@article {pmid40621498, year = {2025}, author = {Chong, J and Zhou, Y and Li, Z and Li, X and Zhang, J and Cao, H and Ma, J and Ge, L and Zhong, H and Sun, J}, title = {Hyodeoxycholic acid modulates gut microbiota and bile acid metabolism to enhance intestinal barrier function in piglets.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1610956}, pmid = {40621498}, issn = {2297-1769}, abstract = {Oral bile acids, particularly hyodeoxycholic acid (HDCA), serve as critical drivers for gut microbial community maturation in mice. In the first study, Cy5-labeled HDCA combined with fluorescence imaging revealed rapid gastrointestinal transit of HDCA in piglets, contrasting with its delayed absorption observed in mice. In the second study, the effects of the oral HDCA supplementation on microbiota-host metabolic interactions were investigated using four piglet model groups: OPM-HDCA (naturally born, raised germ-free (GF), and orally administered HDCA), OPM-CON (naturally born, raised GF, and orally administered PBS), SPF-HDCA (naturally born, raised GF, and received fecal microbiota transplantation (FMT) and HDCA), and SPF-CON (naturally born, raised GF with FMT but no HDCA). The results demonstrated that HDCA administration at 0.2 mg/mL suppressed body weight gain in piglets, which was alleviated by FMT. HDCA significantly altered gut microbiota composition in SPF piglets, markedly increasing the Lactobacillus abundance (37.97% vs. 5.28% in SPF-CON) while decreasing the proportion of Streptococcus (28.34% vs. 38.65%) and pathogenic family Erysipelotrichaceae (0.35% vs. 17.15%). Concurrently, HDCA enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin, Occludin) and suppressing pro-inflammatory cytokines (TNF-α, IL-1β). Additionally, HDCA significantly upregulated ileal gene expression of CYP7A1 (cytochrome P450 family 7 subfamily A member 1) and TGR5 (G protein-coupled bile acid receptor 1) in both SPF-HDCA and OPM-HDCA groups compared to their respective controls (p < 0.05). These findings demonstrate that HDCA exerts microbiota-dependent effects on growth performance, intestinal barrier function, and bile acid metabolism in piglets. Although 0.2 mg/mL HDCA treatment suppressed body weight gain, it potentially enhanced intestinal barrier integrity by activating the TGR5 signaling pathway and increasing the abundance of beneficial bacteria such as Lactobacillus. These results also highlight the critical role of early-life gut microbiota in nutritional interventions, providing a basis for developing precision nutritional strategies targeting intestinal microbial ecology in piglets.}, }
@article {pmid40619451, year = {2025}, author = {Yan, F and Niu, Z}, title = {Impacts of pollution on coral bacterial and metabolites diversity across Dapeng Cove of South China sea.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24107}, pmid = {40619451}, issn = {2045-2322}, mesh = {*Anthozoa/microbiology/metabolism ; China ; Animals ; *Bacteria/metabolism/classification/genetics ; Seawater/microbiology/chemistry ; Biodiversity ; Environmental Monitoring ; Oceans and Seas ; }, abstract = {Coastal ecosystems are increasingly threatened by anthropogenic activities, including sewage discharge and tourism-related pollution, which alter microbial diversity and biochemical cycles. This study applied molecular techniques to examine the coral microbial diversity, and metabolite composition of seawater across five sites (A-E) in Dapeng Cove, South China Sea, to assess pollution impacts. Sites A and B, within the yacht tourism area, exhibited high microbial diversity, dominated by Synechococcus and Rhodobacteraceae, with minimal pollution effects. Site C, inside a domestic drainage channel, showed moderate pollution, with elevated nitrite (NO2) and nitrate (NO3) levels, microbial taxa linked to organic matter degradation, and increased hydroxy acids and indoles. Sites D and E, located in main sewage channels, experienced severe pollution, characterized by high salinity, low dissolved oxygen, and dominance of pollution-tolerant bacteria such as Exiguobacterium and Tepidibacter. Metabolite analysis revealed elevated fatty acyls, organonitrogen compounds, and amino acids at these sites, highlighting strong anthropogenic influence. Beta diversity analysis (NMDS and ANOSIM) confirmed distinct microbial community structures, while KEGG pathway analysis indicated shifts in metabolic functions, with enrichment in xenobiotic biodegradation and anaerobic respiration in sewage-impacted areas. These findings underscore the detrimental effects of wastewater discharge on microbial ecology and biochemical functions. Urgent interventions, including improved wastewater management and regular environmental monitoring, are recommended to mitigate pollution effects. Future research integrating multi-omics approaches is necessary to evaluate the long-term ecological consequences of pollution and climate variability on coastal microbial communities.}, }
@article {pmid40614873, year = {2025}, author = {Lu, X and Gao, Y and Liu, X and Sun, Y and Zhen, G}, title = {Unlocking microbial community succession and key influencing factors during bioelectrocatalytically-driven simultaneous removal of ammonia nitrogen and sulfate from wastewater.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132934}, doi = {10.1016/j.biortech.2025.132934}, pmid = {40614873}, issn = {1873-2976}, abstract = {Ammonia nitrogen (NH4[+]-N) and sulfate (SO4[2][-]) removal by Anaerobic ammonium oxidation (Anammox) and sulfate-reducing bacteria (SRB) was studied in dual-chamber microbial electrolysis cells (MECs). Appropriate anode potential stimulation promoted biofilm formation and enhanced extracellular polymeric substances fluorescence, facilitating electron transfer. The highest NH4[+]-N removal (81.1 %) was achieved at the anode potential of 0.6 V vs. Ag/AgCl after 50 days, coinciding with the increase in electroactive Candidatus_Brocadia from 1.1 % to 27.4 %. Simultaneously, SO4[2][-] removal reached 77.0 %, supported by cathodic biofilms dominated by SRB (Desulfofustis, Desulfomicrobium, and Desulfatirhabdium). Automated machine learning and principal co-ordinates analysis identified the anode potential as the key factor shaping microbial ecology. The appropriate anode potential (0.4-0.6 V vs. Ag/AgCl) promoted cathodic sulfidogenesis, indirectly enhancing electron flow and supporting Anammox process at the anode. These findings demonstrate that MECs hold great promise for simultaneously enhancing anaerobic ammonia oxidation bacteria and SRB activities, enabling efficient NH4[+]-N and SO4[2][-] removal.}, }
@article {pmid40614496, year = {2025}, author = {Brotto, AC and Kurt, H and Chandran, K}, title = {Impacts of intermittent and continuous aeration modes on performance, substrate dynamics, and microbial ecology of mainstream nitrification processes.}, journal = {Water research}, volume = {285}, number = {}, pages = {124123}, doi = {10.1016/j.watres.2025.124123}, pmid = {40614496}, issn = {1879-2448}, abstract = {Intermittent and continuous aeration strategies in combination with solids retention time (SRT) were investigated in terms of their impact on the performance and ecology of mainstream nitrification. Two lab-scale reactors (R1 and R2) were seeded with the same inoculum and subjected to intermittent aeration and continuous low aeration, respectively at statistically similar air-supply rates. For both reactors, SRT was progressively decreased from 8 d during Phase I to 4 and 2.5 d during Phases II and III, respectively. Compared to R2 (93 ± 4.8 %), R1 achieved more stable and higher ammonia oxidation (99 ± 0.13 %) averaged across SRTs. In R1, Nitrosospira were the dominant AOB, while in R2, AOB were a combination of Nitrosospira and Nitrosomonas. Among NOB, Nitrospira were more abundant than Nitrobacter for both R1 and R2 across SRTs. Intermittent aeration in R1 supported higher relative abundance of Comammox Nitrospira than R2. Notably, the enrichment patterns for nitrifying bacteria in the two reactors reflected distinct drivers (beyond microbial kinetics), including inoculum composition, extant oxygen or nitrogen concentrations or both. Overall, intermittent aeration strategies are integral to the design of biological nitrogen removal processes, although other considerations such as operational feasibility and process emissions might ultimately influence operating strategies.}, }
@article {pmid40614494, year = {2025}, author = {Mol, Z and Waegenaar, F and Pluym, T and Vermeir, P and Van Langenhove, H and De Gusseme, B and Boon, N and Walgraeve, C and Demeestere, K}, title = {Effect of biofilm, temperature and type of source water on the formation of haloanisoles in a pilot drinking water distribution system.}, journal = {Water research}, volume = {285}, number = {}, pages = {124078}, doi = {10.1016/j.watres.2025.124078}, pmid = {40614494}, issn = {1879-2448}, abstract = {Taste and odor deviations in tap water affect many consumers and cause a preference for bottled water. However, since tap water is more sustainable than bottled water, these issues should be solved and prevented rapidly. Haloanisoles (HAs) have a very low odor threshold concentration (sub ng.L[-1]) and are of considerable concern since they are mainly formed in drinking water distribution systems (DWDS). Understanding their formation and influencing factors is a crucial aspect of addressing these odor problems. Therefore, this study uses a DWDS pilot to closely mimic the complex situation in real DWDS and investigates the (microbial) formation of six HAs regarding biofilm cell density and composition, temperature, and type of source water. Ten to thirty times higher formation was observed when a stable biofilm (5 months, 10 times more biomass) was present, compared to a young biofilm (2 weeks). With a spiked halophenol (HP) concentration of 0.1 mg.L[-1], the HA concentrations produced by a young biofilm were already within the OTC range. The mature biofilm contained a higher variety of HA-producing microorganisms and more O-methyltransferase genes to convert the precursors (HPs) into HAs. Higher temperatures (24 °C instead of 16 °C) increased the formation of each HA by a factor of 2 to 4, although still low HP-HA conversion ratios were observed (0.2 %). Regardless of the temperature and the type of source water, a clear pattern is observed in the type of HAs formed, with 2,3,4-trichloroanisole being the most abundant. This study finally investigated the effectiveness of flushing to mitigate these odorous compounds in DWDS and concludes that their partitioning between the biofilm and water phase affects the performance of flushing procedures.}, }
@article {pmid40614303, year = {2025}, author = {Ferrocino, I and Buzzanca, D and Pagiati, L and Kazou, M and Georgalaki, M and Hatzopoulos, I and Tsakalidou, E}, title = {The microbial terroir of the Greek olive varieties.}, journal = {International journal of food microbiology}, volume = {441}, number = {}, pages = {111332}, doi = {10.1016/j.ijfoodmicro.2025.111332}, pmid = {40614303}, issn = {1879-3460}, abstract = {The microbial terroir of Greek olive varieties remains underexplored. In this study, 62 samples of olive fruits, collected across the harvest period 2019-2020, were analyzed by high-throughput sequencing. The samples represented 38 olive varieties collected from geographically well distributed regions of Greece. Analysis of the bacterial composition revealed that the geographical area was a significant factor in discriminating samples. The core microbiota included Erwinia, Pseudomonas, and members of the Enterobacteriaceae family. Furthermore, a notable variation in bacterial taxa abundances associated with the geographic location was observed. The sampling area was a key discriminant factor for the mycobiota, and the core mycobiota comprised Alternaria, Taphrina, Candida, Wickerhamomyces anomalus and Penicillium. Finally, Redundancy Analysis (RDA) revealed a notable association between environmental characteristics and microbial composition. Specifically, tree age was associated with certain bacterial and fungal taxa (Pearson's correlation p-value adj.[FDR] < 0.05).}, }
@article {pmid40613821, year = {2025}, author = {Saini, N and Ghosh, A and Bhadury, P}, title = {Linking Plastic Degradation Potential and Resistance Gene Abundance in Bacterioplankton Community of the Sundarbans Estuarine Ecosystem.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf067}, pmid = {40613821}, issn = {1574-6968}, abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.}, }
@article {pmid40610473, year = {2025}, author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV}, title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23763}, pmid = {40610473}, issn = {2045-2322}, support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; }, mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; }, abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.}, }
@article {pmid40607773, year = {2025}, author = {Tao, Y and Liu, D and Shi, Q and Sun, Q and Liu, C and Zeng, X}, title = {Lead exposure in relation to gut homeostasis, microbiota, and metabolites.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0037225}, doi = {10.1128/aem.00372-25}, pmid = {40607773}, issn = {1098-5336}, abstract = {Lead (Pb) is a hazardous heavy metal with no known safe threshold for exposure or consumption, posing significant risks to human health. Pb exposure can cause multiple system damage, depending on exposure levels, duration, and its high bioavailability and bioaccumulative potential. Gastrointestinal tract serves as a primary site for Pb absorption, making it particularly vulnerable to Pb-induced damage, including disruption of gut microbiota composition and metabolic function. This study briefly summarizes the detrimental effects of Pb gut homeostasis, microbial ecology, and host metabolism, which, in turn, further contribute to systemic toxicity. Notably, Pb exposure compromises intestinal barrier integrity, increasing gut permeability and facilitating the translocation of harmful biomolecules into systemic circulation, thereby exacerbating organ dysfunction. Importantly, we underscore that dietary and nutritional interventions such as fiber, probiotic, and vitamin C supplementation is a practicable and effective strategy for mitigating or preventing Pb toxicity.}, }
@article {pmid40606160, year = {2025}, author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D}, title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1639190}, doi = {10.3389/fmicb.2025.1639190}, pmid = {40606160}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].}, }
@article {pmid40605266, year = {2025}, author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG}, title = {A review of engraftment assessments following fecal microbiota transplant.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2525478}, doi = {10.1080/19490976.2025.2525478}, pmid = {40605266}, issn = {1949-0984}, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.}, }
@article {pmid40603778, year = {2025}, author = {Brinck, JE and Sinha, AK and Laursen, MF and Dragsted, LO and Raes, J and Uribe, RV and Walter, J and Roager, HM and Licht, TR}, title = {Intestinal pH: a major driver of human gut microbiota composition and metabolism.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {40603778}, issn = {1759-5053}, abstract = {In the human gastrointestinal tract, pH is a key factor in shaping gut microbial composition and activity, while also being influenced by microbial metabolism. pH varies substantially along the gastrointestinal tract within an individual and between different individuals due to a combination of host, diet, microbial and external factors. The importance of pH on microbiota composition and metabolic response has been widely explored over the past century. Here, we review the literature to explore the major physiological and dietary factors that influence pH along the gastrointestinal tract. From a microbial ecology perspective, we discuss how gastrointestinal pH affects microbiota composition and metabolism. We explore mechanisms by which pH can influence bacterial acid response systems, gene expression and the production of microbial metabolites important for health. Finally, we review the literature regarding the potential role of gastrointestinal pH in human diseases. We propose that we can advance our understanding of the gut microbiota in health and disease by considering gastrointestinal pH. We argue that pH-mediated gut microbial metabolic variation is highly important for predicting and manipulating metabolic output relevant to human health.}, }
@article {pmid40602916, year = {2025}, author = {Puche, E and Roger, B and Vargas-Sánchez, M and Sánchez-Carrillo, S and Rodrigo, MA}, title = {Freshwater macrophyte type (macroalgae versus phanerogams) mainly determines detritus-derived greenhouse gases production: A microcosm experiment.}, journal = {Journal of environmental sciences (China)}, volume = {157}, number = {}, pages = {674-689}, doi = {10.1016/j.jes.2025.01.015}, pmid = {40602916}, issn = {1001-0742}, mesh = {*Greenhouse Gases/analysis/metabolism ; *Seaweed ; Ecosystem ; Methane/analysis ; Fresh Water ; Carbon Dioxide/analysis ; Eutrophication ; *Environmental Monitoring ; *Air Pollutants/analysis ; }, abstract = {Freshwater ecosystems are crucial in the global emissions of greenhouse gases (GHGs) such as CH4. Macrophytes are the main organic matter (i.e., detritus) supplier to the sediment of these systems, thus controlling CH4 production. However, species-specific differences (structure and composition) may determine contrasting patterns of detritus transformation into CH4. Furthermore, eutrophication can affect the degradation and, consequently, CH4 production. We performed a 64-day microcosm experiment with anoxic incubations of detritus from seven phylogenetically different macrophytes (two charophytes, filamentous algae -Spirogyra, Cladophora-, three submerged plants and an amphibious one), under two trophic conditions (oligo- versus eutrophic) and with/without sediment. We assessed the CH4 and CO2 production and the changes in the detritus quality at the end of the experiment. The ranking in the mean cumulative CH4 production was: Chara hispida > Nitella hyalina > Najas marina ≈ Teucrium scordium > Stuckenia pectinata ≈ Myriophyllum spicatum > filamentous algae, and it was related to the detritus quality. GHGs maximum production rates were 1.6 (N. marina)-1.2 (C. hispida) mmol CH4/(g OC·day) and 1.7 (N. marina)-1.5 (C. hispida) mmol CO2/(g OC·day). The CO2:CH4 ratio was biased towards CO2 during the first 10 days (average ratio of 200) and fell afterwards to about 1 for all macrophyte species and treatments. The sediment favored detritus decomposition (probably due to the "positive priming effect"), increasing GHGs production. The influence of nutrient enrichment was not evident. Delving into the macrophyte detritus quality-GHGs production relationship is needed to forecast the GHGs emissions in macrophyte-dominated systems.}, }
@article {pmid40602642, year = {2025}, author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E}, title = {Long-term Organic Fertilization Shields Soil Prokaryotes from Metal Stress While Mineral Fertilization Exacerbates It.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126747}, doi = {10.1016/j.envpol.2025.126747}, pmid = {40602642}, issn = {1873-6424}, abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral<unfertilized<mineral+organic<organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30% upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50 to 100% in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.}, }
@article {pmid40602621, year = {2025}, author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X}, title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70139}, doi = {10.1111/1758-2229.70139}, pmid = {40602621}, issn = {1758-2229}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.}, }
@article {pmid40602574, year = {2025}, author = {Mu, D and Chen, Q and Gao, B and Xu, H and Chen, W and Wang, K and Wu, X and Yan, C and Zhang, S and Ke, S}, title = {Oxidized chitosan: Combining an "Adhesion-and-Kill" antibacterial strategy with immunoregulation and angiogenesis to enhance methicillin-resistant Staphylococcus Aureus-infected wound healing.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {145664}, doi = {10.1016/j.ijbiomac.2025.145664}, pmid = {40602574}, issn = {1879-0003}, abstract = {The emergence of antibiotic-resistant bacteria, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant challenge in clinical wound management due to their resistance to conventional antibiotics and ability to form persistent biofilms. This study explores the antibacterial properties and wound-healing potential of oxidized chitosan (OCTS), fabricated by oxidizing chitosan with hydrogen peroxide (H2O2), which introduces carboxyl groups to enhance its solubility, adhesion, and antibacterial activity. In vitro experiments demonstrate that OCTS exhibits lower MIC concentration (20 mg/mL vs. 80 mg/mL), superior bactericidal efficiency, stronger adhesion to MRSA, and greater biofilm inhibition than conventional chitosan (CTS), while retaining excellent biocompatibility and hemocompatibility. Multi-omics analyses (proteomics and metabolomics) reveal that OCTS disrupts key metabolic, structural, and redox pathways in MRSA. In a MRSA infection model on mouse skin, OCTS effectively eradicated MRSA in wound sites, reduced inflammation, promoted M2 macrophage polarization, and enhanced angiogenesis, culminating in a rapid wound healing rate of 89.2 ± 3.0 % by day 7. Its low cytotoxicity and excellent biosafety in mice further support its clinical translation. These findings highlight OCTS as a promising multifunctional biomaterial for MRSA-infected wound management, integrating antibacterial, immunoregulatory, and regenerative functions through a unique adhesion-and-kill mechanism.}, }
@article {pmid40602118, year = {2025}, author = {Liu, Z and Wen, J and Liu, Z and Su, Z and Wu, Z and Shen, H and Wei, H and Zhang, J}, title = {Tire microplastics rather than polystyrene microplastics reduce soil microbial diversity and network complexity and stability, and induce microbial homogenization.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138945}, doi = {10.1016/j.jhazmat.2025.138945}, pmid = {40602118}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution poses escalating threats to soil biodiversity, yet its impacts on microbial community structure, stability, and assembly are far from fully understood, limiting the comprehensive assessment of MPs risks. This study investigated effects of polystyrene (PS) and tire particle (TP) MPs (0, 1 %, 5 %; w/w) on soil microbial communities in a maize-planted system, evaluating shifts in diversity, network architecture, and assembly processes. Our results demonstrated that high-concentration (5 %) PS MPs significantly enhanced bacterial α-diversity by promoting some taxa (e.g., Planctomycetes, Betaproteobacteria), and increased bacterial network complexity. In contrast, 5 % TP MPs reduced bacterial and fungal diversity, destabilized bacterial networks, and induced taxonomic homogenization. TP MPs amplified deterministic assembly processes by elevating homogeneous selection contribution while reducing stochastic drift, thereby driving microbial community convergence. Bacterial and fungal community structure shifts under TP MPs correlated with soil stoichiometric alterations, including depleted nitrate nitrogen and available phosphorus, and elevated pH, contents of dissolved organic carbon, ammonium nitrogen, and total carbon. These findings highlight the divergent ecological risks posed by PS and TP MPs, and underscore the urgent need for prioritized mitigation of TP MPs pollution in agroecosystems to preserve microbial functional integrity.}, }
@article {pmid40601059, year = {2025}, author = {Chao, LL and Shih, CM}, title = {Molecular Survey and Genetic Identification of Wolbachia Endosymbionts in Dwelling-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Taiwan.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {69}, pmid = {40601059}, issn = {1432-184X}, support = {NSTC 113-2320-B-037-010; NSTC 114-2923-B-037-001//National Science and Technology Council/ ; }, mesh = {Animals ; *Wolbachia/genetics/classification/isolation &amp; purification/physiology ; *Culex/microbiology ; Taiwan ; *Symbiosis ; Phylogeny ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {The genetic identity of Wolbachia endosymbionts was determined in dwelling-caught Culex quinquefasciatus from Taiwan. A total of 370 Cx. quinquefasciatus (245 females and 125 males) was initially screened for Wolbachia infection targeting the universal 16S gene, and the positive samples were further identified their genogroup by a nested-polymerase chain reaction assay to amplify the group-specific Wolbachia surface protein (wsp) gene. In general, 44.59% of Cx. quinquefasciatus was detected with Wolbachia endosymbionts, and 43.2% (54/125) in male and 45.31% (111/245) in female. The group-specific detection was observed in 2.16% (8/370), 41.35% (153/370), and 1.08% (4/370) with groups A, B, and co-infection (A&amp;B), respectively. Phylogenetic analysis revealed that the genetic identities of these Taiwan strains were genetically similar to the groups A and B of Wolbachia with the high sequence homogeneity of 98.7-100% and 96.5-99.8%, respectively. Genetic relatedness is clearly discriminated using both methods of maximum likelihood (ML) and unweighted pair group with arithmetic mean (UPGMA). This study demonstrates the initial genetic identity of Wolbachia endosymbionts with a low prevalence (2.16%) of group A and a high prevalence (41.35%) of group B in dwelling-caught Cx. quinquefasciatus of Taiwan. Because the Cx. quinquefasciatus had been known as a vector for various viral pathogens, the possible impacts of Wolbachia endosymbionts on vector competence of Cx. quinquefasciatus in Taiwan need to be further identified.}, }
@article {pmid40601038, year = {2025}, author = {He, T and Chen, Y and Wang, Y and Peng, Z and Mou, Y and Wang, L}, title = {Responses of Microbial Community to Heterogeneous Dissolved Organic Nitrogen Constituents in the Hyporheic Zones of Treated Sewage-Dominated Rivers.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {71}, pmid = {40601038}, issn = {1432-184X}, support = {2021YFB2600200//National Key Research and Development Project of China/ ; grant number 52170159//National Natural Science Foundation of China/ ; No. BE2022601//Key Research and Development Program of Jiangsu Province/ ; 2016-JNHB-007//the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Six Talent Peaks Project in Jiangsu Province/ ; }, mesh = {*Sewage/microbiology/chemistry ; *Nitrogen/metabolism/analysis ; China ; *Rivers/microbiology/chemistry ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Microbial Consortia ; }, abstract = {The hyporheic zone (HZ) of treated sewage-dominated rivers serves as a critical biogeochemical hotspot for dissolved organic nitrogen (DON) transformation, yet the mechanisms linking DON chemodiversity to microbial community dynamics remain poorly resolved. This study integrated spectroscopic fingerprinting, machine learning, and partial least squares path modeling (PLS-PM) to unravel the interactions between redox-stratified DON fractions and microbial consortia in two effluent-impacted rivers (Xi'an, China). The results revealed that DOM spectral parameters associated with distinct DON characteristics posed distinct effects on microbial communities, with the communities in oxic zones largely impacted by autobiogenic, aromatic, and protein-like DON, while the communities in suboxic zones were more intensely impacted by the humification degree of DON. Microbial communities exhibited redox-dependent niche differentiation; i.e., keystone taxa in oxic zones (e.g., Gamma-Proteobacteria) drove nitrogen assimilation, while suboxic taxa (e.g., Verrucomicrobia) prioritized stress-resistant D-amino acid metabolism. PLS-PM demonstrated that biomarkers exerted stronger control on nitrogen cycling (|path coefficients|> 0.6, P < 0.05) than keystone taxa, with summer communities showing higher model fit. Treated sewage-derived DON fostered specialized consortia through biochemical trade-offs, i.e., methionine recycling in oxic zones versus peptidoglycan modification in suboxic zones, thus highlighting the critical role of HZ in mitigating nitrogen pollution. These findings advance predictive modeling of DON-microbe interactions in anthropogenically perturbed aquatic ecosystems.}, }
@article {pmid40601033, year = {2025}, author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S}, title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {70}, pmid = {40601033}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; }, abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.}, }
@article {pmid40600875, year = {2025}, author = {Yao, J and Wang, H and Fang, J and Shan, S and Joseph, SD and van Zwieten, L and Zhu, K and Chen, D and Jia, H}, title = {Distribution Hotspots, Formation Mechanisms, and Ecological Effects of Reactive Oxygen Species in Soil and Sediment: A Critical Review.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00581}, pmid = {40600875}, issn = {1520-5851}, abstract = {Reactive oxygen species (ROS), including superoxide radical (O2[•-]), hydrogen peroxide (H2O2), hydroxyl radical ([•]OH), and singlet oxygen ([1]O2), are commonly present in soil and sediment, playing a crucial role in the nutrient biogeochemical cycle, pollutant transformation, and microbial ecology. Previous reviews mainly emphasized ROS toxicity and Fenton chemistry-related reactions, neglecting a comprehensive understanding of ROS distribution and hotspots, formation mechanisms, and ecological effects. Here, the most advanced in situ and ex situ detection methods of ROS in soil and sediment are first summarized to address these gaps. ROS hotspots are identified as active microinterfaces and oxic-anoxic fluctuation zones by graphing the distribution of ROS in soil and sediment. Second, ROS formation processes and mechanisms are outlined, which involve natural organic matter (NOM) and biochar (acting as electron shuttle, geobattery, geoconductor, and photosensitizer), transition metals (mainly via Fenton and Fenton-like reactions), and microbes (producing extracellular ROS and mediating NOM decomposition or metal oxides reduction). Further, as for the ecological effects of ROS, they impact the microbial community, nutrient cycle, and the transformation of organic pollutants and multivalence heavy metals. Finally, we call for more future research that focuses on developing rapid and in situ ROS detection techniques, elucidating the interactive ROS formation mechanisms by trace environmental components, analyzing ecological consequences in ROS hotspots, and practically applying ROS in soil and sediment. A comprehensive understanding of the ROS formation process in soil and sediment is crucial for the study of soil carbon sequestration and natural remediation processes in the context of global green and low-carbon development.}, }
@article {pmid40600721, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, development, and validation of new fluorescent strains for studying oral streptococci.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0016825}, doi = {10.1128/spectrum.00168-25}, pmid = {40600721}, issn = {2165-0497}, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest, as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single-cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without the addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.IMPORTANCEStreptococci are among the earliest colonizers of the soft and hard tissues of the oral cavity and are contributors to the oral health status of the host, with involvement in dental caries, endodontic infections, periodontal disease, and the development of oral cancer. Strains genetically modified to produce fluorescent proteins that can be either visualized through microscopy imaging or quantified by their specific fluorescent intensity signal are critical tools toward the study of individual or mixed-species cultures. Our report here details the development and testing of several new strains of fluorescent oral streptococci that can be utilized in the study of microbial ecology, increasing both the availability of tools and documenting experimental approaches toward in vitro assay applications such as the study of intermicrobial interactions.}, }
@article {pmid40600175, year = {2025}, author = {Etesami, H}, title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100421}, pmid = {40600175}, issn = {2666-5174}, abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.}, }
@article {pmid40600142, year = {2025}, author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W}, title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516393}, pmid = {40600142}, issn = {1664-302X}, abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.<br><br>METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.<br><br>RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.<br><br>CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.}, }
@article {pmid40600059, year = {2025}, author = {Liu, J and Yao, P and Liu, J and Ren, G and Zhang, XH and Liu, J}, title = {Habitat and lifestyle affect the spatial dynamics of prokaryotic communities along a river-estuary-sea continuum.}, journal = {mLife}, volume = {4}, number = {3}, pages = {305-318}, pmid = {40600059}, issn = {2770-100X}, abstract = {Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river-estuary-sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.}, }
@article {pmid40598447, year = {2025}, author = {Bulzu, PA and Henriques Vieira, H and Ghai, R}, title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {154}, pmid = {40598447}, issn = {2049-2618}, support = {25-15920S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 24-11998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; }, abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.<br><br>RESULTS: We leveraged long-read sequencing to recover large (200-600&#xa0;Mb), high-quality, and highly repetitive (>&#x2009;60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.<br><br>CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.}, }
@article {pmid40594354, year = {2025}, author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO}, title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22448}, pmid = {40594354}, issn = {2045-2322}, support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; }, abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.}, }
@article {pmid40594086, year = {2025}, author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S}, title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22408}, pmid = {40594086}, issn = {2045-2322}, support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; }, mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; }, abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.}, }
@article {pmid40591097, year = {2025}, author = {Gisriel, CJ and Schluchter, WM and Gan, F and Golbeck, JH and Ho, MY and Shen, G and Soulier, NT and Thiel, V and Ward, DM and Zhao, J and Zhang, S}, title = {Remembering Don Bryant (1950-2024).}, journal = {Photosynthesis research}, volume = {163}, number = {4}, pages = {37}, pmid = {40591097}, issn = {1573-5079}, }
@article {pmid40589459, year = {2025}, author = {Ametefe, EN and Thorsen, L and Danwonno, H and Agoha, RK and Glover, RLK and Dzogbefia, VP and Jespersen, L}, title = {Molecular Characterization of Culturable Yeasts and Nonspore-Forming Bacteria Associated With Fermented Kapok Seeds (Kantong), a Traditional Food Condiment in Ghana.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {6452183}, pmid = {40589459}, issn = {2314-5765}, abstract = {Fermented kapok seeds, known as kantong in northern Ghana, serve as a traditional food condiment which provides flavor and improves the protein content of soups. In this study, the occurrence of yeasts, lactic acid bacteria (LAB), and other nonspore-forming bacteria in kantong was investigated. Microbial enumeration and phenotypic characterizations on isolated strains were performed. Molecular methods were also employed for grouping and identification of strains, and these included random amplification of polymorphic DNA (RAPD) using Escherichia coli phage-derived M13 primer (M13-PCR typing), repetitive element PCR typing (rep-PCR), and 16S rRNA gene sequencing. After a 48-h fermentation period, microbial load ranged from 4.77 ± 0.11 to 8.9 ± 0.1 log10 CFU/g. The pH of the fermenting condiment decreased from 6.5 to 4.7 during the fermentation period. A total of 190 LAB, 53 enterobacteria, and 39 yeasts were identified at species levels using both phenotypic and molecular methods. The LAB included Pediococcus acidilactici, Weissella paramesenteroides, Pediococcus pentosaceus, Weissella confusa, and Lactiplantibacillus plantarum; the enterobacteria isolated were Acinetobacter baumannii, Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, and Enterobacter cloacae; and the yeasts identified were Nakaseomyces glabratus, Cyberlindnera fabianii, Pichia kudriavzevii, and Saccharomyces cerevisiae. This work presents fermented kapok seeds as a reservoir of microorganisms, some of which could possess some technological properties which could be harnessed to enhance the nutritional value of Ghanaian foods as well as improve gut health as probiotics. It also reveals the presence of enterobacteria in this spontaneous fermentation, thus impacting the safety of the product and the need for starter culture development.}, }
@article {pmid40589000, year = {2025}, author = {Sharma, H and Al Noman, A and Ahmad, I and Tonni, SD and Mim, TJ and Afrose, F and Sharma, PD and Parvez, A and Tamanna, S and Al Azad, M and Pathak, R}, title = {Bridging Mind and Gut: The Molecular Mechanisms of microRNA, Microbiota, and Cytokine Interactions in Depression.}, journal = {Current gene therapy}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115665232361169250617192348}, pmid = {40589000}, issn = {1875-5631}, abstract = {Depression is a complex psychiatric disorder that arises from various underlying biological mechanisms. In this review, the role of microRNAs (miRNAs) in modulating gut microbiotacytokine communication and their potential to unravel the pathophysiology of depression and develop novel therapeutic strategies are discussed. MiRNAs are small non-coding RNA molecules that have emerged as key regulators in the bidirectional signaling of the gut-brain axis by modulating gene expression and fine-tuning an intricate dialogue between the microbiota, immune system, and central nervous system. Results show how gut microbiota can shape miRNA expression in brain regions involved in mood regulation; conversely, evidence is accumulating, elucidating how miRNA perturbations can shape microbial ecology. Gut bacteria-derived short-chain fatty acids (SCFAs) fuel this nexus by exerting effects on neurogenesis, neurotransmitter synthesis, neuroinflammation, affective behavior alterations, and depressive-like phenotypes. Pro-inflammatory cytokines such as IL-6, TNF-α, and IL-1β are also known to be associated with depressive symptoms related to altered expression patterns of specific miRNAs across these disorders. This review exposes the novel potential biomarkers and therapeutic targets/strategies to develop innovative methods in the diagnosis and treatment of depression by exploring bidirectional relations among miRNAs, gut microbiota, and cytokines. The knowledge of these molecular networks and pathways has provided the opportunity for designing new-generation therapeutics such as phytobiotics, probiotics, psychobiotics, diet therapies, and nanomedicine based on miRNAs from a future perspective, which will revolutionize the management of mental disorders.}, }
@article {pmid40586542, year = {2025}, author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER}, title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0025725}, doi = {10.1128/msphere.00257-25}, pmid = {40586542}, issn = {2379-5042}, abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.<br><br>IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.}, }
@article {pmid40586525, year = {2025}, author = {Taylor, CC and Parks, ST}, title = {There and back again: navigating the return to in-person lab work post-pandemic for the Hybrid Microbial Ecology Course-based Undergraduate Research Experience (H-ME-CURE).}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0024924}, doi = {10.1128/jmbe.00249-24}, pmid = {40586525}, issn = {1935-7877}, abstract = {The Microbial Ecology Course-based Undergraduate Research Experience (ME-CURE) has evolved over time to accommodate student needs and experiences. Prior to the COVID-19 pandemic, the lab was fully in-person, with a shift to in silico, remote learning from 2020 to 2023. In 2024, the ME-CURE was further adapted to return to in-person learning while maintaining some of the remote learning pedagogy. Significantly, the 2024 Hybrid ME-CURE (H-ME-CURE) built upon the findings of prior iterations of the lab such that students in the 2024 cohort entered with lab isolates, primers, and pathways that were ready for testing. This novel version of the ME-CURE synthesized years of in-person and remote, in silico learning to yield a deeper understanding of microbial pathways and improved molecular data including novel gene sequences for further testing. The goal of this work is to provide the tools that were used to help build the H-ME-CURE by combining past in-person and in silico learning methods of the ME-CURE.}, }
@article {pmid40585502, year = {2025}, author = {Zhu, M and Zhang, F and Qiu, Z and Zhao, S and Gao, S}, title = {White Light Orchestrates Mycoparasitic and Infection Activities by Regulating Expression of Effectors in Trichothecium roseum.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {7}, pages = {e70396}, pmid = {40585502}, issn = {2048-7177}, abstract = {The fungal developmental processes are orchestrated by white light. Despite the genome assembly of Trichothecium roseum being available, the underlying molecular mechanisms of the white light-mediated developments of T. roseum remain obscure. It was found that white light impaired mycoparasitic activities against the wheat powdery mildew fungus and infection processes on tomato fruits in T. roseum. In vitro and in vivo, white light significantly impaired colony expansion and dramatically increased conidiation of T. roseum. RNA-seq analysis of T. roseum conidia was profiled to illustrate the light-mediated expression of genes. A total of 153 and 666 differentially expressed genes were identified between conidia treated with or without white light at 48- and 96-h post inoculation (hpi). Among genome-wide identified effectors, 8 and 36 effectors were differentially regulated by white light at 48 and 96 hpi, respectively. The core effectors, Tro004101, Tro006854, Tro008316, and Tro004104 were commonly downregulated by white light. Notably, white light regulated gene expression in key metabolic pathways including tryptophan metabolism (3 genes) and tyrosine metabolism (5 genes), as well as the HOG-MAPK signaling cascade. These results demonstrated that white light-compromised T. roseum mycoparasitic and infection activities might be achieved by regulating specific effector expression and differentially modulating metabolism and HOG-MAPK pathways. The genes detected by our transcriptome analysis may be crucial for mycoparasitism and infection by T. roseum and thus serve as targets for future functional analysis. Our findings provide new insights into the white light-orchestrated developments of an important agricultural and economical fungus and will potentially support efforts for the study of fungal effectors.}, }
@article {pmid40584121, year = {2025}, author = {Barrero, MAO and Varón-López, M and Peñuela-Sierra, LM}, title = {Competing microorganisms with exclusion effects against multidrug-resistant Salmonella Infantis in chicken litter supplemented with growth-promoting antimicrobials.}, journal = {Veterinary world}, volume = {18}, number = {5}, pages = {1127-1136}, pmid = {40584121}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The widespread use of antibiotic growth promoters (AGPs) in poultry production has been implicated in altering gut microbiota and promoting the excretion of multidrug-resistant (MDR) bacteria into the environment. Salmonella enterica serovar Infantis (Salmonella Infantis [S.I]), a prevalent zoonotic pathogen, has demonstrated increasing resistance in poultry systems. This study aimed to evaluate the efficacy of natural control microorganisms (NCM), Bacillus subtilis and Lactobacillus plantarum, in reducing the abundance of MDR S.I in fresh chicken litter from birds raised with or without AGP supplementation. It also examined how physicochemical properties and microbial dynamics influence pathogen persistence.<br><br>MATERIALS AND METHODS: Microcosms were constructed using litter from broilers raised under two dietary regimes (with and without avilamycin). Treatments included combinations of AGP, S.I, and NCM. Bacterial enumeration was performed using selective media, and whole-genome sequencing of S.I was conducted to characterize antimicrobial resistance and virulence genes. Physicochemical parameters (pH, humidity, temperature, and ammonia) were measured and correlated with microbial loads. Antagonistic activity of NCM strains was assessed using agar diffusion assays.<br><br>RESULTS: Genome analysis revealed that S.I carried multiple resistance genes (e.g., blaCTX-M-65, tet(A), and sul1) and efflux systems conferring MDR. In vitro assays showed strong antagonism by L. plantarum and moderate activity by B. subtilis. In microcosms, S.I counts significantly decreased in the presence of both AGP and NCM, indicating synergistic inhibition. Conversely, in the absence of AGP, NCM had a limited effect. Statistical analyses showed strong correlations between microbial groups and physicochemical variables, particularly during later production stages.<br><br>CONCLUSION: The application of B. subtilis and L. plantarum in chicken litter significantly reduced S.I colonization under AGP supplementation, suggesting their potential as biocontrol agents. These findings support the development of integrated litter management strategies to mitigate zoonotic and resistant pathogen dissemination, particularly in AGP-using systems. However, the effectiveness of such interventions may vary across farms due to differences in microbial ecology and environmental conditions.}, }
@article {pmid40583496, year = {2025}, author = {Crull, S and Hammer, E and Mann, AE and O'Connell, LM and Soule, A and Griffith, E and Blouin, T and Brigmon, RL and Richards, VP}, title = {Seasonal Host Shifts for Legionella Within an Industrial Water-Cooling System.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70132}, doi = {10.1111/1758-2229.70132}, pmid = {40583496}, issn = {1758-2229}, support = {89303321CEM000080//Office of Environmental Management/ ; //The Laboratory Directed Research and Development (LDRD) program within the Savannah River National Laboratory (SRNL)/ ; }, mesh = {Seasons ; *Legionella/genetics/isolation &amp; purification/physiology/classification ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; RNA, Ribosomal, 18S/genetics ; Acanthamoeba ; Phylogeny ; }, abstract = {Legionella is a genus of environmental bacteria containing pathogenic species such as Legionella pneumophila that are responsible for Legionnaires' disease, a potentially fatal respiratory infection. Disease aetiology can involve Legionella replication intracellularly within protists and this study aimed to characterise the Legionella-protist relationship to develop novel outbreak prevention targets. Water and sediment samples were collected from a water-cooling tower in South Carolina over a 6-month period. Concomitantly, multiple environmental parameters were recorded. Bacterial and eukaryotic communities were characterised using 16S rRNA gene V4 region and a 252 bp fragment of 18S rRNA gene, respectively. Co-occurrence network analyses were performed to elucidate Legionella-protist correlations through time. We found that Legionella correlated with different protists as the seasons progressed. Acanthamoeba correlated with Legionella in early spring followed by Vannella and Korotnevella in late spring and early summer, and were joined by Echinamoeba in mid-summer. Vannella and Acanthamoeba are known potential hosts for Legionella, while Korotnevella is a potential undocumented host. Of the environmental parameters, temperature showed strong correlation with protists genera, suggesting that Legionella abundance was driven by temperature-dependent protist availability. Our results highlight ecological shifts that are associated with elevated Legionella levels, which offers potential targets to help predict and prevent disease outbreaks.}, }
@article {pmid40583058, year = {2025}, author = {Cornet, L and Zaidi, SS and Li, J and Ngapout, Y and Shakir, S and Meunier, L and Callot, C and Marande, W and Hanikenne, M and Rombauts, S and Van de Peer, Y and Vanderschuren, H}, title = {A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {185}, pmid = {40583058}, issn = {1474-760X}, support = {F.4515.17//Fonds De La Recherche Scientifique - FNRS/ ; 1.B456.20//Fonds De La Recherche Scientifique - FNRS/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent/ ; }, mesh = {*Manihot/genetics/virology ; *Disease Resistance/genetics ; *Plant Diseases/genetics/virology ; *Haplotypes ; *Chromosomes, Artificial, Bacterial/genetics ; Genome, Plant ; Chromosome Mapping ; }, abstract = {BACKGROUND: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging.<br><br>RESULTS: In the present study, we generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps reveals discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC-guided approach to assess cassava genome assemblies significantly improves the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences.<br><br>CONCLUSIONS: The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.}, }
@article {pmid40581745, year = {2025}, author = {Richter, I and Büttner, H and Hertweck, C}, title = {Endofungal Bacteria as Hidden Facilitators of Biotic Interactions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf128}, pmid = {40581745}, issn = {1751-7370}, abstract = {Fungi play pivotal roles in ecology and human health, driving nutrient cycling, supporting antibiotic production, and posing threats through toxin production. Less well-recognized, however, is their ability to harbour endosymbiotic bacteria. Advances in genomics and microscopy have revealed the prevalence of endofungal bacteria across diverse fungal phyla, though their functions are primarily inferred from genomic and transcriptomic studies. Recent functional research has begun to shed light on their influence on fungal pathogenicity, physiology, and ecology. These findings raise fundamental questions about the establishment and benefits of bacterial-fungal endosymbiosis, as well as the role of endosymbionts in mediating fungal interactions with other organisms. This review provides an in-depth analysis of the molecular mechanisms involved in the establishment and persistence of these symbioses. It also summarizes the current understanding of how endofungal bacteria impact fungal interactions with other organisms. For instance, endofungal bacteria contribute to the beneficial effects of fungi on plant health and fitness, protect fungal hosts from fungivorous predators, and enhance fungal virulence against plants, animals, and humans. These discoveries highlight the need for holistic investigations into bacterial-fungal endosymbiosis to fully understand their role in natural ecosystems. A deeper understanding of these multipartite partnerships offers exciting opportunities to improve ecosystem management, food safety, disease control, and crop productivity.}, }
@article {pmid40580837, year = {2025}, author = {Zhou, B and Niu, C and Mao, W and Wang, X and Wu, Z and Wang, Z}, title = {An electrochemical anaerobic dynamic membrane bioreactor for enhanced sludge digestion: Unveiling molecular interactions and microbial mechanisms.}, journal = {Water research}, volume = {285}, number = {}, pages = {124080}, doi = {10.1016/j.watres.2025.124080}, pmid = {40580837}, issn = {1879-2448}, abstract = {This study investigated the effects of stepwise external voltages on an electrochemical anaerobic dynamic membrane bioreactor (EC-AnDMBR) for anaerobic digestion of waste activated sludge. Increasing the applied voltage greatly mitigated membrane fouling, reduced the transmembrane pressure increase rate and enhanced both volatile solids digestion and biogas production. The dynamic membrane structure became looser with fewer biofouling substances, attributed to a 42.6 % increase in the sludge-membrane interaction energy barrier at higher voltages. Electrochemical analysis revealed improved electroactivity of the anaerobic sludge, as evidenced by increased conductivity and reduced internal resistance. The proton-coupled electron transfer (PCET) pathway was promoted, indicated by a significant increase in the hydrogen/deuterium kinetic isotope effect from 616 to 25,990. Molecular simulations of dissolved organic matter (DOM) showed an enrichment of amide and quinone groups, along with stronger hydrogen-bonding and π-cation interactions, which may contribute to the PCET process. Moreover, elevated voltages promoted more deterministic microbial community assembly and reduced upstream microbial immigration. Gene upregulation in organic metabolism, electron/proton transport, and methanogenesis further supported enhanced digestion performance via PCET pathway. These findings offer valuable insights into the molecular mechanisms and microbial ecology of EC-AnDMBR systems, advancing the development of more efficient and sustainable sludge treatment technologies.}, }
@article {pmid40578101, year = {2025}, author = {Liu, B and Jia, M and Nauwynck, W and Wang, J and Kundu, K and Springael, D and Boon, N}, title = {Hydrogen-powered bacteria enhance organic micropollutant degradation under starvation conditions.}, journal = {Water research}, volume = {285}, number = {}, pages = {124052}, doi = {10.1016/j.watres.2025.124052}, pmid = {40578101}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) occur in natural aquatic environments at trace concentrations with suspected adverse effects on the ecosystem and human health. Microbial biodegradation plays a crucial role in OMP-elimination from drinking water resources. However, long-term OMP-biodegradation remains challenging since the metabolic activity of degrading strains is restricted by energy-limited conditions in treatment systems. Molecular hydrogen (H2) has been identified as a universally available energy source utilized by various bacteria under nutrient-starved conditions, and it can be hypothesized that H2 might also support OMP-degrading microbes when other energy carriers are scarce. The potential of H2 as a supporting energy source for OMP-degradation was tested by examining its effect on the biodegradation of 2,6-dichlorobenzamide (BAM) by Aminobacter niigataensis MSH1 and on the physiological status of the MSH1 cells during both nongrowth-linked (500 μg BAM/L) and growth-linked (10,000 μg BAM/L) regimes. MSH1 cells used as inoculum were either not or pre-exposed to H2 and were harvested at different growth phases. During the nongrowth-linked BAM biodegradation, MSH1 pre-exposed to H2 exhibited a 1.2 to 1.5-fold higher initial specific BAM biodegradation rate, resulting in more rapid BAM removal, likely due to the retention of more metabolically active cells, as suggested by a cell vitality assay. During the growth-linked biodegradation, MSH1 pre-exposed to H2 demonstrated accelerated growth with a 1.5-fold higher maximum specific growth rate, which coincided with an improved BAM removal. The positive effects of H2 were only evident for MSH1 cells harvested either at the stationary and/or starvation phase. Evidence of H2 metabolism was supported by H2 consumption measurements. Collectively, this study reveals that microbial H2 metabolism enables OMP-degrading bacteria to sustain metabolic activity under starvation conditions, offering a novel strategy to enhance long-term OMP-biodegradation.}, }
@article {pmid40577691, year = {2025}, author = {Quellhorst, HE and Ponce, MA and Holguin Rocha, AF and Sakka, MK and Tsintzou, G and Maille, JM and Vagelas, I and Madesis, P and Athanassiou, CG and Scully, ED and Zhu, KY and Morrison, WR}, title = {The capacity of 3 stored product insect species to vector microbes after increasing dispersal periods.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf123}, pmid = {40577691}, issn = {1938-291X}, support = {2024-67012-42439//USDA-NIFA/ ; }, abstract = {Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), and Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae) are 3 important stored product pests of maize, but there has been little work evaluating how they vector microbes. While there has been some work assessing the microbial ecology of S. zeamais, none has directly assessed whether they transfer microbes to new food patches. Thus, we evaluated the ability of both species to vector microbes when given the opportunity to forage on sterilized potato dextrose agar dishes after a 0, 24, or 72 h dispersal period in a sterilized container. We subsequently photographed the dishes at 3 and 5 d after introduction and quantified the microbial growth using ImageJ. In addition, we isolated unique morphotypes of fungi, extracted DNA and amplified the internal transcribed spacer 5/4 intergenic spacer region, then sequenced to determine fungal identity. We found that 3 species readily vectored several plant pathogenic microbes, including 21 taxa from more than 11 genera, notably Aspergillus spp. Increasing dispersal period (0, 24, 72 h) resulted in a third less microbial growth (mean microbial growth or mean greyscale value from 0 to 255) by S. zeamais after 72 h, while for P. truncatus it resulted in a 2.7-fold increase in microbial growth. Dispersal by S. zeamais (0, 24, 72 h) resulted in 6.6-fold more microbial growth than dispersal by P. truncatus. There was 1.5- to 3.7-fold more microbial growth after 5 d than 3 d by each species. This research has important implications for food safety in the postharvest environment, especially for maize production, storage, and processing.}, }
@article {pmid40577531, year = {2025}, author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS}, title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf126}, pmid = {40577531}, issn = {1751-7370}, abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.}, }
@article {pmid40577477, year = {2025}, author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X}, title = {Global health risks lurking in livestock resistome.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadt8073}, pmid = {40577477}, issn = {2375-2548}, mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.}, }
@article {pmid40501655, year = {2025}, author = {Chen, J and Pfeifer, K and Steensen, K and Crooke, AM and Wolfram, M and Bobonis, J and Lopatina, A and Bartlau, N and Hussain, FA and Balskus, EP and Polz, MF and Blainey, PC}, title = {Bacterial peptide deformylase inhibitors induce prophages in competitors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40501655}, issn = {2692-8205}, support = {R01 GM132564/GM/NIGMS NIH HHS/United States ; }, abstract = {While antibiotics mediate chemical warfare among microbes, their roles in the wild extend beyond direct growth inhibition(1). Some antibiotics have the potential to mediate interference competition by triggering a bacterial stress response that subsequently activates endogenous viruses integrated in bacterial genomes (prophages). Canonically, this activation is regulated by the SOS response upon DNA damage. Here we show that a metabolite produced by natural isolates of Vibrio ordalii circumvents the SOS response by directly triggering prophage induction in other Vibrio species, co-occurring in the same environment. While the metabolite was previously classified as a broad-spectrum antibiotic, we observe how it acts as a peptide deformylase inhibitor that specifically induces certain prophages, even when target bacterial cells carry multiple other prophages. Its biosynthetic gene cluster, or ord cluster, also encodes its own peptide deformylase (OrdE) which provides self-immunity to producer strains. Likewise, among natural Vibrio isolates that carry similar prophages, resistance against the ord metabolite was found in those that had acquired a divergent second peptide deformylase. Finally, we show that prophage induction by the ord cluster prevents slower-growing producer strains from being outcompeted by their otherwise fast-growing competitors if they carry an inducible prophage. Thus, we demonstrate how natural products play additional impactful roles in communities beyond antibiotic activity and that prophage induction serves as an interference competition strategy, sustaining community diversity.}, }
@article {pmid40576334, year = {2025}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL}, title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf055}, pmid = {40576334}, issn = {1751-7370}, abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.}, }
@article {pmid40573780, year = {2025}, author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F}, title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/plants14121790}, pmid = {40573780}, issn = {2223-7747}, support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; }, abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.}, }
@article {pmid40572127, year = {2025}, author = {Mohammadi, T and Ely, B}, title = {Dolichocephalovirinae Phages Exist as Episomal Pseudolysogens Across Diverse Soil Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572127}, issn = {2076-2607}, abstract = {Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices.}, }
@article {pmid40569388, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of viral landscape phylogeography approaches.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2506743122}, doi = {10.1073/pnas.2506743122}, pmid = {40569388}, issn = {1091-6490}, mesh = {Phylogeography/methods ; *RNA Viruses/genetics ; Phylogeny ; Genome, Viral ; Computer Simulation ; }, abstract = {The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40569073, year = {2025}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W}, title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).}, journal = {mSystems}, volume = {}, number = {}, pages = {e0060325}, doi = {10.1128/msystems.00603-25}, pmid = {40569073}, issn = {2379-5077}, abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.<br><br>IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.}, }
@article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf129}, pmid = {40568985}, issn = {1751-7370}, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index (PS index) from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory (PICO) to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e., disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, }
@article {pmid40567269, year = {2025}, author = {Mohamadi Nasrabadi, A and Eckstein, D and Mettke, P and Ghanem, N and Kallies, R and Schmidt, M and Mothes, F and Schaefer, T and Graefe, R and Bandara, CD and Maier, M and Liebert, UG and Richnow, H and Herrmann, H}, title = {A Virus Aerosol Chamber Study: The Impact of UVA, UVC, and H2O2 on Airborne Viral Transmission.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {6}, pages = {648-658}, pmid = {40567269}, issn = {2833-8278}, abstract = {The COVID-19 pandemic highlighted the urgent need to control airborne virus transmission, particularly in indoor environments with limited ventilation. This study evaluates the effectiveness of UVA and UVC irradiation, along with hydrogen peroxide (H2O2), in inactivating aerosolized viruses. A 19 m[3] virus aerosol simulation chamber, replicating indoor conditions, was used to simulate human respiratory emissions by aerosolizing Escherichia phage T4 (T4 phages) embedded in a pig mucin medium that mimics respiratory aerosols. Results showed a clear, dose-dependent reduction in viral genome copies with UVC exposure, where a dose of 129.9 mJ/cm[2] reduced over 99% of the viral genome copies. Although less efficient, UVA still contributed to virus inactivation, reducing detectable phages to 20% at 513.30 J/cm[2]. Mucin provided a protective effect, making virus removal more challenging. Hydrogen peroxide enhanced disinfection, with 1.6 ppm reducing viral genome copies by 78%, and higher concentrations (up to 16 ppm) achieving over 99% reduction in the dark condition. The combination of UVA/UVC with H2O2 further enhanced disinfection, eliminating detectable virus genome copies entirely. These findings underscore the potential for using combined UV light and chemical treatments to effectively mitigate airborne viral transmission in enclosed spaces.}, }
@article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, doi = {10.1002/vms3.70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.<br><br>OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.<br><br>METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24&#xa0;h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.<br><br>RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p&#xa0;<&#xa0;0.05). Thyme pulp exhibited the highest NH3-N levels (75.14&#xa0;mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93&#xa0;mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, }
@article {pmid40564363, year = {2025}, author = {Luo, G and Cheng, Y and Xu, Y and Liu, J and Yang, W and Liu, J and Guo, B and Zhu, H}, title = {Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/ani15121815}, pmid = {40564363}, issn = {2076-2615}, support = {32202622//National Natural Science Foundation of China/ ; 32102542//National Natural Science Foundation of China/ ; CX(24)1012//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 2025SKLAB6-17//Open project of State Key Laboratory of Animal Biotech Breeding/ ; }, abstract = {This study investigates the effect of monochromatic light on the body weight (BW), melatonin concentration and its receptors expression levels, intestinal health, and gut microorganisms of Yangzhou geese. Green light (GL) significantly increased BW, melatonin and its receptor expression levels, villus height (VH) and villus height/crypt depth (VH/CD) ratio, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) activities, as well as the abundance of Synergistota and Prevotellaceae_UCG-001, compared with white light (WL). Blue light (BL) significantly increased the mRNA expression of melatonin membrane receptor 1a (Mel1a) and nuclear receptor 1α (RORα), VH and VH/CD ratio, CAT activity, cecal microbes diversity, and decreased malondialdehyde (MDA) levels. Red light (RL) significantly decreased average daily feed intake, reduced the abundances of Synergistota and Prevotellaceae_UCG-001, and increased Mel1a and RORα mRNA expression levels, MDA content, and cecum microbial diversity. Moreover, melatonin levels were significantly higher in the GL and BL groups compared to RL. Furthermore, the mRNA expression levels of Claudin-10, Occludin, and occludens-1 (ZO-1) were significantly upregulated under GL or BL exposures compared to the WL group, whereas RL only enhanced the expression levels of ZO-1. Spearman's correlation analysis revealed that the relative abundance of Prevotellaceae_UCG-001 exhibited positive correlations with BW, melatonin and its receptors expression, gut health, and antioxidant capacity. Overall, these findings suggested that GL exposure enhanced melatonin synthesis and its receptors expression, modulated intestinal homeostasis and microbial ecology, and ultimately increased goose BW.}, }
@article {pmid40562244, year = {2025}, author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL}, title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132877}, doi = {10.1016/j.biortech.2025.132877}, pmid = {40562244}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 %-48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.}, }
@article {pmid40561955, year = {2025}, author = {Yasin, MU and Muhammad, S and Chen, N and Hannan, F and Afzal, M and Haider, Z and Ali, B and Ahmad, I and Rehman, M and Gan, Y}, title = {Nano-engineered biochar enhances soil microbial interactions and maize transcriptomic pathways for cadmium detoxification.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139029}, doi = {10.1016/j.jhazmat.2025.139029}, pmid = {40561955}, issn = {1873-3336}, abstract = {Cadmium (Cd) contamination threatens agroecosystems and food security by degrading soil health, inducing plant oxidative stress, and reducing crop yields. Sustainable strategies integrating biochar (BC) with nanoparticles (NPs) for Cd immobilization and soil-plant-microbe restoration remain underexplored. Here, we demonstrate the efficacy of BC, nano-silicon (nSi), and nano-iron (nFe) to immobilize Cd, improve soil health and reprogram maize stress responses in Cd-contaminated soil. Soil Cd bioavailability, microbial networks, and maize transcriptomes were analyzed under varying BC-nSi-nFe formulations. Among these formulations, the BC + 25 % nSi + 75 % nFe + Cd (T6) composite reduced bioavailable Cd by 21 %, raised soil pH from 6.21 to 6.98, and enhanced soil enzyme activities (118-139 %). T6 improved maize biomass (115-119 %), reduced shoot Cd accumulation (78 %), and suppressed oxidative stress (67-75 % ROS reduction). This study presents transcriptomic evidence showing that BC-NPs composites mitigate Cd stress and modulate maize antioxidant defense and phytohormone signaling pathways, offering new insights into the molecular mechanisms underlying improved plant resilience. Soil microbial networks shifted toward metal-resistant taxa, with enriched glutathione metabolism and nitrogen fixation. BC-NPs composites offer a multidimensional remediation strategy, integrating nanomaterial science, microbial ecology, and plant molecular biology to mitigate Cd toxicity. This approach enhances soil-plant resilience, supporting sustainable agriculture in contaminated ecosystems.}, }
@article {pmid40561631, year = {2025}, author = {Ma, X and Li, Y and Niu, L and Grossart, HP and Shang, J and Zheng, J and Wu, J}, title = {Salinity regulates nutrient cycling via top-down and bottom-up forces in artificial cut-off tidal channels: Insights from multitrophic microbiota.}, journal = {Water research}, volume = {285}, number = {}, pages = {124037}, doi = {10.1016/j.watres.2025.124037}, pmid = {40561631}, issn = {1879-2448}, abstract = {Artificial cut-off of natural tidal meanders for flood control has substantially altered microbial communities and their role in nutrient cycling, yet the lack of comprehensive investigations into these specific anthropogenic impacts introduces greater uncertainty regarding the resultant water quality of nutrient-enriched estuaries. Here, we investigated how planktonic multitrophic microbiota and their mediated nutrient cycling respond to artificial meander cut-off using the environmental DNA (eDNA) approach. Results showed that despite the decline in α diversity of multitrophic microbiota, the nutrient cycling potential of the water column was enhanced 2.91-fold in the straight tidal channel. The artificial cut-off restructured the microbial food web, with trophic transfer efficiency from basal species to protozoa increasing. Salinity was identified to be the key environmental driver, mitigating the negative impact of decreased biodiversity on estuarine nutrient cycling potential by intensifying protozoan predation on heterotrophic bacteria (top-down forces). Additionally, salinity further enhanced environmental selection (bottom-up forces), reducing heterotrophic bacterial diversity while promoting the proliferation of functional microbial taxa, such as Comamonadaceae, Chitinophagaceae, and Rhodocyclaceae. This study offers novel insights into nutrient cycling in artificial straight tidal channels and provides critical foundations for optimizing restoration and management strategies in anthropogenically modified tidal river.}, }
@article {pmid40560449, year = {2025}, author = {de Meireles, DA and Souza, T and de A A Carneiro, K and da S Fraga, V and de O Dias, B and da S Batista, D and Martins, EL and de Lima, AFL and Dos Santos Nascimento, G and Campos, MCC}, title = {Treated Wastewater Irrigation Enhances Plant Biomass, Soil Fertility, and Rhizosphere Microbial Activity in C4 and CAM species Grown on a Degraded Planosol.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {804}, pmid = {40560449}, issn = {1573-2959}, mesh = {*Wastewater/chemistry ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Biomass ; *Waste Disposal, Fluid/methods ; Brazil ; }, abstract = {The Brazilian semi-arid region, marked by erratic rainfall and severely degraded soils, presents critical challenges for sustainable agriculture. In this context, the reuse of treated domestic wastewater-collected from a septic tank and anaerobic filter system-offers a promising strategy to enhance plant productivity and rehabilitate soil conditions, particularly within the Caatinga biome. This study evaluated the long-term (four-year) effects of irrigation with pure water versus treated domestic wastewater on plant dry biomass, soil fertility, and rhizospheric microbial activity in a degraded Planosol. Two plant types were assessed: a C4 species (Mimosa caesalpiniifolia) and a CAM species (Opuntia atropes). Results demonstrated that treated wastewater irrigation significantly increased dry biomass, with a 12.18% increase in the C4 species and a 29.33% increase in the CAM species. Soil chemical fertility improved notably, with wastewater application raising soil pH by 5.0%, increasing soil organic carbon by 87.9%, and enhancing nutrient availability, including nitrogen, potassium, magnesium, and sodium. A 37.5% reduction in exchangeable aluminum further indicated mitigation of soil acidity. Microbial responses varied between species: while soil respiration increased in both rhizospheres-more prominently in CAM species-microbial biomass carbon rose significantly in the C4 rhizosphere but declined in CAM, suggesting species-specific microbial interactions. These findings support the potential of treated domestic wastewater as a nutrient-rich, low-cost irrigation alternative for improving plant performance and soil quality in semi-arid degraded lands. Nevertheless, potential risks-including salinity build-up and pathogen persistence-necessitate long-term monitoring and further environmental safety assessments. By integrating plant physiology, soil chemistry, and microbial ecology, this study offers a comprehensive approach to evaluating wastewater reuse as a sustainable agricultural and ecological restoration practice in the Caatinga biome.}, }
@article {pmid28732554, year = {2017}, author = {De Vuyst, L and Van Kerrebroeck, S and Leroy, F}, title = {Microbial Ecology and Process Technology of Sourdough Fermentation.}, journal = {Advances in applied microbiology}, volume = {100}, number = {}, pages = {49-160}, doi = {10.1016/bs.aambs.2017.02.003}, pmid = {28732554}, issn = {0065-2164}, mesh = {Bread/analysis/*microbiology ; Fermentation ; Food Handling ; Lactobacillus/genetics/*metabolism ; *Microbiota ; Triticum/*metabolism/microbiology ; Yeasts/genetics/*metabolism ; }, abstract = {From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.}, }
@article {pmid40559796, year = {2025}, author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV}, title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/vetsci12060559}, pmid = {40559796}, issn = {2306-7381}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.}, }
@article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, doi = {10.3390/md23060242}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, }
@article {pmid40558970, year = {2025}, author = {Vieira, RIM and Peixoto, ADS and Monclaro, AV and Ricart, CAO and Filho, EXF and Miller, RNG and Gomes, TG}, title = {Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/jof11060458}, pmid = {40558970}, issn = {2309-608X}, support = {00193-00002388/2023-21//Foundation for Research Support of the Federal District/ ; }, abstract = {Microbial decomposition of persistent natural compounds such as phenolic lignin and polysaccharides in plant cell walls plays a crucial role in the global carbon cycle and underpins diverse biotechnological applications. Among microbial decomposers, fungi from the Ascomycota and Basidiomycota phyla have evolved specialized mechanisms for efficient lignocellulosic biomass degradation, employing extracellular enzymes and synergistic fungal consortia. Fungal coculture, defined as the controlled, axenic cultivation of multiple fungal species or strains in a single culture medium, is a promising strategy for industrial processes. This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. Lignocellulosic biomass conversion into fuels, energy, and biochemicals is central to the bioeconomy, integrating advanced biotechnology with sustainable resource use. Recent advancements in -omics technologies, including genomics, transcriptomics, and proteomics, have facilitated detailed analysis of fungal metabolism, uncovering novel secondary metabolites and enzymatic pathways activated under specific growth conditions. This review highlights the potential of fungal coculture systems to advance sustainable biomass conversion in alignment with circular bioeconomy goals.}, }
@article {pmid40557448, year = {2025}, author = {Lingua, MS and Sabatino, ME and Cuatrin, A and Salvucci, E and Blajman, JE and Páez, RB and Wunderlin, DA and Baroni, MV}, title = {From waste to worth: stability, bioaccessibility, and cellular antioxidant activity of microencapsulated red grape pomace phenolics.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70010}, pmid = {40557448}, issn = {1097-0010}, support = {//This work was supported by the National Institute of Agricultural Technology (INTA, Argentina) (Projects 2019-PD-I152-A537 and 2019-PE-I150-A5) and the National Agency of Scientific and Technological Promotion (FONCyT, Argentina), and Argentine Wine Corporation (COVIAR) (Project PICTO-COVIAR-2017-0123)./ ; }, abstract = {BACKGROUND: Red grape pomace (RGP) is a recognized winery by-product due to its phenolic profile with valuable antioxidant power and beneficial health properties. Following the latest trends in food science and technology, this study valorizes the use of RGP to obtain a food ingredient rich in antioxidant phenolics. An integrated approach was proposed, investigating the production by spray drying of easy-to-handle microparticles, rich in stable compounds with antioxidant properties demonstrated after simulated digestion using in vitro assays and Caco-2 cells. The changes in microbiota composition after fermentation were also studied.<br><br>RESULTS: Among investigated wall materials, maltodextrin/skimmed milk powder (1:1) 300&#x2009;g&#x2009;L[-1] offered the highest drying yield, appropriate moisture, solubility, and adequate microparticle morphology, as well as the best stability of polyphenols. Encapsulation improved the protection of phenolic compounds and the in vitro antioxidant capacity during 120&#x2009;days of storage at 4 and 25&#x2009;&#xb0;C, as compared to those unencapsulated. Microencapsulated polyphenols bioaccessibility was evident in 15 out of 22 compounds initially quantified, with 6.6% potentially absorbed. The polyphenols from microcapsules modulated positively the microbial ecology after colonic fermentation. Those derived from intestinal digestion demonstrated the highest capacity to reduce the reactive oxygen species under oxidative stress conditions in Caco-2 cells.<br><br>CONCLUSION: RGP could be used in the development of new food ingredients as a potential candidate for health promotion. This represents the first report on the benefits of RGP microcapsules as a food ingredient, validating its final biological effects in a cellular model considering the processing and digestion effects. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40556886, year = {2025}, author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM}, title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570127}, doi = {10.3389/fmicb.2025.1570127}, pmid = {40556886}, issn = {1664-302X}, abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.}, }
@article {pmid40556136, year = {2025}, author = {Long, Y and Li, Y and Zhang, J and Liu, J and Han, Q and Cao, Y and Jiang, Y and Liu, C and Hu, Y and Wang, G and Zhang, X and Jin, J and Semenov, M and Han, G and Liu, X and Yu, Z}, title = {Unconventional Nitrogen Fixation and Adaptive Genomics of a New Neorhizobium glycines sp. nov., A Promising Soybean Symbiont.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70046}, pmid = {40556136}, issn = {1365-3040}, support = {//This study was funded by the National Key R &amp; D Program of China (2021YFD1500400), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020201), National Natural Science Foundation of China (32172123, 42207399)./ ; }, }
@article {pmid40555367, year = {2025}, author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM}, title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250729}, doi = {10.1098/rspb.2025.0729}, pmid = {40555367}, issn = {1471-2954}, support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; }, mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.}, }
@article {pmid40553410, year = {2025}, author = {Bota, JL and Baum, C and Gawronski, S and Grafe, TU and Kerth, G and Schöner, MG and Schöner, CR}, title = {UV treatment of the digestive fluid of Nepenthes hemsleyana pitcher plants affects their digestive process, possibly via reducing microbial inquilines.}, journal = {Oecologia}, volume = {207}, number = {7}, pages = {108}, pmid = {40553410}, issn = {1432-1939}, support = {SCHO1740/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Ultraviolet Rays ; Animals ; Digestion/radiation effects ; }, abstract = {Interactions with microbes are ubiquitous, and many of them are essential for the survival and success of plants. In Nepenthes pitcher plants, they occur as part of a diverse community of organisms, so-called inquilines, that live inside the digestive fluid of the pitcher traps. However, evidence is ambiguous regarding the role of microbial inquilines: they may complement the plants' prey digestion, fix atmospheric N, act as competitors that reduce plant-available nutrients or affect the plants in other ways unrelated to the breakdown of prey. In a field experiment on Borneo, we investigated the effect of UV disinfection of the digestive fluid on prey digestion of N. hemsleyana that captures and digests insects as well as bat faeces in its pitchers. We show that in the short term, the photosynthetic performance of plants with UV-treated digestive fluids decreases compared to untreated plants, likely due to lower abundances of microbial inquilines. However, at the end of 2 months, responses of pitcher plants with UV-treated and untreated digestive fluids tend to equalise. Nutrient source, whether from insects or bat faeces, does not influence prey digestion. We expect our findings to be a starting point for unveiling the ecological role of microbial inquilines in pitcher plants and how they interact with other inquiline groups of higher trophic levels. Ultimately, this will also help to improve understanding of the functioning and evolution of convergent interactions in other carnivorous plants.}, }
@article {pmid40553254, year = {2025}, author = {Wu, BX and Ma, JY and Huang, XC and Liang, XS and Ning, BL and Wu, Q and Wang, SZ and Zhou, JH and Fu, WB}, title = {Acupuncture as A Potential Therapeutic Approach for Tourette Syndrome: Modulation of Neurotransmitter Levels and Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {}, number = {}, pages = {}, pmid = {40553254}, issn = {1993-0402}, abstract = {OBJECTIVE: To investigate the effects of acupuncture on the neurotransmitter levels and gut microbiota in a mouse model of Tourette syndrome (TS).<br><br>METHODS: Thirty-six male C57/BL6 mice were randomly divided into 4 groups using a random number table method: 3,3'-iminodipropionitrile (IDPN) group, control group, acupuncture group, and tiapride group, with 9 mice in each group. In the IDPN group, acupuncture group, and tiapride group, mice received daily intraperitoneal injections of IDPN (300 mg/kg body weight) for 7 consecutive days to induce stereotyped behaviors. Subsequently, in the acupuncture intervention group, standardized acupuncture treatment was administered for 14 consecutive days to IDPN-induced TS model mice. The selected acupoints included Baihui (DU 20), Yintang (DU 29), Waiguan (SJ 5), and Zulinqi (GB 41). In the tiapride group, mice were administered tiapride (50 mg/kg body weight) via oral gavage daily for 14 consecutive days. The control group, IDPN group, and acupuncture group received the same volume of saline orally for 14 consecutive days. Stereotypic behaviors were quantified through behavioral assessments. Neurotransmitter levels, including dopamine (DA), glutamate (Glu), and aspartate (ASP) in striatal tissue were measured using enzyme-linked immunosorbent assay. Dopamine transporter (DAT) expression levels were additionally quantified through quantitative polymerase chain reaction (qPCR). Gut microbial composition was analyzed through 16S ribosomal RNA gene sequencing, while metabolic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: Acupuncture administration significantly attenuated stereotypic behaviors, concurrently reducing striatal levels of DA, Glu and ASP concentrations while upregulating DAT expression compared with untreated TS controls (P<0.05 or P<0.01). Comparative analysis identified significant differences in Muribaculaceae (P=0.001), Oscillospiraceae (P=0.049), Desulfovibrionaceae (P=0.001), and Marinifilaceae (P=0.014) following acupuncture intervention. Metabolomic profiling revealed alterations in 7 metabolites and 18 metabolic pathways when compared to the TS mice, which involved various amino acid metabolisms associated with DA, Glu, and ASP.<br><br>CONCLUSIONS: Acupuncture demonstrates significant modulatory effects on both central neurotransmitter systems and gut microbial ecology, thereby highlighting its dual therapeutic potential for TS management through gut-brain axis regulation.}, }
@article {pmid40548738, year = {2025}, author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N}, title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0197324}, doi = {10.1128/spectrum.01973-24}, pmid = {40548738}, issn = {2165-0497}, abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.<br><br>IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.}, }
@article {pmid40545777, year = {2025}, author = {VanWallendael, A and Wijewardana, C and Bonnette, J and Vormwald, L and Fritschi, FB and Boe, A and Chambers, S and Mitchell, RB and Rouquette, FM and Wu, Y and Fay, PA and Jastrow, JD and Lovell, JT and Juenger, TE and Lowry, DB}, title = {Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70313}, pmid = {40545777}, issn = {1469-8137}, support = {DE-AC02-06CH11357//Biological and Environmental Research/ ; DE-SC0014156//Biological and Environmental Research/ ; DE-SC0017883//Biological and Environmental Research/ ; DE-SC0018409//Biological and Environmental Research/ ; 1832042//Division of Environmental Biology/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host-parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a 'host reciprocal transplant' framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.}, }
@article {pmid40542918, year = {2025}, author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y}, title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40542918}, issn = {1869-1889}, abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.}, }
@article {pmid40542710, year = {2025}, author = {Susukida, S and Miyazawa, K and Ichikawa, H and Muto, K and Yoshimi, A and Kumagai, T and Kato, Y and Abe, K}, title = {Improved Mixing Properties of Stirred Fermentation of an Aspergillus oryzae Hyphal Dispersion Mutant.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.70004}, pmid = {40542710}, issn = {1097-0290}, support = {//This study was supported by the Institute for Fermentation, Grant/Award Number: L-2018-2-014; Japan Science and Technology Agency-Adaptable and Seamless Technology Transfer Program through target-driven R&amp;D, Grant/Award Number: JPMJTM19Y4; JSPS KAKENHI, Grant/Award Number: JP20H02895; and New Energy and Industrial Technology Development Organization, Grant/Award Number: JPNP20011./ ; }, abstract = {The complexity of mechanical and biological processes in filamentous fungal fermentation remains a major obstacle to improving product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) and multi-omics analysis to characterize the AGΔ-GAGΔ strain during fermentation in a stirred-tank bioreactor. CFD simulations revealed large gas cavities behind the impeller blades and severe compartmentalization in both wild-type and AGΔ-GAGΔ cultures. However, shear stress distribution was broader and gas cavity formation was lower in the AGΔ-GAGΔ strain than in the wild type. The simulation results were consistent with measurements of volumetric oxygen mass transfer coefficients (KLa) and mixing times. Transcriptome analysis revealed upregulation of TCA-cycle genes in AGΔ-GAGΔ relative to the wild type. Analysis of intracellular and extracellular metabolites indicated distinct metabolic profiles associated with oxygen availability. Our findings highlight the critical role of hydrodynamics in fungal fermentation and demonstrate the potential of strain engineering for improving mixing characteristics.}, }
@article {pmid40540980, year = {2025}, author = {Noviello, D and Amoroso, C and Vecchi, M and Facciotti, F and Caprioli, F}, title = {Curing inflammatory bowel diseases: breaking the barriers of current therapies- emerging strategies for a definitive treatment.}, journal = {Current opinion in immunology}, volume = {95}, number = {}, pages = {102593}, doi = {10.1016/j.coi.2025.102593}, pmid = {40540980}, issn = {1879-0372}, abstract = {Chronic intestinal inflammation in inflammatory bowel diseases (IBD) reflects the interplay of genetic predisposition, immune dysregulation, microbial imbalance, and epithelial barrier defects. Current therapies for IBD primarily focus on controlling inflammation necessitating lifelong treatment and face a 'therapeutic ceiling' due to primary and secondary loss of efficacy over time. Immune-mediated approaches do not address additional pathogenic mechanisms, such as impairment of epithelial barrier and gut microbial ecology. Thus, innovative strategies are required to foster the field closer to a definitive cure. This review discusses novel strategies to overcome current therapeutic limitations, including immune reset via hematopoietic stem cell transplantation and B cell-targeted therapies, antigen-specific interventions such as chimeric antigen receptor T cells and tolerogenic vaccines, and intestinal epithelial barrier restoration. We also explore microbiota-based strategies - ranging from fecal microbiota transplantation to engineered consortia and bacteriophages - and discuss the adjunctive role of diet. Together, we outline a potential research roadmap toward a potential cure for IBD.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; }, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40539105, year = {2025}, author = {Zhang, Z and Shi, Z and Zheng, L and Zhang, H}, title = {Remediation of acetochlor-contaminated maize field soil using Serratia odorifera AC-1 fertilizer: effects on soil microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1510157}, pmid = {40539105}, issn = {1664-302X}, abstract = {Acetochlor is a chloroacetamide herbicide that is widely applied in corn fields. Nevertheless, the long-term usage of acetochlor in the soil leads to residues, which severely affect the germination of corn seeds and the growth of seedlings, and even exert an influence on the soil microbial community. Microbial degradation of acetochlor is the principal approach for restoring the soil microbial ecology. In this study, the Serratia odorifera AC-1 strain was isolated and identified from the soil for the degradation of residual acetochlor in the soil. To enhance the degradation efficiency, a solid microbial agent was prepared by using activated carbon as a carrier and the AC-1 strain at a 1:1 ratio and applied to the soil for degradation and remediation experiments. The content of the microbial cells in the solid microbial agent was 1.49 × 106 CFU/g after 120 days of preparation. The application of the AC-1 solid microbial agent significantly influenced the relative abundance of soil microbial communities (Actinobacteria, Firmicutes, and Proteobacteria), increasing the diversity of bacterial populations in the soil. The experimental results indicated that after the application of the AC-1 solid microbial agent, the plant height, stem diameter, and photosynthetic efficiency of corn seedlings under acetochlor stress were significantly elevated. When the application rate of the AC-1 solid microbial agent was 5.00 mg/kg, the stem diameter of corn increased by 56.4% compared with the control group. When the acetochlor concentration in the soil was 6.65 mg/kg, the DT50 value of the AC-1 solid microbial agent was 2.28 days. This study clarified the degradation mechanism and remediation capacity of the Serratia odorifera AC-1 strain in acetochlor-contaminated soil and proposed a new strategy to improve the stability and degradation efficiency of the microbial strain by optimizing the immobilization technology of the strain on activated carbon. This research provides a scientific basis and technical guidance for the future application of bioremediation technology in the field environment to remove pesticide residues, restore soil health, and enhance crop productivity.}, }
@article {pmid40537563, year = {2025}, author = {Embury, EL and Romero-Olivares, AL}, title = {Fungi Follow Flora, Bacteria Track the Seasons: A Tale of a Changing Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {68}, pmid = {40537563}, issn = {1432-184X}, support = {R16 GM146585/GM/NIGMS NIH HHS/United States ; 1R16GM146585//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2312226//National Science Foundation Building Research Capacity in Biology/ ; }, mesh = {Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota ; Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Biodiversity ; }, abstract = {Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions.}, }
@article {pmid40536564, year = {2025}, author = {Parret, L and Simoens, K and Horemans, B and De Vrieze, J and Smets, I}, title = {Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {149}, pmid = {40536564}, issn = {1432-0614}, support = {C24/18/043//KU Leuven/ ; FWO-G032321N//Fonds Wetenschappelijk Onderzoek/ ; FWO- 1191022N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Flocculation ; *Wastewater/microbiology ; Coculture Techniques/methods ; Sewage/microbiology ; *Bacteria/metabolism/growth &amp; development ; Bioreactors/microbiology ; Alginates ; *Water Purification/methods ; *Nitrogen/metabolism ; Nitrification ; Microbial Consortia ; }, abstract = {Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points ∙ Studying flocculation with a model consortium is feasible ∙ Alginate entrapment leads to strong microcolony formation of nitrifiers ∙ FISH by itself is not suitable to study aggregation of a coculture.}, }
@article {pmid40536143, year = {2025}, author = {Timmis, K and Williams, P and Karahan, ZC and López-García, P and Rainey, P and Chavarria, M and Greening, C and Steward, K and Hallsworth, JE and Pereira, CS and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H}, title = {Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice.}, journal = {Microbial biotechnology}, volume = {18}, number = {6}, pages = {e70180}, pmid = {40536143}, issn = {1751-7915}, mesh = {*Periodicals as Topic/standards ; Peer Review, Research/standards ; Humans ; }, abstract = {Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it seeks new knowledge, there is little or no benchmark for appraisal of the plausibility or validity of the immediate conclusions drawn from new information gained, no instant confirmation. For this and other reasons, the science ethos requires the highest level of rigour to ensure the highest level of probability that new findings are true, or at least the most plausible under the prevailing circumstances and state of knowledge. Research is only as good as its degree of rigour. Rigour comes through intensive and comprehensive scientific training and mentoring that teaches critical and agnostic evaluation of new results, self-scrutiny and self-criticism. Additional rigour comes via independent scrutiny and validation: peer review of results and interpretations submitted as publications, and peer repetition of key experiments. However, the current proliferation of publication vehicles whose business model is based on maximisation of papers published, and the revenue stream of article processing charges (APCs) they generate, is promoting an insidious degradation of rigour and quality standards of reviewing-editing practices. Such predatory practices result in the systematic degradation of research quality and its "truthfulness". Moreover, they undermine the science ethos and threaten to create a new generation of scientists that lack this ethos. These trends will inevitably progressively erode public trust in scientists and the research ecosystem. This Editorial is a call for action to all actors, in particular leaders, in scientific research to oppose predatory practices in science dissemination-to restrict the operational space of those responsible for such practices-in order to restore and maintain research rigour and the science ethos and to prevent a downward spiral of research quality. It proposes two linked actionable solutions to the problem, one for the "pull" element of predatory practices and one for the "push" element of research ecosystem management practices, especially those promoting the publish or perish mentality, that drive authors to publish in journals with predatory practices. To counter the "pull", we propose a solution based on the principle of prevention, rather than cure, and list a number of essential policy decisions and actions that should be taken at all levels of the science chain/cloud to achieve this. A central plank of the concept is journal accreditation, without which a journal would be ineligible for payment of APCs from public funds. For accreditation, a journal would need to convincingly demonstrate adoption of a prescribed journal code of conduct. Ideally, accreditation would also be required for inclusion in journal indexing and ranking services and bibliographic databases. To counter the "push", we propose a top-down imposition of a cultural change in science management that ensures merit-based success of scientists and their careers, research best practice, improved education and mentoring of younger scientists in the science ethos and greater support of them in their careers. This must include explicit recognition of the crucial role of peer reviewing for the good health of the research enterprise, its incentivisation and appropriate appreciation of the time and effort involved. To orchestrate this change, we propose the creation of a multi-stakeholder alliance whose brief is to develop the framework and implementation strategy for changes in the research ecosystem. This Editorial also exhorts all actors to embrace the principle of publish less, publish better and to use public funding provided by tax revenues more effectively to perpetually raise the bar of science quality, dissemination and potential to advance humanity.}, }
@article {pmid40534981, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF}, title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71595}, pmid = {40534981}, issn = {2045-7758}, abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.}, }
@article {pmid40533683, year = {2025}, author = {Rios-Reyes, A and Gonzalez-Lozano, KJ and Cabral-Miramontes, JP and Hernandez-Gonzalez, JJ and Rios-Sosa, A and Alvarez-Gutierrez, PE and Mireles-Torres, SP and Batista-García, RA and Arechiga-Carvajal, ET}, title = {Exploration of Plant and Microbial Life at "El Chichonal" Volcano with a Sustainable Agriculture Prospection.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {67}, pmid = {40533683}, issn = {1432-184X}, support = {700634//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 2055419//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 1081508//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 315114//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 252373/SEP-CONACYT//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CBF2023-2024-3120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Fungi/isolation &amp; purification/classification/genetics ; Agriculture ; Soil/chemistry ; *Volcanic Eruptions ; Bacillus cereus/isolation &amp; purification/genetics ; Plant Roots/microbiology ; Microbiota ; }, abstract = {Active volcanic environments represent extreme habitats with underexplored potential for microbial bioprospecting. This study aimed to characterize pioneer vegetation and associated microbial diversity in the crater of "El Chichonal" volcano, with an emphasis on their potential applications in sustainable agriculture. A physicochemical analysis of the soil was performed, identifying acidic and nutrient-poor conditions. Three pioneer plant species were described: Tibouchina longifolia (dominant) and Poaceae spp. (co-dominant), and Palhinhaea cernua (non-dominant). A total of 311 microorganisms were predominantly bacteria, were isolated from soil, root, stem, and water samples. Bacillus cereus and Priestia megaterium were molecularly identified, and in vitro assays demonstrated their ability to fix nitrogen, produce auxins, and antagonize fungal pathogens (Alternaria solani, Botrytis cinerea, and Colletotrichum gloeosporioides). These results suggest that microorganisms adapted to extreme volcanic environments could be promising sources of plant growth-promoting bacteria (PGPB) with application in biological control.}, }
@article {pmid40533475, year = {2025}, author = {Wollrab, S and Schmidt, SR and Woodhouse, J and Kasprzak, P and Berger, SA and Beyer, U and Bodenlos, M and Dalchow, J and Degebrodt, M and Ganzert, L and Gonsiorczyk, T and Huth, E and Kiel, C and Küchler, L and Krienitz, L and Lentz, M and Mach, E and Mallok, U and Nejstgaard, JC and Papke, M and Penske, A and Pinnow, S and Roßberg, R and Ronneberger, D and Sachtleben, M and Scheffler, A and Grossart, HP and Casper, P and Gessner, MO and Koschel, R}, title = {Fifty years of limnological data on Lake Stechlin, a temperate clearwater lake.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1028}, pmid = {40533475}, issn = {2052-4463}, abstract = {We present 50 years of monitoring data on water quality of Lake Stechlin, a deep, dimictic hardwater lake in northeastern Germany known for its exceptionally clear water. Although located in a forested catchment, the lake has undergone major changes in recent decades, including a period of massive heating of surface water when receiving cooling water from a nearby nuclear power plant (1966-1990), accompanied by a greatly shortened water residence time from more than 40 years to less than 300 days. These changes are superimposed by a long-term trend of surface water warming and a concomitant decrease in winter ice cover. Total phosphorus concentrations have quadrupled since 2010 and zones of deep-water oxygen depletion have greatly expanded. The presented dataset covers basic water-chemical and physical records taken at monthly to fortnightly intervals from 1970 to 2020, documenting limnological changes during that period. Furthermore, it serves as a valuable basis to assess and project potential consequences of climate change and other types of environmental change on deep clearwater lakes in temperate climates.}, }
@article {pmid40531665, year = {2025}, author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S}, title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006815}, pmid = {40531665}, issn = {1466-5034}, mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; }, abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).}, }
@article {pmid40531656, year = {2025}, author = {Bou Orm, E and Mukherjee, S and Rifa, E and Créach, A and Grec, S and Bayle, S and Benezet, JC and Bergeret, A and Malhautier, L}, title = {Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70102}, pmid = {40531656}, issn = {1758-2229}, mesh = {*Biodiversity ; *Fungi/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Bacteria/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Cannabis/microbiology/metabolism ; Pectins/metabolism ; Glycoside Hydrolases/metabolism ; Microbiota ; }, abstract = {Hemp field retting is a bioprocess that facilitates fibre extraction by degrading pectin and other matrix components surrounding fibre bundles. However, traditional methods rely on empirical practices, often resulting in inconsistent fibre quality. This study investigates the biodiversity-function relationship in the hemp retting ecosystem to identify microbial and enzymatic indicators for improved process control. Over six weeks of field retting, we monitored bacterial and fungal community dynamics using high-throughput sequencing and assessed enzymatic activity profiles. Our results revealed a sequential enzymatic pattern: pectinases (e.g., polygalacturonase) dominated early stages, followed by hemicellulases (β-xylosidase, β-galactosidase), and later cellulases. These enzymatic shifts were reflected in the changes in microbial community composition, with pectinolytic bacteria (e.g., Proteobacteria) dominating the initial phases and cellulolytic fungi (e.g., Ascomycota) becoming more prevalent later. Our results identified specific microbial taxa correlated with optimal retting, suggesting their potential as bioindicators for monitoring retting. Specifically, key bacterial genera such as Pseudomonas and Sphingomonas, and fungal genera like Cladosporium, were associated with distinct enzymatic profiles. Our findings offer new insights into the microbial ecology of retting, providing both microbial and enzymatic indicators that could inform the development of monitoring strategies for process control, ultimately contributing to more consistent hemp fibre production.}, }
@article {pmid40530365, year = {2025}, author = {Akdur Öztürk, E and Guadano-Procesi, I and Figueiredo, AM and Godfrey, A and Gentekaki, E and Tsaousis, AD and Carmena, D and Dogruman-Al, F}, title = {A protocol for mapping Blastocystis epidemiology and diagnostics from One Health perspective.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {133}, pmid = {40530365}, issn = {2732-5121}, abstract = {Blastocystis is a globally prevalent gut protist colonising over a billion people worldwide, yet its epidemiology, transmission dynamics, and clinical significance remain underexplored. This protocol represents the first step of a large-scale effort to map Blastocystis epidemiology and diagnostic practices across Europe through the COST Action CA21105: Blastocystis under One Health. By assessing diagnostic methodologies across clinical, veterinary, and environmental sectors, this work sets the foundation for future research and standardisation. Here, we highlight key findings, challenges, and a roadmap for improving Blastocystis detection, ultimately influencing global health policies and microbial ecology studies.}, }
@article {pmid40530126, year = {2025}, author = {Wu, WJ and Wang, K and Yang, YV and Yang, X}, title = {Identification of neuronal synapse-related signatures and potential therapeutic drugs in colorectal cancer based on machine learning algorithms and molecular docking.}, journal = {Translational cancer research}, volume = {14}, number = {5}, pages = {2737-2757}, pmid = {40530126}, issn = {2219-6803}, abstract = {BACKGROUND: Nervous system-cancer interactions can regulate tumorigenesis, invasion, and metastasis. However, specific biomarkers for targeting neuron synapse in colorectal cancer (CRC) remain unexplored. This study aims to develop a neuronal synapse-related signature (NSRS) to predict survival in CRC patients, identify potential therapeutic drugs, and explore its clinical applications.<br><br>METHODS: We collected neuronal synapse genes (NSGs) from the Molecular Signatures Database (MSigDB) and published mass spectrometry data. Using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator Cox regression (LASSO-Cox), we identified prognostic NSGs and constructed a NSRS through multivariate Cox regression. Functional enrichment analysis revealed the molecular characteristics of NSRS subgroups. Additionally, xCell and ESTIMATE algorithms quantified the abundance of 54 cell subtypes and assessed the tumor immune microenvironment (TIME) of the two NSRS subgroups. Finally, drug prediction and molecular docking identified candidate drugs with therapeutic potential.<br><br>RESULTS: Seven key prognostic NSGs were identified, and an independent, stable NSRS model was constructed. Kaplan-Meier survival curves indicated that the high NSRS group had poorer outcomes (log-rank test, P<0.05). Functional enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, hypoxia, and inflammation features in the high NSRS group. xCell and ESTIMATE analyses showed a more complex TIME and lower tumor purity in the high NSRS group, highlighting the role of neuro-tumor interactions in CRC. Drug prediction and molecular docking suggested alprostadil, dihydroergocristine, and nocodazole as candidate drugs for CRC treatment.<br><br>CONCLUSIONS: This is the first study to develop neuron synapse-related biomarkers from the perspective of neuron-cancer interactions using machine learning. We constructed a robust NSRS model and identified candidate drugs targeting prognostic NSGs, providing new insights into CRC prognosis and treatment.}, }
@article {pmid40529576, year = {2025}, author = {Sanz-López, C and Amato, M and Torrent, D and Borrego, M and Anza, M and Bibiso, M and Grijalva-Vallejos, N and Vilanova, C and Porcar, M and Pascual, J}, title = {Microbial ecology of selected traditional Ethiopian fermented products.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570914}, pmid = {40529576}, issn = {1664-302X}, abstract = {The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.}, }
@article {pmid40529573, year = {2025}, author = {Ma, R and Zhang, Z and Wang, J and Han, Y and Li, K and Hou, M and Lei, Y and Xiong, S and Yang, B and Zhi, X and Jiao, Y and Lin, T and Zhang, S and Li, Y}, title = {Mitigating gaseous nitrogen emissions in cotton fields through green manure and reduced nitrogen fertilization.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615142}, pmid = {40529573}, issn = {1664-302X}, abstract = {Integrating green manure with reduced nitrogen (N) fertilization is a promising strategy to mitigate N emissions in intensive cotton cultivation, however, the underlying mechanisms remain poorly understood. This study investigated the effects of three green manure incorporation patterns-no green manure (NG), Orychophragmus violaceus (OVG), and Vicia villosa (VVG)-combined with four N reduction levels (100, 50, 25%, and conventional) on gaseous N emissions (NH3 and N2O), soil physicochemical properties, and bacterial community characteristics using a cotton field experiment in the Yellow River Basin. Results showed that OVG incorporation with 25% N reduction (N2 treatment) significantly reduced total gaseous N emissions by 36.07% on average during the cotton growth period, reducing NH3 and N2O emissions by 13.31-54.11% and 32.25-68.77%, respectively, compared with N2 application without OVG. OVG application also increased the relative abundance of Proteobacteria (28.10%), enhanced heterogeneous selection in bacterial community assembly (200%), and increased the complexity of co-occurrence networks, compared with NG. Compared with conventional N fertilization (N3 treatment), ≥50% N reduction significantly lowered NH3 (>25.51%) and N2O (>32.76%) emissions, reduced the relative abundance of Acidobacteria (-20.23%), simplified co-occurrence networks, and increased homogeneous selection in bacterial assembly (50.00%). Integrating green manure with 25% N reduction substantially reduced gaseous N emissions, which was associated with the enhanced microbial biomass carbon (MBC) and facilitated recruitment of key bacterial taxa (e.g., Sphingosinicella, Azohydromonas, Phototrophicus) within the microbial co-occurrence network. These findings provide insight into how green manure application coupled with N reduction can mitigate gaseous N losses and reshape soil microbial ecology, offering a theoretical basis for sustainable nutrient management during cotton production.}, }
@article {pmid40528722, year = {2025}, author = {Gao, D and Guo, X and Yang, Z and Li, H and Chen, Y and Yang, X and Song, L and Yang, X and Yang, J and Zhou, C}, title = {Effects of Sibiraea laevigate maxim polysaccharides on intestinal flora in immunosuppressed mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.14433}, pmid = {40528722}, issn = {1097-0010}, support = {//The program of Science and Technology Department of Gansu Province (2024ZDPC001, 24YFFA026, 23CXGP0002)/ ; //The innovation Drive assistance project of Gansu for Science and Technology Association (GXH20240328-3)/ ; 2023QB-001//The Young Doctor Fund of Gansu Province/ ; //The youth science and technology talent innovation project of Lanzhou (2023-QN-69)./ ; //The Fundamental Research Funds for the Central Universities of Northwest Minzu University (31920240125-01)./ ; 2024RCXM45//The key talent project of Gansu Province (2024)/ ; }, abstract = {BACKGROUND: The intestinal microbial ecology plays a significant role in maintaining normal physiological function processes and significantly influences the immune system. However, research regarding its effects on gut flora and in vivo immunomodulation is insufficient.<br><br>RESULTS: In this study, cyclophosphamide was administered to mice to establish an immunosuppressed mouse model. The regulatory effects of Sibiraea laevigata maxim polysaccharides (SLMPs) on immunity and intestinal microbiota in the immunosuppressed mouse model were investigated. The results indicated that SLMPs could mitigate spleen and thymus damage, protect immune organs, increase the levels of leukocytes, lymphocytes, neutrophils and monocytes in mouse blood and upregulate the levels of IL-2, IFN-&#x3b3;, TNF-&#x3b1; and IgA in mouse serum. Furthermore, SLMPs can restore intestinal microbial imbalance and enhance the diversity of gut microorganisms in immunosuppressed mice.<br><br>CONCLUSION: The findings from this study indicated that SLMPs could enhance immunity and improve the structure and abundance of intestinal flora in mice. These results provide a theoretical basis for the further development and utilization of SLMPs in immunomodulatory adjuvants and functional foods, thereby promoting their application in these fields. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40528265, year = {2025}, author = {Selak, L and Meier, DV and Marinović, M and Čačković, A and Kajan, K and Pjevac, P and Orlić, S}, title = {Salinization alters microbial methane cycling in freshwater sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {73}, pmid = {40528265}, issn = {2524-6372}, support = {DOK-2018-09-1550//Hrvatska Zaklada za Znanost/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, abstract = {Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.}, }
@article {pmid40528093, year = {2025}, author = {Goswami, R and Sarkar, A and Bandyopadhyay, B and Sadhukhan, S}, title = {Exploring microbial diversity in the Kharasinpur hot spring of West Bengal, India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {608}, pmid = {40528093}, issn = {1573-4978}, mesh = {*Hot Springs/microbiology ; India ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Biodiversity ; Water Microbiology ; Microbiota/genetics ; Hydrogen-Ion Concentration ; Iron/analysis ; }, abstract = {BACKGROUND: Hot springs are natural geothermal environments that harbour thermophilic microorganisms with significant biotechnological potential. Despite extensive studies on many Indian hot springs, Kharasinpur Hot Spring in West Bengal remains totally unexplored in terms of microbial diversity and physicochemical properties.<br><br>METHODS: A total of seven bacterial isolates were obtained from water samples collected at the Kharasinpur Hot Spring. These isolates underwent morphological, physiological, biochemical, and molecular characterization through 16S rRNA gene sequencing. Water samples were analyzed for physicochemical parameters such as temperature, pH, total hardness, iron concentration, salt content, and total dissolved solids (TDS).<br><br>RESULTS: The water temperature was recorded at 65&#xa0;&#xb0;C with a slightly alkaline pH (7.24). The 16S rRNA analysis identified isolates belonging to the phyla Pseudomonadota (e.g., Pseudomonas sp., Hydrogenophaga sp.) and Bacillota (e.g., Staphylococcus sp., Neobacillus sp.). The high iron content in the hot spring water was notable and rendered it unsafe for direct human consumption.<br><br>CONCLUSION: This study provides novel insights into the microbial diversity and physicochemical characteristics of a relatively unstudied Indian hot spring. The findings contribute to broader research efforts on hot spring ecosystems in India, enhancing our understanding of their microbial ecology and potential health implications.}, }
@article {pmid40528049, year = {2025}, author = {Blair, EM and Margalith, NJ and O'Malley, MA}, title = {Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {66}, pmid = {40528049}, issn = {1432-184X}, support = {DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Turtles/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Desert Climate ; Fatty Acids, Volatile/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Biomass ; }, abstract = {Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, including Lachnospiraceae and Enterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.}, }
@article {pmid40527958, year = {2025}, author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK}, title = {AlphaDesign: a de novo protein design framework based on AlphaFold.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40527958}, issn = {1744-4292}, support = {de.NBI project: 031A537B//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.}, }
@article {pmid40525968, year = {2025}, author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA}, title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {6}, pages = {}, pmid = {40525968}, issn = {1465-2080}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; }, abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.}, }
@article {pmid40525847, year = {2025}, author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B}, title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0007125}, doi = {10.1128/jb.00071-25}, pmid = {40525847}, issn = {1098-5530}, abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.}, }
@article {pmid40524759, year = {2025}, author = {Lacerda, AL and Proietti, MC and Kessler, F and Mendes, CR and Secchi, ER and Taylor, JD}, title = {Oceanic regions shape the composition of the Antarctic plastisphere.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {462}, pmid = {40524759}, issn = {2662-4435}, abstract = {Antarctica, once considered pristine, is increasingly threatened by plastic pollution, with debris found in its waters, sediments, sea ice, and biota. Here, we provide a comprehensive molecular survey of both prokaryotic and eukaryotic diversity on plastics around the Antarctic Peninsula, addressing a gap in existing research. Using eDNA metabarcoding, we identified diverse communities, with Pseudomonadota and Bacteroidota dominating prokaryotic communities, while Gyrista (mostly diatoms), Fungi and Arthropods were prevalent among eukaryotes. Geographic location significantly influenced community composition, with differences between the Bransfield Strait and the Gerlache Strait/Bellingshausen Sea. Polymer type and plastic shape did not impact species richness or community structure. These findings offer new insights into the complexity of the Antarctic plastisphere, highlighting potential impacts on biodiversity, ecosystem functions, and the broader implications of marine plastic pollution.}, }
@article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; Pampa Azul A8 Programa "Investigaci&#xf3;n//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Desarrollo e Innovaci&#xf3;n en Ciencias del Mar"//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, }
@article {pmid40523669, year = {2025}, author = {Prakash, O and Chauhan, A and Green, SJ}, title = {The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70108}, pmid = {40523669}, issn = {1758-2229}, support = {2200615//BioXFEL Science and Technology Center/ ; DE-FE0032198//DOE's University Training &amp; Research Program University Coal Research (UCR)/ ; 0000602538//The Department of Energy/ ; //Major Research Project (MJRP) intramural grant from Symbiosis International (Deemed University)/ ; 1901371//National Science Foundation/ ; 2200615//National Science Foundation/ ; W911NF2210145//Department of Defence contract/ ; }, mesh = {Anaerobiosis ; Aerobiosis ; *Oxygen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; Ecosystem ; *Bacterial Physiological Phenomena ; Humans ; }, abstract = {During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host-associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.}, }
@article {pmid40522148, year = {2025}, author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O}, title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70156}, doi = {10.1002/mnfr.70156}, pmid = {40522148}, issn = {1613-4133}, support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; }, abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.}, }
@article {pmid40521244, year = {2025}, author = {Addo, M and Apaame, S and Ghanney, MA and Adu, HK and DeWitt, ME and Addo, SO}, title = {Hepatitis B Infection in Outpatients and Pregnant Women Visiting a Mission Hospital in Ghana.}, journal = {Public health challenges..}, volume = {4}, number = {2}, pages = {e70071}, pmid = {40521244}, issn = {2769-2450}, abstract = {Millions of individuals worldwide suffer from hepatitis B, a serious, potentially fatal liver infection brought on by the hepatitis B virus (HBV). Although vaccines are available for HBV, infections continue to persist in Ghana. This study reports the prevalence of HBV infections in outpatients and pregnant women attending antenatal care at the Seventh-day Adventist (SDA) Hospital in Gbawe, Ghana. This retrospective cohort study involved the review of de-identified medical records of outpatients and pregnant women who visited the hospital between 2022 and 2024. Data on their HBV infection status, sex and age were analysed using R version 4.4.1. A total of 531 outpatients and 768 pregnant women visited the hospital during the study period. The prevalence of HBV infection was 7.5% in outpatients and 3.9% in pregnant women. It was observed that outpatients were more likely to be hepatitis B surface antigen (HBsAg) positive (OR = 2.0, 95%CI = 1.24-3.28, p = 0.005). It was also seen that HBV prevalence increased from 2022 to 2023 and decreased in 2024. There is a need for more educational campaigns to raise awareness of HBV infections, especially in pregnant women due to the risk of mother-to-child transmission. Furthermore, vaccinations need to be made affordable and easily accessible to the general population to ensure maximum coverage within the country.}, }
@article {pmid40518732, year = {2025}, author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M}, title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.14268}, pmid = {40518732}, issn = {1365-2591}, support = {7003589//Region of V&#xe4;sterbotten (Sweden)/ ; 977100//Region of V&#xe4;sterbotten (Sweden)/ ; RV-967705//Region of V&#xe4;sterbotten (Sweden)/ ; }, abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.<br><br>SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.<br><br>KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.}, }
@article {pmid40511921, year = {2025}, author = {Mayer, L and Nikolov, G and Kunert, M and Horn, M and Willemsen, A}, title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0055425}, doi = {10.1128/jvi.00554-25}, pmid = {40511921}, issn = {1098-5514}, abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence in situ hybridization (smFISH) protocol for giant viruses in an Acanthamoeba host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.}, }
@article {pmid40510670, year = {2025}, author = {Barnhart, EP and Douterelo, I and Morgan, MJ and Puzon, GJ}, title = {Editorial: Microbial ecology supporting growth of free-living amoebae in natural and engineered water systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620877}, doi = {10.3389/fmicb.2025.1620877}, pmid = {40510670}, issn = {1664-302X}, }
@article {pmid40509663, year = {2025}, author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR}, title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70117}, pmid = {40509663}, issn = {1462-2920}, support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; }, mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; }, abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.}, }
@article {pmid40509476, year = {2025}, author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P}, title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {40509476}, issn = {2304-8158}, abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.}, }
@article {pmid40507003, year = {2025}, author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A}, title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {40507003}, issn = {2075-4418}, abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.}, }
@article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, }
@article {pmid40504377, year = {2025}, author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H}, title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {65}, pmid = {40504377}, issn = {1432-184X}, support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; }, mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation &amp; purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; }, abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.}, }
@article {pmid40504009, year = {2025}, author = {Schroer, HW and Markland, K and Ling, F and Just, CL}, title = {Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12279-12291}, doi = {10.1021/acs.est.5c03155}, pmid = {40504009}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Microbiota ; Midwestern United States ; Drinking Water ; }, abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.}, }
@article {pmid40502102, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {P. aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502102}, issn = {2692-8205}, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affect rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.}, }
@article {pmid40500964, year = {2025}, author = {Li, S and Wang, T and Liu, M and Ma, T and Li, Y and Liu, J and Liu, Y and Shen, W and Ma, J and Wang, X and Han, X and Wang, H and Zhang, X}, title = {α-Linolenic Acid-Rich Flaxseed Oil Improves Polycystic Ovary Syndrome via Regulating Lipid Metabolism by GPR120-cAMP Pathway and Restoring Gut Microecology.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70136}, doi = {10.1002/mnfr.70136}, pmid = {40500964}, issn = {1613-4133}, support = {82460793//National Natural Science Foundation of China/ ; 82160691//National Natural Science Foundation of China/ ; 2023AAC03216//Ningxia Natural Science Foundation, China/ ; 2023BEG02011//Key Research and Development Program of Ningxia/ ; 2022BSB03112//Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; XZ2021003//Key Laboratory of Fertility Preservation and Maintainance of Ministry of Education of Ningxia Medical University/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects metabolic and reproductive health in women. α-Linolenic acid (ALA)-rich flaxseed oil as a dietary food has been suggested to offer potential therapeutic benefits in managing metabolic disturbances associated with PCOS. This study investigates the effects of ALA-rich flaxseed oil on lipid metabolism and gut microecology in a PCOS rat model. The PCOS model was induced in rats using letrozole, and the animals were then administered ALA-rich flaxseed oil. Metabolomics, transcriptomics, 16S rRNA sequencing, hormonal levels, and markers of metabolic health were assessed. Results showed that ALA-rich flaxseed oil significantly improved lipid metabolism by reducing serum cholesterol and triglycerides. In addition, we found that the improvement in lipid metabolism may be associated with the activation of the GPR120-cAMP pathway. Furthermore, gut microbiota analysis revealed a restoration of gut microbial ecology, with a shift toward a more balanced and healthy microbial composition. ALA-rich flaxseed oil shows promising potential as a dietary intervention for managing metabolic disturbances in PCOS. Its effects on lipid metabolism and gut microecology highlight its nutritional relevance, offering new insights into the dietary management of PCOS and its associated metabolic disorders.}, }
@article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, }
@article {pmid40500405, year = {2025}, author = {Chen, TK and Shiau, YJ}, title = {Effects of Soil Properties and Seasonal Variations on Microbial Communities in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {64}, pmid = {40500405}, issn = {1432-184X}, support = {110-2313-B-002-033-MY3//National Science and Technology Council/ ; }, mesh = {*Wetlands ; Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil/chemistry ; Denitrification ; *Microbiota ; Biodiversity ; Nitrates/analysis ; Sulfates/analysis ; Nitrification ; }, abstract = {Constructed wetlands (CWs) are important ecosystems with numerous benefits such as wastewater treatment, wildlife habitat protection, and stormwater remediation. However, the development of soil microbial communities in CWs over time remains understudied. This study comprehensively investigates microbial diversity and community composition in three constructed wetlands, focusing on the influence of wetland age, soil depth, and environmental factors. The results indicate that both soil depth and seasonal variations significantly affect alpha diversity, particularly in surface soils. The predominant microbial communities, including nitrifying and denitrifying communities, were identified across the studied wetlands. Moreover, sulfate-rich conditions may promote sulfur autotrophic denitrification. Redundancy analysis and multiple linear regression highlighted the distinction between autotrophic and heterotrophic denitrifiers. Soluble organic carbon was identified as a major factor influencing heterotrophic denitrifying bacteria, while sulfate and nitrate levels were more closely associated with autotrophic denitrifying bacteria. Overall, these findings provide valuable insights into microbial community dynamics in CWs and can help optimize wetland management strategies for improved nutrient removal efficiency.}, }
@article {pmid40499249, year = {2025}, author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G}, title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.}, journal = {Journal of psychiatric research}, volume = {189}, number = {}, pages = {171-183}, doi = {10.1016/j.jpsychires.2025.05.046}, pmid = {40499249}, issn = {1879-1379}, abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.<br><br>METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.<br><br>RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.<br><br>DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.}, }
@article {pmid40498465, year = {2025}, author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA}, title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an00130g}, pmid = {40498465}, issn = {1364-5528}, abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.}, }
@article {pmid40498364, year = {2025}, author = {Castledine, M and Esom, C and Van Nieuwenhuyse, B and Djebara, S and Merabishvili, M and Pirnay, JP and Buckling, A}, title = {Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf144}, pmid = {40498364}, issn = {1365-2672}, support = {NE/V012347/1//NERC/ ; NE/S000771/1//NERC/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/virology/isolation &amp; purification ; *Phage Therapy/methods ; Humans ; *Staphylococcal Infections/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; Bacteriophages ; Male ; *Staphylococcus Phages/physiology ; }, abstract = {AIMS: In phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study.<br><br>METHODS AND RESULTS: The patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localized regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites.<br><br>CONCLUSIONS: For this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection.}, }
@article {pmid40495815, year = {2025}, author = {Abiriga, D and Odong, R and Bakyayita, GK and Semyalo, R and Okello, W and Grossart, HP}, title = {The microbiology of Uganda's large freshwater lakes experiencing anthropogenic and climatic perturbations: why it matters-a review.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2048}, pages = {20243072}, pmid = {40495815}, issn = {1471-2954}, mesh = {Uganda ; *Lakes/microbiology ; *Climate Change ; *Anthropogenic Effects ; *Water Microbiology ; Biodiversity ; Bacteria ; }, abstract = {Intensification of pollution of African water resources due to human activities together with climate change has serious implications for Africa's blue economy, biodiversity and human health. Despite these overwhelming threats, there is limited research as evidenced by the underrepresentation of Africa-based data in global ecological and biochemical models. This review, therefore, aims to highlight key challenges and existing research gaps, particularly in Ugandan freshwater ecosystems. We focus on lake microbiology as this scientific field has been greatly underrepresented. Aquatic microorganisms are situated at the base of lake food webs and thus play crucial roles in the evolution and maintenance of water quality, attenuation of pollutants, and control of biogeochemical cycling through the microbial loop. Until now, the microbiology of Ugandan lakes has not been systematically studied. Thus, many open fundamental microbial ecology questions need to be urgently addressed to generate valuable information to advance future research, education, management and policy in Uganda and beyond. These include, but are not limited to: identification of microbial taxa and functional genes in relation to anthropogenic and climatic influence; seasonal and spatial variation in species diversity and functions; diversity and functions of planktonic, sediment, biofilm and mat communities; antimicrobial resistance burden; plastisphere communities; and geomicrobiology.}, }
@article {pmid40493213, year = {2025}, author = {Vila Duplá, M}, title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {63}, pmid = {40493213}, issn = {1432-184X}, mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; }, abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.}, }
@article {pmid40492114, year = {2025}, author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H}, title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1615533}, pmid = {40492114}, issn = {2296-889X}, abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.<br><br>METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.<br><br>RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.<br><br>CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.}, }
@article {pmid40488407, year = {2025}, author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B}, title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf119}, pmid = {40488407}, issn = {1751-7370}, abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.}, }
@article {pmid40487916, year = {2025}, author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI}, title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf086}, pmid = {40487916}, issn = {2730-6151}, abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.}, }
@article {pmid40487326, year = {2025}, author = {Bornbusch, SL and Dami, KA}, title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.}, journal = {F&amp;S reports}, volume = {6}, number = {Suppl 1}, pages = {45-49}, pmid = {40487326}, issn = {2666-3341}, abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.}, }
@article {pmid40483289, year = {2025}, author = {Swain, PP and Subudhi, E and Sahoo, RK}, title = {Heavy Metals and Carbapenem-Resistant Klebsiella pneumoniae in a River System of Odisha, India: Correlation and Integrated Risk Assessment.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {62}, pmid = {40483289}, issn = {1432-184X}, support = {523/2020(BSR)//University Grants Commission/ ; }, mesh = {*Metals, Heavy/analysis ; *Rivers/microbiology/chemistry ; India ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Wastewater/microbiology ; Environmental Monitoring ; Humans ; Microbial Sensitivity Tests ; }, abstract = {The unregulated release of heavy metals and antibiotics into rivers has the potential to significantly impact human health. Infections caused by healthcare-associated pathogen, carbapenem-resistant Klebsiella pneumoniae (CRKP), present a critical challenge to clinical practitioners due to its resistance to last-line antibiotics. In this study, we investigated co-contamination of heavy metals (As, Cd, Cr, Mn, and Pb) and CRKP isolates in water samples from multiple sites along the river receiving wastewater discharge from urban areas of twin-city, Odisha. We used a composite risk scoring framework integrating chemical risks (based on hazard indices (HI) of heavy metals) and biological risks (based on the proportion of CRKP isolates exhibiting multidrug-resistant phenotypes and their multiple antibiotic resistance (MAR) index. Furthermore, Spearman's correlations and redundancy analysis (RDA) were employed to assess the association between heavy metals and antibiotic resistance genes (ARGs). From the total CRKP isolates identified (n = 91), 90.1% and 9.89% exhibited multidrug resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. Sites D2 and C2 were flagged as high-risk sites based on their composite risk scores of 0.735 and 0.699, respectively. Positive correlations were observed between heavy metals and ARGs (blaOXA-48, blaTEM, and blaSHV). The findings raise concern regarding the potential threat of CRKP and heavy metal pollution in river water while also emphasizing the need for integrated assessment to control their release into the environment.}, }
@article {pmid40482721, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Root architecture and the rhizosphere microbiome: Shaping sustainable agriculture.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {359}, number = {}, pages = {112599}, doi = {10.1016/j.plantsci.2025.112599}, pmid = {40482721}, issn = {1873-2259}, abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.}, }
@article {pmid40481550, year = {2025}, author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A}, title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {40}, pmid = {40481550}, issn = {1757-4749}, abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.}, }
@article {pmid40481438, year = {2025}, author = {Babalola, OO and Osuji, IE and Akanmu, AO}, title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {40}, pmid = {40481438}, issn = {2730-6844}, abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).<br><br>DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).}, }
@article {pmid40480043, year = {2025}, author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ}, title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123931}, doi = {10.1016/j.watres.2025.123931}, pmid = {40480043}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Microbiota ; *Bioreactors/microbiology ; Anaerobiosis ; Archaea/genetics ; Bacteria/genetics ; Waste Disposal, Fluid ; }, abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.}, }
@article {pmid40476717, year = {2025}, author = {Baer, J and Little, M and Aquino, J and van der Geer, A and Sánchez-Quinto, A and Ballard, A and Lawrence, C and Carilli, J and Hartmann, A and Rohwer, F}, title = {Viralization as a microbial approach for enhancing coral reef restoration.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf110}, pmid = {40476717}, issn = {1751-7370}, support = {2022717//National Science Foundation/ ; 2209377//National Science Foundation/ ; 9207//Gordon and Betty Moore Foundation/ ; CR20-5175//United States Department of Defense Environmental Security Technology Certification Program/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/virology/growth &amp; development/microbiology ; *Viruses/isolation &amp; purification ; Seawater/chemistry/virology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a "microbialized" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters ("water quality") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term "viralized", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.}, }
@article {pmid40474779, year = {2025}, author = {Green, N and Norwood, A and Sidhe, C and Mutlow, A and Aymen, J and Stiles, R and Bushell, J and Lim, T and Culver, E and Reeder, N and Timmer, M and Connelly, F and Charbonneau, J and McCall, W and Koenig, L and Stein, M and Geist, N and Lambert, MR and Hernández-Gómez, O}, title = {Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, pmid = {40474779}, issn = {1943-3700}, abstract = {Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, US, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the US, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.}, }
@article {pmid40474000, year = {2025}, author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR}, title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {61}, pmid = {40474000}, issn = {1432-184X}, mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation &amp; purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.}, }
@article {pmid40473091, year = {2025}, author = {Santos, FSA and Corgosinho, PHC and de Abreu, FVS and Vaca-Sánchez, MS and Cuevas-Reyes, P and de Faria, ML and Valério, HM and Borges, MAZ}, title = {Assessing the impact of different scale removal methods on the geometric morphometrics of Aedes aegypti wings.}, journal = {Acta tropica}, volume = {268}, number = {}, pages = {107686}, doi = {10.1016/j.actatropica.2025.107686}, pmid = {40473091}, issn = {1873-6254}, abstract = {This work aimed to test different treatments for removing wing scales from Aedes aegypti, and evaluate through geometric morphometrics, if these treatments can modify the wing venation morphometric pattern. The treatments were wing agitation in mineral water and NaOH (sodium hydroxide) saline solution using a mini-ultrasound, and manual wing scales removal using a size zero (0) tip brush. We propose an alternative method for mounting wings on slides using glycerin. We conclude that glycerin use for slide mounting provides better optics and translucency, and that treatments with NaOH saline solution and water can impair morphometric analysis of wings. The size zero (0) tip brush treatment efficiently removed wing scales, improving wing structure visualization without causing significant modifications to the specimens.}, }
@article {pmid40471139, year = {2025}, author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C}, title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {9}, pages = {}, pmid = {40471139}, issn = {1540-9538}, support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; }, mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention &amp; control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; }, abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.}, }
@article {pmid40469738, year = {2025}, author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D}, title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576898}, pmid = {40469738}, issn = {1664-302X}, abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.<br><br>METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.<br><br>RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.<br><br>DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.}, }
@article {pmid40469504, year = {2025}, author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , }, title = {The microbiologist's guide to metaproteomics.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70031}, pmid = {40469504}, issn = {2770-596X}, abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.}, }
@article {pmid40468430, year = {2025}, author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE}, title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {60}, pmid = {40468430}, issn = {2524-6372}, support = {#2014/21772-4 and #2014/14935-4//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Funda&#xe7;&#xe3;o Agrisus/ ; }, abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.<br><br>RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M&#x2009;+&#x2009;PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.<br><br>CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.}, }
@article {pmid40467851, year = {2025}, author = {Rakotonindrina, V and Andriamananjara, A and Razafimbelo, T and Okamoto, T and Sarr, PS}, title = {Land Cover and Seasonal Variations Shape Soil Microbial Communities and Nutrient Cycling in Madagascar Tropical Forests.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {60}, pmid = {40467851}, issn = {1432-184X}, mesh = {*Soil Microbiology ; Seasons ; Madagascar ; *Forests ; Soil/chemistry ; Tropical Climate ; Nitrogen/analysis/metabolism ; Carbon/analysis ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/genetics/classification/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phosphorus/analysis/metabolism ; Trees ; Ecosystem ; }, abstract = {Understanding how land cover and seasonal variations influence soil microbial communities and nutrient cycling is crucial for sustainable land management in tropical forests. However, such investigations are limited in Madagascar's tropical ecosystems. This study investigated the impacts of land cover types and seasonal variations on soil properties and microbial communities in the tropical forest region of Andasibe, Madagascar. Soil samples were collected from four land cover types-tree fallow (TSA), shrub fallow (SSA), eucalyptus forest (EUC), and degraded land (TM)-across three seasonal periods: the dry season, the start of the rainy season, and the end of the rainy season. Both land cover and sampling season affected soil pH and available P, whereas total nitrogen, soil organic carbon, and the C/N ratio were affected only by land cover. The soil organic carbon and total nitrogen concentrations were greater in TM. NextSeq sequencing of the 16S rRNA gene and ITS regions of the nuclear rRNA operon revealed distinct microbial community compositions across land covers, with greater diversity in the TSA and SSA. Bacteria are more sensitive to seasonal changes than are fungi, with phosphate-solubilizing (gcd) and phosphate-mineralizing (phoD) genes being more abundant in the rainy season, emphasizing the role of microbes in nutrient availability under different climatic conditions. Principal component analysis highlighted SSA as a hotspot for microbial activity, reinforcing the potential of shrub ecosystems in soil restoration. These findings reveal strong land cover and seasonal effects on soil microbial functions, with implications for nutrient cycling, ecosystem resilience, and sustainable land management in tropical forest landscapes.}, }
@article {pmid40467767, year = {2025}, author = {Yan, Z and Yao, Y and Xu, Q and He, X and Zhou, X and Wang, H}, title = {Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca).}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {864}, pmid = {40467767}, issn = {2399-3642}, mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; Feces/microbiology ; *Bacteria/genetics/classification ; }, abstract = {The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.}, }
@article {pmid40467587, year = {2025}, author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y}, title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5186}, pmid = {40467587}, issn = {2041-1723}, support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; }, abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.}, }
@article {pmid40467261, year = {2025}, author = {Cabezas-Terán, K and Grootaert, C and Van Camp, J and Ortiz, J and Ruales, J and Donoso, S and Van de Wiele, T}, title = {Bioaccessibility of β-carotene during in vitro co-digestion of encapsulated mango peel carotenoids with milk.}, journal = {Food research international (Ottawa, Ont.)}, volume = {214}, number = {}, pages = {116576}, doi = {10.1016/j.foodres.2025.116576}, pmid = {40467261}, issn = {1873-7145}, mesh = {*Mangifera/chemistry ; *beta Carotene/pharmacokinetics/metabolism ; *Milk/chemistry/metabolism ; *Digestion ; Animals ; Biological Availability ; *Fruit/chemistry ; *Carotenoids ; Particle Size ; }, abstract = {β-carotene is a carotenoid with provitamin A activity whose digestive stability and bioaccessibility prior to intestinal absorption are important to fully exploit its health benefits. Microencapsulation protects carotenoids, but there is a lack of information on the extent to which its characteristics and interactions with complex food matrices could impact the carotenoid micellization during digestion. We evaluated the effect of milk fat content on the in vitro bioaccessibility of β-carotene from microparticles containing carotenoids from mango peel. The microparticles tested contained solvent-extracted carotenoids and supercritical fluid-extracted carotenoids, and were separately co-digested with whole, semi-skimmed and skimmed milks. Bioaccessibility was assessed using an in vitro digestion method adapted to carotenoids. β-carotene recoveries after in vitro digestions ranged from 79.6 to 102.2 %, with the highest values corresponding mainly to microparticles with the lowest initial β-carotene concentration. β-carotene bioaccessibilities ranged from 8.8 to 75.5 %, the highest values being obtained mainly when the microparticles were co-digested with whole milk, especially when those containing supercritical fluid-extracted carotenoids were used. The bioaccessibility-enhancing effect of the milk fat was explained by the higher concentration of free fatty acids in the micellar phase, while the better results in the microparticles containing supercritical-fluid-extract was attributed to the lower initial concentration of β-carotene. In conclusion, increasing the milk fat content increased the bioaccessibility of encapsulated β-carotene from mango peel, further determining that, a lower initial concentration of β-carotene in the microparticles resulted in higher bioaccessibility.}, }
@article {pmid40467013, year = {2025}, author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S}, title = {Targeted analysis of metagenomes: divide and conquer.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108619}, doi = {10.1016/j.biotechadv.2025.108619}, pmid = {40467013}, issn = {1873-1899}, abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targeted methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.}, }
@article {pmid40465274, year = {2025}, author = {Hassen, B and Hammami, S}, title = {Environmental phages: ecosystem dynamics, biotechnological applications and their limits, and future directions.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf136}, pmid = {40465274}, issn = {1365-2672}, support = {//IRESA/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Ecosystem ; *Biotechnology/methods/trends ; Gene Transfer, Horizontal ; Bacteria/virology ; *Environmental Microbiology ; }, abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange, and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.}, }
@article {pmid40464990, year = {2025}, author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H}, title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {59}, pmid = {40464990}, issn = {1432-184X}, support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; }, mesh = {*Rhizosphere ; *Seeds/microbiology/growth &amp; development ; *Soil Microbiology ; *Atractylodes/microbiology/growth &amp; development ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Seedlings/microbiology/growth &amp; development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation &amp; purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.}, }
@article {pmid40463892, year = {2025}, author = {Shepherd, RM and Oliverio, AM}, title = {The Biogeography of Apicomplexan Parasites in Tropical Soils.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71478}, pmid = {40463892}, issn = {2045-7758}, abstract = {Parasitic protists such as Apicomplexa, an abundant group of soil protists, contribute to ecosystem processes and nutrient cycling in belowground soil systems through their obligate symbioses with soil Metazoa. Yet despite the importance of soil parasites, the biodiversity and biogeography of Apicomplexa in belowground systems remain poorly characterized. Leveraging 205 soils collected across a rainfall gradient spanning the isthmus of Panama, we sought to understand the distribution of soil Apicomplexa lineages and how abiotic (e.g., soil and climatic) and biotic (e.g., soil Metazoa) factors relate to their diversity and structure. Apicomplexa were highly heterogeneous across the samples and comprised 30% of the soil protist community on average. Soil pH, along with phosphorus and magnesium, best explained the overall distribution of Apicomplexa. Soil Metazoa distributions also corresponded to Apicomplexa distributions, and many Metazoan taxa co-occurred with particular Apicomplexa, which may reflect ecological interactions (such as parasitism) or shared habitat preferences. These results highlight the potential roles of both soil and climatic variables and putative hosts in structuring parasite distributions in belowground tropical systems. Our work builds a broader understanding of Apicomplexa biodiversity in tropical soils and sheds light on environmental factors that may contribute to shaping their distribution in belowground systems. These results help inform our understanding of the importance of parasites in tropical forest soils.}, }
@article {pmid40463148, year = {2025}, author = {Usman, H and Molaei, M and House, S and Haase, MF and Dennis, CL and Niepa, THR}, title = {Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.17.654660}, pmid = {40463148}, issn = {2692-8205}, abstract = {UNLABELLED: Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing currently unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover novel biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semi-permeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for discovering previously uncultured or unknown microbial species.<br><br>TEASER: Engineered magnetic nanocultures support microbial growth and magnetic separation from complex environments.}, }
@article {pmid40462960, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40462960}, issn = {2692-8205}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40462143, year = {2025}, author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F}, title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.}, journal = {Plant methods}, volume = {21}, number = {1}, pages = {79}, pmid = {40462143}, issn = {1746-4811}, abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.}, }
@article {pmid40461733, year = {2025}, author = {Ruiz-Blas, F and Friese, A and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A}, title = {The Deep Subsurface Biosphere and its Substrates Along a One-Million-Year Ferruginous Lake Archive.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {58}, pmid = {40461733}, issn = {1432-184X}, support = {KA 2293/8-1//Deutsche Forschungsgemeinschaft/ ; VU 94/1-1//Deutsche Forschungsgemeinschaft/ ; P2GEP2_148621//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Indonesia ; *Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; Iron/analysis/metabolism ; Biodiversity ; }, abstract = {Lake Towuti, Indonesia, is an ancient stratified lake with ferruginous (iron-rich, sulfate-poor) anoxic bottom water conditions and a long depositional record affected by redox changes in the water column and sediments. As modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry, and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep subsurface biosphere along a one-million-year lacustrine archive. Electron acceptors in the pore water became depleted at shallow depths, resulting in a drastic decrease in cell densities in the fermentative zone, where Bathyarchaeia dominate the microbial community composition. Although alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across successive lithologies, indicating that sediment composition subsequent to deposition also affects diversity. The upper sediments (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. Deeper sediments (20-70 mblf) contained low-diversity microbial communities adapted to nutrient scarcity. In contrast, deepest lacustrine sediments (70-100 mblf) contained an increased microbial diversity reflecting greater availability of organic matter of terrestrial origin. Despite Bathyarchaeia being prime constituents of the deep subsurface biosphere, increased diversity in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom ooze, peat). This demonstrated that depositional conditions remained traceable, while stratified microbial communities drove reductive diagenesis.}, }
@article {pmid40461630, year = {2025}, author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W}, title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19484}, pmid = {40461630}, issn = {2045-2322}, support = {1815//OeNB Jubil&#xe4;umsfonds/ ; }, mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.}, }
@article {pmid40459550, year = {2025}, author = {Wu, Y and Zhang, F and Zhang, S and Zhang, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Curvularia spicifera causing black rot on Ipomoea batatas in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-25-0477-PDN}, pmid = {40459550}, issn = {0191-2917}, abstract = {Ipomoea batatas (sweet potato) is an annual herb originating from South America and the large and small Antilles. It is widely cultivated in tropical and subtropical regions around the world and is widely grown in most parts of China. As an edible plant with rich nutrition, I. batatas has high economic and medicinal value (Suhendy et al. 2023). In September 2023, black rot-like disease signs and symptoms were observed on the roots of I. batatas in a farmland (about 6667 m2) located in Kaifeng city, Henan Province, China. The roots showed irregular brown or dark spots on the surface, extending to the internal center, and brown to black necrosis. Additionally, above-ground parts of infected plants showed symptoms such as yellowing and wilting of leaves, brown spots on stems, and stunted growth. Around 80 % of monitored plant roots (n = 200) exhibited the symptoms. Infected roots were cut into pieces and then placed on potato dextrose agar (PDA) (light/dark, 16 h/8 h; temperature, 18°C). After a period of 3-10 days, single hyphal tips of each fungal colony were placed on PDA and incubated for another 5-10 days (Paul et al. 2021). Colonies of the fungal pathogen on PDA reached 50 mm in diameter within 7 days, dark gray on the inner side, dark brown extending to the edge, irregular round edge, with abundant aerial mycelium, cotton-like, irregularly convex upward, undulating. The conidia were brown, ellipsoid to oval, 8 to 19 × 3 to 6 μm (n = 50). Morphologically similar isolates with characteristics consistent with those of Curvularia spicifera (Cui et al. 2020) were recovered from 87% of symptomatic root tissues (n=100). The internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from three independent isolates (CSZM202101, CSZM202102, and CSZM202103) of the fungus were amplified and sequenced with primers ITS1/ITS4 (Seliger et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were deposited in GenBank (Accession No. OR885691, PV056889, PV056568, PQ839726, PV072835 and PV02836). BLASTn analysis showed that the ITS and GAPDH sequences had 100% (ITS, 516/516; GAPDH, 508/508) identity with C. spicifera (OQ845826 and CBS 274.52 JN192387) from maize (Ram et al. 2024) and pearl millet (S. et al. 2024), respectively. The phylogenetic analysis clearly illustrated that these isolates clustered with the sequences of a representative reference strain of C. spicifera(CBS 274.52, GenBank accession number JN192387). Therefore, the morphological, molecular and phylogenetic analysis indicated that the pathogen was C. spicifera. To complete Koch's postulates, pathogenicity experiments were carried out by inoculating spore suspension (106 spores mL-1) into the wounded roots (n=10) of I. batatas plants. Sterile distilled water treated wounded roots (n=10) served as control. One to two days after inoculation, visible mycelia were produced at the inoculation sites of I. batatas. Inoculated roots showed black rot signs 21 days post-inoculation; controls were unaffected. This was confirmed in three repeated pathogenicity tests. To our knowledge, this is the first report of black rot caused by C. spicifera on I. batatas in China. The emergence of the black rot pathogen could harm valuable food crops and reduce agricultural productivity in China. Accurate identification of the black rot fungus is essential for devising effective disease management strategies and supporting future control of C. spicifera in China.}, }
@article {pmid40459301, year = {2025}, author = {Zhang, J and Guo, Z and Liu, J and Pan, X and Huang, Y and Cui, X and Wang, Y and Jin, Y and Sheng, J}, title = {Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70111}, doi = {10.1111/1462-2920.70111}, pmid = {40459301}, issn = {1462-2920}, support = {KFJ-SW-YW043-2//Field Station Basic Research Project of the Chinese Academy of Sciences/ ; 42107145//National Natural Science Foundation of China/ ; 42407410//National Natural Science Foundation of China/ ; 0270756100ZX//Jiangsu Agricultural Biodiversity Cultivation and Utilization Research Center/ ; CX (22) 2002//Jiangsu Agricultural Science and Technology Innovation Fund/ ; CX (23) 3105//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 3220220039//Pilot Project for Mineral-Land Integration of Jiangsu Province/ ; //Jiangsu Provincial Territorial Ecological Monitoring/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; *Desiccation ; Biodiversity ; *Microbiota ; }, abstract = {Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial-environmental relationships at large scales.}, }
@article {pmid40456365, year = {2025}, author = {Zhao, X and Van Overbeek, L and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M}, title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.}, journal = {Journal of food protection}, volume = {88}, number = {7}, pages = {100551}, doi = {10.1016/j.jfp.2025.100551}, pmid = {40456365}, issn = {1944-9097}, mesh = {Humans ; *Food Safety ; Food Microbiology ; Food Contamination/prevention &amp; control ; }, abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental, and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from preharvest plant production to postharvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterization (to subspecies, or even strain level) needing a multimethod approach, (iii) hazard characterization should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviors coexist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens), or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multiperspective approach are the foundation for every successful conversation when plant science meets food safety.}, }
@article {pmid40456197, year = {2025}, author = {Song, W and Lin, L and Oh, S and Grossart, HP and Yang, Y}, title = {Tire wear particles in aquatic environments: From biota to ecosystem impacts.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126059}, doi = {10.1016/j.jenvman.2025.126059}, pmid = {40456197}, issn = {1095-8630}, mesh = {*Ecosystem ; Biota ; Microplastics ; *Water Pollutants, Chemical ; Animals ; }, abstract = {Tire wear particles (TWPs), mainly generated through friction between tires and road surfaces, represent a major source of traffic-related microplastic pollution, posing threats to biota and ecosystem functions. These particles are a complex mixture of toxic compounds, including heavy metals (e.g., zinc) and organic compounds (e.g., 6-PPD), and their diverse leachates exacerbate their ecological impacts. This review collates current knowledge on the occurrence of TWPs and their leachates in aquatic systems, emphasizing their toxicological effects on species and cascading ecological consequences at the community and ecosystem levels. TWP concentrations in aquatic environments span several orders of magnitude, ranging from 10[-5] to 10[4] mg/L in water via pyrolysis-GC/MS. TWPs and their leachates induce oxidative stress, DNA damage, and alter immune responses of aquatic biota, while disrupting feeding behavior, reproduction, and survival. At the ecosystem level, TWPs and their leachates cause shifts in species composition, reduce biodiversity, and alter trophic interactions, destabilizing natural food web dynamics through selective pressure that promotes tolerant taxa and triggers cascading ecological effects. Their presence significantly influences carbon and nitrogen cycling, with environmentally relevant concentrations could promote primary producers, while higher concentrations inhibit photosynthetic nitrogen-fixing biota, disrupt microbial communities, and impair processes such as denitrification and carbon mineralization. Their toxicological and ecological impacts are likely to be intensified by global environmental change, highlighting the need for long-term studies under realistic environmental conditions to better understand underlying mechanisms and develop effective mitigation strategies.}, }
@article {pmid40453667, year = {2025}, author = {Yang, H and Shao, C and Liu, Z and Zhang, X and Liu, Y and Xiao, J and Tang, L}, title = {Cold- and hot-classified botanical drugs differentially modulate gut microbiota: linking TCM emic classification to microbial ecology.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1545619}, pmid = {40453667}, issn = {1663-9812}, abstract = {INTRODUCTION: Traditional Chinese Medicine (TCM) classifies botanical drugs based on their thermal properties (an emic classification system), categorizing them as "cold" (e.g., "clearing heat" for anti-inflammatory effects) or "hot" (e.g., "warming the middle" for metabolic enhancement). However, the specific roles of these botanical drugs in restoring gut microbiota dysbiosis remain unclear. This study aimed to explore whether TCM-classified cold and hot botanical drugs differentially restore gut microbiota dysbiosis and host physiology in antibiotic-treated mice.<br><br>METHODS: Mice with antibiotic-induced dysbiosis were treated with eight TCM-classified botanical drugs (four cold: Rheum palmatum L., Scutellaria baicalensis Georgi, Senna alexandrina Mill., Coptis chinensis Franch.; four hot: Codonopsis pilosula (Franch.) Nannf., Astragalus membranaceus (Fisch.) Bunge, Angelica sinensis (Oliv.) Diels, Panax ginseng C.A.Mey.) for 20&#xa0;days. Gut microbiota were analyzed via 16S rRNA sequencing on days 5, 10, 15, and 20, alongside physiological parameters including blood glucose, serum lipids, TNF-&#x3b1;, adiponectin, and intestinal histomorphology.<br><br>RESULTS: By day 20, all botanical drugs restored the diversity and ranking of dominant genera (those with >10% abundance, such as Lactobacillus and unclassified Muribaculaceae). However, cold-classified drugs, traditionally associated with anti-inflammatory effects, selectively enriched anti-inflammatory taxa, including Akkermansia and Bifidobacterium. In contrast, hot-classified drugs, linked to metabolic enhancement, promoted metabolic-modulating genera such as Clostridia and Eubacterium coprostanoligenes. These differential enrichments corresponded with the therapeutic principles defined by TCM: cold-classified drugs reduced serum TNF-&#x3b1; levels (P < 0.01), demonstrating anti-inflammatory effects, whereas hot-classified drugs improved lipid profiles (TG: P < 0.001), thereby promoting metabolic modulation.<br><br>DISCUSSION: TCM-classified cold and hot botanical drugs universally stabilize dominant microbiota while differentially modulating low-abundance taxa. The enrichment of Akkermansia (cold) and Clostridia (hot) offers a microbiota-driven validation of TCM's empirical classification framework. These findings connect traditional knowledge with microbial ecology, underscoring the potential of TCM-guided microbiota modulation for precision therapies.}, }
@article {pmid40450024, year = {2025}, author = {Masigol, H and Solbach, MD and Pourmoghaddam, MJ and Ahadi, R and Mostowfizadeh-Ghalamfarsa, R and Taheri, SR and Tobias-Hünefeldt, SP and Bonkowski, M and Grossart, HP}, title = {A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19124}, pmid = {40450024}, issn = {2045-2322}, mesh = {*Lakes/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Forests ; *Oomycetes/genetics/classification/isolation &amp; purification ; Ecosystem ; Germany ; Phylogeny ; Fresh Water/microbiology ; }, abstract = {Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.}, }
@article {pmid40448709, year = {2025}, author = {Samaniego, T and La Torre, R and Orjeda, G and Ramirez, JL}, title = {Lima Megacity's Influence on Aquatic Microbial Communities in the Rímac River: Dominance Over Spatial and Seasonal Variations.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {57}, pmid = {40448709}, issn = {1432-184X}, support = {B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; }, mesh = {*Rivers/microbiology ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Peru ; *Microbiota ; *Water Microbiology ; Environmental Monitoring ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The Rímac River, a vital watershed on the Peruvian coast, is confronted with substantial environmental challenges stemming from intensive exploitation and widespread contamination. As the primary source of water for Lima, supplying approximately 80% of the city's needs, the river is heavily impacted by pollutants from domestic, hospital, industrial, and mining effluents. These contaminants introduce microbiota that pose significant public health risks. This study utilizes 16S rRNA gene metabarcoding to characterize the bacterial communities along the Rímac River, examining both spatial (upper, middle, and lower basins) and temporal (dry and rainy seasons) variations. Over a year-long sampling period, DNA sequencing revealed pronounced microbiological differences between the Metropolitan and Regional zones, primarily driven by anthropogenic activities. Key findings include a significant reduction in microbial diversity and an increase in pathogenic bacteria within the Metropolitan zone, while the influence of seasonal variations and altitudinal gradients was comparatively minor. Betaproteobacteria emerged as the most abundant class across most samples. Notably, Aliarcobacter cryaerophilus, an indicator of fecal contamination and a potential public health hazard, was predominantly detected in the Metropolitan zone. These results underscore the necessity for comprehensive monitoring of the Rímac River's microbiota, incorporating advanced molecular techniques to effectively track and mitigate pollution. The study emphasizes the urgent need for robust water quality management strategies to protect this critical resource, ensuring the health and sustainability of Lima and its surrounding regions.}, }
@article {pmid40446899, year = {2025}, author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F}, title = {Nanoplastics under the charge effects: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage and microbial ecology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {381}, number = {}, pages = {126566}, doi = {10.1016/j.envpol.2025.126566}, pmid = {40446899}, issn = {1873-6424}, mesh = {Animals ; *Microplastics/toxicity ; Larva/drug effects/growth &amp; development ; *Intestines/drug effects ; *Ranidae/growth &amp; development ; *Water Pollutants, Chemical/toxicity ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; }, abstract = {Nanoplastics (NPs) are contaminants that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged Polystyrene-NPs (PS-NH2, 30 nm) and negatively charged Polystyrene-NPs (PS-COOH, 30 nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage and microbial ecology. The results demonstrated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increased their body weight and body length. Compared to PS-COOH, PS-NH2 exposure resulted in more adverse intestinal tissue damage, manifested by more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, thereby indirectly causing more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study revealed the effects of different charged NPs exposure on the growth of tadpoles and their intestinal toxicity, clarified the potential connections between gut microbiota and glucose-lipid metabolism, and provided a new perspectives on the health risks of NPs in amphibians.}, }
@article {pmid40446767, year = {2025}, author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A}, title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.}, journal = {Water research}, volume = {284}, number = {}, pages = {123887}, doi = {10.1016/j.watres.2025.123887}, pmid = {40446767}, issn = {1879-2448}, abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.}, }
@article {pmid40446743, year = {2025}, author = {Jansriphibul, K and Krohn, C and Ball, AS}, title = {Sources of variability for viability PCR using propidium monoazide.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128224}, doi = {10.1016/j.micres.2025.128224}, pmid = {40446743}, issn = {1618-0623}, mesh = {*Propidium/analogs &amp; derivatives/chemistry ; *Azides/chemistry ; *Microbial Viability ; *Polymerase Chain Reaction/methods/standards ; DNA, Bacterial/isolation &amp; purification/genetics ; *Bacteria/genetics/isolation &amp; purification ; Environmental Microbiology ; }, abstract = {The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.}, }
@article {pmid40446651, year = {2025}, author = {O'Connor, L and Minogue, E and Carolan, S and Darcy, G and Chueiri, A and Faherty, M and Morton, J and Mc Donagh, F and Singh, NK and Venkateswaran, K and Miliotis, G and Smith, TJ}, title = {Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116905}, doi = {10.1016/j.diagmicrobio.2025.116905}, pmid = {40446651}, issn = {1879-0070}, abstract = {Pantoea piersonii a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting. This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of P. piersonii. The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.}, }
@article {pmid40445193, year = {2025}, author = {Cisneros, M and Blanco-Fuertes, M and Lluansí, A and Brotons, P and Henares, D and Pérez-Argüello, A and González-Comino, G and Ciruela, P and Mira, A and Muñoz-Almagro, C}, title = {Synergistic inhibition of pneumococcal growth by Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum: insights into nasopharyngeal microbial interactions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0013825}, doi = {10.1128/spectrum.00138-25}, pmid = {40445193}, issn = {2165-0497}, abstract = {Streptococcus pneumoniae is a nasopharynx colonizer that can invade sterile tissues, causing invasive pneumococcal disease (IPD). Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum are commensal bacteria commonly isolated from the nasopharynx of healthy children, potentially playing a protective role. This study aims to analyze the effects of D. pigrum and C. pseudodiphtheriticum on S. pneumoniae in vitro growth. Pneumococcal strains were collected from IPD patients and healthy carriers in Catalonia (2016-2023). D. pigrum and C. pseudodiphtheriticum strains were isolated from a healthy child's nasopharynx. S. pneumoniae was co-cultured with each commensal bacterium in triplicate experiments. Pneumococcal growth was quantified using a real-time PCR assay targeting the lytA gene. The effect of commensal bacteria on pneumococcal growth was evaluated using a linear mixed-effect regression model. Twenty-eight pneumococcal strains expressing 24 different serotypes and 27 clonal types were analyzed (18 isolated in blood and 10 in nasopharyngeal aspirate). Pneumococcal growth was decreased by D. pigrum (β = -0.763, 95% confidence interval [CI]: -0.94 to -0.59, P < 0.0001) and C. pseudodiphtheriticum (β = -0.583, 95% CI: -0.76 to -0.41, P < 0.0001). The combined presence of both had a stronger inhibitory effect (β = -0.971, 95% CI: -1.15 to -0.79, P < 0.0001). No association was found between isolation site or serotype with pneumococcal growth. D. pigrum and C. pseudodiphtheriticum significantly reduced pneumococcal growth, with a synergistic effect when combined. This antagonistic effect supports the potential protective factor of healthy nasopharyngeal microbiota against IPD and the development of these microorganisms as probiotics.IMPORTANCEInvasive pneumococcal disease (IPD) is a significant worldwide health challenge. The present study highlights the significant inhibitory effect of two commensal bacteria, Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum, on pneumococcal growth, with a stronger effect observed when both bacteria are present together. Through testing different strains of S. pneumoniae and the implementation of a robust statistical model, this research advances in the knowledge of microbial ecology and provides evidence to support the development of the use of these commensal bacteria as probiotics. These results emphasize the possibility of using the nasopharyngeal microbiota's natural interactions to mitigate the risk of IPD.}, }
@article {pmid40444437, year = {2025}, author = {Pan, Y and Tao, Y and Yang, X and Du, S and Ding, H and Li, J and Jia, H and Chen, H}, title = {Underlying mechanisms of spatial distribution of prokaryotic community in surface seawater from Arctic Ocean to the Sea of Japan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0051725}, doi = {10.1128/spectrum.00517-25}, pmid = {40444437}, issn = {2165-0497}, abstract = {Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.}, }
@article {pmid40442489, year = {2025}, author = {Ostap-Chec, M and Antoł, W and Bajorek, D and Berbeć, E and Moroń, D and Rapacz, M and Miler, K}, title = {Meta-Analysis and Experimental Evidence Reveal No Impact of Nosema ceranae Infection on Honeybee Carbohydrate Consumption.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {56}, pmid = {40442489}, issn = {1432-184X}, support = {Preludium 2021/41/N/NZ8/02917//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Nosema/physiology ; Hemolymph/chemistry/metabolism ; Feeding Behavior ; Trehalose/metabolism/analysis ; *Carbohydrate Metabolism ; }, abstract = {Honeybees (Apis mellifera) are indispensable pollinators for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens threatening their survival and ecosystem services. Among these pathogens, Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in the organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioral defenses, such as self-medicating with antimicrobial substances available in their environment. We hypothesized that bees infected with N. ceranae might compensate behaviorally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused by N. ceranae does not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.}, }
@article {pmid40440849, year = {2025}, author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B}, title = {Bacterial composition of dust deposited in Qatar: A seasonal study.}, journal = {The Science of the total environment}, volume = {985}, number = {}, pages = {179766}, doi = {10.1016/j.scitotenv.2025.179766}, pmid = {40440849}, issn = {1879-1026}, mesh = {Qatar ; *Dust/analysis ; Seasons ; *Bacteria/classification ; *Air Microbiology ; *Environmental Monitoring ; RNA, Ribosomal, 16S/analysis ; *Microbiota ; *Air Pollutants/analysis ; }, abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.}, }
@article {pmid40439420, year = {2025}, author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW}, title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0030125}, pmid = {40439420}, issn = {1098-5336}, mesh = {*Kelp/microbiology/growth &amp; development ; *Bacteria/isolation &amp; purification/classification/genetics ; *Microbiota ; Edible Seaweeds ; Laminaria ; }, abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.<br><br>IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.}, }
@article {pmid40437905, year = {2025}, author = {Ni, J and Yang, Z and Sun, X and Cui, Q and Zhang, R and Lu, H and Wu, Z and Zhu, J and Mao, H and Liu, K and Tang, C and Wang, C and Xing, C and Zhu, J}, title = {Probiotic Akkermansia muciniphila alleviates acute kidney injury by protecting the intestinal barrier and modulating gut microbiota and metabolites.}, journal = {Journal of biomedical research}, volume = {}, number = {}, pages = {1-12}, doi = {10.7555/JBR.39.20250162}, pmid = {40437905}, issn = {1674-8301}, abstract = {Acute kidney injury (AKI) is a critical condition with limited effective therapies. Akkermansia muciniphila (A. muciniphila) is a probiotic with multiple beneficial effects, including epithelial cell tight junctions regulation. Since renal pathophysiology is associated with gut barrier integrity, we hypothesized that A. muciniphila may have potential preventive effects on AKI. We established a lipopolysaccharide (LPS)-induced AKI mouse model to evaluate the effects of A. muciniphila. Our findings showed that pretreatment with A. muciniphila significantly attenuated kidney injury, as evidenced by reduced serum creatinine and urea nitrogen levels, alongside diminished tubular necrosis and apoptosis. A. muciniphila preserved the intestinal barrier integrity and induced marked shifts in gut microbial ecology and the metabolome. A. muciniphila induced notably an increase in the relative abundance of phylum Proteobacteria while a decrease of Bacteroidetes. At the genus level, Prevotella, Faecalibaculum, Moraxella and Lactobacillus were more abundant in A. muciniphila-pretreated mice. Metabolomic analysis revealed that A. muciniphila altered the gut metabolome affecting modulation of pathways, including tyrosine metabolism, alanine/aspartate/glutamate homeostasis, cancer-related carbon flux, and GABAergic synaptic signaling. In conclusion, our findings demonstrate A. muciniphila's renoprotective effects through gut-kidney axis modulation, laying the foundation for subsequent studies to verify the connection between gut microbiota and AKI.}, }
@article {pmid40436193, year = {2025}, author = {Lacerda, AL and Casotti, R and Briand, JF and Lenoble, V and Muniategui-Lorenzo, S and Kessler, F and Barre, A and Moscoso-Pérez, CM and Fernández-González, V and Andrade-Garda, JM and Murano, C and Donnarumma, V and Oreste, E and Joyce, H and Hannon, C and Nash, R and Orange, F and Frias, J and Pedrotti, ML}, title = {The plastisphere: a comprehensive description of geographic and temporal community patterns across the Mediterranean Sea and the Atlantic Ocean.}, journal = {Environmental research}, volume = {282}, number = {}, pages = {121929}, doi = {10.1016/j.envres.2025.121929}, pmid = {40436193}, issn = {1096-0953}, abstract = {Plastic pollution is a global ecological threat, not only as physical debris but also as a novel substrate hosting microbial communities, known as "plastisphere". Polymer type (virgin vs. recycled), combined with environmental variations, may influence both early and mature colonization stages. While biogeography has been identified as a key driver of the plastisphere community structure, prior research often relied on isolated studies with no methodological standardization or on opportunistic sampling. Here, this study stands out by conducting a simultaneous and harmonized investigation across environmentally distinct sites in the Mediterranean Sea and the Atlantic Ocean. Three polymers (LDPE, PP-PC, PLA) were incubated in situ, across six locations. Using standardized protocols and eDNA metabarcoding (16S and 18S rRNA), we assessed how biogeography, environmental variables, polymer type, and exposure time shape the diversity and composition of prokaryotic and eukaryotic communities colonizing plastics. Incubations lasted up to one year, with sampling at 7, 30 and 90 days, covering all four seasons. Microbial colonization in all plastics occurred within 7 days, but community richness and maturity fluctuated across sites and seasons. Proteobacteria, Bacteroidia and Planctomycetes were the dominant prokaryotes, while Ciliophora, Cercozoa and Dinoflagellata dominated eukaryotes. Taxa with potential for plastic biodegradation (e.g., Oleibacter, Alcanivorax) and pathogenicity (e.g., Pseudomonas, Candida) were identified, highlighting the plastisphere's ecological role. This dataset represents the most comprehensive assessment of marine plastisphere diversity to date, allowing the understanding of species occurrence and their interactions, influence on ecological processes and the emerging health risks of the plastisphere, which should be considered when developing global strategies to mitigate ocean plastic pollution.}, }
@article {pmid40435560, year = {2025}, author = {Fazio, NA and Albertin, W and Masneuf-Pomarede, I and Randazzo, CL and Caggia, C}, title = {Structure of culturable indigenous yeast population and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts during spontaneous fermentation of Etna vineyards grapes.}, journal = {International journal of food microbiology}, volume = {440}, number = {}, pages = {111282}, doi = {10.1016/j.ijfoodmicro.2025.111282}, pmid = {40435560}, issn = {1879-3460}, mesh = {*Vitis/microbiology ; Fermentation ; *Genetic Variation ; *Wine/microbiology ; *Saccharomyces cerevisiae/genetics/isolation &amp; purification/metabolism/classification ; *Yeasts/genetics/isolation &amp; purification/classification/metabolism/growth &amp; development ; Italy ; Microsatellite Repeats ; Farms ; }, abstract = {The microbial diversity of indigenous yeasts plays a fundamental role in the spontaneous fermentation of wines, contributing to the concept of microbial terroir and potentially influencing the sensory profile of the final product. This study explores the yeast ecology and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts in four wineries located on two different sides of Mount Etna, a region of unique viticultural significance due to its volcanic soils and diverse microclimatic conditions. A total of 454 yeast isolates were obtained from spontaneous fermentations of different grape varieties, and identified as belonging to 18 distinct species. The spontaneous fermentation was characterized by an initial dominance of non-Saccharomyces yeasts, especially Hanseniaspora uvarum and Metschnikowia pulcherrima, followed by a gradual dominance of S. cerevisiae at later stages. Microsatellite genotyping revealed significant genetic diversity among S. cerevisiae strains, with some distinct genetic patterns associated with Italian winery environments. Additionally, H. uvarum exhibited significant genetic variation but lacked clear geographic clustering, suggesting complex ecological and enological interactions. Statistical analyses of microbial diversity indices indicated that vineyard-specific factors, including altitude, soil composition, and agronomic practices, may influence yeast community structure among the four wineries. These findings provide new insights into the microbial ecology of Etna wines and highlight the potential of indigenous yeast populations for maintaining and enhancing regional wine identity.}, }
@article {pmid40432969, year = {2025}, author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ}, title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589263}, pmid = {40432969}, issn = {1664-302X}, abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.}, }
@article {pmid40431577, year = {2025}, author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P}, title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431577}, issn = {2306-7381}, support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; }, abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.}, }
@article {pmid40431542, year = {2025}, author = {Karukayil Gopalakrishnan, N and Pappuswamy, M and Meganathan, G and Shanmugam, S and Pushparaj, K and Balasubramanian, B and Kim, IH}, title = {Influence of Probiotic Administration in Canine Feed: A Comprehensive Review.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431542}, issn = {2306-7381}, abstract = {Dogs are cherished companions, and in today's world, pets are increasingly regarded as family members. Pet owners are placing growing emphasis on their animals' health, particularly for dogs. Probiotics, which are living bacteria that benefit the host when given in sufficient quantities, have drawn a lot of interest in the veterinary nutrition community due to their beneficial effects on companion animals, including dogs. This study emphasizes the advantages of adding probiotics to canine diets in order to enhance the health of the gut flora and the technologies used to incorporate probiotics into canine feed. It looks at the best ways to deal with common dog health problems, highlighting probiotics as a helpful substitute for antibiotics, which can have serious adverse effects, encourage bacterial resistance, and disturb the gut's microbial ecology, which is necessary for digesting. Such disruptions are linked to chronic inflammatory enteropathy and obesity in dogs. This paper also examines biotechnological advancements in probiotic incorporation methods in dog feed, aiming to optimize their health benefits. Probiotic feed supplements may thus represent a promising approach to advancing canine health care, providing a natural adjunct to conventional treatments and preventive measures.}, }
@article {pmid40431287, year = {2025}, author = {Zhong, J and Ran, Q and Han, Y and Gan, L and Dong, C}, title = {Biosynthetic Mechanisms of Plant Chlorogenic Acid from a Microbiological Perspective.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431287}, issn = {2076-2607}, support = {32360029//the National Science Foundation of China/ ; 32400111//the National Science Foundation of China/ ; Qiankehe Foundation-ZK (2024) General 091//he Guizhou Provincial Basic Research Program (Natural Science)/ ; }, abstract = {Chlorogenic acid (CGA), a phenolic compound with diverse bioactivities, plays a crucial role in plant defense mechanisms and has significant therapeutic potential in human inflammatory and cardiovascular diseases. The biosynthesis and accumulation of CGA in plants result from a complex interplay between internal factors (e.g., hormones, enzymes, and genes) and external factors (e.g., microbial interactions, drought, and temperature fluctuations). This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and the interaction between bacteria and fungi. In addition, our review summarizes the challenges currently present in the research and proposes a series of innovative strategies. These include in-depth investigations into the molecular mechanisms of microbial regulation of plant gene expression, gene editing, development of microbial inoculants, construction of synthetic microbial communities, and exogenous application of plant hormones.}, }
@article {pmid40431158, year = {2025}, author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE}, title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431158}, issn = {2076-2607}, support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.}, }
@article {pmid40427685, year = {2025}, author = {Chen, Z and Zhong, Y and Chen, L and Liu, W and Lin, C and Chen, Y and Wang, X}, title = {HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.}, journal = {Biology}, volume = {14}, number = {5}, pages = {}, pmid = {40427685}, issn = {2079-7737}, support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 02-408-2304-05037XM and 02-408-240603131063//Plan on Enhancing Scientific Research in Guangzhou Medical University/ ; 202201020203//Guangzhou Science and Technology Program/ ; }, abstract = {While periodontitis is increasingly linked to systemic disorders through the oral-gut axis, the molecular mediators driving gut microbiota dysbiosis and barrier disruption remain elusive. Hepatocyte growth factor (HGF), a novel regulator of inflammatory bone loss in periodontitis, may serve as a critical communicator between oral infection and distal intestinal pathology. This study investigates how HGF overexpression modulates the gut microbial ecosystem and intestinal barrier integrity in a transgenic periodontitis model. In this study, we combined 16S rRNA sequencing of fecal microbiota with comprehensive gut barrier assessments, including systemic markers (D-lactate, LPS, and DAO ELISA), structural integrity (villous morphology), and molecular analysis (ZO-1, occludin, and NOD2 immunohistochemistry), using HGF-overexpressing transgenic (HGF-Tg) mice with periodontitis. The results demonstrated that HGF increased gut permeability in the context of periodontitis, as evidenced by elevated serum levels of D-lactate and LPS compared to wild type (WT) mice. In addition, gut villous morphology disorder was observed in HGF-Tg mice with periodontitis. HGF also diminished the protein level of occludin and upregulated NOD2 expression in mice with periodontitis. Moreover, HGF-Tg mice with periodontitis exhibited significant dysbiosis of gut microbiota, with reduced levels of probiotics (e.g., Faecalibaculum). Notably, HGF also increased the enrichment of the periodontitis-associated pathogens (e.g., Desulfovibrio and Streptococcus) in the gut. Microbial functions, particularly metabolic pathways, were significantly altered by HGF when periodontitis occurred. Some microorganisms like g_Desulfovibrio may play a role in gut barrier disorder in HGF-Tg mice with periodontitis. Overall, our findings position HGF as a novel orchestrator of oral-gut crosstalk, where its overexpression reshapes gut microbial ecology toward a "leaky gut" phenotype to compromise intestinal barrier integrity, further deepening our understanding of the oral-gut axis.}, }
@article {pmid40427319, year = {2025}, author = {Xu, C and Guo, X and Li, L}, title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {10}, pages = {}, pmid = {40427319}, issn = {2076-2615}, abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.}, }
@article {pmid40426572, year = {2025}, author = {Touati, A and Ibrahim, NA and Mairi, A and Kirat, H and Basher, NS and Idres, T}, title = {One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40426572}, issn = {2079-6382}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.}, }
@article {pmid40423845, year = {2025}, author = {Pérez-Gómez, O and Domínguez-Maqueda, M and García-Márquez, J and Moriñigo, M&#xc1; and Tapia-Paniagua, ST}, title = {Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {55}, pmid = {40423845}, issn = {1432-184X}, support = {PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Shewanella/metabolism/physiology/genetics ; *Biofilms/growth &amp; development/drug effects ; Glycogen/metabolism ; }, abstract = {Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.}, }
@article {pmid40423805, year = {2025}, author = {Meehan, DE and O'Toole, PW}, title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {54}, pmid = {40423805}, issn = {1432-184X}, support = {GOIPG/2024/5035//Taighde &#xc9;ireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; }, abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.}, }
@article {pmid40423261, year = {2025}, author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T}, title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf107}, pmid = {40423261}, issn = {1525-3163}, abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.}, }
@article {pmid40422247, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR Shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum-Sensing Inhibition.}, journal = {Cells}, volume = {14}, number = {10}, pages = {}, pmid = {40422247}, issn = {2073-4409}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; 5R01AI177555-02/GF/NIH HHS/United States ; N/A//Massachusetts General Hospital Research Scholar Award/ ; }, mesh = {*Quorum Sensing/genetics ; *Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism ; Humans ; *Bacterial Proteins/metabolism/genetics ; Biofilms/growth &amp; development ; Virulence ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Pseudomonas Infections/microbiology ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40421462, year = {2025}, author = {Liu, RZ and Zhao, XY and Feng, B and Zhao, WS and Li, MY and Yu, XF and Hu, SP and Li, RP and Gao, JL and Borjigin, Q}, title = {Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1590686}, pmid = {40421462}, issn = {1664-302X}, abstract = {INTRODUCTION: Straw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.<br><br>METHODS: We investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers' shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.<br><br>RESULTS: The study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).<br><br>DISCUSSION: The study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.}, }
@article {pmid40419814, year = {2025}, author = {Srivastava, AK and Riaz, A and Jiang, J and Li, X and Uzair, M and Mishra, P and Zeb, A and Zhang, J and Singh, RP and Luo, L and Chen, S and Yang, S and Zhao, Y and Xie, X}, title = {Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions.}, journal = {Rice (New York, N.Y.)}, volume = {18}, number = {1}, pages = {41}, pmid = {40419814}, issn = {1939-8425}, support = {[2022]091//Guizhou Provincial Youth Science and Technology Talents Growth Project/ ; }, abstract = {Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.}, }
@article {pmid40419768, year = {2025}, author = {Keegstra, JM and Landry, ZC and Zweifel, ST and Roller, BRK and Baumgartner, DA and Carrara, F and Martínez-Pérez, C and Clerc, EE and Ackermann, M and Stocker, R}, title = {Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.}, journal = {Nature microbiology}, volume = {10}, number = {6}, pages = {1393-1403}, pmid = {40419768}, issn = {2058-5276}, support = {542395FY22//Simons Foundation/ ; 542379FY22//Simons Foundation/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 205321 207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40 225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; *Aquatic Organisms/physiology/metabolism ; Biomass ; Carbon Cycle ; *Bacterial Physiological Phenomena ; }, abstract = {Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.}, }
@article {pmid40417422, year = {2025}, author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M}, title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.}, journal = {Nature water}, volume = {3}, number = {5}, pages = {590-604}, pmid = {40417422}, issn = {2731-6084}, abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.}, }
@article {pmid40413948, year = {2025}, author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T}, title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.}, journal = {Food chemistry}, volume = {488}, number = {}, pages = {144871}, doi = {10.1016/j.foodchem.2025.144871}, pmid = {40413948}, issn = {1873-7072}, mesh = {Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; Taste ; *Coffee/microbiology/chemistry/metabolism ; Humans ; *Saccharomyces boulardii/metabolism ; Anaerobiosis ; *Coffea/microbiology/chemistry/metabolism ; Bacteria/metabolism/isolation &amp; purification/classification/genetics ; Flavoring Agents/metabolism/chemistry ; }, abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.}, }
@article {pmid40413198, year = {2025}, author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {858}, pmid = {40413198}, issn = {2052-4463}, support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; }, abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.}, }
@article {pmid40412969, year = {2025}, author = {Yan, W and Gu, L and Yue, X and Zhong, H and Wang, D}, title = {Vertical distribution of intracellular protoporphyrin IX in coastal sediment cores: Implications for sedimentology and microbial community composition.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {712-724}, doi = {10.1016/j.jes.2024.11.014}, pmid = {40412969}, issn = {1001-0742}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Protoporphyrins/analysis ; *Microbiota ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; }, abstract = {Protoporphyrin IX (PPIX), a basic porphyrin system found in nature, all "porphyrin-type" tetrapyrroles with a biological function are biosynthetically derived thereof. PPIX is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Determining the biotic and abiotic factors that influence marine microbial growth and community structure is critical for understanding global biogeochemical cycles. Here, we present vertical profiles of intracellular PPIX and four derivative products (Chlorophyll-a/b and Pheophytin-a/b) from two coastal sediment cores, alongside ancillary geochemical and 16S rRNA microbial community data. Our findings indicated that PPIX is present in the natural sediment environment and displays a decreasing trend with depth, revealing a significant positive correlation with both organic matter and microbial abundance. Co-occurrence networks revealed that the environmental distribution of PPIX was positively correlated with the microbial porphyrin producer (high genetic completeness), but negatively correlated with auxotrophs (absence or low genetic completeness). It emphasized the critical role of PPIX as a biological molecule involved in key physiological processes. These results suggest that PPIX is a prominent component of the shared extracellular metabolite pool, especially in anoxic marine sediments where it exists at physiologically relevant concentrations for microbial metabolism. This study highlighted the significance of PPIX in microbial ecology and its potential impact on biogeochemical cycles in marine sedimentary environments.}, }
@article {pmid40412391, year = {2025}, author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F}, title = {The contribution of pelagic fungi to ocean biomass.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.05.004}, pmid = {40412391}, issn = {1097-4172}, abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.}, }
@article {pmid40411587, year = {2025}, author = {Kelleher, LA and Anderson, Z and Stratford, JA and Fortunato, CS}, title = {Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {53}, pmid = {40411587}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Grassland ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Pennsylvania ; *Solidago/microbiology ; Plant Roots/microbiology ; Biodiversity ; Hydrogen-Ion Concentration ; }, abstract = {Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.}, }
@article {pmid40410028, year = {2025}, author = {Vareschi, S and Jaut, V and Vijay, S and Allen, RJ and Schreiber, F}, title = {Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.012}, pmid = {40410028}, issn = {1878-4380}, abstract = {The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.}, }
@article {pmid40408931, year = {2025}, author = {Conall Holohan, B and Trego, A and Keating, C and Bressani-Ribeiro, T and Chernicharo, CL and Daigger, G and Galdi, SM and Knörle, U and Paissoni, E and Robles, A and Rogalla, F and Shin, C and Soares, A and Smith, AL and Szczuka, A and Hughes, D and O'Flaherty, V}, title = {Anaerobic microbial core for municipal wastewater treatment - the sustainable platform for resource recovery.}, journal = {Current opinion in biotechnology}, volume = {94}, number = {}, pages = {103317}, doi = {10.1016/j.copbio.2025.103317}, pmid = {40408931}, issn = {1879-0429}, abstract = {The requirement for carbon neutrality and bioresource recovery has shifted our views on water treatment from health and pollution avoidance to one of sustainability with water and nutrient circularity. Despite progress, the current process of wastewater treatment is linear, based on core aerobic microbiology, which is unlikely to be carbon neutral due to its large use of energy and production of waste sludge. Here, we outline a shift from aerobic to anaerobic microbiology at the core of wastewater treatment and resource recovery, illustrating the state-of-the-art technologies available for this paradigm shift. Anaerobic metabolism primarily offers the benefit of minimal energy input (up to 50% reduction) and minimal biomass production, resulting in up to 95% less waste sludge compared with aerobic treatment, which is increasingly attractive, given dialogue surrounding emerging contaminants in biosolids. Recent innovative research solutions have made ambient (mainstream) anaerobic treatment a ready substitute for the aerobic processes for municipal wastewater in temperate regions. Moreover, utilising anaerobic treatment as the core carbon removal step allows for more biological downstream resource recovery with several opportunities to couple the process with (anaerobic) nitrogen and phosphorus recovery, namely, potential mainstream anaerobic ammonium oxidation (anammox) and methane oxidation (N-DAMO). Furthermore, these technologies can be mixed and matched with membranes and ion-exchange systems, high-value biochemical production, and/or water reuse installations. As such, we propose the reconfiguration of the wastewater treatment plant of the futurewith anaerobic microbiology. Mainstream anaerobic treatment at the core of a truly sustainable platform for modern municipal wastewater treatment, facilitating circular economy and net-zero carbon goals.}, }
@article {pmid40408805, year = {2025}, author = {Bi, W and Butardo, V and Sha, G and Zhang, H and Wu, X and Wang, L}, title = {Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review.}, journal = {Waste management (New York, N.Y.)}, volume = {204}, number = {}, pages = {114894}, doi = {10.1016/j.wasman.2025.114894}, pmid = {40408805}, issn = {1879-2456}, abstract = {Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.}, }
@article {pmid40408146, year = {2025}, author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP}, title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {5}, pages = {}, pmid = {40408146}, issn = {1367-4811}, support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; }, abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.}, }
@article {pmid40407874, year = {2025}, author = {Velthuis, M and Zoccarato, L and Veraart, AJ and Monaghan, MT and Funke, E and Verdonschot, P and Grossart, HP and Hilt, S}, title = {Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {52}, pmid = {40407874}, issn = {1432-184X}, support = {Veni.202.053//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Biofilms/growth &amp; development/radiation effects ; *Fungi/classification/genetics/radiation effects/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota/radiation effects ; *Light ; *Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism ; Nitrogen/metabolism/analysis ; Carbon/metabolism/analysis ; Phosphorus/metabolism/analysis ; Biodiversity ; Plant Leaves/microbiology ; Phenols/analysis/metabolism ; }, abstract = {Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.}, }
@article {pmid40407873, year = {2025}, author = {Van Heurck, B and Cardenas, DV and Hylén, A and Jankowska, E and Cole, DB and Montserrat, F and Kreuzburg, M and Romaniello, SJ and Meysman, FJR}, title = {Microbial Community Structure in Contrasting Hawaiian Coastal Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {51}, pmid = {40407873}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology/chemistry ; Hawaii ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology/chemistry ; Bays/microbiology/chemistry ; Biodiversity ; }, abstract = {Microbe-mineral interactions play a fundamental role in marine sediments and global biogeochemical cycles. Here, we investigated the sediment microbial communities in two contrasting field sites on Big Island, Hawaii (USA), that differ in their bay morphology and sediment grain size distributions: Papakōlea Beach (exposed, finer sediment) and Richardson Ocean Park (sheltered, coarser sediment). We selected three stations within each bay and characterized the mineral and chemical composition of the sediment and porewater, and used 16S rRNA amplicon sequencing of the V4V5 hypervariable region to investigate the naturally occurring microbial communities. Microbial community structure differed significantly between the two bays, rather than within each bay, whereby microbial diversity was markedly lower at Papakōlea compared to Richardson. We correlated environmental variables to microbial community structure in order to identify the key drivers of community differences between and within the two bays. Our study suggests that differing physico-chemical properties of the sediment and porewater, resulting from the contrasting bay morphologies and geophysical drivers, are the main factors influencing microbial community structure in these two bays. Papakōlea Beach is a naturally occurring "green sand" beach, due to its high olivine content. This site was selected in the broader context of a field campaign investigating olivine as a source mineral for ocean alkalinity enhancement (OAE), a carbon dioxide removal technology. Our results highlight the complexity of marine sediment environments, with implications for the monitoring, reporting and verification of future field trials involving olivine addition for ocean alkalinity enhancement.}, }
@article {pmid40406230, year = {2025}, author = {Li, M and Meng, Z and Li, J and Zhang, X and Wang, Y and Li, X and Yang, Y and Li, Y and Yang, X and Chen, X and Fan, Y}, title = {Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19364}, pmid = {40406230}, issn = {2167-8359}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; China ; *Soil Microbiology ; *Betula/microbiology ; Stochastic Processes ; Biodiversity ; Rhizosphere ; DNA, Fungal/genetics ; Mycobiome ; }, abstract = {The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China.}, }
@article {pmid40405772, year = {2025}, author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S}, title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.}, journal = {International journal of surgery (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/JS9.0000000000002502}, pmid = {40405772}, issn = {1743-9159}, abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.<br><br>MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25%&#xa0;=&#xa0;&#x3a9;1, 50%&#xa0;=&#xa0;&#x3a9;2, 75%&#xa0;=&#xa0;&#x3a9;3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of &#x3a9;3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.<br><br>RESULTS: RYGB and &#x3a9;1&amp;2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (&#x3a9;3) resulted in 100% mortality. The &#x3a9;3 procedure induced bacterial translocation of enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in &#x3a9;3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved &#x3a9;3 one-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.<br><br>CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.}, }
@article {pmid40405300, year = {2025}, author = {He, T and Moukarzel, R and Fu, M and Yang, M and Du, R and Zhao, J and Liu, J and Wu, J and Deng, W and Zhu, Y and Yang, M and Zhu, S and Du, F}, title = {Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {56}, pmid = {40405300}, issn = {2524-6372}, support = {32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 2018HA009//Yunnan Provincial Academician Exploration Funding Project/ ; }, abstract = {Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.}, }
@article {pmid40404904, year = {2025}, author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {50}, pmid = {40404904}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology/blood ; *Metabolome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Cloaca/microbiology ; *Ponds/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; Fresh Water ; }, abstract = {The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.}, }
@article {pmid40403739, year = {2025}, author = {Kramer, SJ and Jones, EL and Estapa, ML and Paul, NL and Rynearson, TA and Santoro, AE and Sudek, S and Durkin, CA}, title = {Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40403739}, issn = {1751-7370}, support = {#986836//Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology/ ; 80NSSC21K0015//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC18K1431//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC17K0716//NASA Ocean Biology and Biogeochemistry/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phytoplankton/genetics/metabolism/classification ; *Diatoms/metabolism/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Pacific Ocean ; Atlantic Ocean ; *Carbon/metabolism/analysis ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to identify mechanistic links between surface communities and carbon export in the North Pacific and North Atlantic Oceans. Phytoplankton 18S rRNA gene sequences were sampled over a 1-month period in surface seawater and within bulk-collected and individually isolated sinking particles using mesopelagic sediment traps (100-500 m). Nearly all phytoplankton amplicon sequence variants exported from the surface were packaged in large (>300 μm) particles. Individually, each of these particles contained only a few distinct phytoplankton amplicon sequence variants, but collectively, large particles transported about half of the surface taxonomic diversity into the mesopelagic. The relative sequence abundances of the surface community detected within particles were quantitatively related to measured carbon fluxes: a linear model based on the relative sequence abundance of just two pigment-based phytoplankton taxa, diatoms and photosynthetic Hacrobia, was predictive of carbon flux magnitude. These two taxa were also enriched in the ecologically distinct particle classes that had the greatest influence on carbon export magnitude. As global, hyperspectral ocean color satellites begin to quantify these taxonomic groups in the surface ocean, the relationship of these taxa to carbon fluxes demonstrated here may help in developing more accurate algorithms to estimate global carbon export in the ocean.}, }
@article {pmid40402470, year = {2025}, author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ}, title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.}, journal = {Letters in applied microbiology}, volume = {78}, number = {5}, pages = {}, doi = {10.1093/lambio/ovaf070}, pmid = {40402470}, issn = {1472-765X}, mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.}, }
@article {pmid40402324, year = {2025}, author = {Mizeriene, G and Lygis, V and Prospero, S}, title = {Oomycete Diversity and Ecology in Declining Alder Stands in Switzerland.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {49}, pmid = {40402324}, issn = {1432-184X}, support = {Project Code 14.035//Sciex-NMSch Fellowship/ ; }, mesh = {Switzerland ; *Alnus/microbiology/parasitology ; *Oomycetes/classification/isolation &amp; purification/genetics ; *Biodiversity ; *Soil Microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Phytophthora/isolation &amp; purification/classification/genetics ; Phylogeny ; Pythium/isolation &amp; purification/genetics/classification ; }, abstract = {In this study, we assessed the occurrence and diversity of four oomycete genera (Phytophthora, Phytopythium, Pythium, and Globisporangium) in 13 declining alder (Alnus glutinosa and A. incana) stands in Switzerland. For this, we sampled and analyzed soil from tree rhizosphere, water from streams and rivers along which the stands were located, and symptomatic alder bark. The overall isolation rate was 47.2%, with a total of 400 oomycete isolates recovered at all 13 sites. The highest incidence of oomycete isolates was in soil samples (baiting, 82.5% isolation rate), followed by water (baiting, 14.7%), and bark (direct isolation, 2.7%). Of all recovered oomycete isolates, 90.3% could be successfully assigned to a known species, for a total of 23 species identified, including both preferential saprotrophs and pathogens. Among all genera, Phytophthora was the most abundant with 273 isolates (75.6%), followed by Phytopythium, Pythium, and Globisporangium. Oomycete species diversity showed a significant variation among substrates. Only one species-Phytophthora lacustris-was abundant in all substrates, while 16 species were restricted to a specific substrate, mainly soil. The rhizosphere of symptomatic alder trees harbored the most diverse oomycete community, highlighting once again the importance of soil as a reservoir for these microorganisms. Only two Phytophthora species were isolated from alder bark lesions, namely, P. × alni, the known causal agent of alder decline, and P. lacustris. The low recovery rate of P. × alni might be due to attempts to isolate it from old, inactive lesions, but may also suggest that alder decline might be caused by other oomycetes infecting the root system of the trees.}, }
@article {pmid40402315, year = {2025}, author = {Mitchell, JK and Matthee, S and Ndhlovu, A and Miller, M and Buss, P and Matthee, CA}, title = {The Microbiome and Coxiella Diversity Found in Amblyomma hebraeum and Dermacentor rhinocerinus Ticks Sampled from White Rhinoceros.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {48}, pmid = {40402315}, issn = {1432-184X}, mesh = {Animals ; *Microbiota ; *Perissodactyla/parasitology/microbiology ; *Amblyomma/microbiology ; *Coxiella/genetics/classification/isolation &amp; purification ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; South Africa ; Coxiella burnetii/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; }, abstract = {The microbiome and the prevalence of the pathogenic bacterium Coxiella burnetii in ticks associated with white rhinoceros, Ceratotherium simum, is unknown. Targeted Illumina 16S rRNA amplicon sequencing was used to characterize the bacterial microbiome diversity found within 40 Amblyomma hebraeum and 40 Dermacentor rhinocerinus ticks collected from 40 white rhinoceros individuals in the Kruger National Park, South Africa. Specific emphasis was also given to further investigate the prevalence of the pathogenic C. burnetti in these tick species. At the phylum level, Proteobacteria dominated both tick microbiomes, followed by Actinobacteria and Firmicutes; Coxiella was the most abundant genus within A. hebraeum and Rickettsia within D. rhinocerinus. While alpha diversity did not differ significantly between the two tick species, beta diversity revealed significant species-specific differences in bacterial community composition. Additionally, there was no correlation between sampling region and microbiome diversity or composition for either tick species. Twenty-five Coxiella amplicon sequence variants (ASVs) were identified, forming three distinct monophyletic Coxiella clades and a fourth single ASV lineage. The Coxiella clades showed a correlation to tick species identity with D. rhinocerinus harboring significantly greater Coxiella diversity than A. hebraeum-potentially indicative of different coevolutionary pathways between the bacteria and their respective hosts. PCR of the IS1111 transposase gene for 238 ticks detected a 66.1% (56.7-74.4%) prevalence for C. burnetii in D. rhinocerinus compared to 55.8% in A. hebraeum (46.5-64.8%). These findings support a notion that each tick species is characterized by its own microbiome community composition and that both A. hebraeum and D. rhinocerinus may act as reservoirs and potential vectors of C. burnetii to white rhinoceros.}, }
@article {pmid40402178, year = {2025}, author = {Salazar, J and González, J and Riofrío, R and Siavichay, F and Carrera, M and Mogrovejo, A and Barrera-Galicia, G and Valdez-Tenezaca, A}, title = {MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {47}, pmid = {40402178}, issn = {1432-184X}, support = {PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; }, mesh = {Ecuador ; Animals ; *Skin/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; *Anura/microbiology ; Biodiversity ; }, abstract = {Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.}, }
@article {pmid40401940, year = {2025}, author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Pérez-Santos, N and Borrero-Villabol, SJ and Rodríguez-Ramos, J and Nieves-Rivera, AM and Rios-Velazquez, C}, title = {Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0002225}, pmid = {40401940}, issn = {2576-098X}, abstract = {Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.}, }
@article {pmid40401939, year = {2025}, author = {Darden, B and Johnson, G and Busch, G and Sharma, I}, title = {Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0088224}, pmid = {40401939}, issn = {2576-098X}, support = {2205569//National Science Foundation/ ; }, abstract = {We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.}, }
@article {pmid40401933, year = {2025}, author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S}, title = {Genomic insights into novel predatory myxobacteria isolated from human feces.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0214724}, doi = {10.1128/spectrum.02147-24}, pmid = {40401933}, issn = {2165-0497}, abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.}, }
@article {pmid40400674, year = {2025}, author = {Kokociński, M and Graco-Roza, C and Jasser, I and Karosienė, J and Kasperovičienė, J and Kobos, J and Koreivienė, J and Mankiewicz-Boczek, J and Soininen, J and Szczurowska, A}, title = {Environmental factors determining the distribution patterns of invasive Raphidiopsis raciborskii and R. mediterranea in central east Europe.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533716}, pmid = {40400674}, issn = {1664-302X}, abstract = {OBJECTIVE: In recent decades, the invasive cyanobacteria Raphidiopsis raciborskii and Raphidiopsis mediterranea have expanded their distribution globally, particularly in temperate regions. Understanding the ecological drivers of Raphidiopsis distribution is imperative to addressing the challenges associated with these species. Here, we aimed to characterize the distribution and biomass of R. raciborskii and R. mediterranea across 112 lakes in Poland and Lithuania in relation to local and regional factors.<br><br>RESEARCH DESIGN AND METHODS: Integrated water samples were collected from 102 Polish and 10 Lithuanian lakes from different regions for phytoplankton and chemical analyses. The lakes varied in surface area, and exhibited diverse mixing regimes, trophic states, and morphometries. Phytoplankton was identified and quantified using a Fuchs-Rosenthal or Nageotte chamber. Additionally, we characterized the degree of human pressures the climatic constraints experienced by each lake.<br><br>RESULTS: R. raciborskii occurrence has increased in eastern regions of Poland but biomass is relatively low compared to western Poland, likely due to lower air temperatures and nutrient concentrations, especially phosphorus. In contrast, R. mediterranea only occurred in a small number of lakes in Poland, and in a single lake in Lithuania, with no relation to measured local and regional variables.<br><br>CONCLUSIONS: Our study shows contrasting patterns in the distribution of two invasive cyanobacteria species in Europe, highlighting the importance of climate and nutrients to the distribution of R. raciborskii, the most widespread species, and providing relevant information for decision making and conservation strategies.}, }
@article {pmid40399330, year = {2025}, author = {Liang, X and Yang, S and Radosevich, M and Wang, Y and Duan, N and Jia, Y}, title = {Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {82}, pmid = {40399330}, issn = {2055-5008}, support = {42377306//National Natural Science Foundation of China/ ; 2023JH3/10200009//Natural Science Foundation of Liaoning Province/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; }, mesh = {*Bacteriophages/physiology ; Phenotype ; *Bacteria/virology/metabolism/genetics ; Ecosystem ; *Host Microbial Interactions ; *Microbiota ; }, abstract = {Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.}, }
@article {pmid40398824, year = {2025}, author = {Massaro, A and Peruzzo, A and Zacometti, C and Zancato, M and Piro, R and Losasso, C and Tata, A and Peron, G}, title = {Exploring the crosstalk between gut microbiota and stool metabolome in omnivorous, vegetarian, and vegan diets: A pilot study.}, journal = {The Journal of nutritional biochemistry}, volume = {144}, number = {}, pages = {109965}, doi = {10.1016/j.jnutbio.2025.109965}, pmid = {40398824}, issn = {1873-4847}, abstract = {Gut microbiota (GM) and fecal metabolome are shaped by different dietary regimens. Nevertheless, outlining generalized patterns is challenging, due to the intrinsic heterogeneity of individual dietary choices. In this work, the fecal metabolome of adult volunteers consuming omnivorous (n=44), vegetarian (n=29), and vegan diets (n=25) for at least 12 months was characterized. The crosstalk among diet, GM and fecal metabolome was also investigated correlating metabolomics and metataxonomics data. Untargeted metabolomic profiles were correlated with metataxonomics data previously acquired on the same stool samples. The sphingomyelin SM(d18:2/18:1-2OH) and phosphoethanolamines from animal-based food were associated to the omnivorous diet and were negatively correlated to beneficial Bacteroides ovatus and Odoribacter genus. Plant glycerides, sterols, triterpenes, and oleic-linoleic acid were associated with the vegan diet. Oleic-linoleic acid was positively correlated with Alistipes putredinis. Chenodeoxycholic acid, a primary bile acid, was identified as a marker of vegan diet, while ketolithocholic acid, a secondary bile acid, was associated to the omnivorous diet. This latter was also negatively correlated to B.ovatus. Overall, results confirm that assessing markers of dietary regimens instead of specific food categories is challenging, especially if volunteers' diet is not strictly monitored. However, the integration of metabolomics and metataxonomic data allows to better understand the effects of specific food components on the GM and represents a suitable approach for further molecular investigation in nutrition.}, }
@article {pmid40394467, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {Correction: The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {671}, pmid = {40394467}, issn = {1471-2229}, }
@article {pmid40394206, year = {2025}, author = {Khurshid, H and Jamshaid, MB and Salahuudin, Z and Sibtain, K and Fayyaz, I and Ameer, A and Kerbiriou, C and Mckirdy, S and Malik, SN and Gerasimidis, K and Noreen, Z and Javed, S and Tariq, A and Ijaz, UZ and Tariq, A}, title = {Gut microbial ecology and function of a Pakistani cohort with Iron deficiency Anemia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17532}, pmid = {40394206}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; MR/Z50628X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anemia, Iron-Deficiency/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Humans ; Pakistan/epidemiology ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Iron/metabolism ; Bacteria/genetics/classification ; Diet ; }, abstract = {Iron deficiency anemia (IDA) is a major public health concern among women of reproductive age leading to high maternal mortality. Pakistan being one of the Lower -Middle income countries (LMIC) is facing this challenge tremendously. The objective of this study is to determine the impact of IDA on gut microbial diversity as well as its relationship with microbial metabolites.16 S rRNA gene profiling of healthy and IDA affected meconium samples was performed with additional meta-data collected through questionnaire. The anemia was linked to different dietary parameters through chi-square test of independence and Generalized Linear Latent Variable Model (GLLVM). Anaerobic bacterial genera such as Coprococcus, Anaerovoracaceae, strongly associated with anemia and negatively correlated with red meat and fish consumption. Moreover, these microbes positively correlated with branched short chain fatty acids (BSCFAs) production. BSCFAs have strong implications in metabolic disorders. This study provides a snapshot of how anemia modulates gut microbial diversity and microbial metabolites production which may have an impact on iron metabolism.}, }
@article {pmid40393817, year = {2025}, author = {Pantigoso, HA and Ossowicki, A and Stringlis, IA and Carrión, VJ}, title = {Hub metabolites at the root-microbiome interface: unlocking plant drought resilience.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.007}, pmid = {40393817}, issn = {1878-4372}, abstract = {Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.}, }
@article {pmid40393246, year = {2025}, author = {Liu, X and Li, Y and Yuan, C and Zhao, Y and Zhou, L and Yan, Y and Ren, J and Liu, Q}, title = {Sophocarpine suppresses MAPK-mediated inflammation by restoring gut microbiota in colorectal cancer.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {143}, number = {}, pages = {156833}, doi = {10.1016/j.phymed.2025.156833}, pmid = {40393246}, issn = {1618-095X}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; Animals ; Humans ; Mice ; *Alkaloids/pharmacology ; Fecal Microbiota Transplantation ; Inflammation/drug therapy ; Cell Line, Tumor ; Male ; Mice, Inbred BALB C ; *Antineoplastic Agents, Phytogenic/pharmacology ; MAP Kinase Signaling System/drug effects ; Dysbiosis/drug therapy ; Xenograft Model Antitumor Assays ; Mice, Nude ; p38 Mitogen-Activated Protein Kinases/metabolism ; Matrines ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), as one of the most common cancers globally, poses a significant challenge to public health due to its high incidence and mortality rates. This underscores the need for continuous exploration of new therapeutic targets and effective drugs. Sophocarpine (SC), a natural compound derived from traditional Chinese medicine, holds considerable therapeutic potential in the treatment of CRC, however, the relevant mechanisms remains unclear.<br><br>PURPOSE: This study aims to explore the anti-tumor effects of SC against CRC by modulating gut microbiota, and uncover potential mechanisms linking SC's therapeutic effects to gut microbiota regulation by analyzing the impact of SC on microbiota composition and CRC progression.<br><br>MATERIAL: This study explores the impact of SC on the gut microbiota in CRC by constructing subcutaneous xenograft tumors of CRC and integrating 16S rRNA sequencing and RNA transcriptomic sequencing. The fecal microbiota transplantation (FMT) mouse model was used to validate the biological function of SC in correcting gut microbiota dysbiosis to treat CRC. Subsequently, we conducted in vitro studies on the molecular mechanisms by which SC regulates the gut microbiota as an effective hallmark of CRC treatment, using lipopolysaccharide (LPS) to simulate an inflammatory gut microbiota environment and P38 MAPK knockdown cell line.<br><br>RESULTS: SC significantly inhibited CRC cell proliferation with IC50 values of 2.547&#xb1;0.256 &#x3bc;M for HCT116 and 2.851&#xb1;0.332 &#x3bc;M for LoVo cells. In vivo experiments demonstrated that SC effectively suppressed tumor growth in xenograft models. 16S rRNA sequencing revealed that SC modulated gut microbiota composition, particularly affecting Bacteroides and Alistipes populations. SC significantly reduced the levels of inflammatory factors and inhibited the MAPK signaling pathway, as evidenced by decreased p-JNK, p-p38 MAPK, and p-NF-&#x3ba;B p65 expression.<br><br>CONCLUSIONS: Current clinical practice still lacks effective therapeutic agents targeting CRC through gut microbiota modulation. This study presents the first evidence that SC, a natural compound, exhibits dual-action therapeutic efficacy against CRC progression by simultaneously modulating gut microbial composition and suppressing MAPK pathway-mediated inflammatory responses. These findings highlight SC's novel therapeutic potential as a promising microbiota-regulating candidate for CRC intervention, offering an innovative approach that bridges microbial ecology with cancer signaling pathways.}, }
@article {pmid40387954, year = {2025}, author = {Warren, ML and Tsuji, K and Decker, LE and Kishi, M and Yang, J and Howe, AC and Fukami, T}, title = {Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {46}, pmid = {40387954}, issn = {1432-184X}, support = {1656518//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Bees/microbiology ; Animals ; *Plant Nectar ; *Bacteria/classification/isolation &amp; purification/genetics ; *Flowers/microbiology ; Japan ; *Mouth/microbiology ; Seasons ; Gastrointestinal Microbiome ; }, abstract = {Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.}, }
@article {pmid40387916, year = {2025}, author = {González-Villalobos, E and de Almeida Kumlien, ACM and Sànchez-Melsió, A and Balcázar, JL}, title = {Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Onyar River, Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {41}, pmid = {40387916}, issn = {1432-184X}, support = {CVU: 441304//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 792686//European Union's Horizon 2020 Research and Innovation Programme under the Marie Sk&#x142;odowska-Curie/ ; SGR 01282//Generalitat de Catalunya/ ; }, mesh = {Spain ; *Rivers/microbiology/virology ; *Bacteriophages/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/virology/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Geologic Sediments/microbiology/virology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; DNA, Viral/genetics ; }, abstract = {This study aimed to investigate the presence and abundance of antibiotic resistance genes (ARGs) in bacterial and phage DNA fractions from sediment samples collected from the Onyar River, both before and after its passage through the urban area of Girona (northeast Spain). Genes conferring resistance to β-lactams, fluoroquinolones, macrolides, sulfonamides, and tetracyclines were quantified using quantitative PCR. Our findings showed that ARGs are present in both bacterial and phage DNA fractions, with a higher abundance in the bacterial fraction. Notably, our analysis revealed an increased abundance of the sulfonamide resistance gene sulI in the phage DNA fraction when comparing samples collected before and after the river's passage through the city. Although similar trends were observed for other ARGs (e.g., qnrS and sulII), these differences were not statistically significant (p > 0.05). These findings emphasize the importance of phages as potential reservoirs or vehicles for ARGs in environmental settings. Further research is needed to elucidate the factors that influence gene transfer dynamics and the persistence of ARGs within phages.}, }
@article {pmid40385475, year = {2025}, author = {Li, J and Zhou, L and Xiao, Z}, title = {Advances in the study of Ophiopogon japonicus polysaccharides: structural characterization, bioactivity and gut microbiota modulation regulation.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1583711}, pmid = {40385475}, issn = {1663-9812}, abstract = {Ophiopogon japonicus polysaccharides (OJPS), the principal bioactive constituents isolated from Ophiopogon japonicus, demonstrate substantial physiological efficacy. OJPS is characterized by a high molecular weight, typically ranging from 2.48 to 324.7 kDa. Emerging evidence indicates that OJPS modulates the composition and structural organization of the gut microbiota, thereby maintaining intestinal barrier integrity and enhancing both gastrointestinal and systemic homeostasis. Moreover, OJPS and its metabolic derivatives engage in dynamic interactions with microbial communities, mediating cellular signaling cascades and endocrine regulation to elicit hypoglycemic effects. Despite these findings, comprehensive analyses of OJPS extraction and purification methodologies, structural elucidation, biological functionalities, and mechanistic insights into its crosstalk with the gut microbiota remain scarce. This review systematically synthesizes contemporary knowledge pertaining to the preparation, structural attributes, bioactivity, and mechanistic underpinnings of OJPS, with particular emphasis on its dual regulatory role in host physiology and gut microbial ecology.}, }
@article {pmid40384051, year = {2025}, author = {Khafagy, ES and Saqr, AA and Almutairy, BK and Aldawsari, MF and Lila, ASA and Ibrahim, TS and Hegazy, WAH and Salem, IM}, title = {Repurposing Nitroimidazoles: A New Frontier in Combatting Bacterial Virulence and Quorum Sensing via In Silico, In Vitro, and In Vivo Insights.}, journal = {Drug development research}, volume = {86}, number = {3}, pages = {e70101}, doi = {10.1002/ddr.70101}, pmid = {40384051}, issn = {1098-2299}, support = {//The authors extend their appreciation to Prince Sattam bin Abdulaziz University for funding this research work through the project number (PSAU/2024/03/29653)./ ; }, mesh = {*Quorum Sensing/drug effects ; Animals ; Biofilms/drug effects ; *Drug Repositioning ; Humans ; Molecular Docking Simulation ; Virulence/drug effects ; *Nitroimidazoles/pharmacology ; Mice ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; HeLa Cells ; Chromobacterium/drug effects ; Molecular Dynamics Simulation ; Pseudomonas aeruginosa/drug effects ; Female ; Indoles/metabolism ; }, abstract = {The global antibiotic resistance crisis demands innovative strategies targeting bacterial virulence rather than survival. Quorum sensing (QS), a key regulator of virulence and biofilm formation, offers a promising avenue to mitigate resistance by disarming pathogens without bactericidal pressure. This study investigates the repurposing of nitroimidazoles as anti-QS and anti-virulence agents at subminimum inhibitory concentrations (sub-MICs). In Silico analyses, including molecular docking and molecular dynamics (MD) simulations, were performed to investigate ligand-receptor interactions with structurally distinct Lux-type QS receptors and assess binding stability and conformational dynamics over time. In Vitro assays evaluated the effects of representative nitroimidazoles, metronidazole (MET) and secnidazole (SEC), on QS-controlled phenotypes, including violacein production in Chromobacterium violaceum and biofilm formation and protease activity in Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella enterica, and Proteus mirabilis. In Vivo efficacy was assessed using a murine infection model and HeLa cell invasion assays. Molecular docking revealed high-affinity binding to QS receptors, corroborating their mechanistic interference. Sub-MIC MET/SEC significantly suppressed violacein synthesis, biofilm biomass, and protease secretion in Gram-negative pathogens. Both compounds reduced bacterial invasiveness in HeLa cells and In Vivo protected mice from lethal P. aeruginosa infections. Crucially, nitroimidazoles attenuated virulence without affecting bacterial viability, preserving microbial ecology. These findings position nitroimidazoles as dual-function agents; antimicrobial at bactericidal doses and anti-virulence at sub-MICs. Their validated efficacy across In Silico, In Vitro, and In Vivo models underscores their potential as adjunctive therapies, bridging the gap between drug repurposing and next-generation anti-infective development.}, }
@article {pmid40383311, year = {2025}, author = {Zhu, L and Huang, K and Bai, T and Xia, H}, title = {Bacteriophages enhance the transformation of dissolved organic matter during vermicomposting of sludge.}, journal = {Bioresource technology}, volume = {432}, number = {}, pages = {132694}, doi = {10.1016/j.biortech.2025.132694}, pmid = {40383311}, issn = {1873-2976}, mesh = {*Sewage/microbiology/chemistry ; *Bacteriophages/physiology/metabolism ; *Composting/methods ; *Organic Chemicals/metabolism ; Biodegradation, Environmental ; Carbon ; Solubility ; }, abstract = {Vermicomposting is an eco-friendly technology for treating sewage sludge, however its efficiency in transforming biological material is often constrained. This study investigates the potential of bacteriophages to enhance the transformation of dissolved organic matter (DOM) during sludge vermicomposting. Fresh dewatered sludge treated with bacteriophages (VP) were compared to untreated controls (CK) over a 30 days' vermicomposting. The results showed that bacteriophage inoculation led to a 58.17 % reduction in dissolved organic carbon (DOC), significantly higher than the 10.67 % reduction in the CK group (P < 0.05). Additionally, the DOM stability indices in the VP treatment were significantly decreased by 30.95 % (P < 0.05), alongside an increased humification rate. Partial least squares path modeling (PLS-PM) revealed that bacteriophages played a pivotal role in accelerating DOM degradation by selectively lysing specific bacterial populations and altering DOM transformation pathways.}, }
@article {pmid40382531, year = {2025}, author = {Hasegawa, R and Poulin, R and Salloum, PM}, title = {Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {45}, pmid = {40382531}, issn = {1432-184X}, support = {202460294//Japan Society for the Promotion of Science/ ; UOO2113//Marsden Fund/ ; UOO2113//Marsden Fund/ ; }, mesh = {Animals ; *Trematoda/microbiology/classification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Snails/parasitology/microbiology ; Phylogeny ; }, abstract = {Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.}, }
@article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, }
@article {pmid40380820, year = {2025}, author = {Lakamp, AD and Neujahr, AC and Fernando, SC and Snelling, WM and Spangler, ML}, title = {Short communication: imputation accuracy of host genomic data from metagenomic sequence information.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, doi = {10.1093/jas/skaf175}, pmid = {40380820}, issn = {1525-3163}, mesh = {Animals ; Cattle/genetics ; *Metagenomics/methods ; Genotype ; Sequence Analysis, DNA/veterinary ; }, abstract = {Metagenomic sequencing is the process of extracting all the genomic information from a given sample. Most metagenomic studies remove any host reads as a matter of course. However, host reads can be used as the basis for genotype imputation to obtain whole genomic sequences. The accuracy of these imputed genotypic calls from a bovine ocular sample was determined by comparing results to those from a commercial array. Overall, imputed genotype calls proved to have a high concordance with array genotype calls (average concordance of 83% and correlation of 0.81 with no filtering). Accuracy increased as filters for host read depth and imputed call confidence were implemented. With filters in place, the average percent concordance was 98% (88% to 99%) while the mean correlation was 0.98 (0.89 to 0.99). Further, identity verification of the metagenomic samples can be carried out if the host is genotyped on another platform.}, }
@article {pmid40379949, year = {2025}, author = {Onaka, H}, title = {Unlocking hidden bioactive compounds: from indolocarbazole and RiPP biosynthesis to the activation of cryptic secondary metabolism via microbial interactions.}, journal = {The Journal of antibiotics}, volume = {}, number = {}, pages = {}, pmid = {40379949}, issn = {1881-1469}, abstract = {Actinomycetes, particularly Streptomyces, are soil microorganisms that produce diverse secondary metabolites with pharmaceutical applications, such as antibiotics and anticancer drugs. These metabolites play important roles in microbial competition and survival. This review highlights three major aspects of actinomycete secondary metabolism: (1) the biosynthesis of indolocarbazoles, (2) the biosynthesis of RiPPs (ribosomally synthesized and post-translationally modified peptides), and (3) the activation of secondary metabolism through microbial interactions. Indolocarbazoles, including staurosporine and rebeccamycin, are potent inhibitors of kinases and DNA topoisomerase I, with potential as anticancer agents. Their biosynthetic pathways involve multiple enzymatic steps, notably carbon-carbon bond formation catalyzed by cytochrome P450 enzymes. RiPPs such as goadsporin and lactazole are highly modular peptide natural products; structural gene modification enables the generation of diverse analogs. A cell-free one-pot synthesis platform has been developed for efficient analog production. To activate cryptic biosynthetic pathways, we employed a combined-culture strategy using actinomycetes and mycolic acid-containing bacteria, resulting in the discovery of 42 novel compounds. Genetic and physiological data indicate that physical contact, rather than diffusible signaling, is essential for induction. These insights emphasize the importance of microbial interactions in natural product biosynthesis and offer new directions for drug discovery through synthetic biology and microbial ecology.}, }
@article {pmid40376461, year = {2025}, author = {Davis, RA and Mafune, KK and Winkler, MKH}, title = {Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1565940}, pmid = {40376461}, issn = {1664-302X}, abstract = {Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.}, }
@article {pmid40373669, year = {2025}, author = {Rescan, M and Gros, M and Borrego, CM}, title = {Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria.}, journal = {Water research}, volume = {282}, number = {}, pages = {123720}, doi = {10.1016/j.watres.2025.123720}, pmid = {40373669}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects ; Temperature ; Salinity ; Sewage/microbiology ; *Bacteria/drug effects ; Population Dynamics ; }, abstract = {City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.}, }
@article {pmid40373649, year = {2025}, author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B}, title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.}, journal = {Chemosphere}, volume = {381}, number = {}, pages = {144483}, doi = {10.1016/j.chemosphere.2025.144483}, pmid = {40373649}, issn = {1879-1298}, mesh = {*Wastewater/microbiology/chemistry ; *Sewage/microbiology ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis/metabolism ; Bioreactors/microbiology ; Hospitals ; Bacteria/classification/genetics ; Fungi/classification ; *Microbiota ; Cities ; Aerobiosis ; Pharmaceutical Preparations/analysis ; }, abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.}, }
@article {pmid40373419, year = {2025}, author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS}, title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.}, journal = {Meat science}, volume = {226}, number = {}, pages = {109848}, doi = {10.1016/j.meatsci.2025.109848}, pmid = {40373419}, issn = {1873-4138}, mesh = {*Meat Products/microbiology/analysis ; *Food Microbiology ; *Sodium Chloride/analysis ; *Food Handling/methods ; Animals ; Metagenomics ; Microbiota ; Bacteria ; Food Preservation/methods ; }, abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.}, }
@article {pmid40372110, year = {2025}, author = {Rohrhofer, J and Wolflehner, V and Schweighardt, J and Koidl, L and Stingl, M and Zehetmayer, S and Séneca, J and Pjevac, P and Untersmayr, E}, title = {Gastrointestinal Barrier Disruption in Post-COVID Syndrome Fatigue Patients.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16593}, pmid = {40372110}, issn = {1398-9995}, support = {//WE&amp;ME Foundation/ ; //Medizinisch-Wissenschaftlicher Fond des Buergermeisters der Bundeshauptstadt Wien/ ; }, abstract = {BACKGROUND: Post-COVID Syndrome (PCS) is the term for a condition with persistent symptoms in a proportion of COVID-19 patients after asymptomatic, mild, or severe disease courses. Numbers vary, but the current estimate is that after COVID-19 approximately 10% develop PCS. The aim of our study was to evaluate the impact of SARS-CoV-2 infection on the gastrointestinal (GI) tract and associations with the development of PCS with fatigue, post-exertional malaise (PEM), orthostatic dysregulation, autonomous dysregulation, and/or neurocognitive dysregulation.<br><br>METHODS: By combining medical record data from a prospective observational study with symptom analysis before, during, and after SARS-CoV-2 infection, we aimed to identify potential risk factors and predictive markers for PCS. Additionally, we analyzed blood, saliva, and stool samples from this well-characterized PCS patient cohort to biologically validate our findings.<br><br>RESULTS: We identified significant associations between pre-existing GI complaints and the development of PCS Fatigue. PCS patients showed higher LBP/sCD14 ratios, lower IL-33 levels, and higher IL-6 levels compared to control groups. Our results highlight the critical role of the GI tract in PCS development of post-viral Fatigue.<br><br>CONCLUSION: We propose that the viral infection disrupts pathways related to the innate immune response and GI barrier function, evidenced by intestinal low-grade inflammation and GI barrier leakage. Monitoring GI symptoms and markers before, during, and after SARS-CoV-2 infection is crucial for identifying predictive clinical phenotypes in PCS. Understanding the interaction between viral infections, immune responses, and gut integrity could lead to more effective diagnostic and treatment strategies, ultimately reducing the burden on PCS patients.}, }
@article {pmid40367785, year = {2025}, author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J}, title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138594}, doi = {10.1016/j.jhazmat.2025.138594}, pmid = {40367785}, issn = {1873-3336}, abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.}, }
@article {pmid40366158, year = {2025}, author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB}, title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0174924}, pmid = {40366158}, issn = {2379-5077}, mesh = {*Soil Microbiology ; Forests ; *Fires ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Soil/chemistry ; *Tracheophyta ; *Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenome ; Virome ; }, abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.<br><br>IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.}, }
@article {pmid40366134, year = {2025}, author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X}, title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0037525}, pmid = {40366134}, issn = {2379-5077}, support = {SCW1039//U.S. Department of Energy/ ; 1939//Joint Genome Institute/ ; 50220//Facilities Integrating collaborations for User Science/ ; }, mesh = {*Diatoms/growth &amp; development/microbiology ; *Microbiota ; *Eutrophication ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Flavobacteriaceae/genetics/metabolism ; Metagenomics ; }, abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.}, }
@article {pmid40366070, year = {2025}, author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW}, title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.}, journal = {European journal of endocrinology}, volume = {192}, number = {5}, pages = {603-611}, doi = {10.1093/ejendo/lvaf081}, pmid = {40366070}, issn = {1479-683X}, support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; *Bariatric Surgery ; Energy Metabolism/physiology ; Fatty Acids, Volatile/metabolism/blood ; *Gastrointestinal Microbiome/physiology ; *Obesity, Morbid/surgery/metabolism/microbiology ; Positron Emission Tomography Computed Tomography ; Weight Loss/physiology ; }, abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.<br><br>METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.<br><br>RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.<br><br>CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).}, }
@article {pmid40361280, year = {2025}, author = {Wan, SH and Xu, Y and Xu, W and Leung, SKK and Yu, EYN and Yung, CCM}, title = {Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70107}, pmid = {40361280}, issn = {1462-2920}, support = {AoE/P-601/23-N//Research Grants Council of Hong Kong/ ; }, mesh = {*Vibrio/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ecosystem ; Hong Kong ; Temperature ; Salinity ; Chaperonin 60/genetics ; Bays/microbiology ; }, abstract = {Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (10[4]-10[7] copies/mL) compared to coastal waters (10[2]-10[4] copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.}, }
@article {pmid40359204, year = {2025}, author = {Ghyselinck, J and Verstrepen, L and Rakebrandt, M and Marynissen, S and Daminet, S and Marzorati, M}, title = {In vitro fermentation of yeast cell walls (mannan-oligosaccharide) and purified β-glucans modulates the colonic microbiota of dogs with inflammatory bowel disease and demonstrates protective effects on barrier integrity and anti-inflammatory properties.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0322877}, pmid = {40359204}, issn = {1932-6203}, mesh = {Animals ; Dogs ; *Inflammatory Bowel Diseases/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Mannans/metabolism/pharmacology ; *beta-Glucans/pharmacology/metabolism ; Prebiotics ; *Saccharomyces cerevisiae/metabolism/chemistry ; *Cell Wall/metabolism/chemistry ; Humans ; Fermentation ; *Colon/microbiology ; Caco-2 Cells ; *Anti-Inflammatory Agents/pharmacology ; *Oligosaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by a disruption of intestinal homeostasis, chronic inflammation, and dysbiosis. Prebiotic supplementation may be useful for managing IBD in dogs. The aim of the study is to investigate the effects of two prebiotics, Biolex MB40 or Leiber Beta-S, on the gut microbiota isolated from three dogs with IBD, using the Colon-on-a-plate technology. Biolex MB40 and Leiber Beta-S contain concentrated 1,3-1,6- β-D-glucan isolated from the Saccharomyces cerevisiae cell walls. Biolex MB40 also contains mannan-oligosaccharide (MOS). Wells of the Colon-on-a-plate set up were inoculated with fecal suspensions and supplemented with either Biolex MB40 and Leiber Beta-S, or no test product (blank). Following 48h incubation, bacterial metabolites were measured and 16S rRNA targeted gene sequencing was performed. Colonic supernatants were added to a Caco-2/THP1 co-culture model to evaluate their effects on barrier integrity upon inflammation-induced barrier disruption and interleukin (IL)-10 production. Acetate and propionate concentrations were significantly increased versus blank with Biolex MB40, and biologically relevant numerical increases were observed with Leiber Beta-S supplementation. A donor-dependent, biologically relevant increase in butyrate was observed with both test products versus blank. Alpha diversity and microbiota biomass were increased, as well as the abundance of the five predominant phyla with both test products relative to blank. The greatest increases in abundance were observed for the Bacteroidetes and Firmicutes phyla. Fermentation of both test products had a protective effect on the gut epithelial barrier (measured by transepithelial electrical resistance) that was donor dependent. IL-10 production was significantly increased with Biolex MB40 supplementation for all donors, and with Leiber Beta-S supplementation for one donor. These in vitro findings confirm a prebiotic effect for both products and suggest that supplementation with either Biolex MB40 or Leiber Beta-S may have beneficial effects on the gut microbiota of dogs with IBD.}, }
@article {pmid40358239, year = {2025}, author = {Waegenaar, F and Pluym, T and Vermeulen, E and De Gusseme, B and Boon, N}, title = {Impact of flushing procedures on drinking water biostability and invasion susceptibility in distribution systems.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0068625}, pmid = {40358239}, issn = {1098-5336}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; Belgium ; *Water Purification/methods ; *Bacteria/drug effects/growth &amp; development ; *Water Microbiology ; Water Supply ; Halogenation ; Sodium Hypochlorite/pharmacology ; Chlorine ; }, abstract = {UNLABELLED: Ensuring high-quality drinking water remains challenging, as complaints about odors, discoloration, or contamination persist. In Belgium and beyond, traditional flushing is a common curative strategy that involves discharging large water volumes through hydrants while the network remains in use. In some cases, free chlorine (0.5 mg/L) is added, and consumers are advised not to drink the water. However, flushing can alter water biostability, potentially increasing susceptibility to microbial invasion. This study used a pilot-scale drinking water distribution system with three identical 100 m polyvinyl chloride(PVC) loops (DN 80 mm) to assess the impact of flushing with and without chlorination as practiced in chlorinated networks. Loop 1 was flushed with tap water and sodium hypochlorite (NaOCl), followed by two non-chlorinated flushes, loop 2 was unflushed, and loop 3 underwent three flushes. Biostability was assessed using online flow cytometry, and susceptibility to bacterial invasion (Aeromonas media, Pseudomonas putida, and Serratia fonticola) was evaluated in the days following flushing. The water had a 7-day residence time. Results showed that chlorinated flushing promoted microbial regrowth (3.8 × 10[5] vs 2.0 × 10[5] and 1.6 × 10[5] cells/mL for loops 1, 2, and 3, respectively), primarily of resident Sphingopyxis spp. Biofilm cell densities (~4 × 10[6] cells/cm[2]) remained stable across conditions. Bacterial indicators declined over time, with P. pudita and S. fonticola surviving longer (>100 hours) than A. media (13 hours). Decay rates were highest in chlorinated loops, likely due to increased microbial competition. For example, the decay constant of S. fonticola at 20°C was -0.082 h[-1], -0.042 h[-1], and -0.027 h[-1] for loops 1, 2, and 3, respectively.<br><br>IMPORTANCE: Traditional flushing is used as a curative strategy to solve unwanted quality issues during distribution, yet its impact on microbial biostability remains poorly understood. This study provides critical insights into how traditional flushing, both with and without chlorination, influences microbial regrowth and susceptibility to invasion. Findings reveal that chlorinated flushing promotes the regrowth of resident drinking water bacteria while accelerating the decay of introduced unwanted bacterial indicators, emphasizing the complex trade-off between microbial control and system stability. Understanding these dynamics is essential for optimizing flushing procedures, minimizing unintended consequences, and improving distribution system resilience.}, }
@article {pmid40358205, year = {2025}, author = {An, Y and Garcia, SL and Hambäck, PA}, title = {Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0172324}, pmid = {40358205}, issn = {2379-5077}, support = {#2019-4980//Vetenskapsr&#xe5;det/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Ovum/microbiology ; Larva/microbiology ; }, abstract = {UNLABELLED: Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.<br><br>IMPORTANCE: We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.}, }
@article {pmid40356667, year = {2025}, author = {Martínez-Mota, R and Vásquez-Aguilar, AA and Hernández-Rodríguez, D and Suárez-Domínguez, EA and Krömer, T}, title = {Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19376}, pmid = {40356667}, issn = {2167-8359}, mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Mexico ; *Bromeliaceae/microbiology ; *Bacteria/genetics/classification ; Ecosystem ; }, abstract = {BACKGROUND: Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.<br><br>METHODS: We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.<br><br>RESULTS: The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.<br><br>CONCLUSIONS: Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.}, }
@article {pmid40356640, year = {2025}, author = {Sun, Z and Hu, Y and Yang, YX and Lei, MY and Han, ZM and Cheng, L and Wang, W and Han, M and Lyu, ZL and Yang, LM}, title = {Changes in the diversity of ginseng endophyte flora driven by Fusarium solani.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554706}, pmid = {40356640}, issn = {1664-302X}, abstract = {Endophytic flora serves a crucial function as a secondary line of defense against pathogen invasion in plants. To investigate the mechanisms underlying the relationship between changes in endophytic flora and ginseng root rot, exhumate beneficial endophytic bacteria, and explore biological management approaches for ginseng root rot. In this study, we used Illumina high-throughput sequencing and bioinformatics analysis to investigate the characteristics and differences in endophytic microbial community structure between healthy ginseng (HG) and diseased ginseng (BLS) after Fusarium solani infection. The findings revealed that as ginseng root rot increased, the diversity and richness of endophytic bacterial communities increased before decreasing, but the diversity and richness of endophytic fungal communities decreased. The dominating bacterial phylum in ginseng roots was Proteobacteria, which declined in quantity as the disease progressed. Ascomycota was the dominating fungal phylum among endophytes, and its prevalence grew as the disease progressed. At the genus level, the relative abundance of Rhodococcus, Stenotrophomonas, Variovorax, and Achromobacter species increased with the occurrence of ginseng root rot, in contrast, Pantoea and Pseudomonas species decreased in relative abundance as the prevalence of ginseng root rot increased. The relative abundance of the pathogenic fungi Gibberella, Nectria, Ilyonectria, and Alternaria in ginseng roots increased as the disease progressed. Endophytic fungal LEfSe research revealed that Neonectria was the particular biomarker discovered in the highly susceptible group. Additionally, commensal nutrient-type fungi appeared to be absent in moderately susceptible ginseng, but pathognomic nutrient-type fungi grew, coupled with potentially pathogenic fungi, exacerbating the condition. These results suggest that there is a pattern of response of ginseng endophytic microbial diversity to disease infestation. In this work, we investigated the impact of varying degrees of root rot on ginseng's endophytic flora structure. The study's findings give a theoretical framework for understanding the microecological processes of ginseng root rot via the lens of microbial ecology and applying biological control tools.}, }
@article {pmid40356172, year = {2025}, author = {Cardinali, F and Rampanti, G and Harasym, J and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A}, title = {Comprehensive profiling of smoked cheese from raw goat's milk handcrafted in Lower Silesia (Poland).}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116398}, doi = {10.1016/j.foodres.2025.116398}, pmid = {40356172}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; Fatty Acids/analysis ; Volatile Organic Compounds/analysis ; Poland ; *Milk/microbiology/chemistry ; *Food Microbiology ; *Food Handling/methods ; Consumer Behavior ; Humans ; *Smoke ; Colony Count, Microbial ; }, abstract = {This study aimed to explore the distinctive characteristics of smoked cheese made from raw goat's milk, labelled "Produkt polski" and crafted in the Lower Silesia region of Poland. A comprehensive range of analyses was performed, including physico-chemical and morpho-textural evaluations, microbial counts, and a metataxonomic investigation to uncover the microbial diversity occurring in the cheese. The volatile organic compounds (VOCs) and the total fatty acid composition were also determined. Additionally, a consumer test based on a hedonic scale was conducted to capture the subjective experience of the product's appeal. The cheese samples revealed water activity (aw) ranging between 0.901 ± 0.003 and 0.926 ± 0.001, with pH levels between 5.08 ± 0.15 and 5.44 ± 0.01. Regarding fatty acid composition, all of the smoked cheeses displayed a similar profile, with saturated fatty acids dominating (SFA, ∼75 %), followed by monounsaturated (MUFA, ∼22 %) and polyunsaturated fatty acids (PUFA, ∼3 %). Microbial analysis revealed thriving populations, including lactococci (up to 8.63 ± 0.07 log colony-forming units g[-1]), thermophilic cocci (up to 6.85 ± 0.08 log cfu g[-1]), lactobacilli (up to 9.50 ± 0.04 log cfu g[-1]), enterococci (up to 5.93 ± 0.00 log cfu g[-1]), and eumycetes (up to 2.68 ± 0.48 log cfu g[-1]). Metataxonomic analysis identified dominant bacterial taxa such as Lactobacillus, Lactococcus, and Leuconostoc, as well as Carnobacterium and Lacticaseibacillus. Among the 24 lactic acid bacteria cultures isolated, the closest relatives to Enterococcus, Lacticaseibacillus, Lactococcus, and Leuconostoc were identified. Some isolates demonstrated promising pro-technological traits, positioning them as potential adjunct cultures for improving fermented dairy products. The volatile profile of the smoked cheese was particularly intriguing, with a total of 87 VOCs detected, categorized as esters (18), ketones (14), hydrocarbons (11), acids (10), phenols (11), alcohols (8), furans (5), lactones (4), aldehydes (3), and other compounds (3). Sensory evaluation revealed a moderate appreciation for the cheese's appearance, whereas the smoked flavor elicited the most varied scores, highlighting its strong impact on consumer preference.}, }
@article {pmid40356145, year = {2025}, author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q}, title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116488}, doi = {10.1016/j.foodres.2025.116488}, pmid = {40356145}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; }, abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.}, }
@article {pmid40354775, year = {2025}, author = {Frazier, CF and Harris, TD and DelSontro, T and Grossart, HP and Sturm, BSM and Murry, JM and Ising, A}, title = {Phytoplankton abundance and methane emissions are minimally impacted by environmentally-relevant glyphosate concentrations in small-scale outdoor mesocosms.}, journal = {Water research}, volume = {283}, number = {}, pages = {123764}, doi = {10.1016/j.watres.2025.123764}, pmid = {40354775}, issn = {1879-2448}, abstract = {Glyphosate is one of the most widely applied agrochemicals in North America and can be directly transported via runoff into non-target aquatic habitats. Yet, our understanding of how this herbicide affects aquatic ecosystems is limited; past studies have often focused on single species effects and/or used herbicide concentrations several orders of magnitude higher than what has been reported in contaminated aquatic systems. Further, glyphosate in aquatic systems has the potential to alter greenhouse gas emissions (methane) if it is broken down for phosphate utilization by bacteria under specific environmental conditions (i.e., oxygen, nutrient concentrations). In this study, we assessed the temporal changes in nutrients, phytoplankton, copy number of genes associated with breakdown of glyphosate or production of methane (phnJ, mcrA), and methane concentrations in 12-day mesocosms with amendments of glyphosate, nitrogen, and/or phosphorus. We found glyphosate at environmentally-relevant concentrations (∼4 ug/L) did not confer changes in overall ratios and total concentrations of nutrients, or abundance of any major phytoplankton group (cyanobacteria, diatoms, green algae), methane concentration or flux, or gene copy numbers of phnJ and mcrA. Our results suggest that the relatively low concentrations of glyphosate we used (relative to levels used in toxicological studies) did not cause major changes over short time periods in mesocosms, and that the potential for glyphosate to increase greenhouse gas emissions in aquatic systems requires specific conditions to occur and may not be universal in contaminated systems.}, }
@article {pmid40354740, year = {2025}, author = {Rodrigo, MA and Puche, E and Muñoz-Colmenares, M and Sánchez-Carrillo, S}, title = {Vascular macrophytes versus charophytes: how the macrophyte type and warming affect the sediment microbial community and the production of greenhouse gases.}, journal = {Journal of environmental management}, volume = {386}, number = {}, pages = {125654}, doi = {10.1016/j.jenvman.2025.125654}, pmid = {40354740}, issn = {1095-8630}, mesh = {*Greenhouse Gases ; *Geologic Sediments/microbiology ; Global Warming ; Carbon Dioxide ; Ecosystem ; Microbiota ; }, abstract = {In the global warming context, adaptive management strategies involve the conservation and restoration of inland waters by planning the reintroduction of macrophytes to substantially mitigate greenhouse gas emissions (GHG). The selection of appropriate species is crucial. We studied the influence of two submerged macrophyte species on GHG production, sediment-oxygen microprofiles, and microbial community composition under two thermal regimes by means of a microcosm experiment. We chose the phanerogam Myriophyllum spicatum, more typical of meso-eutrophic habitats, and the charophyte Chara hispida, more frequent in oligotrophic waters and belonging to a much less studied macrophyte group, which, moreover, exhibit contrasting functional traits (i.e., roots versus rhizoids). The presence of both macrophyte types considerably reduced the diurnal diffusive CO2 emissions due to their photosynthetic activity compared to bare-sediment situations. The radial oxygen loss of M. spicatum roots provided aerobic-microaerobic conditions beyond the first sediment centimeter, in contrast to more anoxic sediments created by C. hispida. As a result of this, each type of macrophyte determined a particular sediment microbiome. Despite dissolved CH4 being greater in the presence of plants, no statistical differences in CH4 diffusive flux caused by the presence or absence of plants was found. We demonstrated how the presence, or not, of macrophytes is more important than warming (in our case with a temperature difference of 3 °C) in relation to GHG emissions. Both species, being perennial, provide ecosystem services year-round and are strong candidates for management strategies aimed at transforming new or restored aquatic ecosystems into carbon sinks.}, }
@article {pmid40353721, year = {2025}, author = {Pellitier, PT and Kling, MM and Qin, C and Van Nuland, ME and Zhu, K and Peay, KG}, title = {Wind Patterns Influence the Dispersal and Assembly of North American Soil Fungal Communities.}, journal = {Ecology letters}, volume = {28}, number = {5}, pages = {e70130}, doi = {10.1111/ele.70130}, pmid = {40353721}, issn = {1461-0248}, support = {1845544//Directorate for Biological Sciences/ ; 1926335//Directorate for Biological Sciences/ ; 2010897//Directorate for Biological Sciences/ ; 2244711//Directorate for Biological Sciences/ ; }, mesh = {*Wind ; *Soil Microbiology ; *Fungi/physiology/genetics ; North America ; *Mycobiome ; Spores, Fungal/physiology ; Climate Change ; Models, Biological ; }, abstract = {Wind is the primary dispersal mechanism of most fungal spores but is rarely considered in studies of fungal communities, limiting inference of assembly mechanisms and forecasting responses to climate change. We compiled wind-connectivity models-'windscapes'-to model potential dispersal of fungal spores at the continental scale and linked them with a molecular dataset of North American soil fungi. Our analyses demonstrate that prevailing windflow patterns exhibit a significantly stronger signal on fungal community structure than do geographic distances amongst sites. Notably, the signature of wind was detectable for mushrooms and fungi producing primarily wind-dispersed spores. Contrastingly, fungi primarily reliant on animal dispersal exhibited a strong signature of geographic distance but not wind-connectivity. Additionally, we show that directionally 'downwind' sites are more diverse than comparatively 'upwind' sites. Altogether, our findings suggest that future wind patterns will shape the adaptation potential of fungal communities dispersing into suitable climatic niches.}, }
@article {pmid40353658, year = {2025}, author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0074925}, pmid = {40353658}, issn = {2150-7511}, support = {FJC2019-041362-I, RyC2021-031775-I//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2019-110011RB-C33, PID2023-146919NB-C21//MEC | Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; }, mesh = {Arctic Regions ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; *Nitrogen Cycle ; *Archaea/metabolism/genetics/classification ; Phytoplankton/growth &amp; development/metabolism ; Metagenomics ; Canada ; *Chemoautotrophic Growth ; Seasons ; Metagenome ; }, abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.}, }
@article {pmid40352645, year = {2025}, author = {Quinn, LK and Sharma, K and Faber, KT and Orphan, VJ}, title = {Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.}, journal = {PNAS nexus}, volume = {4}, number = {5}, pages = {pgaf118}, pmid = {40352645}, issn = {2752-6542}, abstract = {Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and [13]C enrichment in microorganisms, highlighting the potential to directly couple D2O or [13]C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.}, }
@article {pmid40352477, year = {2025}, author = {Coltman, BL and Motheramgari, K and Tatto, N and Gasser, B}, title = {Identification and functional analysis of growth rate associated long non-coding RNAs in Komagataella phaffii.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1693-1705}, pmid = {40352477}, issn = {2001-0370}, abstract = {Long non-coding RNAs (lncRNAs) are a regulatory feature that have been reported to operate on both transcriptional and translational levels. With DNA-based prediction still limited, lncRNAs are most reliably identified through genome-guided mapping of RNA-Seq data. Reports of lncRNAs in yeast have been increasing in recent years and changes in their expression levels have often been associated with stressful conditions. As the transition to near zero-growth conditions likely imposes stress, we used RNA-Seq data from the non-conventional, biotechnologically established yeast Komagataella phaffii, cultivated in glucose-limited retentostats, to identify the expression of lncRNAs. Using an adapted bioinformatics pipeline, we identified 168 mostly novel lncRNAs from the K. phaffii retentostat RNA-Seq data, 36 of which demonstrate likely growth-associated expression changes. lncRNA expression levels were associated to that of possible interaction partners, in both cis and trans, suggesting potential roles in regulatory adaptations. Our analysis indicates that lncRNAs likely contribute to how K. phaffii responds to changing environmental conditions, as exemplified here by the adaptation to extremely slow growth.}, }
@article {pmid40349898, year = {2025}, author = {Moghaddam, ZS and Dehghan, A and Halimi, S and Najafi, F and Nokhostin, A and Naeini, AE and Akbarzadeh, I and Ren, Q}, title = {Bacterial Extracellular Vesicles: Bridging Pathogen Biology and Therapeutic Innovation.}, journal = {Acta biomaterialia}, volume = {200}, number = {}, pages = {1-20}, doi = {10.1016/j.actbio.2025.05.028}, pmid = {40349898}, issn = {1878-7568}, mesh = {*Extracellular Vesicles/metabolism ; Humans ; *Bacteria/metabolism ; Animals ; Drug Delivery Systems ; *Host-Pathogen Interactions ; }, abstract = {The main role of bacterial extracellular vesicles (BEVs) has been associated with various processes such as intercellular communication and host-pathogen interactions. This comprehensive review explores the multifaceted functions of BEVs across different biological domains, emphasizing their dual nature as contributors to disease and potential vehicles for therapeutic intervention. We examine the intricate interactions of BEVs within bacterial communities and between bacteria and hosts, their involvement in disease development through cargo delivery mechanisms, and their beneficial impact on microbial ecology. The review also highlights BEVs' applications in biomedical field, where they are revolutionizing vaccine development, targeted drug delivery, and cancer therapy. By utilizing the inherent properties of BEVs for controlled drug release, targeted antigen delivery, and immune modulation, they offer a promising frontier in precision medicine. In addition, the diagnostic potential of BEVs is explored through their utility as biomarkers, providing valuable insights into disease states and treatment efficacy. Looking forward, this review underscores the challenges and opportunities in translating BEV research to clinical practice, promoting the need of standardized methods in BEV characterization and scaling up production. The diverse abilities of BEVs, ranging from contributing to pathogen virulence to driving therapeutic innovation, highlight their potential as a cornerstone in the future of biomedical advancements. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are emerging as pivotal players in both pathogenesis and therapeutic innovation. This review explores their dual nature as agents of disease and as promising biomaterials for biomedical applications, and provides a comprehensive survey on their involvement in disease mechanisms and microbial ecology, and their potential in biomedical applications such as vaccine development, targeted drug delivery, cancer therapy, and diagnosis. It highlights the complex interactions of BEVs within bacterial communities and between bacteria and hosts. This review also addresses current advancements, challenges, and opportunities in translating BEV research into clinical practice. The insights presented here position BEVs as a cornerstone in the future of biomedical advancements, advocating for standardized methods in BEV characterization and scalable production techniques.}, }
@article {pmid40348966, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {615}, pmid = {40348966}, issn = {1471-2229}, support = {C24E/19/052//KU Leuven/ ; }, mesh = {*Hypocreales/physiology ; Animals ; Plant Leaves/metabolism/microbiology ; Herbivory ; Metabolome ; *Capsicum/microbiology/metabolism ; Plant Roots/microbiology/metabolism ; Plant Defense Against Herbivory ; }, abstract = {BACKGROUND: Plant-beneficial fungi play an important role in enhancing plant health and resistance against biotic and abiotic stresses. Although extensive research has focused on their role in eliciting plant defences against pathogens, their contribution to induced resistance against herbivorous insects and the underlying mechanisms remain poorly understood. In this study, we used insect bioassays and untargeted metabolomics to investigate the impact of root inoculation of sweet pepper with the plant-beneficial fungus Trichoderma harzianum T22 on direct defence responses against the insect herbivore Nezara viridula.<br><br>RESULTS: We observed reduced relative growth rate of N. viridula on leaves of fungus-inoculated plants, with no change in mortality. Untargeted metabolomic analyses revealed that inoculation with T. harzianum did not affect the leaf metabolome in the absence of herbivory five weeks after inoculation. However, compared to non-inoculated plants, inoculated plants exhibited significant metabolic alterations in herbivore-damaged leaves following N. viridula feeding, while changes in the metabolic profile of distant leaves were less pronounced. Notably, metabolites involved in the shikimate-phenylpropanoid pathway, known to be involved in plant defence responses, displayed higher accumulation in damaged leaves of inoculated plants compared to non-inoculated plants.<br><br>CONCLUSION: Our results indicate that root inoculation with T. harzianum T22 affects plant defences against N. viridula, leading to reduced insect performance. Metabolite-level effects were primarily observed in damaged leaves, suggesting that the priming effect mainly results in localized metabolite accumulation at the site of attack. Future research should focus on identifying the detected compounds and determining their role in impairing N. viridula performance.}, }
@article {pmid40347612, year = {2025}, author = {Rodríguez-Seijo, A and Pérez-Rodríguez, P and Arias-Estévez, M and Gómez-Armesto, A and Conde-Cid, M and Santás-Miguel, V and Campillo-Cora, C and Ollio, I and Lloret, E and Martínez-Martínez, S and Zornoza, R and Waeyenberge, L and Schrader, S and Brandt, KK and Loit, K and Põldmets, M and Shanskiy, M and Peltoniemi, K and Hagner, M and Calviño, DF}, title = {Occurrence, persistence and risk assessment of pesticide residues in European wheat fields: A continental scale approach.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138291}, doi = {10.1016/j.jhazmat.2025.138291}, pmid = {40347612}, issn = {1873-3336}, abstract = {Pesticide residues in agricultural soils represent an environmental concern that requires special attention due to their potential ecological and public health risks. We analyzed 614 pesticides in 188 wheat fields across Europe subjected to both conventional and organic farming systems. At least one pesticide residue was detected in 141 soils. Seventy-eight pesticides or their metabolites were detected. The presence of pesticides was significantly higher in both number and concentration in conventional fileds (up to 0.98 mg kg[-1]) compared to organically managed sites (up to 0.40 mg kg[-1]). A total of 88 % of conventional fields and 63 % of organic fields contained two or more pesticides. Conversion from conventional to organic farming does not guarantee that soils will be pesticide-free in the short term. Fenbutatin oxide was the most frequently detected pesticide in both farming systems, followed by AMPA. Other substances, such as boscalid, epoxiconazole, diflufenican, tebuconazole, dinoterb, bixafen, and DEET, were found in ≥ 10 % of samples. Some Persistent Organic Pollutants, including dieldrin, endosulfan sulphate, and chlorpyrifos, were also detected. Ecological risks were higher in conventionally managed fields, with 46 % exhibiting high-risk levels, compared to just 1 % in organic fields. Epoxiconazole and boscalid were the substances with the highest risk levels.}, }
@article {pmid40347236, year = {2025}, author = {Qi, W and Song, W and Qi, R and Li, Y and Yang, H and Li, Y and Chang, Z}, title = {Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {43}, pmid = {40347236}, issn = {1432-184X}, support = {2021-XBQNXZ-001//The West Light Foundation of Chinese Academy of Science/ ; DD20242544//The Ecological Protection and Restoration Support Survey Project of China Geological Survey/ ; }, mesh = {*Soil Microbiology ; China ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; Desert Climate ; Agriculture ; *Microbiota ; Farms ; Mycobiome ; }, abstract = {Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.}, }
@article {pmid40347194, year = {2025}, author = {Su, QY and Zhang, JT and Gao, HJ and Zhang, Y and Luo, J and Cao, TY and Yang, MY and Zhang, SX}, title = {Mechanism and clinical utility of abatacept in the treatment of rheumatoid arthritis.}, journal = {Expert opinion on drug safety}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/14740338.2025.2505542}, pmid = {40347194}, issn = {1744-764X}, abstract = {INTRODUCTION: Abatacept, a biological disease-modifying antirheumatic drug(bDMARD), has demonstrated unique and effective therapeutic properties for rheumatoid arthritis (RA).<br><br>AREAS COVERED: This review offers an in-depth examination of the mechanism by which abatacept exerts its effects in RA treatment and assesses its efficacy and safety based on a range of studies. We conducted a comprehensive search of PubMed, Embase databases, Web of Science, the Cochrane Library, MEDLINE, Wanfang Data, and CNKI from the time the databases were created until 30 July 2024.<br><br>EXPERT OPINION: By modulating the CD28 and CD80/CD86 costimulatory signaling pathways, abatacept is instrumental in regulating immune cells and cytokines implicated in the pathogenesis RA. Longitudinal studies have highlighted its capacity to mitigate disease advancement and maintain joint functionality. The most frequently reported adverse effects associated with abatacept are headache, nausea, and upper respiratory tract infections, which are typically self-resolving. The incidence of serious infections was not high, mainly various types of bacterial pneumonia. Comparative safety analyses of abatacept with other DMARDs yield encouraging results. As our understanding of the mechanism of action of abatacept improves, we may be able to better identify appropriate biologic therapies and advanced combination therapies for RA patients and ultimately improve patient outcomes.}, }
@article {pmid40346393, year = {2025}, author = {Leiter, N and Wohlschläger, M and Versen, M and Harter, SD and Kießlich, T and Lederer, F and Clauß, S and Schlosser, D and Armanu, EG and Eberlein, C and Heipieper, HJ and Löder, MGJ and Laforsch, C}, title = {Effects of defined organic layers on the fluorescence lifetime of plastic materials.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {40346393}, issn = {1618-2650}, support = {FKZ 031B0828A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 391977956 - SFB 1357//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Plastics have become an integral part of modern life, and linked to that fact, the demand for and global production of plastics are still increasing. However, the environmental pollution caused by plastics has reached unprecedented levels. The accumulation of small plastic fragments-microplastics and nanoplastics-potentially threatens organisms, ecosystems, and human health. Researchers commonly employ non-destructive analytical methods to assess the presence and characteristics of microplastic particles in environmental samples. However, these techniques require extensive sample preparation, which represents a significant limitation and hinders a direct on-site analysis. In this context, previous investigations showed the potential of fluorescence lifetime imaging microscopy (FLIM) for fast and reliable identification of microplastics in an environmental matrix. However, since microplastics receive an environmental coating after entering nature, a challenge arises from organic contamination on the surface of microplastic particles. How this influences the fluorescence signal and the possibility of microplastic detection are unknown. To address this research gap, we exposed acrylonitrile butadiene styrene (ABS) and polyethylene terephthalate (PET) plastic samples to peptides, proteins, bacteria, and a filamentous fungus to induce organic contamination and mimic environmental conditions. We analyzed the fluorescence spectra and lifetimes of the samples using fluorescence spectroscopy and frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM), respectively. Our results demonstrate that reliably identifying and differentiating ABS and PET was possible via FD-FLIM, even in the presence of these biological contaminations. These findings highlight the potential of this technique as a valuable tool for environmental monitoring and plastic characterization, offering a rapid and efficient alternative to currently used analytical methods.}, }
@article {pmid40345255, year = {2025}, author = {Feng, J and Zhang, C and Bao, J and Xu, Q and Gan, Y and Hu, Y}, title = {A modified variable flip angle release device for endoscopic titanium clips.}, journal = {Endoscopy}, volume = {57}, number = {S 01}, pages = {E396-E397}, pmid = {40345255}, issn = {1438-8812}, support = {2024GZL-CX58//Xiamen High-quality Development Medical Innovation Fund/ ; }, }
@article {pmid40343125, year = {2025}, author = {Tóth, VR}, title = {The impact of epiphytic algae on the foliar traits of Potamogeton perfoliatus.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1561709}, pmid = {40343125}, issn = {1664-462X}, abstract = {This study investigated the effect of epiphyton on foliar traits of a submerged rooted macrophyte, Potamogeton perfoliatus, in a shallow freshwater lake, highlighting its influence on the ecological dynamics of littoral zones in aquatic ecosystems. It was shown that the limnological characteristics of the sampling sites (water chlorophyll-a, total suspended matter and coloured dissolved organic matter content) had no significant effect on the average values of epiphytic algal content found on pondweed leaves, while influencing the plasticity of these data. The responses of morphological and physiological traits of submerged macrophytes to accumulated epiphyton demonstrate the complexity of their relationship: epiphyton colonisation had no relevant effect on leaf morphology (except leaf length) and leaf pigment content (except Chl-a/Chl-b ratio), however, this study highlights the significant influence of epiphytic algal biomass on photophysiological traits of submerged macrophyte leaves, as 5 out of 6 photophysiological traits were affected. The results highlight the importance of considering epiphyte colonisation when seeking to understand the ecological functioning of littoral aquatic ecosystems. Furthermore, the complex interactions between epiphytes and submerged rooted macrophytes should be considered in integrated lake management and environmental protection policies. These interactions play an important, though ambiguous role in shaping habitat variability and overall ecosystem health in littoral zones.}, }
@article {pmid40341906, year = {2025}, author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J}, title = {Macroecological patterns in experimental microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013044}, pmid = {40341906}, issn = {1553-7358}, mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; }, abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.}, }
@article {pmid40338317, year = {2025}, author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A}, title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {42}, pmid = {40338317}, issn = {1432-184X}, support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; }, mesh = {*Endophytes/genetics/isolation &amp; purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation &amp; purification/physiology ; *Ascomycota/genetics/isolation &amp; purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; }, abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.}, }
@article {pmid40336837, year = {2025}, author = {Couch, CE and Xavier, R and Beechler, BR}, title = {Editorial: Parasite, host, and microbiome interactions in natural host systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589627}, doi = {10.3389/fmicb.2025.1589627}, pmid = {40336837}, issn = {1664-302X}, }
@article {pmid40335733, year = {2025}, author = {Guo, Y and Tian, L and Zhu, X and Liu, S and Wang, L and Li, W}, title = {Antagonism of Bacillus velezensis ZGE166 Against the Pathogenic Fungi Causing Corm Rot Disease in Saffron (Crocus sativus L.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {40}, pmid = {40335733}, issn = {1432-184X}, mesh = {*Bacillus/physiology/genetics/isolation &amp; purification ; *Crocus/microbiology/growth &amp; development ; Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; Soil Microbiology ; *Antibiosis ; *Fungi/physiology ; Genome, Bacterial ; Phylogeny ; }, abstract = {Saffron can be infected with pathogenic fungi that cause corm rot as it grows and multiplies, which can reduce the quality and yield of saffron. Corm rot has become one of the most serious diseases of saffron. In this study, rhizosphere bacteria were isolated from saffron rhizosphere soil, and bacteria exhibiting antagonistic effects against corm rot pathogenic fungi were screened using in vitro plate co-culture assays and dual-compartment agar plate systems. Selected strains were further evaluated for hydrolase activity determination and PGP potential assessment. Among them, Bacillus velezensis showed the best disease resistance activity. The degradative enzyme production and some beneficial characteristics of Bacillus velezensis for plant growth promotion were evaluated. It was found that Bacillus velezensis possesses nitrogen fixing, NH3-producing, IAA production, and ACC-deaminating enzymes. The whole genome sequence of this strain was annotated and analyzed. The genome of Bacillus velezensis consists of a circular chromosome of 3,908,025 bp base pairs, with a guanine and cytosine content of 46.64%. There are 3737 protein-coding genes, including 86 tRNA genes, 27 rRNA genes, and 85 sRNA genes. The genome also contains four genomic islands, two pre-phages, and one transposon. The prediction of the secondary metabolic accumulation gene cluster demonstrated that the genome sequence of ZGE166 encodes 12 gene clusters involved in the synthesis of secondary metabolites, including macrolactin H, bacillaene, fengycin, difficidin, and bacillibactin. In summary, strain ZGE166 Bacillus velezensis has the potential to be developed as a biological agent.}, }
@article {pmid40335388, year = {2025}, author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R}, title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.004}, pmid = {40335388}, issn = {1878-4372}, abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.}, }
@article {pmid40334664, year = {2025}, author = {Sandin, MM and Renaudie, J and Suzuki, N and Not, F}, title = {Extant diversity, biogeography, and evolutionary history of Radiolaria.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {2524-2538.e6}, doi = {10.1016/j.cub.2025.04.032}, pmid = {40334664}, issn = {1879-0445}, mesh = {*Biological Evolution ; *Biodiversity ; *Fossils ; Phylogeny ; *Plankton/classification/physiology/genetics ; Phylogeography ; }, abstract = {Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons left an extensive fossil record extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography, and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B, and Rad-C. We suggest that most of this undescribed diversity comprises skeleton-less life forms or endosymbionts, explaining their elusive, yet abundant, nature. Phylogenetic analyses highlight the need for a major revision of high-level Radiolaria taxonomy, including placement of Collodaria within the order Nassellaria. Global metabarcoding surveys show that Radiolaria contributes more than 12% to the total eukaryotic community, displaying distinct biogeographic patterns with the skeleton-less lineages at depth and photosymbiont-bearing lineages in the surface. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (mya), the development of the skeleton in the early Paleozoic (∼500 mya), and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 mya), related to geological periods of oligotrophy and anoxia. The results presented here provide a robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.}, }
@article {pmid40333193, year = {2025}, author = {Hodžić, A and Kunert, M and Berry, D}, title = {Protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization.}, journal = {STAR protocols}, volume = {6}, number = {2}, pages = {103814}, pmid = {40333193}, issn = {2666-1667}, mesh = {*In Situ Hybridization, Fluorescence/methods ; Animals ; *Bacteria/isolation &amp; purification/genetics ; *Ticks/microbiology ; *Gastrointestinal Tract/microbiology ; }, abstract = {The tick gut harbors a relatively diverse microbial community that includes commensal, beneficial, and pathogenic bacterial species. Here, we present a protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization. We describe steps for tick dissection, tissue fixation, hybridization, washing, and mounting. We then detail procedures for microscopy imaging of the whole-mounted samples. Although the procedure is designed for gut tissue samples, it can be readily modified for use with other tissue types. For complete details on the use and execution of this protocol, please refer to Hodžić et al.[1].}, }
@article {pmid40333163, year = {2025}, author = {Touati, A and Ibrahim, NA and Idres, T}, title = {Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333163}, issn = {2076-0817}, support = {IMSIU-DDRSP2501//The Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, mesh = {Humans ; *Staphylococcal Infections/microbiology/drug therapy ; Virulence/drug effects ; *Staphylococcus aureus/drug effects/pathogenicity/physiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms/drug effects/growth &amp; development ; *Virulence Factors/antagonists &amp; inhibitors/metabolism ; Quorum Sensing/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity ; Animals ; }, abstract = {Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.}, }
@article {pmid40333144, year = {2025}, author = {Plewa-Tutaj, K and Chmielewska, Z and Twarużek, M and Kosicki, R and Soszczyńska, E}, title = {An Analysis of the Mycotoxins, Cytotoxicity, and Biodiversity of Airborne Molds Belonging to Aspergillus Genera Isolated from the Zoological Garden.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333144}, issn = {2076-0817}, support = {"MINIATURA 6," grant 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; }, mesh = {*Mycotoxins/toxicity/analysis ; *Aspergillus/isolation &amp; purification/classification/genetics/metabolism ; *Air Microbiology ; *Biodiversity ; Animals ; Humans ; }, abstract = {The present study aimed to identify airborne molds of the Aspergillus genus and to determine the secondary metabolite profiles and toxicity of dominant fungal species isolated from various locations in the Wroclaw Zoological Garden. Air samples were collected using a MAS-100 air sampler and analyzed for fungal colony-forming units (CFU). Morphological and molecular methods, including ITS sequencing, were employed for dominant mold identification. The most frequently encountered species were A. fumigatus and A. niger, while A. pseudoglaucus and A. nomius were the least common. The high prevalence of species from sections Nigri, Flavi, and Fumigati suggests their adaptability to the zoo environment. A total of 17 Aspergillus isolates were analyzed for both their capacity to induce cellular toxicity and their production of mycotoxins. The results indicated that all isolates exhibited cellular toxicity, with 70.6% displaying levels of toxicity that were medium to high. Furthermore, the mycotoxicological analysis revealed that only A. fumigatus strains were capable of producing mycotoxins, specifically gliotoxin. The study underscores the discrepancy between the levels of toxicity and the production of mycotoxins, thereby suggesting the presence of additional cytotoxic metabolites. These findings emphasize the need for a comprehensive understanding of the complex interplay between fungal metabolites and their consequences for human health.}, }
@article {pmid40333133, year = {2025}, author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO}, title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333133}, issn = {2076-0817}, support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; }, abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.}, }
@article {pmid40332344, year = {2025}, author = {Figueiredo, JEF and Marins, MS and Silva, FC and Ribeiro, VP and Diniz, GdFD and Rodrigues, VA and Oliveira-Paiva, CA and Lana, UGdP and Ferreira, LVS and Sousa Tinoco, SMd and Cruz-Magalhães, V}, title = {Draft genome of the endophytic Bacillus velezensis CNPMS-22 isolated from maize leaves.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0127924}, pmid = {40332344}, issn = {2576-098X}, abstract = {Bacillus velezensis has been widely used as a biocontrol agent and plant growth promoter in agricultural bio-inputs. The genome of the endophytic bacterial strain CNPMS-22 isolated from maize leaves was sequenced, and the results showed that the strain is a Bacillus velezensis species.}, }
@article {pmid40329925, year = {2025}, author = {Razzaq Meo, S and Van de Wiele, T and Defoirdt, T}, title = {Indole signaling in Escherichia coli: a target for antivirulence therapy?.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2499573}, pmid = {40329925}, issn = {1949-0984}, mesh = {*Indoles/metabolism/pharmacology ; *Escherichia coli/drug effects/metabolism/pathogenicity/genetics ; Humans ; *Signal Transduction/drug effects ; *Escherichia coli Infections/microbiology/drug therapy ; Virulence/drug effects ; Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics/antagonists &amp; inhibitors ; Animals ; Escherichia coli Proteins/metabolism/genetics ; Biofilms/drug effects/growth &amp; development ; }, abstract = {Pathogenic Escherichia coli are a major cause of infections in both humans and animals, leading to conditions such as severe diarrheal diseases, urinary tract infections, enteritis, and septicemia. To combat bacterial infections, antibiotics are widely utilized. However, the extensive and inappropriate use of antibiotics has fueled the development and spread of antibiotic resistance, posing a significant challenge to the effective treatment of E. coli. There is consequently an urgent need to explore alternative therapies to control such infections. This review provides an overview of the recent findings concerning indole signaling in E. coli. E. coli uses indole as a quorum sensing molecule, and indole signaling has been reported to decrease various virulence factors in pathogenic E. coli, including motility, biofilm formation, adherence to host cells, expression of the LEE pathogenicity island, and formation of attaching and effacing lesions. This makes indole signaling an interesting target for the development of new therapeutics in the framework of antivirulence therapy. Both natural and synthetic indole analogues have been explored as potential virulence inhibitors. This alternative approach could be advantageous, as it will exert less selective pressure for resistance development than conventional antibiotics.}, }
@article {pmid40329550, year = {2025}, author = {Jenkins, GB and Boyd, ES and Danchin, A and Hervé, V and Huggett, MJ and Sánchez, &#xc1; and Trevorrow, P}, title = {Environmental Microbiology and Environmental Microbiology Reports: Two Journals, One Goal.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70078}, doi = {10.1111/1462-2920.70078}, pmid = {40329550}, issn = {1462-2920}, }
@article {pmid40329526, year = {2025}, author = {Ory, F and Dainat, B and Würgler, O and Wenger, F and Roetschi, A and Braillard, L and Charrière, JD and Dietemann, V}, title = {Ecology and Pathogenicity for Honey Bee Brood of Recently Described Paenibacillus melissococcoides and Comparison With Paenibacillus dendritiformis, Paenibacillus thiaminolyticus.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70089}, pmid = {40329526}, issn = {1758-2229}, mesh = {Bees/microbiology ; Animals ; *Paenibacillus/pathogenicity/genetics/isolation &amp; purification/classification ; Virulence ; Spores, Bacterial ; Paenibacillus larvae ; Phylogeny ; Larva/microbiology ; }, abstract = {Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.}, }
@article {pmid40327698, year = {2025}, author = {Clegg, T and Gross, T}, title = {Cross-feeding creates tipping points in microbiome diversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {19}, pages = {e2425603122}, pmid = {40327698}, issn = {1091-6490}, mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; }, abstract = {A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many functionally distinct populations. This process is driven in part by the cross-feeding networks that help to structure these systems, in which consumers use resources to fuel their metabolism, creating by-products which can be used by others in the community. Understanding the effects of cross-feeding presents a major challenge, as it creates complex interdependencies between populations which can be hard to untangle. We address this problem using the tools of network science to develop a structural microbial community model. Using methods from percolation theory, we identify feasible community states for cross-feeding network structures in which the needs of consumers are met by metabolite production across the community. We identify tipping points at which small changes in structure can cause the catastrophic collapse of cross-feeding networks and abrupt declines in microbial community diversity. Our results are an example of a well-defined tipping point in a complex ecological system and provide insight into the fundamental processes shaping microbiomes and their robustness. We further demonstrate this by considering how network attacks affect community diversity and apply our results to show how the apparent difficulty in culturing the microbial diversity emerges as an inherent property of their cross-feeding networks.}, }
@article {pmid40327084, year = {2025}, author = {Zhang, M and Hu, Y and Ma, Y and Hou, T and Wang, J and Che, Q and Chen, B and Wang, Q and Feng, G}, title = {Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {39}, pmid = {40327084}, issn = {1432-184X}, mesh = {*Gossypium/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Agricultural Irrigation/methods ; Biodiversity ; Desert Climate ; Microbiota ; Alkaline Phosphatase/genetics ; }, abstract = {Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.}, }
@article {pmid40324073, year = {2025}, author = {Hoffman, PF}, title = {Ecosystem relocation on Snowball Earth: Polar-alpine ancestry of the extant surface biosphere?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {20}, pages = {e2414059122}, pmid = {40324073}, issn = {1091-6490}, support = {EAR-0417422//NSF (NSF)/ ; }, mesh = {*Ecosystem ; Earth, Planet ; Oceans and Seas ; Ice Cover ; Fossils ; Biological Evolution ; }, abstract = {Geological observations informed by climate dynamics imply that the oceans were 99.9% covered by light-blocking ice shelves during two discrete, self-reversing Snowball Earth epochs spanning a combined 60 to 70 Myr of the Cryogenian Period (720 to 635 Ma). The timescale for initial ice advances across the tropical oceans is ~300 y in an ice-atmosphere-ocean general circulation model in Cryogenian paleogeography. Areas of optically thin oceanic ice are usually invoked to account for fossil marine phototrophs, including macroscopic multicellular eukaryotes, before and after each Snowball, but different taxa. Ecosystem relocation is a scenario that does not require thin marine ice. Assume that long before Cryogenian Snowballs, diverse supra- and periglacial biomes were established in polar-alpine regions. When the Snowball onsets occurred, those biomes migrated in step with their ice margins to the equatorial zone of net sublimation. There, they prospered and evolved, their habitat areas expanded, and the cruelty of winter reduced. Nutrients were supplied by dust (loess) derived from cozonal ablative lands where surface winds were strong. When each Snowball finally ended, those biomes were mostly inundated by the meltwater-dominated and rapidly warming lid of a nutrient-rich but depauperate ocean. Some taxa returned to the mountaintops while others restocked the oceans. This ecosystem relocation scenario makes testable predictions. The lineages required for post-Cryogenian biotic radiations should be present in modern polar-alpine biomes. Legacies of polar-alpine ancestry should be found in the genomes of living organisms. Examples of such tests are highlighted herein.}, }
@article {pmid40323108, year = {2025}, author = {Oz, A and Mairesse, O and Raikin, S and Hanani, H and Mor, H and Dafny Yelin, M and Sharon, I}, title = {Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora.}, journal = {mSphere}, volume = {10}, number = {5}, pages = {e0001125}, pmid = {40323108}, issn = {2379-5042}, support = {Accelerator project//The JCA Foundation/ ; }, mesh = {*Erwinia amylovora/genetics ; *Pyrus/microbiology ; *Flowers/microbiology ; *Microbiota ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; Bacteria/classification/genetics ; }, abstract = {Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.}, }
@article {pmid40322584, year = {2025}, author = {Zschaubitz, E and Schröder, H and Glackin, CC and Vogel, L and Labrenz, M and Sperlea, T}, title = {A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1636-1647}, pmid = {40322584}, issn = {2001-0370}, abstract = {Next-Generation Sequencing methods like DNA metabarcoding enable the generation of large community composition datasets and have grown instrumental in many branches of ecology in recent years. However, the sparsity, compositionality, and high dimensionality of metabarcoding datasets pose challenges in data analysis. In theory, feature selection methods improve the analyzability of eDNA metabarcoding datasets by identifying a subset of informative taxa that are relevant for a certain task and discarding those that are redundant or irrelevant. However, general guidelines on selecting a feature selection method for application to a given setting are lacking. Here, we report a comparison of feature selection methods in a supervised machine learning setup across 13 environmental metabarcoding datasets with differing characteristics. We evaluate workflows that consist of data preprocessing, feature selection and a machine learning model by their ability to capture the ecological relationship between the microbial community composition and environmental parameters. Our results demonstrate that, while the optimal feature selection approach depends on dataset characteristics, feature selection is more likely to impair model performance than to improve it for tree ensemble models like Random Forests. Furthermore, our results show that calculating relative counts impairs model performance, which suggests that novel methods to combat the compositionality of metabarcoding data are required.}, }
@article {pmid40322503, year = {2025}, author = {Mandal, A and Ghosh, A and Kumar, G and Bhadury, P}, title = {Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111554}, pmid = {40322503}, issn = {2352-3409}, abstract = {Sundarbans, the world's largest contiguous mangrove wetland, a UNESCO World Heritage Site and a RAMSAR site formed on the delta of Ganga-Brahmaputra-Meghna (GBM) and influenced by coastal water entering from the Bay of Bengal contribute immensely to biodiversity and blue economy. To track the changes driven by natural and anthropogenic stressors, sediment based environmental DNA (eDNA) biomonitoring of benthic foraminifera communities, an important biological group sensitive to changes, has been initiated along with estimation of dissolved nutrients from estuarine surface water of Sundarbans. In pre-monsoon of 2022 (June), sediment cores and surface water were collected as well as in situ environmental parameters were measured from two pre-designated sampling points of Sundarbans to elucidate the benthic foraminifera community based on sediment eDNA approach. Based on Oxford Nanopore Technologies (ONT) sequencing in MinION platform, high abundance of Sorites sp., Elphidium excavatum, Textularia gramen, Quinqueloculina sp. and Trochammina hadai were detected. The increasing nutrient concentrations and elucidated benthic foraminiferal signals can contribute towards tracking the state of ecological health of Sundarbans. This study is aimed at generating baseline information on mangrove benthic foraminifera communities using sediment eDNA based high-throughput sequencing.}, }
@article {pmid40319780, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {282}, number = {}, pages = {123751}, doi = {10.1016/j.watres.2025.123751}, pmid = {40319780}, issn = {1879-2448}, mesh = {*Water Purification ; *Drinking Water/microbiology ; Filtration ; *Sand ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Netherlands ; Bacteria ; }, abstract = {Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.}, }
@article {pmid40319213, year = {2025}, author = {Liu, Y and Hu, Y and Ma, B and Wang, Z and Wei, B}, title = {Gut Microbiota and Exercise: Probiotics to Modify the Composition and Roles of the Gut Microbiota in the Context of 3P Medicine.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {38}, pmid = {40319213}, issn = {1432-184X}, mesh = {*Probiotics/administration &amp; dosage/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Exercise/physiology ; Athletic Performance/physiology ; Precision Medicine ; Animals ; }, abstract = {Prolonged and intense physical activity can trigger stress response mechanisms across various physiological systems-including the cardiovascular, respiratory, gastrointestinal, musculoskeletal, and neuroendocrine systems-disrupting energy metabolism, immune function, redox balance, and hormonal regulation. Critically, when not accompanied by adequate recovery, such exertion may impair rather than enhance athletic performance. In parallel, there has been growing interest in probiotics as natural, safe, and accessible dietary supplements with the potential to support performance and recovery. Emerging evidence highlights the pivotal role of the gut microbiome in mediating communication along the gut-brain and gut-muscle axes, thereby influencing not only metabolic and immune functions but also neuromuscular adaptation and fatigue resistance. This review explores the mechanisms through which probiotics may enhance exercise performance, mitigate exercise-induced fatigue, and improve physiological adaptation via modulation of inflammation, oxidative stress, and metabolic signaling pathways. Framed within the context of predictive, preventive, and personalized medicine (3P medicine), this paper emphasizes the diagnostic and therapeutic potential of personalized probiotic strategies in optimizing athletic performance through the qualitative and quantitative assessment of microbiota and host responses.}, }
@article {pmid40316823, year = {2025}, author = {Ben Ammar, FE and Hkiri, AE and Zaafouri, K and Saidane Bchir, F and Hamdi, M}, title = {Enhanced growth of Chlorella sorokiniana on ash-enriched treated wastewater for large-scale lipid and chlorophyll a production using a hybrid raceway photobioreactor.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {21}, pages = {12610-12629}, pmid = {40316823}, issn = {1614-7499}, mesh = {*Chlorella ; *Wastewater ; *Photobioreactors ; Lipids ; Chlorophyll A ; Microalgae ; Biomass ; }, abstract = {Nutrient concentration in microalgal cultivation media greatly influences microalgal growth and macromolecules production. In the present study, treated urban wastewater was used as a medium for Chlorella sorokiniana, incorporating mineral components and ashes in batch culture. The aim was to assess the combined effect of nutrients on microalgal growth, Chlorophyll a content, and lipid production using customized experimental design and response surface methodology. Another objective was to evaluate response improvement after using hybrid raceway photobioreactor HRPBR. The results showed that the highest microalgal biomass growth as well as the highest Chlorophyll a and lipid concentrations was obtained using 2015 mg. L[-1]of NaNO3 and 2086.76 mg. L[-1] of NaHCO3 with a mineral solution concentration of 120 mg. L[-1]. After the HRPBR cultivation, Chlorophyll a content increased from 40.26 to 65.04 mg. L[-1] and the lipid content rose from 37 to 40% and then to 68% under starvation conditions. In these circumstances, the FA profile of Chlorella sorokiniana became in line with the requirements of the European biodiesel standard. Thus, the low-cost nutrient sources for culture medium formulation can be used to culture C. sorokiniana as an efficient strain for sustainable and cost-effective biofuel production.}, }
@article {pmid40312782, year = {2025}, author = {Kynast, D and Reverey, F and Ganzert, L and Grossart, HP and Lischeid, G and Kolb, S}, title = {Detectable land use impact on methanotrophs and methanogens in kettle hole sediments but not on net methane production potentials.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {6}, pages = {}, pmid = {40312782}, issn = {1574-6941}, support = {465808595//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation &amp; purification ; Microbiota ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Soil Microbiology ; Soil/chemistry ; Agriculture ; Biodiversity ; Forests ; }, abstract = {Kettle holes (KHs) are dynamic freshwater systems and potential sources of the greenhouse gas methane. Due to their small size (<1 hectare), KHs are subject to inorganic and organic matter input from their terrestrial surroundings, governed by land use. Matter inputs include inorganic solutes that are alternative electron acceptors and impact on methanotrophs and methanogens. Thus, they might affect methane net production. We sampled 10 kettle hole sediments embedded in landscapes with either agricultural or forest land use and determined their (i) potential net methane production rates, (ii) the composition of their microbial communities, and (iii) physicochemical soil parameters. Potential net methane production did not significantly differ by land use type but between single KHs. However, land use type had a strong impact on methanotroph and methanogen and on total bacterial and archaeal microbiota structure. Relative abundances of methanotrophs and methanogens were significantly higher in agricultural KHs, and their relative abundances were among the most influential variables projecting net methane production potentials along with nutrient status and water content. Land use type was thus identified as a major factor that impacts the structure and biodiversity of general and methane-cycling microbiota, but it did not affect net methane production potentials.}, }
@article {pmid40312547, year = {2025}, author = {Hu, L and Zhang, K and Xu, Y and Zheng, X and Waterman, JM and Ouyang, X and Wu, Z and Shen, Z and He, Y and Ma, B and Robert, CAM and Raaijmakers, JM and Ye, M and Erb, M and Xu, J}, title = {Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.}, journal = {Nature plants}, volume = {11}, number = {5}, pages = {1001-1017}, pmid = {40312547}, issn = {2055-0278}, support = {32372775//National Natural Science Foundation of China (National Science Foundation of China)/ ; 200355//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Oxylipins/metabolism ; *Cyclopentanes/metabolism ; *Herbivory ; *Volatile Organic Compounds/metabolism ; *Plant Leaves/metabolism ; *Zea mays/physiology/metabolism/growth &amp; development ; Soil Microbiology ; Soil/chemistry ; Animals ; Rhizosphere ; }, abstract = {Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.}, }
@article {pmid40310547, year = {2025}, author = {Calcagnile, M and Quarta, E and Sicuro, A and Pecoraro, L and Schiavone, R and Tredici, SM and Talà, A and Corallo, A and Verri, T and Stabili, L and Alifano, P}, title = {Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {37}, pmid = {40310547}, issn = {1432-184X}, support = {ARS01_01053//Ministero dell'Istruzione e del Merito/ ; ARS01_01053//Ministero dell'Istruzione e del Merito/ ; CUP B83C22002930006//European Union Next Generation EU (PNRR)/ ; }, mesh = {Animals ; *Bacillus/physiology/genetics ; *Cichlids/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Bacteria/classification/genetics/isolation &amp; purification ; Animal Feed/analysis ; }, abstract = {In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.}, }
@article {pmid40309103, year = {2025}, author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F}, title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575405}, pmid = {40309103}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.<br><br>METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.<br><br>DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.}, }
@article {pmid40307095, year = {2025}, author = {Zhang, D and Gao, JT and Zhou, SG}, title = {Microbial electrotaxis: rewiring environmental microbiomes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.005}, pmid = {40307095}, issn = {1878-4380}, abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.}, }
@article {pmid40305681, year = {2025}, author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC}, title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40305681}, issn = {1751-7370}, mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; }, abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.}, }
@article {pmid40304437, year = {2025}, author = {Kardish, MR and Stachowicz, JJ}, title = {More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70086}, pmid = {40304437}, issn = {1758-2229}, support = {//UC Davis Center for Population Biology/ ; OCE 1829992//National Science Foundation/ ; //National Science Foundation GRFP/ ; TG-DEB160008//Extreme Science and Engineering Discovery Environment (XSEDE)/ ; //Gordon and Betty Moore Foundation/ ; }, mesh = {*Zosteraceae/microbiology ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.}, }
@article {pmid40303429, year = {2025}, author = {Zhao, C and Zhang, J and Chen, Y and Yang, L and Chen, H and Liang, Y and Wang, W and He, S and Luo, Y and Zhang, J and Zhang, H and Yang, S and Guo, G and Dai, W and Yang, Z and Chen, J and Zhou, Y and Khan, WU and Liu, G and Jiang, Y and Zhu, T and Xu, Y and García-Caparros, P and Van de Peer, Y and Xue, JY and Chen, C and Zhang, L and Chen, F}, title = {Water lily pond: a multiomics database for water lilies.}, journal = {Horticulture research}, volume = {12}, number = {6}, pages = {uhaf076}, pmid = {40303429}, issn = {2662-6810}, }
@article {pmid40302853, year = {2025}, author = {Gharbi, D and Neumann, FH and Podile, K and McDonald, M and Linde, JH and Frampton, M and Liebenberg, JL and Cilliers, S and Mmatladi, T and Nkosi, P and Paledi, K and Piketh, S and Staats, J and Burger, RP and Havenga, H and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa.}, journal = {Frontiers in allergy}, volume = {6}, number = {}, pages = {1568669}, pmid = {40302853}, issn = {2673-6101}, abstract = {BACKGROUND: Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom.<br><br>OBJECTIVES: This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom.<br><br>METHODS: Skin prick tests (SPTs) were performed on 202 adults aged 18-64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed.<br><br>RESULTS: Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus.<br><br>DISCUSSION &amp; CONCLUSION: This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.}, }
@article {pmid40301344, year = {2025}, author = {Zhu, C and Wu, L and Ning, D and Tian, R and Gao, S and Zhang, B and Zhao, J and Zhang, Y and Xiao, N and Wang, Y and Brown, MR and Tu, Q and ,  and Ju, F and Wells, GF and Guo, J and He, Z and Nielsen, PH and Wang, A and Zhang, Y and Chen, T and He, Q and Criddle, CS and Wagner, M and Tiedje, JM and Curtis, TP and Wen, X and Yang, Y and Alvarez-Cohen, L and Stahl, DA and Alvarez, PJJ and Rittmann, BE and Zhou, J}, title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4006}, pmid = {40301344}, issn = {2041-1723}, support = {EF-2025558//National Science Foundation (NSF)/ ; 32371724//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82202299//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872218//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Wastewater/microbiology ; Humans ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.}, }
@article {pmid40301151, year = {2025}, author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C}, title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {36}, pmid = {40301151}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; }, abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.}, }
@article {pmid40301143, year = {2025}, author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K}, title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {35}, pmid = {40301143}, issn = {1432-184X}, support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; }, mesh = {Animals ; *Skin/microbiology ; Seasons ; *Bacteria/classification/isolation &amp; purification/genetics ; *Bufo marinus/microbiology ; *Microbiota ; Ecosystem ; Australia ; Animals, Wild/microbiology ; Animals, Zoo/microbiology ; }, abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.}, }
@article {pmid40300605, year = {2025}, author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH}, title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.}, journal = {Current biology : CB}, volume = {35}, number = {10}, pages = {2282-2294.e11}, doi = {10.1016/j.cub.2025.03.073}, pmid = {40300605}, issn = {1879-0445}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteriophages/physiology/genetics ; *Lysogeny ; Mice ; Animals ; *Bacteria/virology/genetics ; *Virome ; }, abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.}, }
@article {pmid40299544, year = {2025}, author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA}, title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.}, journal = {Journal of phycology}, volume = {61}, number = {3}, pages = {633-649}, pmid = {40299544}, issn = {1529-8817}, support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; }, mesh = {*Microbiota ; *Kelp/microbiology/growth &amp; development/physiology ; *Germ Cells, Plant/growth &amp; development/microbiology ; Hot Temperature ; Stress, Physiological ; }, abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.}, }
@article {pmid40298441, year = {2025}, author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N}, title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0070525}, pmid = {40298441}, issn = {2150-7511}, support = {no. 31870111//National Natural Science Foundation of China/ ; no. 41830318//National Natural Science Foundation of China/ ; no. 32300001//National Natural Science Foundation of China/ ; no. 2022A1515010625//Natural Science Foundation of Guangdong Province/ ; no. 2021A1515012468//Natural Science Foundation of Guangdong Province/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; *Archaea/genetics/classification/isolation &amp; purification/metabolism ; *Geologic Sediments/microbiology ; Metagenomics ; Metagenome ; Mining ; Phylogeny ; Acids ; Phylogeography ; }, abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.}, }
@article {pmid40297467, year = {2025}, author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19120}, pmid = {40297467}, issn = {2167-8359}, mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, }
@article {pmid40294427, year = {2025}, author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y}, title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {18}, pages = {8922-8938}, doi = {10.1021/acs.est.5c01214}, pmid = {40294427}, issn = {1520-5851}, mesh = {*Nitrification ; Bacteria/metabolism ; Nitrogen ; Wastewater ; Nitrites/metabolism ; Ammonia/metabolism ; }, abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.}, }
@article {pmid40294268, year = {2025}, author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X}, title = {Exposure and health risks of livestock air resistomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {18}, pages = {e2403866122}, pmid = {40294268}, issn = {1091-6490}, support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; }, mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; }, abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.}, }
@article {pmid40293502, year = {2025}, author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L}, title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {34}, pmid = {40293502}, issn = {1432-184X}, support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; }, mesh = {China ; *Wetlands ; *Soil Microbiology ; Soil/chemistry ; Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.}, }
@article {pmid40287826, year = {2025}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, pmid = {40287826}, issn = {1362-4962}, support = {DBI1356288NSF//NSF/ ; }, mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; }, abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.}, }
@article {pmid40287775, year = {2025}, author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W}, title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {105}, pmid = {40287775}, issn = {2049-2618}, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.}, }
@article {pmid40287657, year = {2025}, author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA}, title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {408}, pmid = {40287657}, issn = {1471-2164}, support = {310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; }, abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.<br><br>RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.<br><br>CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.}, }
@article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, }
@article {pmid40287414, year = {2025}, author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ}, title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3940}, pmid = {40287414}, issn = {2041-1723}, support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; }, mesh = {*Urinary Catheters/microbiology/adverse effects ; Humans ; *Urinary Tract Infections/microbiology/prevention &amp; control/etiology ; *Catheter-Related Infections/microbiology/prevention &amp; control ; *Urinary Catheterization/adverse effects ; Computer Simulation ; *Bacteria/growth &amp; development ; Urinary Bladder/microbiology ; Models, Theoretical ; Models, Biological ; Time Factors ; }, abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.}, }
@article {pmid40286617, year = {2025}, author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS}, title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.}, journal = {The Science of the total environment}, volume = {979}, number = {}, pages = {179495}, doi = {10.1016/j.scitotenv.2025.179495}, pmid = {40286617}, issn = {1879-1026}, mesh = {*Particulate Matter/analysis ; *Microbiota ; *Environmental Monitoring ; *Air Pollutants/analysis ; Fungi ; Bacteria ; *Air Microbiology ; Seoul ; }, abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.}, }
@article {pmid40285533, year = {2025}, author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A}, title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70211}, doi = {10.1111/gcb.70211}, pmid = {40285533}, issn = {1365-2486}, support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; }, mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; }, abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.}, }
@article {pmid40284744, year = {2025}, author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N}, title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284744}, issn = {2076-2607}, support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; }, abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.}, }
@article {pmid40284675, year = {2025}, author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y}, title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284675}, issn = {2076-2607}, support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; }, abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.}, }
@article {pmid40284595, year = {2025}, author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA}, title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284595}, issn = {2076-2607}, support = {3090-31630-006//USDA-ARS CRIS/ ; }, abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.}, }
@article {pmid40280843, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Plant-microbe interactions: plants modulating their defenses.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.001}, pmid = {40280843}, issn = {1878-4372}, abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.}, }
@article {pmid40280003, year = {2025}, author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ}, title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.}, journal = {Water research}, volume = {281}, number = {}, pages = {123684}, doi = {10.1016/j.watres.2025.123684}, pmid = {40280003}, issn = {1879-2448}, mesh = {*Filtration ; *RNA, Ribosomal, 16S/genetics ; *Water Purification/methods ; *Drinking Water/microbiology ; Microbiota ; }, abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.}, }
@article {pmid40279085, year = {2025}, author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y}, title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.}, journal = {Molecular diversity}, volume = {}, number = {}, pages = {}, pmid = {40279085}, issn = {1573-501X}, support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; }, abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.}, }
@article {pmid40277367, year = {2025}, author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW}, title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0222224}, pmid = {40277367}, issn = {1098-5336}, support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; }, mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Methane/metabolism ; *Bacteria/metabolism/classification/genetics ; Electron Transport ; Electrons ; Quinones/metabolism ; Acetates/metabolism ; Riboflavin/metabolism ; Archaea/metabolism ; Microbiota ; }, abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.}, }
@article {pmid40277363, year = {2025}, author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J}, title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0245624}, pmid = {40277363}, issn = {1098-5336}, support = {No. 2022B1111030001//Guangdong key Research and Developement program/ ; No. CARS-46//China Agricultural Research System/ ; No. 32473201//National Natural Science Foundation of China/ ; No. 2022YFE0203900//National Key Research and Development Program of China/ ; No. 2023A1515110395//Guangdong Province Basic and Applied Basic Research Found project/ ; No. 2024B1212040007//Science and Technology Plan Project of Guangdong Province/ ; }, mesh = {*Bacillus/genetics/classification/isolation &amp; purification/physiology/metabolism ; Phylogeny ; *Geologic Sediments/microbiology ; China ; Genome, Bacterial ; *Seawater/microbiology ; Cold Temperature ; Multigene Family ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; }, abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.}, }
@article {pmid40276016, year = {2025}, author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P}, title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100385}, pmid = {40276016}, issn = {2666-5174}, abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.}, }
@article {pmid40275504, year = {2025}, author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL}, title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf017}, pmid = {40275504}, issn = {1557-7023}, abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.}, }
@article {pmid40273553, year = {2025}, author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J}, title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.}, journal = {International journal of food microbiology}, volume = {437}, number = {}, pages = {111204}, doi = {10.1016/j.ijfoodmicro.2025.111204}, pmid = {40273553}, issn = {1879-3460}, mesh = {*Vegetables/microbiology ; France ; *Fruit/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; *Fungi/isolation &amp; purification/classification/genetics ; *Food Microbiology ; Family Characteristics ; Seasons ; Biodiversity ; Food Contamination/analysis ; }, abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.}, }
@article {pmid40270585, year = {2025}, author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L}, title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf057}, pmid = {40270585}, issn = {2730-6151}, abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.}, }
@article {pmid40270532, year = {2025}, author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F}, title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {4}, pages = {380-391}, pmid = {40270532}, issn = {2833-8278}, abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.}, }
@article {pmid40268300, year = {2025}, author = {Goyal, A and Chure, G}, title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70094}, pmid = {40268300}, issn = {1462-2920}, mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; }, abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.}, }
@article {pmid40267173, year = {2025}, author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T}, title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.}, journal = {Annual review of phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-phyto-111424-090412}, pmid = {40267173}, issn = {1545-2107}, abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.}, }
@article {pmid40266732, year = {2025}, author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX}, title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266732}, issn = {2075-4450}, support = {Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.}, }
@article {pmid40266381, year = {2025}, author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH}, title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {33}, pmid = {40266381}, issn = {1432-184X}, support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; }, abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.}, }
@article {pmid40262702, year = {2025}, author = {Zhang, S and Sun, C}, title = {Ecological divergence of marine bacteria Alteromonas mediterranea.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108359}, doi = {10.1016/j.ympev.2025.108359}, pmid = {40262702}, issn = {1095-9513}, mesh = {*Phylogeny ; *Alteromonas/genetics/classification ; Ecosystem ; Evolution, Molecular ; Seawater/microbiology ; Sequence Analysis, DNA ; Gene Transfer, Horizontal ; Ecotype ; Phylogeography ; }, abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.}, }
@article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microbiota ; *Water Microbiology ; Temperature ; Drinking Water/microbiology ; Seasons ; }, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, }
@article {pmid40261360, year = {2025}, author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ}, title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {32}, pmid = {40261360}, issn = {1432-184X}, support = {HR22C1605//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; }, abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.}, }
@article {pmid40261136, year = {2025}, author = {Elias Masiques, N and De Vrieze, J and Hemeryck, LY and Vanhaecke, L and De Smet, S and Van Hecke, T}, title = {Dietary fiber mitigates the differential impact of beef and chicken meat consumption on rat intestinal health.}, journal = {Food &amp; function}, volume = {16}, number = {10}, pages = {3949-3962}, doi = {10.1039/d5fo00900f}, pmid = {40261136}, issn = {2042-650X}, mesh = {Animals ; Rats ; *Dietary Fiber/metabolism ; Male ; Chickens ; Gastrointestinal Microbiome ; Cattle ; *Red Meat/analysis ; Oxidative Stress ; Colon/metabolism/microbiology ; Rats, Wistar ; Oligosaccharides/metabolism ; *Meat/analysis ; Fermentation ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {In this rat feeding study, it was hypothesized that the impact of red (vs. white) meat consumption on gut health is more pronounced in fiber-deprived diets, whereas fiber-rich diets may attenuate meat-related differences. For this purpose, rats were fed a red (beef) or white (chicken) meat diet with and without fructo-oligosaccharides (FOS) for three weeks. Gut health was assessed through colonic microbiota, fermentation metabolites, oxidative stress, inflammation, DNA adducts and histology. In rats on the fiber-deprived diets, beef consumption resulted in higher abundance of mucin-degrading bacteria Akkermansia and lower blood glutathione levels compared to chicken-fed rats. Adding FOS to the meat diets modulated the gut microbiota and fermentation metabolites, affected oxidative stress and inflammation markers in tissues and blood, increased colon length, and reduced fat deposition and liver weight. Thus, results showed that the dietary context should be considered when evaluating the impact of red meat consumption on gut health.}, }
@article {pmid40260087, year = {2025}, author = {Matsumura, E and Kato, H and Hara, S and Ohbayashi, T and Ito, K and Shingubara, R and Kawakami, T and Mitsunobu, S and Saeki, T and Tsuda, S and Minamisawa, K and Wagai, R}, title = {Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1557188}, pmid = {40260087}, issn = {1664-302X}, abstract = {Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.}, }
@article {pmid40259028, year = {2025}, author = {Hsieh, YE and Yang, SY and Liu, SL and Wang, SW and Wang, WL and Tang, SL and Yang, SH}, title = {Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {31}, pmid = {40259028}, issn = {1432-184X}, support = {MOST 111-2621-B-029 -002 -MY3//National Science and Technology Council, Taiwan/ ; MOST 110-2611-M-002-024//National Science and Technology Council/ ; }, mesh = {*Carbonates/metabolism/chemistry ; Hydrogen-Ion Concentration ; Salinity ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Chemical Precipitation ; }, abstract = {Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.}, }
@article {pmid40258091, year = {2025}, author = {Hashem, I and Wang, J and Van Impe, JFM}, title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012974}, pmid = {40258091}, issn = {1553-7358}, mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; }, abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.}, }
@article {pmid40257249, year = {2025}, author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS}, title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.}, journal = {Microbiology resource announcements}, volume = {14}, number = {5}, pages = {e0133524}, pmid = {40257249}, issn = {2576-098X}, support = {/NASA/NASA/United States ; }, abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.}, }
@article {pmid40253969, year = {2025}, author = {Achouri, H and Derguini, A and Idres, T and Selamoglu, Z and Hamadi, NB and Jalouli, M and Elfalleh, W and Bendif, H and Badraoui, R and Boufahja, F and Dellali, M}, title = {Impact of climate change on the toxicity of bisphenol A in Mytilus galloprovincialis and assessment of phycoremediation using Nannochloropsis salina via a multi-biomarker strategy and modeling.}, journal = {Marine pollution bulletin}, volume = {216}, number = {}, pages = {118010}, doi = {10.1016/j.marpolbul.2025.118010}, pmid = {40253969}, issn = {1879-3363}, mesh = {Animals ; *Mytilus/drug effects ; *Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Water Pollutants, Chemical/toxicity ; Biomarkers/metabolism ; *Climate Change ; *Stramenopiles ; Oxidative Stress ; Lipid Peroxidation ; Bisphenol A Compounds ; }, abstract = {In the current study, the mussels Mytilus galloprovincialis, exposed to four varying temperatures (17, 20, 23, and 26 °C), were contaminated with 50 μg/L of bisphenol A both with and without Nannochloropsis salina. The toxicity evaluation is determined by quantifying various biomarkers related to oxidative stress, neurotoxicity, and cellular damage. The key findings indicate that the toxicity of bisphenol A is heightened by rising temperature. The impact of bisphenol A is most evident at 26 °C, leading to excessive production of reactive oxygen species, depletion of non-enzymatic antioxidants, and activation of antioxidant enzymes (catalase and glutathione-S-transferase). The rise in malondialdehyde levels confirms lipid peroxidation caused by bisphenol A and intensified by thermal stress. These findings have been supported by strong molecular interactions between bisphenol A and lectin mytilec apo-form and proximal thread matrix protein 1 from M. galloprovincialis following the computational modeling assay. The incorporation of N. salina as a food additive helped, firstly, to mitigate the stress effects and, secondly, resulted in a noticeable enhancement of oxidative balance and filtration ability, along with decreased lipid peroxidation.}, }
@article {pmid40252751, year = {2025}, author = {Tuts, L and Heyndrickx, M and Becue, I and Boon, N and De Maesschalck, P and Rasschaert, G}, title = {Tracking antibiotics and antibiotic-resistant E. coli in the aquatic environment linked to agriculture.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126265}, doi = {10.1016/j.envpol.2025.126265}, pmid = {40252751}, issn = {1873-6424}, mesh = {*Escherichia coli/drug effects ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; *Agriculture ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Bacterial ; Groundwater/microbiology/chemistry ; Water Microbiology ; }, abstract = {The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic-resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01-10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16 % of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20 % to 48 %. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.}, }
@article {pmid40251008, year = {2025}, author = {Rizaludin, MS and Díaz, ASL and Zweers, H and Raaijmakers, JM and Garbeva, P}, title = {Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40251008}, issn = {1574-6941}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Plant Roots/microbiology/chemistry/metabolism ; *Botrytis/physiology ; *Solanum lycopersicum/microbiology/genetics/chemistry ; *Microbiota ; *Volatile Organic Compounds/metabolism/analysis ; *Plant Diseases/microbiology ; Rhizosphere ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; Soil Microbiology ; }, abstract = {The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.}, }
@article {pmid40250533, year = {2025}, author = {Rosario Rodero, MD and Steyer, JP and Pérez-Bernal, MF and Verstraete, W and Escudié, R and Capson-Tojo, G}, title = {Dinitrogen fixation by open purple non-sulfur bacteria cultures for protein production: Diazotrophy boosts photoheterotrophic uptake rates.}, journal = {Bioresource technology}, volume = {430}, number = {}, pages = {132554}, doi = {10.1016/j.biortech.2025.132554}, pmid = {40250533}, issn = {1873-2976}, mesh = {*Nitrogen Fixation/physiology ; Biomass ; Rhodopseudomonas/metabolism ; Nitrogen/metabolism ; Heterotrophic Processes ; Light ; *Bacterial Proteins/biosynthesis ; }, abstract = {Purple non-sulfur bacteria (PNSB) offer a sustainable alternative to current inefficient protein production systems thanks to their high yields. This study explored the potential of specialized diazotrophic PNSB open cultures for protein production, benchmarking their performance against ammonium-grown PNSB and other diazotrophs. While diazotrophic yields (0.85-0.93 gCODbiomass·gCODsubstrate[-1]; COD being chemical oxygen demand) were slightly lower than non-diazotrophic (∼1.0), they were over double those of heterotrophic-diazotrophic rhizobacteria, with full N recovery as biomass (∼1.0 gNbiomass·gNfixed[-1]). Photoheterotrophic-diazotrophic uptake rates were the fastest ever reported for PNSB and any other diazotroph (e.g., 5.20 ± 0.83 vs. 2.64 ± 0.34 gCODsubstrate·gCODbiomass[-1]·d[-1] for PNSB on NH4[+]). Optimal rates required high light intensities, aligning with diazotrophic energy demands. Photoheterotrophic-diazotrophic conditions were highly selective, enriching a specialized Rhodopseudomonas palustris strain. Biomass protein contents and essential amino acid metrics confirmed nutritional suitability for humans. This work lays the background for exploiting PNSB's potential to address global protein demands through sustainable nitrogen fixation.}, }
@article {pmid40248914, year = {2025}, author = {Zhang, RG and Shang, HY and Milne, RI and Almeida-Silva, F and Chen, H and Zhou, MJ and Shu, H and Jia, KH and Van de Peer, Y and Ma, YP}, title = {SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.}, journal = {Nucleic acids research}, volume = {53}, number = {7}, pages = {}, pmid = {40248914}, issn = {1362-4962}, support = {2022YFF1301700//National Key Research and Development Program/ ; KIBXD202401//Kunming Institute of Botany, Chinese Academy of Sciences/ ; //Light of West China/ ; 202101BC070003//Key Basic Research Programs of Yunnan Province/ ; 2022SJ07X-03//PSESP/ ; }, mesh = {*Synteny/genetics ; *Genomics/methods ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; Polyploidy ; Algorithms ; Plants/genetics ; }, abstract = {With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.}, }
@article {pmid40248762, year = {2025}, author = {Flores, C and Millard, S and Seekatz, AM}, title = {Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.}, journal = {Current clinical microbiology reports}, volume = {12}, number = {1}, pages = {9}, pmid = {40248762}, issn = {2196-5471}, abstract = {PURPOSE OF REVIEW: This review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward.<br><br>RECENT FINDINGS: Recent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states.<br><br>SUMMARY: Despite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.}, }
@article {pmid40247944, year = {2025}, author = {Sun, Y and Sun, S and Zahid, MS and Qiu, Q and Wang, L and Wang, S}, title = {Root-applied brassinosteroid and salicylic acid enhance thermotolerance and fruit quality in heat-stressed 'Kyoho' grapevines.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1563270}, pmid = {40247944}, issn = {1664-462X}, abstract = {INTRODUCTION: The increasingly severe global greenhouse effect has become an irreversible trend, significantly impacting viticulture regions through heat stress during various grape growth stages, especially under protected cultivation conditions where high temperatures frequently occur. Therefore, studying the impact of heat stress on grapevine growth and fruit quality across the entire growth and development period, along with effective mitigation measures, is crucial.<br><br>METHODS: In this study, three-year-old 'Kyoho' grapevines were used as experimental materials, with four treatment groups: a control group, a hightemperature group (heat stress, HT), a high-temperature + brassinolide group (BR), and a high-temperature + salicylic acid group (SA). During the flowering, young berry swelling, and veraison stages, BR and SA were applied via nutrient solutions every seven days.<br><br>RESULTS: The results demonstrated that BR restored the maximum photosynthetic rate (Amax) to 96.14% of CK by the 18th day of flowering, significantly outperforming SA's recovery rate of 86.64%. Both treatments maintained light saturation points (1200 &#x3bc;mol&#x2022;m[&#x207b;&#xb2;]&#x2022;s[&#x207b;&#xb9;]) and CO2 saturation thresholds equivalent to CK. The decline in PSII photochemical efficiency (Fv/Fm) was reduced from 18% in HT to 5-8% in BR/SA-treated groups, with BR showing minimal deviation (2.3%) from CK during veraison, effectively mitigating PSII photoinhibition caused by heat stress. Furthermore, both treatments reduced leaf malondialdehyde (MDA) content, minimizing membrane lipid peroxidation, while increasing soluble protein (SP) content to protect leaves. Under heat stress, BR notably improved the fruit set rate by 22.67% compared to HT (SA: 13%), promoted berry expansion, and enhanced the accumulation of sugars and anthocyanins in the fruit skin, with SA showing similar, though slightly less pronounced, effects.<br><br>DISCUSSION: These findings provide valuable theoretical insights into the use of exogenous hormones in root nutrient solutions as a strategy to mitigate the adverse effects of heat stress in grape production.}, }
@article {pmid40247820, year = {2025}, author = {Liu, M and Yao, X and Wang, H and Xu, X and Kong, J and Wang, Y and Chen, W and Bai, H and Wang, Z and Setati, ME and Crauwels, S and Blancquaert, E and Fan, P and Liang, Z and Dai, Z}, title = {Carposphere microbiota alters grape volatiles and shapes the wine grape typicality.}, journal = {The New phytologist}, volume = {246}, number = {5}, pages = {2280-2294}, doi = {10.1111/nph.70152}, pmid = {40247820}, issn = {1469-8137}, support = {NXNYYZ202101//Agricultural Breeding Project of Ningxia Hui Autonomous Region/ ; U20A2041//National Natural Science Foundation of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 2021YFE0109500//National Key Research and Development Program of China/ ; YSBR-093//CAS Project for Young Scientists in Basic Research/ ; }, mesh = {*Vitis/microbiology/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Microbiota ; Fruit/microbiology/genetics/metabolism ; *Wine/microbiology ; Sphingomonas/physiology ; Transcriptome/genetics ; Metabolome ; Gene Expression Regulation, Plant ; }, abstract = {While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.}, }
@article {pmid40247656, year = {2025}, author = {Bonazzi, E and De Barba, C and Lorenzon, G and Maniero, D and Bertin, L and Barberio, B and Facciotti, F and Caprioli, F and Scaldaferri, F and Zingone, F and Savarino, EV}, title = {Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {19}, number = {5}, pages = {563-576}, doi = {10.1080/17474124.2025.2495087}, pmid = {40247656}, issn = {1747-4132}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Precision Medicine ; Animals ; Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/microbiology/diagnosis ; *Inflammatory Bowel Diseases/therapy/microbiology/diagnosis ; *Crohn Disease/therapy/microbiology/diagnosis ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.<br><br>AREAS COVERED: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.<br><br>EXPERT OPINION: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.}, }
@article {pmid40246153, year = {2025}, author = {Bharathan, A and Arafath, Y and Fathima, A and Hassan, S and Singh, P and Kiran, GS and Selvin, J}, title = {Implication of environmental factors on the pathogenicity of Vibrio vulnificus: Insights into gene activation and disease outbreak.}, journal = {Microbial pathogenesis}, volume = {204}, number = {}, pages = {107591}, doi = {10.1016/j.micpath.2025.107591}, pmid = {40246153}, issn = {1096-1208}, mesh = {*Vibrio vulnificus/pathogenicity/genetics/drug effects ; Humans ; *Vibrio Infections/epidemiology/microbiology ; *Disease Outbreaks ; Virulence Factors/genetics ; Climate Change ; Virulence/genetics ; Gene Expression Regulation, Bacterial ; Temperature ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Animals ; Biofilms/growth &amp; development ; }, abstract = {Climate change, particularly rising sea surface temperatures and altered salinity levels has contributed to the increased prevalence of Vibrio vulnificus infections in humans and marine life. This opportunistic pathogen thrives in warm, estuarine environments, and its virulence is influenced by temperature-dependent gene expression, such as the activation of pVvBt2. Elevated temperatures and iron availability enhance pathogenicity by upregulating key virulence factors, including hemolysin, exotoxins, and biofilm-associated genes. Climate-driven shifts in microbial ecology have also facilitated the global expansion of V. vulnificus, leading to more frequent outbreaks and an increasing threat to public health. The unregulated use of antibiotics has also contributed to the emergence of resistant strains, complicating treatment strategies. This review explores the complex interplay between climate change and the molecular mechanisms driving V. vulnificus pathogenicity, global gene expression responses, and the implications for disease outbreaks. We also discuss current and emerging therapeutic approaches, including antibiotic stewardship and vaccine development, to mitigate the rising health risks posed by this climate-sensitive pathogen.}, }
@article {pmid40244660, year = {2025}, author = {Narla, AV and Hwa, T and Murugan, A}, title = {Dynamic coexistence driven by physiological transitions in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {16}, pages = {e2405527122}, pmid = {40244660}, issn = {1091-6490}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; R35GM151211//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 542387//Simons Foundation (SF)/ ; 2029480//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; 2317138//NSF | MPS | Division of Physics (PHY)/ ; }, mesh = {*Ecosystem ; *Models, Biological ; Biomass ; *Microbiota/physiology ; *Microbial Interactions/physiology ; Bacteria/growth &amp; development ; }, abstract = {Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.}, }
@article {pmid40243315, year = {2025}, author = {Weng, L and Cui, Y and Jian, W and Zhang, Y and Pang, L and Cao, Y and Zhou, Y and Liu, W and Lin, H and Tao, Y}, title = {Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.}, journal = {Microbiology spectrum}, volume = {13}, number = {6}, pages = {e0251824}, pmid = {40243315}, issn = {2165-0497}, support = {31901116//National Natural Science Foundation of China/ ; 2022A1515012345//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Dental Caries/microbiology ; *Microbiota/genetics ; Child, Preschool ; Saliva/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Dental Plaque/microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Candida albicans/isolation &amp; purification ; }, abstract = {UNLABELLED: Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. In this study, we aimed to investigate the microbial diversity and inter-kingdom interactions in severe early childhood caries (S-ECC) and assess the influence of environmental factors such as salivary pH and trace elements. We analyzed 61 children aged 3-4 years with complete deciduous dentition, evaluating salivary pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced salivary pH.<br><br>IMPORTANCE: This study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with S-ECC and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, our findings revealed an association between Veillonella sp., Propionibacterium sp., and Candida sp. and reduced salivary pH. This provides novel insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.}, }
@article {pmid40241747, year = {2025}, author = {Takahashi, M and Hiraoka, S and Matsumoto, Y and Shibagaki, R and Ujihara, T and Maeda, H and Seo, S and Nagasaki, K and Takeuchi, H and Matsuzaki, S}, title = {Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112264}, pmid = {40241747}, issn = {2589-0042}, abstract = {Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.}, }
@article {pmid40240613, year = {2025}, author = {Dhungana, I and Nguyen, NH}, title = {Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {30}, pmid = {40240613}, issn = {1432-184X}, support = {HAW08042-H//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; *Fungi/classification/growth &amp; development/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; Zea mays/growth &amp; development/microbiology ; *Archaea/classification/growth &amp; development/genetics/isolation &amp; purification ; *Microbiota ; Tropical Climate ; Crops, Agricultural/growth &amp; development/microbiology ; Lactuca/growth &amp; development/microbiology ; Mustard Plant/growth &amp; development/microbiology ; }, abstract = {Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.}, }
@article {pmid40239902, year = {2025}, author = {Ma, H and Chen, S and Lv, L and Ye, Z and Yang, J and Wang, B and Zou, J and Li, J and Ganigué, R}, title = {Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.}, journal = {Bioresource technology}, volume = {429}, number = {}, pages = {132543}, doi = {10.1016/j.biortech.2025.132543}, pmid = {40239902}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Biofilms/growth &amp; development ; *Nitrogen/isolation &amp; purification/metabolism ; Aerobiosis ; Bioreactors/microbiology ; *Biotechnology/methods ; Biomass ; }, abstract = {Three parallel sequencing batch reactors (control, small-sized polyurethane sponge (PUS) (3.0 mm), and large-sized PUS (10.0 mm)) were used to investigate aerobic granular biofilm (AGB) characteristics. Results show that 10.0 mm PUS facilitated rapid formation of large-sized AGB (AGBL), which exhibited higher biomass concentration (8.5 g/L) and faster settling velocity (69.2-159.3 m/h) than aerobic granular sludge (AGS) (3.2 g/L and 38.6-80.0 m/h). The AGBL system also maintained long-term structural stability with a lower instability coefficient (0.004-0.018 min[-1]) than AGS (0.053-0.090 min[-1]). Additionally, during long-term operation, the AGBL system achieved excellent removal efficiencies for NH4[+]-N (99.6 ± 0.4 %) and total nitrogen (92.3 ± 2.6 %), and exhibited a lower sludge yield (0.05 gVSS/gCOD) than AGS (0.14 gVSS/gCOD). The larger size and compact structure of AGBL increased anoxic/anaerobic zones, enriching denitrifying and hydrolytic/fermentative bacteria. These findings highlight AGBL with large PUS as a more promising biotechnology for practical applications than conventional AGS.}, }
@article {pmid40238873, year = {2025}, author = {Bukhdruker, S and Gushchin, I and Shevchenko, V and Kovalev, K and Polovinkin, V and Tsybrov, F and Astashkin, R and Alekseev, A and Mikhaylov, A and Bukhalovich, S and Bratanov, D and Ryzhykau, Y and Kuklina, D and Caramello, N and Rokitskaya, T and Antonenko, Y and Rulev, M and Stoev, C and Zabelskii, D and Round, E and Rogachev, A and Borshchevskiy, V and Ghai, R and Bourenkov, G and Zeghouf, M and Cherfils, J and Engelhard, M and Chizhov, I and Rodriguez-Valera, F and Bamberg, E and Gordeliy, V}, title = {Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.}, journal = {Science advances}, volume = {11}, number = {16}, pages = {eadu5303}, pmid = {40238873}, issn = {2375-2548}, mesh = {*Protons ; *Rhodopsins, Microbial/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Proton Pumps/chemistry/metabolism ; Protein Conformation ; }, abstract = {Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.}, }
@article {pmid40238292, year = {2025}, author = {Zhang, Y and Lin, H and Xiong, Y and Zhang, Z and Zeng, L and Liu, Z}, title = {Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238292}, issn = {2304-8158}, support = {2024HX118//Horizontal project of Shaoyang University/ ; 2024JJ7497//Foundation regional joint fund of Hunan Province natural Science/ ; 202401001313//The teaching reform research project of Hunan Province in 2024/ ; 2022YFE0111200//Innovation and transformation of key technologies for efficient preparation of catechin oxidation polymerization products/ ; }, abstract = {Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.}, }
@article {pmid40238218, year = {2025}, author = {Zhadyra, S and Tao, F and Xu, P}, title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238218}, issn = {2304-8158}, abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.}, }
@article {pmid40237447, year = {2025}, author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC}, title = {The case for microbiome stewardship: what it is and how to get there.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0006225}, pmid = {40237447}, issn = {2379-5077}, support = {//University of Guelph Institute of Environmental Research/ ; R15 DK133826/DK/NIDDK NIH HHS/United States ; 191753/CAPMC/CIHR/Canada ; //Canada Research Chairs/ ; 7004439, ME022329//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; //Natural Sciences and Engineering Research Council of Canada/ ; NIH/NIDDK 1R15DK133826-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Agriculture ; Anti-Bacterial Agents ; Ecosystem ; *Microbiota ; Public Health ; }, abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.}, }
@article {pmid40235320, year = {2025}, author = {Bahram Wlia, A and Majedi, S}, title = {Optimizing hygiene and microbial aspect of paper recycling: a sustainable approach for environmental conservation.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {3}, pages = {151-157}, doi = {10.14715/cmb/2025.71.3.18}, pmid = {40235320}, issn = {1165-158X}, mesh = {*Recycling/methods ; *Paper ; *Hygiene ; *Bacteria/isolation &amp; purification/classification/genetics ; *Conservation of Natural Resources/methods ; Iraq ; Waste Management/methods ; }, abstract = {This study explores microbial dynamics in paper recycling, emphasizing the significance of sustainable practices for environmental preservation. Samples were collected from various urban waste sources in Erbil city, Kurdistan Region, Iraq, including materials such as pizza boxes, cigarette packets, and coffee cups. Pure bacterial colonies were isolated using standard methods, and their morphological and physiological traits were characterized through biochemical tests. Identification of bacterial species followed established protocols. The study identified diverse bacterial species associated with paper waste, highlighting potential hygiene concerns in the recycling process. The findings of this study contribute to understanding the microbial ecology associated with paper waste and recycling processes. By optimizing hygiene measures and gaining insights into the microbial communities present, this research underscores the importance of sustainable practices in paper recycling to mitigate environmental impacts and promote a healthier ecosystem. Policies for future waste management and reduction of environmental risks have been proposed.}, }
@article {pmid40234253, year = {2025}, author = {Yao, B and Mou, X and Li, Y and Lian, J and Niu, Y and Liu, J and Lu, J and Li, Y and Li, Y and Wang, X}, title = {Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {29}, pmid = {40234253}, issn = {1432-184X}, support = {23JRRA672//Youth Science and Technology Fund Program of Gansu Province/ ; 2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 22JR5RA076//Gansu Province Natural Science Foundation Program/ ; }, mesh = {*Soil Microbiology ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Ecosystem ; *Microbiota ; Biodiversity ; *Mycobiome ; China ; High-Throughput Nucleotide Sequencing ; }, abstract = {A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.}, }
@article {pmid40230839, year = {2025}, author = {Zhao, T and Wang, C and Liu, Y and Li, B and Shao, M and Zhao, W and Zhou, C}, title = {The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1555414}, pmid = {40230839}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Polysaccharides/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; *Immunomodulation ; Cytokines/metabolism ; }, abstract = {Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.}, }
@article {pmid40229524, year = {2025}, author = {Sakae, K and Kitagami, Y and Matsuda, Y}, title = {Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {28}, pmid = {40229524}, issn = {1432-184X}, support = {2023-4099//Japan Science Society/ ; JRMJSP2137//Japan Science and Technology Agency/ ; 24K01796//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/growth &amp; development/physiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Ericaceae/microbiology/growth &amp; development ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.}, }
@article {pmid40228732, year = {2025}, author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH}, title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126245}, doi = {10.1016/j.envpol.2025.126245}, pmid = {40228732}, issn = {1873-6424}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.}, }
@article {pmid40227232, year = {2025}, author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M}, title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40227232}, issn = {2050-084X}, support = {Fellowship//Schmidt Family Foundation/ ; K08 DK110532/DK/NIDDK NIH HHS/United States ; R01DK135707/NH/NIH HHS/United States ; Fellowship//National Defense Science and Engineering Graduate/ ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; Graduate Research Fellowship Program//National Science Foundation/ ; K08DK110532/NH/NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; Odyssey Award//Smith Family Foundation/ ; R01DK130836/NH/NIH HHS/United States ; }, mesh = {Animals ; *Paneth Cells/metabolism/physiology ; Mice ; *Neuroglia/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Myelin Proteolipid Protein/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; *Enteric Nervous System/physiology ; Mice, Inbred C57BL ; Male ; Female ; }, abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions (Prochera and Rao, 2023). To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express the gene Proteolipid protein 1 (PLP1) in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.}, }
@article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, pmid = {40223273}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, }
@article {pmid40222749, year = {2025}, author = {Belda, I and Izquierdo-Gea, S and Benitez-Dominguez, B and Ruiz, J and Vila, JCC}, title = {Wine Fermentation as a Model System for Microbial Ecology and Evolution.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70092}, pmid = {40222749}, issn = {1462-2920}, support = {//Center for Computational, Evolutionary and Human Genomics, Stanford University. Postdoc Fellowship to Jean CC VIla/ ; FPU21/06830//Spanish Ministry of Science, Innovation and Universities/ ; PID2019-105834GA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2022-138343NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PRE2022-103063//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {*Wine/microbiology ; *Fermentation ; *Biological Evolution ; Microbiota ; *Bacteria/metabolism/genetics ; Ecosystem ; Models, Biological ; Ecology ; }, abstract = {In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.}, }
@article {pmid40220383, year = {2025}, author = {Li, C and Zhu, L and Axe, L and Li, M}, title = {Acclimation of sludge-derived biofilms for effective removal of emerging contaminants: Impacts of inoculum source and carbon supplementation.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138235}, doi = {10.1016/j.jhazmat.2025.138235}, pmid = {40220383}, issn = {1873-3336}, mesh = {*Biofilms ; *Sewage/microbiology ; *Carbon ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; Sulfamethoxazole/metabolism ; Carbamazepine/metabolism ; Waste Disposal, Fluid/methods ; Acclimatization ; }, abstract = {Contaminants of emerging concern (CECs) have gathered significant public attention due to their widespread occurrence, high persistence, and increasing exposure potential. In this study, we used polyethylene biocarriers for acclimating biofilms from singular or combined activated sludges collected from three wastewater treatment plants (R, P, and L) over 5 month-long cycles. The acclimated biofilms achieved an average removal rate at 0.333, 0.313, and 0.185 week[-1] for N, N-diethyl-meta-toluamide (DEET), sulfamethoxazole (SMX), and carbamazepine (CBZ), respectively, when external carbon was supplemented, which were significantly higher (p < 0.05) than biofilms that did not receive external carbons. Metabolite screening revealed SMX transformation through ipso-hydroxylation and acetyl conjugation, while CBZ degradation could be initiated by epoxidation. Significant but slower degradation rates (0.024∼0.031 week[-1]) were observed for aminotriazole (AMT), lidocaine (LDC), and trimethoprim (TMP), whereas atrazine (ATZ) exhibited minimal removal, highlighting its high recalcitrance. Biofilms acclimated from individual R and P sludges, with external carbon supplementation, attained the greatest removal efficiencies for 7 CECs. Multivariate statistical correlations (p < 0.05) identified potential degraders, including Sphingomonas and Zoogolea for AMT, Labrys and Koazkia for CBZ, and Asprobacter, unclassified Cyclobacteriaceae (ELB16-189) and Bryobacteraceae (Fen-178) for LDC. Abundance distribution of potential degraders among biofilms revealed that Sludge R favored the enrichment of key degraders for AMT, CBZ and LDC, while Sludge P was more conducive to acclimating CBZ degraders. This study advances our understanding of strategies in biofilm acclimation to improve CEC removal and provides insights into degradation pathways and associated microbial communities for future research.}, }
@article {pmid40220189, year = {2025}, author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A}, title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {27}, pmid = {40220189}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; }, abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.}, }
@article {pmid40216640, year = {2025}, author = {Huttunen, KL and Malazarte, J and Jyväsjärvi, J and Lehosmaa, K and Muotka, T}, title = {Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {26}, pmid = {40216640}, issn = {1432-184X}, support = {356403//Research Council of Finland/ ; 318230//Research Council of Finland/ ; 318230//Research Council of Finland/ ; }, mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; *Plankton/classification/genetics ; Soil Microbiology ; Ecosystem ; Seasons ; }, abstract = {Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.}, }
@article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7517-7529}, pmid = {40214404}, issn = {1520-5851}, mesh = {Animals ; Aquaculture ; Archaea ; Ecosystem ; Iceland ; *Microbiota ; Norway ; *Aquatic Organisms/microbiology ; }, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, }
@article {pmid40209676, year = {2025}, author = {Schell, LD and Carmody, RN}, title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {4}, pages = {470-483}, doi = {10.1016/j.chom.2025.03.009}, pmid = {40209676}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; }, abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.}, }
@article {pmid40208324, year = {2025}, author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN}, title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {25}, pmid = {40208324}, issn = {1432-184X}, support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; }, abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.}, }
@article {pmid40208265, year = {2025}, author = {DiPietri, VT and Grady, ZS and Frost, AN and Stitzel, SE and Sivey, JD}, title = {Toilet Bowl Cleaning Tablets as Sources of Chlorine, Bromine, and Disinfection Byproducts in Wastewater.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7646-7655}, doi = {10.1021/acs.est.4c12026}, pmid = {40208265}, issn = {1520-5851}, mesh = {*Chlorine/analysis ; *Wastewater/chemistry ; *Bromine/analysis ; Disinfection ; *Water Pollutants, Chemical/analysis ; Tablets ; *Disinfectants/analysis ; }, abstract = {Commercial toilet bowl cleaning tablets were examined in laboratory systems to characterize their release of active halogens and their potential to form trihalomethanes (THMs) when combined with synthetic sewage. Active halogens (e.g., HOCl, HOBr, and reactive halamines) were quantified via derivatization with 1,3,5-trimethoxybenzene prior to analysis by liquid chromatography. The effects of several variables on halogen release profiles were examined, including pH, ionic strength, temperature, tank solution volume, flushing frequency, and tablet brand. Changes in pH resulted in modest or no appreciable changes in halogen release profiles. Release of active halogens increased as ionic strength decreased and as temperature increased. Tank volume, flushing frequency, and tablet brand had pronounced impacts on halogen release profiles. Maximum measured active chlorine and bromine concentrations in toilet tank water were 189 mg/L as Cl2 and 164 mg/L as Cl2, respectively. Active halogens persisted in toilet bowl water for >24 h. When toilet-tablet-treated water was combined with synthetic sewage, THMs formed at up to 219 ppb with bromine incorporation factors up to 2.86. Active halogens and highly brominated THMs released into wastewater from toilet tablets could have implications for downstream microbial ecology, septic system performance, and overall water quality.}, }
@article {pmid40206699, year = {2025}, author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS}, title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.}, journal = {Polar biology}, volume = {48}, number = {2}, pages = {62}, pmid = {40206699}, issn = {0722-4060}, support = {S10 OD026929/OD/NIH HHS/United States ; }, abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.}, }
@article {pmid40205489, year = {2025}, author = {Soares, A and Rassner, SME and Edwards, A and Farr, G and Blackwell, N and Sass, H and Persiani, G and Schofield, D and Mitchell, AC}, title = {Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205489}, issn = {1574-6941}, support = {//S&#xea;r Cymru/ ; NE/V012991/1//Natural Environment Research Council/ ; }, mesh = {*Sulfur/metabolism ; *Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Coal/microbiology ; *Groundwater/microbiology/chemistry ; *Microbial Consortia ; Oxidation-Reduction ; Seasons ; Phylogeny ; Sulfides/metabolism ; Wales ; Coal Mining ; Mining ; }, abstract = {Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment, thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here, we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidizing Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidizing Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The cooccurrence of pairs of Fe(II)- and S-oxidizing bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.}, }
@article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205473}, issn = {1574-6941}, support = {//DGAPA/ ; IG200319//UNAM/ ; //Instituto de Ecolog&#xed;a, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota/genetics ; Phylogeny ; Ecosystem ; Groundwater/microbiology ; }, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas (PR) and Archean Domes (AD). Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from PR and AD: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and AD: Halanaerobium sp. (63%) and D. halophilus (60%). Furthermore, metagenome-assembled genomes from Ectothiorhodospira genus were found in both AD and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the AD system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, }
@article {pmid40205253, year = {2025}, author = {Dasgupta, M and Paul, R and Chowdhury, P and Mondal, S and Ahmed, J and Mukherjee, C and Das, S and Tribedi, P}, title = {Management of Enterococcus faecalis biofilms: a combinatorial approach with phytochemical.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1131-1143}, pmid = {40205253}, issn = {1678-4405}, support = {TNU/R&amp;D/MP/2021/010//The Neotia University/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Enterococcus faecalis/drug effects/physiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Phytochemicals/pharmacology ; *Benzoquinones/pharmacology ; *Benzaldehydes/pharmacology ; Humans ; }, abstract = {The rapid emergence of antimicrobial resistance in Enterococcus faecalis infections was primarily due to their robust biofilm formation, highlighting the urgent need for meaningful strategies. Since combinatorial application of natural phytochemical often offer promising outcomes in dealing with microbial infections, present study indicated the pharmacological, antimicrobial and antibiofilm potential of combinatorial strategies of natural phytochemical involving cuminaldehyde and thymoquinone against E. faecalis. Towards this direction, in silico analysis suggested that both compounds could show favourable oral bioavailability and high GI absorption, with a considerable solubility and drug-likeness profiles. Furthermore, in vitro antimicrobial assay indicated that the minimum inhibitory concentrations (MIC) of cuminaldehyde and thymoquinone were found to be 500 µg/mL and 30 µg/mL, respectively against E. faecalis. Thereafter, the fractional inhibitory concentration (FIC) index score of 0.73 indicated an additive effect prevailed between cuminaldehyde and thymoquinone, enhancing their antimicrobial potential. Thereafter, sub-MIC doses of cuminaldehyde (40 µg/mL) and thymoquinone (8 µg/mL) were selected to assess their antibiofilm potential. Though the compounds were able to show antibiofilm activity separately, their combination was significantly more effective, reduced biofilm formation by approximately 80%, and decreased production of extracellular polymeric substance (EPS) and protein content by ~ 76% and ~ 70%, respectively. Further studies revealed that the antibiofilm activity of the test compounds could likely to be attributed to the accumulation of reactive oxygen species (ROS) and enhancement of membrane permeability. Taken together, all this experimental observation revealed that combination of these natural compounds could potentially improve the treatment outcomes of biofilm-borne infections of E. faecalis.}, }
@article {pmid40203032, year = {2025}, author = {Timilsina, S and Iruegas-Bocardo, F and Jibrin, MO and Sharma, A and Subedi, A and Kaur, A and Minsavage, GV and Huguet-Tapia, JC and Klein-Gordon, J and Adhikari, P and Adhikari, TB and Cirvilleri, G and de la Barrera, LBT and Bernal, E and Creswell, TC and Doan, TTK and Coutinho, TA and Egel, DS and Félix-Gastélum, R and Francis, DM and Kebede, M and Ivey, ML and Louws, FJ and Luo, L and Maynard, ET and Miller, SA and Nguyen, NTT and Osdaghi, E and Quezado-Duval, AM and Roach, R and Rotondo, F and Ruhl, GE and Shutt, VM and Thummabenjapone, P and Trueman, C and Roberts, PD and Jones, JB and Vallad, GE and Goss, EM}, title = {Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013036}, pmid = {40203032}, issn = {1553-7374}, mesh = {*Xanthomonas/genetics/pathogenicity/classification ; *Plant Diseases/microbiology ; *Solanum lycopersicum/microbiology ; *Genetic Variation ; Phylogeny ; }, abstract = {Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.}, }
@article {pmid40202691, year = {2025}, author = {Pimentel, AC and Cesar, CS and Martins, AHB and Martins, M and Cogni, R}, title = {Wolbachia Offers Protection Against Two Common Natural Viruses of Drosophila.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {24}, pmid = {40202691}, issn = {1432-184X}, mesh = {Animals ; *Wolbachia/physiology ; *Drosophila melanogaster/virology/microbiology ; *Drosophila/virology/microbiology ; Symbiosis ; Female ; }, abstract = {Wolbachia pipientis is a maternally transmitted endosymbiont infecting more than half of terrestrial arthropod species. Wolbachia can express parasitic phenotypes such as manipulation of host reproduction and mutualist phenotypes such as protection against RNA virus infections. Because Wolbachia can invade populations by reproductive manipulation and block virus infection, it is used to modify natural insect populations. However, the ecological importance of virus protection is not yet clear, especially due to scarce information on Wolbachia protection against viruses that are common in nature. We used systemic infection to investigate whether Wolbachia protects its host by suppressing the titer of DMELDAV and DMelNora virus, two viruses that commonly infect Drosophila melanogaster flies in natural populations. Antiviral protection was tested in three systems to assess the impact of Wolbachia strains across species: (1) a panel of Wolbachia strains transfected into Drosophila simulans, (2) two Wolbachia strains introgressed into the natural host D. melanogaster, and (3) two native Wolbachia strains in their natural hosts Drosophila baimaii and Drosophila tropicalis. We showed that certain Wolbachia strains provide protection against DMelNora virus and DMELDAV, and this protection is correlated with Wolbachia density, which is consistent with what has been observed in protection against other RNA viruses. Additionally, we found that Wolbachia does not protect its original host, D. melanogaster, from DMELDAV infection. While native Wolbachia can reduce DMELDAV titers in D. baimaii, this effect was not detected in D. tropicalis. Although the Wolbachia protection-induced phenotype seems to depend on the virus, the specific Wolbachia strain, and the host species, our findings suggest that antiviral protection may be one of the mutualistic effects that helps explain why Wolbachia is so widespread in arthropod populations.}, }
@article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, }
@article {pmid40200306, year = {2025}, author = {Bindels, LB and Watts, JEM and Theis, KR and Carrion, VJ and Ossowicki, A and Seifert, J and Oh, J and Shao, Y and Hilty, M and Kumar, P and Hildebrand, F and Lovejoy, C and Wigley, P and Yu, K and Zhang, M and Zhang, T and Walter, J and Desai, MS and Huws, SA and Schriml, LM and Ravel, J and Fricke, WF and Eloe-Fadrosh, EA and Lee, CK and Clavel, T}, title = {A blueprint for contemporary studies of microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {95}, pmid = {40200306}, issn = {2049-2618}, mesh = {*Microbiota ; *Publishing/standards ; }, abstract = {This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.}, }
@article {pmid40197060, year = {2025}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0327524}, pmid = {40197060}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.}, }
@article {pmid40197052, year = {2025}, author = {Liu, S and Ru, J and Guo, X and Gao, Q and Deng, S and Lei, J and Song, J and Zhai, C and Wan, S and Yang, Y}, title = {Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0124824}, pmid = {40197052}, issn = {2379-5077}, support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 20223BBG74S02//the Key Technology R&amp;D Program of JiangXi Province grant/ ; KY-23ZK01//the Hainan Institute of National Park grant/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Bacteria/genetics/classification ; *Rain ; China ; Fungi/genetics/classification ; Climate Change ; Soil/chemistry ; Grassland ; Biodiversity ; }, abstract = {Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.}, }
@article {pmid40196585, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of novel viral landscape phylogeography approaches.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40196585}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40195174, year = {2025}, author = {Burazerović, J and Jovanović, M and Savković, &#x17d; and Breka, K and Stupar, M}, title = {Finding the Right Host in the Darkness of the Cave-New Insights into the Ecology and Spatio-temporal Dynamics of Hyperparasitic Fungi (Arthrorhynchus nycteribiae, Laboulbeniales).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {23}, pmid = {40195174}, issn = {1432-184X}, support = {451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; }, mesh = {Animals ; *Chiroptera/parasitology/microbiology ; *Caves/microbiology ; *Ascomycota/genetics/isolation &amp; purification/physiology/classification ; *Diptera/microbiology ; Serbia ; Male ; Female ; Phylogeny ; }, abstract = {The aim of this study was to determine the presence of the hyperparasitic fungus Arthrorhynchus nycteribiae and to analyze its spatio-temporal pattern in the two bat flies (Penicillidia conspicua and P. dufourii) parasitizing on bats. We collected 612 samples of bat flies from 400 bats in 20 caves in the Central Balkans. Hyperparasite was identified based on morphological and molecular analyses of rDNA genes (LSU and SSU). A. nycteribiae was reported for the first time in Bosnia and Herzegovina and Montenegro, and confirmed in Serbia. Of the 20 sites examined, we found A. nycteribiae at 11 sites. The prevalence of A. nycteribiae infection in the bats examined was approximately 17%. Miniopterus schreibersii harbored the highest number of bat flies and was the only bat species hosting the infected bat flies of the species P. conspicua. Our results showed significant differences in infection patterns during the different seasons: the highest prevalence of bat flies with hyperparasitic fungi was found in the summer season (23%) and the lowest in spring (2%). Female bat fly hosts showed a significantly higher prevalence of infection than male bat flies. This study makes an important contribution to the knowledge of the distribution of A. nycteribiae and to the understanding of complex parasite-host relationships in the poorly studied areas of the Central Balkans.}, }
@article {pmid40194740, year = {2025}, author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q}, title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101039}, pmid = {40194740}, issn = {2213-2961}, abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.}, }
@article {pmid40186763, year = {2025}, author = {Huang, YD and Zhao, XL and Lin, Y and Ouyang, XM and Cheng, XS and Liang, LY and Huo, YN and Xie, GJ and Lin, JH and Jazag, A and Guleng, B}, title = {Mindin orchestrates the macrophage-mediated resolution of liver fibrosis in mice.}, journal = {Hepatology international}, volume = {}, number = {}, pages = {}, pmid = {40186763}, issn = {1936-0541}, support = {No. 81970460//National Natural Science Foundation of China/ ; No. 2023J011598//Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND &amp; AIMS: Liver disease that progresses to cirrhosis is an enormous health problem worldwide. The extracellular matrix protein Mindin is known to have immune functions, but its role in liver homeostasis remains largely unexplored. We aimed to characterize the role of Mindin in the regulation of liver fibrosis.<br><br>APPROACH &amp; RESULTS: Mindin was upregulated in mice with carbon tetrachloride (CCl4) or thioacetamide (TAA)-induced liver fibrosis, and was primarily expressed in hepatocytes. Global Mindin knockout mice were generated, which were susceptible to liver fibrosis. Notably, Mindin failed to activate hepatic stellate cells directly; however, it played a role in promoting the recruitment and phagocytosis of macrophages, and caused a phenotypic switch toward restorative macrophages during liver fibrosis. Furthermore, Mindin was found to bind to the &#x3b1;M-I domain of CD11b/CD18 heterodimeric receptors. To further explore this mechanism, we created Mindin and CD11b double-knockout (DKO) mice. In DKO mice, phagocytosis was further reduced, and liver fibrosis was markedly exacerbated.<br><br>CONCLUSIONS: Mindin promotes the resolution of liver fibrosis and the Mindin/CD11b axis might represent a novel target for the macrophage-mediated regression of liver fibrosis.}, }
@article {pmid40186595, year = {2025}, author = {Pérez, J and Boyero, L and Pearson, RG and Gessner, MO and Tonin, A and López-Rojo, N and Rubio-Ríos, J and Correa-Araneda, F and Alonso, A and Cornejo, A and Albariño, RJ and Anbalagan, S and Barmuta, LA and Boulton, AJ and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Carneiro, LS and Casas, JJ and Chará-Serna, AM and Chauvet, E and Colón-Gaud, C and Davis, AM and de Eyto, E and Degebrodt, M and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and García, EA and García, G and García, PE and Giller, PS and Gómez, JE and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, CM and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Wanderi, EW and Watson, A and Yule, CM}, title = {Positive Feedback on Climate Warming by Stream Microbial Decomposers Indicated by a Global Space-For-Time Substitution Study.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70171}, doi = {10.1111/gcb.70171}, pmid = {40186595}, issn = {1365-2486}, support = {UAL18-RNM-B006-B//2014-2020 Operational Programme FEDER Andalusia/ ; IT951-16//Eusko Jaurlaritza/ ; IT1471-22//Eusko Jaurlaritza/ ; UIDB/04292/2020//Funda &#xe7; &#xe3;o para a Ci &#xea;ncia e a Tecnologia, Portugal/ ; //UAL-HIPATIA/ ; }, mesh = {*Rivers/microbiology ; *Climate Change ; Temperature ; *Global Warming ; Plants/metabolism ; Carbon Cycle ; }, abstract = {Decomposition of plant litter is a key ecological process in streams, whose contribution to the global carbon cycle is large relative to their extent on Earth. We examined the mechanisms underlying the temperature sensitivity (TS) of instream decomposition and forecast effects of climate warming on this process. Comparing data from 41 globally distributed sites, we assessed the TS of microbial and total decomposition using litter of nine plant species combined in six mixtures. Microbial decomposition conformed to the metabolic theory of ecology and its TS was consistently higher than that of total decomposition, which was higher than found previously. Litter quality influenced the difference between microbial and total decomposition, with total decomposition of more recalcitrant litter being more sensitive to temperature. Our projections suggest that (i) warming will enhance the microbial contribution to decomposition, increasing CO2 outgassing and intensifying the warming trend, especially in colder regions; and (ii) riparian species composition will have a major influence on this process.}, }
@article {pmid40185870, year = {2025}, author = {Ripoll, J and Stenger, PL and Nuñez, NF and Demenois, J and Stokes, A and Gourmelon, V and Dinh, K and Robert, N and Drouin, J and Mournet, P and Léopold, A and Read, J and Gardes, M and Maggia, L and Carriconde, F}, title = {Unexpected microbial diversity in new Caledonia's ultramafic ecosystems with conservation implications in a biodiversity hotspot.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11564}, pmid = {40185870}, issn = {2045-2322}, support = {IAC-SLN Research Collaboration N&#xb0;DE2013-041//Soci&#xe9;t&#xe9; Le Nickel (SLN-Eramet Group)/ ; agreement CSF N&#xb0;1PS2013-CNRT.IAC/BIOINDIC//CNRT "Nickel &amp; son Environnement"/ ; }, mesh = {New Caledonia ; *Biodiversity ; *Soil Microbiology ; *Ecosystem ; Mycorrhizae/genetics/classification ; Conservation of Natural Resources ; Fungi/genetics/classification ; *Bacteria/genetics/classification ; }, abstract = {Soils harbour an incredible diversity of microorganisms that play crucial roles in ecosystem functioning. However, this biodiversity remains largely overlooked, with a poor understanding of how patterns form across landscapes. An eDNA metabarcoding approach was used to identify potential overarching patterns in fungal and bacterial communities from ultramafic ecosystems in New Caledonia, a renowned biodiversity hotspot. Our comprehensive analysis revealed several key findings, notably an important microbial diversity in the extreme environments of iron crust soils. Clear tendencies in phyla composition were also observed, with the fungal groups Ascomycota and Mucoromycota acting as potential indicators of land degradation (only in lateritic soils for Mucoromycota). For bacteria, Chloroflexi was characteristic of open vegetation, while Proteobacteria and Cyanobacteria were observed in higher relative abundances in the closed vegetation. The ectomycorrhizal fungal functional group was also found to be rich and unique, with a hypothetical endemism rate of 87%, and over-represented by the Cortinarius genus in rainforests and maquis (shrublands) dominated by ectomycorrhizal plants. Finally, each ultramafic Massif demonstrated a unique microbial community. Thus, our findings provide valuable insights into microbial ecology and emphasize the need for tailored conservation strategies for this biodiversity hotspot.}, }
@article {pmid40184706, year = {2025}, author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY}, title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.}, journal = {Water research}, volume = {281}, number = {}, pages = {123571}, doi = {10.1016/j.watres.2025.123571}, pmid = {40184706}, issn = {1879-2448}, mesh = {*Ammonia ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Gases ; Food Loss and Waste ; }, abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.}, }
@article {pmid40184705, year = {2025}, author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K}, title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.}, journal = {Water research}, volume = {281}, number = {}, pages = {123553}, doi = {10.1016/j.watres.2025.123553}, pmid = {40184705}, issn = {1879-2448}, mesh = {*Plasmids/genetics ; *Rivers/microbiology ; *Urbanization ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.}, }
@article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40184632}, issn = {1751-7370}, support = {17212124//Hong Kong GRF/ ; }, mesh = {*Eukaryota/classification/genetics/isolation &amp; purification ; *Sewage/microbiology/virology/parasitology ; *Wastewater/microbiology ; Hong Kong ; Metagenomics ; Animals ; Biodiversity ; Phylogeny ; }, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, }
@article {pmid40183581, year = {2025}, author = {Aminian-Dehkordi, J and Dickson, A and Valiei, A and Mofrad, MRK}, title = {MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0165224}, pmid = {40183581}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/physiology ; *Metabolic Networks and Pathways ; *Intestinal Mucosa/microbiology/metabolism ; *Metabolomics/methods ; Models, Biological ; Humans ; Computer Simulation ; }, abstract = {Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present MetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our in-silico platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in E. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.}, }
@article {pmid40179787, year = {2025}, author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M}, title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138061}, doi = {10.1016/j.jhazmat.2025.138061}, pmid = {40179787}, issn = {1873-3336}, mesh = {*Triticum/metabolism/growth &amp; development/drug effects ; *Cadmium/metabolism ; *Silicon/pharmacology/chemistry ; Rhizosphere ; *Soil Pollutants/metabolism ; Microbiota/drug effects ; Soil Microbiology ; }, abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.}, }
@article {pmid40179176, year = {2025}, author = {Lentsch, V and Woller, A and Rocker, A and Aslani, S and Moresi, C and Ruoho, N and Larsson, L and Fattinger, SA and Wenner, N and Barazzone, EC and Hardt, WD and Loverdo, C and Diard, M and Slack, E}, title = {Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {74-81}, pmid = {40179176}, issn = {1095-9203}, support = {176954/SNSF_/Swiss National Science Foundation/Switzerland ; 180953/SNSF_/Swiss National Science Foundation/Switzerland ; 865730/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; Mice ; Adaptive Immunity ; Administration, Oral ; *Antibiosis ; Antibodies, Bacterial/immunology ; *Escherichia coli/immunology/growth &amp; development/physiology ; Escherichia coli Infections/prevention &amp; control/immunology/microbiology ; Gastrointestinal Microbiome ; Immunity, Mucosal ; Mice, Inbred C57BL ; *Salmonella typhimurium/immunology/growth &amp; development/physiology ; *Salmonella Vaccines/immunology/administration &amp; dosage ; Vaccination ; }, abstract = {Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs and for rational microbiota engineering.}, }
@article {pmid40177466, year = {2025}, author = {Hwang, J and Hayward, A and Sofen, LE and Pitz, KJ and Chavez, FP and Edwards, BR}, title = {Daily microbial rhythms of the surface ocean interrupted by the new moon-a lipidomic study.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf044}, pmid = {40177466}, issn = {2730-6151}, abstract = {Lipids are essential biomolecules for cell physiology and are commonly used as biomarkers to elucidate biogeochemical processes over a large range of environments and timescales. Here, we use high-temporal-resolution lipidomic analysis to characterize the surface ocean community in the productive upwelling region overlying the Monterey Bay Canyon. We observed a strong diel signal with a drawdown of lipids at night and an increase during the day that seemed to correspond to wholesale removal of lipids from the surface ocean as opposed to internal metabolism. Individual lipid species were organized into coregulated groups that were interpreted as representing different phytoplankton guilds. Concentrations of long-chained triacylglycerols (TAGs) showed unique patterns over the course of five days. TAGs were used to estimate the amount of energy cycled through the surface ocean. These calculations revealed diurnal carbon cycling that was on scales comparable to net primary production. The diel pattern dissipated from most lipid modules on Day 3 as tidal forcing increased at our site with the advent of the new moon. Pigment analysis indicated that the community shifted from a diatom-dominated community to a more diverse assemblage, including more haptophytes, chlorophytes, and Synechococcus during the new moon. The shift in community appears to promote higher nutritional quality of biomass, with more essential fatty acids in the surface ocean during the spring tide. This analysis showcases the utility of lipidomics in characterizing community dynamics and underscores the importance of considering both diel and tidal timescales when sampling in productive coastal regions.}, }
@article {pmid40177465, year = {2025}, author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE}, title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf030}, pmid = {40177465}, issn = {2730-6151}, abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.}, }
@article {pmid40177402, year = {2025}, author = {Pellengahr, F and Corella-Puertas, E and Mattelin, V and Saadi, N and Bertella, F and Boulay, AM and van der Meer, Y}, title = {Modeling marine microplastic emissions in Life Cycle Assessment: characterization factors for biodegradable polymers and their application in a textile case study.}, journal = {Frontiers in toxicology}, volume = {7}, number = {}, pages = {1494220}, pmid = {40177402}, issn = {2673-3080}, abstract = {INTRODUCTION: With the continuous increase of plastics production, it is imperative to carefully examine their environmental profile through Life Cycle Assessment (LCA). However, current LCA modeling is not considering the potential impacts of plastic emissions on the biosphere. To integrate plastic emissions into LCA, characterization factors are needed that commonly consist of three elements: a fate factor, an exposure factor, and an effect factor. In this context, fate factors quantify the distribution and longevity of plastics in the environment. Research on these fate factors is still limited, especially for biodegradable polymers. Hence, the main objective of this research was to determine the fate factors of biodegradable polymers [poly (lactic acid), poly (butylene succinate), and poly (ε-caprolactam)] based on primary experimental data for the marine environment.<br><br>METHODS: The validity of former research is tested by comparing the degradation evolution of i. macro- and microplastic particles, ii. two different grades of the polymer, and iii. different temperature levels. The degradation data are obtained by monitoring the oxygen consumption over a period of six months in natural seawater. The determined degradation rates are combined with sedimentation, resuspension, and deep burial rates to obtain fate factors. These fate factors are used to develop polymer-specific characterization factors. The resulting characterization factors are tested in an LCA case study of a synthetic sports shirt made from biodegradable polymer fibers. It allows to assess the relative importance of microplastic impacts compared to other life cycle impacts.<br><br>RESULTS AND DISCUSSION: Comparing the resulting specific surface degradation rates indicates that microplastic degradation rates could be overestimated when using macroplastic degradation data. Pertaining to the case study, the results show that the impact on ecosystem quality by microplastic emissions could account for up to 30% of the total endpoint category. Overall, this work aims to foster interdisciplinary collaboration to leverage the accuracy of LCA studies and thus provide guidance for novel material development.}, }
@article {pmid40175811, year = {2025}, author = {Alexander, NR and Brown, RS and Duwadi, S and Womble, SG and Ludwig, DW and Moe, KC and Murdock, JN and Phillips, JL and Veach, AM and Walker, DM}, title = {Leveraging Fine-Scale Variation and Heterogeneity of the Wetland Soil Microbiome to Predict Nutrient Flux on the Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {22}, pmid = {40175811}, issn = {1432-184X}, support = {DEB 1933925//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; sub-award 220858//Natural Resource Conservation Services/ ; Molecular Biosciences Program//Middle Tennessee State University/ ; }, mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Soil/chemistry ; Nitrogen/metabolism ; *Nutrients/metabolism ; Nitrogen Cycle ; Phosphorus/metabolism ; Ecosystem ; Agriculture ; }, abstract = {Shifts in agricultural land use over the past 200 years have led to a loss of nearly 50% of existing wetlands in the USA, and agricultural activities contribute up to 65% of the nutrients that reach the Mississippi River Basin, directly contributing to biological disasters such as the hypoxic Gulf of Mexico "Dead" Zone. Federal efforts to construct and restore wetland habitats have been employed to mitigate the detrimental effects of eutrophication, with an emphasis on the restoration of ecosystem services such as nutrient cycling and retention. Soil microbial assemblages drive biogeochemical cycles and offer a unique and sensitive framework for the accurate evaluation, restoration, and management of ecosystem services. The purpose of this study was to elucidate patterns of soil bacteria within and among wetlands by developing diversity profiles from high-throughput sequencing data, link functional gene copy number of nitrogen cycling genes to measured nutrient flux rates collected from flow-through incubation cores, and predict nutrient flux using microbial assemblage composition. Soil microbial assemblages showed fine-scale turnover in soil cores collected across the topsoil horizon (0-5 cm; top vs bottom partitions) and were structured by restoration practices on the easements (tree planting, shallow water, remnant forest). Connections between soil assemblage composition, functional gene copy number, and nutrient flux rates show the potential for soil bacterial assemblages to be used as bioindicators for nutrient cycling on the landscape. In addition, the predictive accuracy of flux rates was improved when implementing deep learning models that paired connected samples across time.}, }
@article {pmid40175529, year = {2025}, author = {Pascoal, F and Branco, P and Torgo, L and Costa, R and Magalhães, C}, title = {Definition of the microbial rare biosphere through unsupervised machine learning.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {544}, pmid = {40175529}, issn = {2399-3642}, mesh = {*Unsupervised Machine Learning ; *Microbiota ; Machine Learning ; }, abstract = {The microbial rare biosphere, composed of low-abundance microorganisms in a community, lacks a standardized delineation method for its definition. Currently, most studies rely on arbitrary thresholds to define the microbial rare biosphere (e.g., 0.1% relative abundance per sample), hampering comparisons across studies. To address this challenge, we present ulrb (Unsupervised Learning based Definition of the Rare Biosphere), available as an R package. ulrb uses unsupervised machine learning to optimally classify taxa into abundance categories (e.g., rare, intermediate, or abundant) within microbial communities. We show that ulrb is more consistent than threshold-based approaches and can be applied to data derived from common microbial ecology protocols and non-microbial studies. ulrb can be used to identify different types of rarity and is statistically valid for the analysis of various dataset sizes. In conclusion, ulrb discerns rare from abundant organisms in a user-independent manner, finding applicability in selected ecological datasets.}, }
@article {pmid40174026, year = {2024}, author = {Shimano, S and Hiruta, SF and Sánchez-Chávez, DI and Pfingstl, T}, title = {Coastal mites (Oribatida, Ameronothridae) found far from the coast in moss growing on the Cathédrale Notre-Dame de Paris, France, fifty years after their first discovery in this historic site.}, journal = {Zootaxa}, volume = {5556}, number = {1}, pages = {62-71}, doi = {10.11646/zootaxa.5556.1.6}, pmid = {40174026}, issn = {1175-5334}, mesh = {Animals ; *Mites/classification/genetics/anatomy &amp; histology/growth &amp; development/ultrastructure ; Male ; Animal Distribution ; Female ; Ecosystem ; France ; Phylogeny ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; *Bryophyta/parasitology ; }, abstract = {A species of oribatid mite, Ameronothrus maculatus (Michael, 1882), was collected from moss growing on the building of the Cathédrale Notre-Dame de Paris. This species of Ameronothridae is usually found in coastal Holarctic environments. The specimens were studied by Scanning Electron Microscope and could be clearly assigned to this taxon. This population was first discovered by F. Grandjean approximately 50 years ago, and the present record demonstrates that it has persisted despite its habitat being a tourist destination visited by over 14 million people annually. The record of this species far upstream and on anthropogenic structures is rare but not out of the ordinary in Northern Europe where its distribution can reach far beyond the edges of the estuaries. For further confirmation, we obtained DNA sequences for the COI gene (1554 bp, LC848687), and they were almost identical to those of an earlier found and sequenced specimen of A. maculatus from Germany, differing by only a single base. As supplemental information on A. maculatus from Paris, the region includes whole nucleic ribosomal RNA genes (18S, 5.8S, and 28S, LC848688), partial elongation factor 1 alpha (LC848689), and the complete nucleotide sequence of mitochondrion were also determined.}, }
@article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {93}, number = {5}, pages = {e0056924}, pmid = {40172536}, issn = {1098-5522}, support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; }, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, }
@article {pmid40170918, year = {2025}, author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T}, title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549128}, pmid = {40170918}, issn = {1664-302X}, abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.}, }
@article {pmid40168336, year = {2025}, author = {Brangsch, H and Marcordes, S and Busch, A and Weber, M and Wolf, SA and Semmler, T and Höper, D and Calvelage, S and Linde, J and Barth, SA}, title = {Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320499}, pmid = {40168336}, issn = {1932-6203}, mesh = {Animals ; *Mycobacterium avium/genetics/isolation &amp; purification/classification ; *Perissodactyla/microbiology ; Polymorphism, Single Nucleotide ; *Genome, Bacterial ; *Genomics ; Phylogeny ; Multilocus Sequence Typing ; Whole Genome Sequencing ; }, abstract = {Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.}, }
@article {pmid40167801, year = {2025}, author = {Banu, S and Valero, KCW and Rivero, F}, title = {Simulated Heat Waves Affect Cell Fate and Fitness in the Social Amoeba Dictyostelium discoideum.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {21}, pmid = {40167801}, issn = {1432-184X}, support = {#101044202/ERC_/European Research Council/International ; }, mesh = {*Dictyostelium/genetics/growth &amp; development/physiology/cytology ; *Hot Temperature ; Protozoan Proteins/genetics/metabolism ; Spores, Protozoan/growth &amp; development/genetics ; }, abstract = {The effects of heatwaves at organism and population levels have been widely investigated; however, little is known about how they affect the development of cell populations and the fitness of the resulting organism. Disruptions caused by heatwaves are especially critical during early developmental stages in organisms lacking parental developmental protection or care. Here we use the social amoeba Dictyostelium discoideum, a soil microbe with a life cycle that transitions between single-cell and multicellular stages. D. discoideum thrives optimally at 22 °C and elevated temperatures impair (27 °C) or completely arrest (30 °C) growth, development, and spore yield. We established a simulated heatwave model in which vegetative cells were exposed to 27 °C for 3 days and studied the effects on the expression of early and cell type specific developmental genes using real-time quantitative PCR. A single heatwave severely impaired the expression of cyclic AMP-dependent early developmental gene markers (carA, acaA, pkaR, gtaC, tgrC1, and csaA) as well as that of prespore markers (cotB and spiA), while the expression of the prestalk marker ecmA was less affected. When mixed with heat-stressed cells, reporter cells expressing β-galactosidase grown at 22 °C preferentially occupy the spore mass of the fruiting body. Chimera assays of wild-type and reporter cells grown at optimal temperature or subjected to a heatwave confirmed a decreased fitness (contribution to chimeric fruiting bodies). We conclude that exposure of unprotected organisms at the single cell stage to a single heatwave has the potential to negatively impact their ability to cope with environmental extremes.}, }
@article {pmid40167318, year = {2025}, author = {Détain, A and Suzuki, H and Wijffels, RH and Leborgne-Castel, N and Hulatt, CJ}, title = {Snow algae exhibit diverse motile behaviors and thermal responses.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0295424}, pmid = {40167318}, issn = {2150-7511}, support = {No. 319352//Norwegian Research Council/ ; No. 349485//Norwegian Research Council/ ; }, mesh = {*Snow/microbiology ; Temperature ; Microbiota ; Eutrophication ; Phototaxis ; }, abstract = {Snow algal blooms influence snow and glacier melt dynamics, yet the mechanisms involved in community assemblage, development, and dispersal are not well understood. While microbial swimming behavior contributes significantly to the productivity and organization of aquatic and terrestrial microbiomes, the potential impact of algal cell motility in melting snow on the formation of visible, large-scale surface bloom patterns is largely unknown. Here, using video tracking and phototaxis experiments of unique isolates, we evaluated the motility of diverse snow algal taxa from green, red, and golden colored snow blooms in response to light and thermal gradients. We show that many species are efficient cryophilic microswimmers with speed thermal optima below 10°C although taxa with cryotolerant swimming traits were also identified. The significant motility of snow algae at low temperatures, a result of specialized adaptations, supports the importance of active movement in the life histories of algae inhabiting snow meltwater. However, diversity in swimming performance and behavior reveal a range of evolutionary outcomes and sensitivity of motile life stages to dynamic environments.IMPORTANCESwimming motility is a fundamental mechanism that controls the assembly, structure, and productivity of microbiomes across diverse environments and is highly sensitive to temperature. Especially, the role of cell swimming activity in algal bloom formation at the very low temperatures of snowmelt has been hypothesized, but not studied. By examining the movement patterns of snow algae and modeling the thermal response curves of swimming speed, the data reveal the key role of active cell movement that may have further important impacts on the microbial ecology and melt rates of snow and ice in polar and alpine regions.}, }
@article {pmid40162837, year = {2025}, author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ}, title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0259324}, pmid = {40162837}, issn = {1098-5336}, support = {22-08846//Dalio Foundation/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Multigene Family ; Seawater/microbiology ; Gene Transfer, Horizontal ; }, abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.}, }
@article {pmid40162703, year = {2025}, author = {Souza Beraldo, C}, title = {An interactive art activity to promote student reflection and learning about host-microbe interactions.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0006325}, pmid = {40162703}, issn = {1935-7877}, abstract = {The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects-the microbes-are invisible to human eyes. To explore how different factors shape host-microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students' conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint-representing hosts, microbes, and environmental factors, respectively-to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies' meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.}, }
@article {pmid40161817, year = {2025}, author = {Band, VI and Gribonika, I and Stacy, A and Bouladoux, N and Mistry, S and Burns, A and Perez-Chaparro, PJ and Chau, J and Enamorado, M and Nagai, M and Bhushan, V and Golec, DP and Schwartzberg, PL and Hourigan, SK and Nita-Lazar, A and Belkaid, Y}, title = {Sulfide is a keystone metabolite for gut homeostasis and immunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40161817}, issn = {2692-8205}, support = {ZIA AI001115/ImNIH/Intramural NIH HHS/United States ; ZIA AI001132/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.}, }
@article {pmid40160925, year = {2025}, author = {Amirmijani, A and Pordel, A and Dehghani, K and Pourmoghaddam, MJ and Masigol, H and Grossart, HP}, title = {Two new pestalotioid fungi from tropical fruits in Iran.}, journal = {MycoKeys}, volume = {115}, number = {}, pages = {221-240}, pmid = {40160925}, issn = {1314-4049}, abstract = {In a survey of tropical plant diseases in southern and southeastern Iran, samples of diseased Mangiferaindica and Psidiumguava leaves with necrotic symptoms were collected between 2021 and 2022. Six representative isolates of Neopestalotiopsis and Robillarda (three isolates for each) were studied using morphological characteristics as well as multi-locus phylogenetic analysis based on (i) the internal transcribed spacer (ITS) region of the nuclear rDNA, (ii) part of the translation elongation factor 1-alpha (tef1), and (iii) the β-tubulin (tub2). After morphological investigation, our phylogenetic analysis revealed that the Neopestalotiopsis and Robillarda isolates under study differed from all previously described species within these genera. Based on our polyphasic approach, two new species, including Neopestalotiopsisguava sp. nov. from necrotic Mangiferaindica and Robillardakhodaparastii sp. nov. from Psidiumguava are described and illustrated from Iran.}, }
@article {pmid40157674, year = {2025}, author = {Wu, X and Yu, D and Ma, Y and Fang, X and Sun, P}, title = {Function and therapeutic potential of Amuc_1100, an outer membrane protein of Akkermansia muciniphila: A review.}, journal = {International journal of biological macromolecules}, volume = {308}, number = {Pt 4}, pages = {142442}, doi = {10.1016/j.ijbiomac.2025.142442}, pmid = {40157674}, issn = {1879-0003}, mesh = {Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; *Bacterial Outer Membrane Proteins/pharmacology/therapeutic use/chemistry ; Akkermansia ; Probiotics/therapeutic use ; }, abstract = {The gut microbiota-derived protein Amuc_1100, a key outer membrane component of Akkermansia muciniphila, has emerged as a groundbreaking therapeutic agent with unique structural and functional properties. Amuc_1100 exerts multifaceted immune-metabolic effects through novel mechanisms, including modulation of TLR2/4 and JAK/STAT pathways. This review highlights its unique multi-component structure that enables synergistic biological activity, and its pharmacological properties, which underlies its ability to enhance intestinal barrier integrity, restore microbiota balance, and suppress systemic inflammation. Crucially, Amuc_1100 demonstrates unprecedented therapeutic versatility across both intestinal disorders (e.g., inflammatory bowel disease, antibiotic-associated diarrhea) and extraintestinal conditions-notably improving neuropsychiatric symptoms via gut-serotonin axis regulation, combating cancer through CD8+ T cell activation, and mitigating cardiotoxicity via gut-heart immune crosstalk. Emerging innovations in targeted delivery systems, including gut-retentive nano-formulations and engineered probiotic vectors, further amplify its clinical potential. We critically evaluate recent advances distinguishing Amuc_1100's mechanisms from live bacterial interventions. By synthesizing evidence from preclinical models, this work positions Amuc_1100 as a prototype for next-generation microbiome-derived therapeutics, bridging microbial ecology with precision medicine.}, }
@article {pmid40152585, year = {2025}, author = {Wang, F and Luo, J and Zhang, Z and Liu, Y and Sheng, Dh and Zhuo, L and Li, Y-z}, title = {Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0390224}, pmid = {40152585}, issn = {2150-7511}, support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 32070030//MOST | National Natural Science Foundation of China (NSFC)/ ; 32270073//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2022QC001//Natural Science Foundation of Shandong Province ()/ ; BK20230248//JST | Natural Science Foundation of Jiangsu Province(Jiangsu Natural Science Foundation)/ ; }, mesh = {*Myxococcus xanthus/genetics/physiology/immunology ; *Bacterial Toxins/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Toxin-Antitoxin Systems ; Microbial Interactions ; }, abstract = {Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.}, }
@article {pmid40151948, year = {2025}, author = {Šulčius, S and Alzbutas, G and Lukashevich, V}, title = {Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70042}, doi = {10.1111/1462-2920.70042}, pmid = {40151948}, issn = {1462-2920}, support = {S-LL-21-10//Lietuvos Mokslo Taryba/ ; }, mesh = {*Microbiota ; *Bacteriophages/physiology ; *Cyanobacteria/virology/metabolism/genetics/physiology ; *Bacteriolysis ; }, abstract = {Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.}, }
@article {pmid40149089, year = {2025}, author = {Nussbaumer-Pröll, A and Hausmann, B and Weber, M and Pjevac, P and Berry, D and Zeitlinger, M}, title = {A Pilot Study on the Impact of Cranberry and Ascorbic Acid Supplementation on the Urinary Microbiome of Healthy Women: A Randomized Controlled Trial.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149089}, issn = {2079-6382}, abstract = {Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18-40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states.}, }
@article {pmid40149015, year = {2025}, author = {Fournier, P and Pellan, L and Jaswa, A and Cambon, MC and Chataigner, A and Bonnard, O and Raynal, M and Debord, C and Poeydebat, C and Labarthe, S and Delmotte, F and This, P and Vacher, C}, title = {Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {37}, pmid = {40149015}, issn = {2524-6372}, support = {20-PCPA-0010//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.<br><br>RESULTS: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics&#xa0;of this primarily aerial disease.<br><br>CONCLUSION: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.}, }
@article {pmid40148178, year = {2025}, author = {Hodžić, A and Duscher, GG and Alić, A and Beck, R and Berry, D}, title = {Peritrophic matrix: an important determinant of vector competence in hematophagous arthropods.}, journal = {Trends in parasitology}, volume = {41}, number = {5}, pages = {374-386}, doi = {10.1016/j.pt.2025.03.005}, pmid = {40148178}, issn = {1471-5007}, mesh = {Animals ; *Arthropod Vectors/immunology/physiology ; *Arthropods/immunology/physiology/parasitology ; Immunity, Innate ; }, abstract = {The peritrophic matrix (PM) is a non-cellular, glycan-rich structure that lines the gut epithelium of most invertebrates, including arthropod vectors that transmit diseases of public health and veterinary concern. This semipermeable barrier, functionally analogous to the vertebrate mucosal layer, separates the gut lumen from epithelial cells and provides protection against invading pathogens and their toxins. Beyond its mechanical protective role in the gut, the PM plays a crucial part in arthropod innate immunity. Here, we summarize the most recent advances in understanding the molecular mechanisms of vector-pathogen interactions in blood-feeding arthropods and discuss the significance of the PM in modulating vector competence. This knowledge could contribute to the development of novel strategies to control vector-borne infections.}, }
@article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, }
@article {pmid40146382, year = {2025}, author = {Nain, D and Rana, A and Raychoudhury, R and Sen, R}, title = {Parasite-Induced Replacement of Host Microbiota: Impact of Xenos gadagkari Parasitization on the Microbiota of Polistes wattii.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {20}, pmid = {40146382}, issn = {1432-184X}, support = {DST/INSPIRE/03/2021/000175, IF200146//Department of Science and Technology, Ministry of Science and Technology, India/ ; 1061830779//Council of Scientific and Industrial Research, India/ ; CRG-2021/007010//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Wasps/microbiology/physiology/parasitology ; *Microbiota ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Seasons ; *Host-Parasite Interactions ; }, abstract = {The study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behavior. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet a comprehensive study on the microbiota of any species of Polistes or any primitively eusocial wasp is missing. Polistes wattii is an Asian wasp, which hibernates in winter and exhibits a biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite/parasitoid Xenos gadagkari, which changes the morpho-physiology and behavior of their hosts. In this study, we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community of P. wattii and investigate the effects of seasonality, sex, and Xenos parasitism. We show that the microbiota differs in females from solitary foundress spring nests and multiple foundress summer nests. The microbiota also differs in males and females. Finally, we show that X. gadagkari parasitism replaces and homogenizes the microbiota of P. wattii. Unlike the unparasitized wasps, the microbiota of X. gadagkari parasitoids and parasitized wasps are dominated by Wolbachia and Providencia. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show that the microbiota of parasitized P. wattii becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts than previously thought.}, }
@article {pmid40146077, year = {2025}, author = {Savchenko, V and Yu, XA and Polz, MF and Böttcher, T}, title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1H)-quinolone Producers.}, journal = {ACS chemical biology}, volume = {20}, number = {4}, pages = {960-966}, pmid = {40146077}, issn = {1554-8937}, mesh = {*Quinolones/metabolism/chemistry ; Multigene Family ; Phylogeny ; *Comamonadaceae/metabolism/genetics ; }, abstract = {2-Alkyl-4(1H)-quinolones play a key role in bacterial communication, regulating biofilm formation, and virulence. Their antimicrobial properties also support bacterial survival and interspecies competition in microbial communities. In addition to the human pathogen Pseudomonas aeruginosa various species of Burkholderia and Pseudoalteromonas are known to produce 2-alkyl-4(1H)-quinolones. However, the evolutionary relationships of their biosynthetic gene clusters remain largely unexplored. To address this, we investigated the phylogeny of 2-alkyl-4(1H)-quinolone biosynthetic gene clusters, leading to the discovery of Chitinivorax as a fourth genus capable of producing 2-alkyl-4(1H)-quinolones, expanding our knowledge of the diversity of bacteria involved in quinolone-biosynthesis.}, }
@article {pmid40143451, year = {2025}, author = {Jenkins, G and Boyd, ES and Danchin, A and Hervé, V}, title = {Microbiome Notes-Building a Library of Descriptive Microbial Ecology.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70085}, pmid = {40143451}, issn = {1758-2229}, }
@article {pmid40142506, year = {2025}, author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M}, title = {Effects of NatureKnit™, a Blend of Fruit and Vegetable Fibers Rich in Naturally Occurring Bound Polyphenols, on the Metabolic Activity and Community Composition of the Human Gut Microbiome Using the M-SHIME[®] Gastrointestinal Model.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142506}, issn = {2076-2607}, support = {Not applicable//VDF FutureCeuticals, Inc./ ; }, abstract = {This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit[TM]), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME[®] gastrointestinal model. A short-term single-stage colonic M-SHIME[®] experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers.}, }
@article {pmid40142410, year = {2025}, author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL}, title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142410}, issn = {2076-2607}, support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; }, abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).}, }
@article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, }
@article {pmid40138093, year = {2025}, author = {Demeulenaere, &#xc9;}, title = {In search of the microbial path to Terroir: a place-based history of the ecologization of French cheese microbiology, 1990-2000s.}, journal = {History and philosophy of the life sciences}, volume = {47}, number = {2}, pages = {22}, pmid = {40138093}, issn = {1742-6316}, support = {EXORIGINS//Emergence(s) Ville de Paris/ ; }, mesh = {*Cheese/microbiology/history ; France ; History, 20th Century ; *Food Microbiology/history ; Animals ; Milk/microbiology ; Laboratories/history ; }, abstract = {At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get "cleaner" milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor "natural seeding" and enrich milk native microflora. A new approach emerged, namely "practice-driven microbial ecology" (écologie microbienne dirigée), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the "microbial (ecology) turn" described by other authors, highlighting the ecological approach developed in the 1990s-2000s by French microbiologists in search of "the microbial path to terroir".}, }
@article {pmid40137691, year = {2025}, author = {Maitre, A and Mateos-Hernandez, L and Kratou, M and Egri, N and Maye, J and Juan, M and Hodžić, A and Obregón, D and Abuin-Denis, L and Piloto-Sardinas, E and Fogaça, AC and Cabezas-Cruz, A}, title = {Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40137691}, issn = {2076-0817}, mesh = {Animals ; *Ixodes/microbiology/immunology ; *Microbiota/immunology ; Mice ; *Bacterial Vaccines/immunology/administration &amp; dosage ; Vaccines, Subunit/immunology/administration &amp; dosage ; Staphylococcus epidermidis/immunology ; *Lyme Disease/prevention &amp; control/immunology/microbiology ; Borrelia burgdorferi Group/immunology ; Vaccines, Attenuated/immunology/administration &amp; dosage ; Female ; *Tick-Borne Diseases/prevention &amp; control/microbiology/immunology ; }, abstract = {This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.}, }
@article {pmid40134242, year = {2025}, author = {Trombley, J and Celenza, JL and Frey, SD and Anthony, MA}, title = {Arbuscular Mycorrhizal Fungi Boost Development of an Invasive Brassicaceae.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {7}, pages = {4928-4937}, pmid = {40134242}, issn = {1365-3040}, support = {//This study was supported by the Dick George Invasives Fund awarded to S.D.F. and M.A.A. M.A.A. was supported by a Vienna Science and Technology Fund (WWTF) Vienna Research Groups for Young Investigators grant awarded to MAA (VRG22-007)./ ; }, mesh = {*Mycorrhizae/physiology ; *Introduced Species ; *Brassicaceae/growth &amp; development/microbiology ; Symbiosis ; Plant Roots/microbiology/growth &amp; development ; Glucosinolates/metabolism ; Nitrogen/metabolism ; }, abstract = {Invasive plant growth is affected by interactions with arbuscular mycorrhizal fungi (AMF). AMF are mutualists of most land plants but suppress the growth of many plants within the Brassicaceae, a large plant family including many invasive species. Alliaria petiolata (garlic mustard) is a nonnative, nonmycorrhizal Brassicaceae distributed throughout North America in forest understories where native species rely on AMF. If AMF suppress growth of garlic mustard, it may be possible to inoculate AMF to manage invasions. Here, we show that in contrast to expectation, garlic mustard growth nearly doubled in response to AMF inoculation under both laboratory and field conditions. This effect was negatively linked to investments in glucosinolates, a class of defensive compounds. In contrast to typical symbiosis, AMF did not produce arbuscules where nutrient exchange occurs in roots, but AMF inoculation increased plant and soil nitrogen availability. Our findings reveal an adjacent pathway by which AMF promote invasive plant growth without classic symbiotic exchanges. Prior assumptions that garlic mustard suppresses AMF are inadequate to explain invasion success since it benefits from interactions with AMF. This study is the first to demonstrate extensive growth promotion following AMF inoculation in mustard plants, with important implications for invasion biology and agriculture.}, }
@article {pmid40131450, year = {2025}, author = {Sun, L and Guan, W and Tai, X and Qi, W and Zhang, Y and Ma, Y and Sun, X and Lu, Y and Lin, D}, title = {Research Progress on Microbial Nitrogen Conservation Technology and Mechanism of Microorganisms in Aerobic Composting.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {19}, pmid = {40131450}, issn = {1432-184X}, support = {32160756//National Natural Science Foundation of China/ ; GAUfx-04J03//Fuxi Foundation of Gansu Agricultural University/ ; 23CXNN0007//Gansu Province Science and Technology Plan Project Technology Innovation Guidance Program - LuGan Science and Technology Collaboration topic/ ; 2023-3-66//Science and Technology Plan Project of Lanzhou city/ ; GNKJ-2024-46//Research and Application of Supporting Technologies for Gansu Pig Industry/ ; GAU-XKTD-2022-24//The Discipline Team Project of Gansu Agricultural University/ ; }, mesh = {*Composting/methods ; *Nitrogen/metabolism ; *Soil Microbiology ; Aerobiosis ; *Bacteria/metabolism/genetics ; Manure/microbiology ; Soil/chemistry ; Animals ; }, abstract = {With economic development and improvements in living standards, the demand for livestock products has steadily increased, resulting in the generation of large amounts of livestock manure, which seriously pollutes the ecological environment and poses a threat to human health. High-temperature aerobic composting is an effective method for treating livestock manure; however, traditional composting processes often lead to considerable nitrogen loss, reduced efficiency of soil conditioners, and increased emissions of harmful gases. The incorporation of physical, chemical, and biological additives can effectively retain nitrogen within the compost. Among these, microbial agents are particularly noteworthy as they precisely regulate the microbial community structure associated with nitrogen transformation during aerobic composting, altering the abundance of functional genes and enzyme activities involved in nitrogen transformation. This approach significantly reduces nitrogen loss and harmful gas emissions. This paper reviews the application effects of microbial agents on nitrogen retention during aerobic composting and explores the underlying regulatory mechanisms, aiming to provide theoretical guidance and new research directions for the application of microbial agents in enhancing nitrogen retention during aerobic composting.}, }
@article {pmid40129674, year = {2025}, author = {Hussain, N and Ibrahim Al Haddad, AH and Abbass, S and Alfahl, Z}, title = {The potential impact of habitual sleep quality on glycaemic control and inflammation: A study on geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM).}, journal = {Sleep medicine: X}, volume = {9}, number = {}, pages = {100139}, pmid = {40129674}, issn = {2590-1427}, abstract = {Sleep quality and its relationship with glycaemic control is of particular interest in the context of geriatric diabetes. We aimed to investigate the potential impact of habitual sleep quality on glycaemic control status among geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM). A total of 193 geriatric patients recently diagnosed with T2DM in a tertiary-care hospital were selected. A developed questionnaire was used to assess various aspects of sleep quality. Glycaemic control was evaluated through fasting blood glucose levels, HbA1c measurements and number of admissions to the hospital for hypoglycaemic or hyperglycaemic episodes. Patients were divided into Poor Sleep Quality (PSQ, n = 132) and Adequate Sleep Quality (ASQ, n = 61) groups. The PSQ group exhibited significantly worse sleep outcomes, including longer sleep latency (35 ± 9.2 min vs. 15 ± 6.4 min), shorter sleep duration (5 h 42 min vs. 7 h 18 min) and greater use of sleep medications (72 % vs. 22 %). Glycaemic control, measured by HbA1c, was worse in the PSQ group (8.7 ± 1.9 vs. 7.2 ± 1.2; p < 0.01), which also had more frequent severe hypoglycaemic (35 ± 1.4 vs. 8 ± 2.1; p = 0.02) and ketoacidotic episodes (72 ± 1.0 vs. 5 ± 1.1; p = 0.01). These findings suggest an association between poor sleep quality and poorer glycaemic control, with more frequent diabetes-related complications, highlighting the need for further research to explore potential causal relationships and targeted interventions in this population.}, }
@article {pmid40127879, year = {2025}, author = {Mirsalami, SM and Mirsalami, M}, title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {130}, number = {}, pages = {105738}, doi = {10.1016/j.meegid.2025.105738}, pmid = {40127879}, issn = {1567-7257}, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; Phylogeny ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.}, }
@article {pmid40121181, year = {2025}, author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P}, title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf075}, pmid = {40121181}, issn = {1365-2672}, support = {//Pace University Dyson College Office of the Dean/ ; }, mesh = {*Soil Microbiology ; Costa Rica ; *Forests ; Biomass ; *Carbon/metabolism/analysis ; *Fungi/metabolism/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Actinobacteria/metabolism/genetics/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Acidobacteria/metabolism/genetics/isolation &amp; purification ; *Forestry ; Trees ; }, abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the three decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the WRT/LD community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between logging road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.}, }
@article {pmid40120670, year = {2025}, author = {San-Blas, E and Cornejo, MJ and Guerra, M and Olivares, M and Faundez, S and Bastidas, B and Morales-Montero, P and Pizarro, L and Aponte, H and Castaneda-Alvarez, C and Lankin, G}, title = {Where are my nematodes? labelling and visualising entomopathogenic nematodes in vivo using carbon quantum dots.}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108317}, doi = {10.1016/j.jip.2025.108317}, pmid = {40120670}, issn = {1096-0805}, mesh = {Animals ; *Quantum Dots ; *Nematoda ; Carbon ; *Staining and Labeling/methods ; }, abstract = {Identifying single or groups of animals has significantly advanced our understanding of animal biology and ecology. However, labelling is extremely difficult in small animals, like soil invertebrates. Due to the complexity of current methods, the dynamics and interactions of these populations are often studied indirectly. Labelling nematodes or microarthropods such as collembolans or soil acari has been challenging due to the high cost, potential toxicity, genetic modification requirements, cellular processes interference, and photobleaching. In this scenario, no methods can be applied to large numbers of microorganisms at once due to their mentioned practical and biological limitations and cost. In this work we show that quantum carbon dots (Cdots) are effective for labelling infective juveniles (IJs) of entomopathogenic nematodes (EPNs). In in vitro assays the IJs gradually acquired fluorescence, as Cdots accumulated in the lysosome-related organelles from their intestine cells, peaking at day 14, and with no lethal or sub-lethal effects on IJs. Fluorescence was clearly distinguishable from the natural auto-fluorescence of non-labelled IJs and persisted for months in IJs transferred to water. We and non-experts easily differentiated between similar species of EPNs and between two strains of S. feltiae placed in the same matrix (soil or water). We demonstrated for the first time the feasibility of labelling large numbers of IJs (hundreds of thousands/millions) with Cdots at minimal cost without any adverse effects for over a year. Our findings could be the starting point for detailed and large-scale field investigations on nematodes and other small organisms, allowing deeper understanding of their roles in soil ecosystems. This method provides a cost-effective and reliable tool for advancing research in the ecology of soil invertebrates, such as the interactions occurring in communities or between specific organisms, movement and dispersal, population dynamics or ecosystem services in a cryptic environment difficult to study.}, }
@article {pmid40119062, year = {2025}, author = {Acharya, P and Yegon, MJ and Haferkemper, L and Misteli, B and Griebler, C and Vitecek, S and Attermeyer, K}, title = {Leaf Conditioning and Shredder Activity Shape Microbial Dynamics on Fine Particulate Organic Matter Produced During Decomposition of Different Leaf Litter in Streams.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {18}, pmid = {40119062}, issn = {1432-184X}, mesh = {*Plant Leaves/metabolism/chemistry/microbiology ; Acer/metabolism/chemistry ; Animals ; *Rivers/microbiology/chemistry ; Fatty Acids/analysis ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fagus/metabolism ; *Microbiota ; *Particulate Matter/metabolism ; Larva/microbiology ; Alnus/metabolism ; Feces/microbiology/chemistry ; Ecosystem ; Carbon/analysis ; }, abstract = {Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.}, }
@article {pmid40118512, year = {2025}, author = {Gomes, IB}, title = {The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf064}, pmid = {40118512}, issn = {1365-2672}, support = {//FCT/ ; UIDB/00511/2020//MCTES/ ; }, mesh = {*Public Health ; Humans ; *Ecosystem ; *Microbiota ; Animals ; *Microbial Interactions ; One Health ; *Environmental Pollutants ; Bacteria ; Biodegradation, Environmental ; }, abstract = {CONTEXT AND AIMS: Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment.The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of 'One Health.'<br><br>RESULTS: The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance.<br><br>CONCLUSIONS: So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.}, }
@article {pmid40118002, year = {2025}, author = {Wan, W and Grossart, HP and Wu, QL and Xiong, X and Yuan, W and Zhang, W and Zhang, Q and Liu, W and Yang, Y}, title = {Global meta-analysis deciphering ecological restoration performance of dredging: Divergent variabilities of pollutants and hydrobiontes.}, journal = {Water research}, volume = {280}, number = {}, pages = {123506}, doi = {10.1016/j.watres.2025.123506}, pmid = {40118002}, issn = {1879-2448}, mesh = {Ecosystem ; *Environmental Restoration and Remediation ; Water Pollutants, Chemical ; Geologic Sediments ; }, abstract = {Global "Sustainable Development Goals" propose ambitious targets to protect water resource and provide clean water, whereas comprehensive understanding of restoration performance and ecological mechanisms are lacking for dredging adopted for purifying polluted waterbodies and maintaining navigation channels. Here, we conducted a global meta-analysis to estimate ecological restoration consequence of dredging as pollution mitigation and navigation channel maintenance measures using a dataset compiled from 191 articles covering 696 studies and 84 environmental and ecological parameters (e.g., pollutants and hydrobiontes). We confirm that dredging shows negative influences on 77.50% pollutants in the BA model (before dredging vs. after dredging) and 84.21% pollutants in the CI model (control vs. impact) as well as on sediment nutrient fluxes. Additionally, 57.14% attributes (i.e., richness, diversity, biomass, and density) of hydrobiontes in the BA model and 89.47% attributes of hydrobiontes in the CI model responded negatively to dredging. As a result, 76.32% of the pollutants and 61.11% of the hydrobiont attributes responded uniformly to dredging in the BA and CI models. Our findings emphasize that dredging generally decreases pollutants and mitigates algal blooms, controlling phosphorus is easier than controlling nitrogen by dredging, and attributes (i.e., richness, diversity, and biomass) of hydrobiontes (i.e., zooplankton, phytoplankton, and zoobenthos) are density-dependent in dredging-disturbed environments. Our findings broaden our knowledge on ecological restoration performance of dredging as a mitigation measure in global aquatic ecosystems, and these findings might be helpful to use and optimize dredging to efficiently and sustainably purify polluted aquatic ecosystems.}, }
@article {pmid40116066, year = {2025}, author = {Cusenza, BS and Scelfo, G and Licata, G and Capri, FC and Vicari, F and Alduina, R and Villanova, V}, title = {First Insights Into the Biological and Physical-Chemical Diversity of Various Salt Ponds of Trapani, Sicily.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70075}, pmid = {40116066}, issn = {1758-2229}, support = {MSCA_0000011//Next Generation EU/ ; }, mesh = {*Ponds/microbiology/chemistry ; Sicily ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salinity ; Biodiversity ; *Microbiota ; Phylogeny ; DNA, Archaeal/genetics ; Sodium Chloride/analysis ; DNA, Bacterial/genetics ; Ecosystem ; }, abstract = {The salt ponds of Trapani, Sicily, represent an extreme and under-explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical-chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical-chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High-throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter. Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.}, }
@article {pmid40113629, year = {2025}, author = {Moldovan, OT and Levei, E and Ferreira, RL and Silva, MS and Mirea, IC}, title = {Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {17}, pmid = {40113629}, issn = {1432-184X}, support = {PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; GA N&#xb0;101052342//Biodiversa+, the European Biodiversity Partnership/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Groundwater/microbiology ; *Climate Change ; *Bacteria/classification/genetics/isolation &amp; purification ; Brazil ; *Caves/microbiology ; Romania ; Humans ; Tropical Climate ; Biodiversity ; Seasons ; *Microbiota ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; }, abstract = {This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.}, }
@article {pmid40112476, year = {2025}, author = {Xu, RZ and Cao, JS and Cheng, S and Luo, JY and Ni, BJ and Fang, F and Liu, W and Wang, P}, title = {Heterotrophic nitrification-aerobic denitrification strains: An overlooked microbial interaction nexus in the anaerobic-swing-anoxic-oxic (ASAO) plug-flow system.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {125030}, doi = {10.1016/j.jenvman.2025.125030}, pmid = {40112476}, issn = {1095-8630}, mesh = {*Denitrification ; *Nitrification ; Nitrogen/metabolism ; Anaerobiosis ; Aerobiosis ; Heterotrophic Processes ; Bioreactors/microbiology ; Bacteria/metabolism ; Oxygen ; Phosphorus/metabolism ; }, abstract = {This study aims to clarify the overlooked functions of heterotrophic nitrification-aerobic denitrification (HNAD) bacteria in a novel anaerobic-swing-anoxic-oxic (ASAO) continuous plug-flow system. The dissolved oxygen (DO) levels and aerated hydraulic retention time (HRT) varied in the swing zones, providing a more diverse redox environment. High nitrogen (85.0 %) and phosphorus (80.0 %) removal were achieved by enriched HNAD bacteria (e.g., Thauera and Malikia) and phosphate accumulating organisms (PAO, e.g., Rhodocyclus and Azonexus) under middle DO level (1.0-2.0 mg/L) and longer aerated HRT (5.0 h). More importantly, microbial network revealed that HNAD bacteria became a connection point for other functional microorganisms associated with pollutant metabolism, and promoted the cooperation and functional evolution of microbial communities. The microbial ecology analysis captured the high importance of homogeneous selection, diffusion restriction, and drift for microbial community assembly in the ASAO system. Among them, HNAD bacteria contributed to both deterministic and stochastic processes, whereas the community assembly of PAO was mainly affected by the deterministic processes. The upregulation of denitrification genes (i.e., napA, napB, nirS, norB and norC) further confirmed the nitrogen removal contribution of aerobic denitrification by HNAD bacteria. Through this study, a comprehensive analysis of microbial interactions in the ASAO system was achieved, providing valuable insights into the targeted regulation of functional microorganisms in wastewater biological treatment processes.}, }
@article {pmid40112457, year = {2025}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether.}, journal = {Water research}, volume = {280}, number = {}, pages = {123417}, doi = {10.1016/j.watres.2025.123417}, pmid = {40112457}, issn = {1879-2448}, mesh = {*Geologic Sediments/microbiology ; *Microplastics ; *Microbiota/drug effects ; *Halogenated Diphenyl Ethers ; Water Pollutants, Chemical ; }, abstract = {Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.}, }
@article {pmid40109964, year = {2025}, author = {Figueiredo, JEF and Diniz, GFD and Marins, MS and Silva, FC and Ribeiro, VP and Lanza, FE and de Oliveira-Paiva, CA and Cruz-Magalhães, V}, title = {Bacillus velezensis CNPMS-22 as biocontrol agent of pathogenic fungi and plant growth promoter.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522136}, pmid = {40109964}, issn = {1664-302X}, abstract = {INTRODUCTION: Bacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.<br><br>METHODS: This research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.<br><br>RESULTS: CNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.<br><br>CONCLUSION: Our findings highlight the CNPMS-22's potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.}, }
@article {pmid40109356, year = {2025}, author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL}, title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.}, journal = {ACS ES&amp;T engineering}, volume = {5}, number = {3}, pages = {772-781}, pmid = {40109356}, issn = {2690-0645}, abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.}, }
@article {pmid40107140, year = {2025}, author = {Quattrocelli, P and Piccirillo, C and Kuramae, EE and Pullar, RC and Ercoli, L and Pellegrino, E}, title = {Synergistic interaction of phosphate nanoparticles from fish by-products and phosphate-solubilizing bacterial consortium on maize growth and phosphorus cycling.}, journal = {The Science of the total environment}, volume = {973}, number = {}, pages = {179082}, doi = {10.1016/j.scitotenv.2025.179082}, pmid = {40107140}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development ; *Phosphorus/metabolism ; *Phosphates/metabolism ; *Nanoparticles/chemistry ; *Fish Products ; Bacteria/metabolism ; Microbial Consortia ; Animals ; }, abstract = {Phosphate nanomaterials, such as hydroxyapatite/β-tricalcium nanoparticles (nHAs) derived from food industry by-products, offer a sustainable alternative to enhance P-use efficiency in agriculture. However, their limited solubility remains a challenge. This study first investigated the mechanisms of P solubilization of salmon and tuna bones (SnHAs and TnHAs) in fifteen strains of phosphate-solubilizing bacteria (PSB) by an in vitro system. Then, best-performing strains were assembled in a consortium and tested in vivo on maize. We hypothesized that combining nHAs and the PSB consortium inoculated as seed coating (SC) outperforms single treatments alone in promoting plant growth and P cycling, and ensures the establishment in plant-soil system without a bacterial reinforcement (BR) by an additional inoculum suspension. The synergistic effect of nHAs and PSB was proved, improving maize root (+22 %) and total plant biomass (+29 %), as well as P (+32 %) and K (66 %) uptake compared to single treatments. With nHAs and SC, P-use efficiency and recovery increased by 25 % and three-fold, respectively, compared to nHAs alone or with bacterial reinforcement. Consistently, root and substrate bacterial biomass were associated with nHAs plus SC, while nHAs alone or with PSB upregulated PHT1;1 and PHT1;2 transporter genes in maize. Finally, linking the in vitro and in vivo system, we demonstrated that propionic acid production and P-solubilization efficiency of PSB co-applied with nHAs are key drivers of maize growth and P uptake. Our findings indicated that co-applying nHAs and PSB through SC offers a sustainable strategy to improve maize P-use efficiency.}, }
@article {pmid40106821, year = {2025}, author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N}, title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15317}, pmid = {40106821}, issn = {1601-0825}, support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; }, abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.<br><br>METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.<br><br>RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.<br><br>CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.}, }
@article {pmid40106330, year = {2025}, author = {Maguire, M and DeLappe, N and Clarke, C and Touhy, A and Carlino-MacDonald, U and Hutson, A and Cormican, M and Brennan, W and Devane, G and Morris, D and Coughlan, SC and Miliotis, G and Russo, TA and Burke, LP}, title = {Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001373}, pmid = {40106330}, issn = {2057-5858}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/classification/isolation &amp; purification/drug effects ; Animals ; *Klebsiella Infections/microbiology/epidemiology ; Humans ; Virulence/genetics ; Ireland/epidemiology ; Mice ; *Phylogeny ; beta-Lactamases/genetics ; Retrospective Studies ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; Female ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Genomics ; Male ; Genotype ; Aged ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.}, }
@article {pmid40100630, year = {2025}, author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X}, title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {12}, pages = {e2424463122}, pmid = {40100630}, issn = {1091-6490}, mesh = {Phylogeny ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism ; *Adaptation, Physiological ; *Microbiota/genetics ; *Biological Evolution ; Genome, Bacterial ; Energy Metabolism ; Evolution, Molecular ; }, abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.}, }
@article {pmid40099901, year = {2025}, author = {Lysenko, V and Machushynets, NV and van Dam, JL and Sterk, FAC and Speer, A and Ram, AFJ and Slingerland, CJ and Van Wezel, GP and Martin, NI}, title = {Total Synthesis, Structure Elucidation, and Bioactivity Evaluation of the Cyclic Lipopeptide Natural Product Paenilipoheptin A.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2826-2831}, pmid = {40099901}, issn = {1523-7052}, mesh = {*Lipopeptides/chemistry/pharmacology/chemical synthesis ; Molecular Structure ; *Biological Products/chemistry/pharmacology/chemical synthesis ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology/chemistry/chemical synthesis ; Peptides, Cyclic/chemistry/chemical synthesis/pharmacology ; Antifungal Agents/pharmacology/chemistry/chemical synthesis ; Gram-Positive Bacteria/drug effects ; Stereoisomerism ; }, abstract = {In this study, we further investigated the structure of the recently reported cyclic lipopeptide natural product paenilipoheptin A. Here, we disclose the first total synthesis of the compound, allowing for its complete structural assignment. The route developed employs automated SPPS, providing access to the compound in quantities suitable for antibacterial and antifungal testing. These studies unequivocally establish the stereochemical framework of paenilipoheptin A and further reveal that the compound possesses moderate activity against Gram-positive bacteria.}, }
@article {pmid40099871, year = {2025}, author = {Bittleston, L and Gilbert, J and Klassen, J and Mackelprang, R and Mandel, MJ and Newton, RJ and Paudel, A and Rodriguez-Verdugo, A and Shade, A and Wilhelm, RC and Zhang, Y}, title = {Embracing the systems complexity of microbial ecology and evolution: call for papers.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0009125}, doi = {10.1128/msystems.00091-25}, pmid = {40099871}, issn = {2379-5077}, }
@article {pmid40099188, year = {2025}, author = {Silverio, MP and Schultz, J and Parise, MTD and Parise, D and Viana, MVC and Nogueira, W and Ramos, RTJ and Góes-Neto, A and Azevedo, VAC and Brenig, B and Bonelli, RR and Rosado, AS}, title = {Genomic and phenotypic insight into antimicrobial resistance of Pseudomonas fluorescens from King George Island, Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1535420}, pmid = {40099188}, issn = {1664-302X}, abstract = {The genus Pseudomonas includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, Pseudomonas spp. might act as a reservoir of antimicrobial resistance genes, which have been detected even in isolated environments. The aim of this study was to report the antimicrobial susceptibility profile of 25 Pseudomonas fluorescens isolates from soil samples collected on King George Island (Antarctic Peninsula), and to select non-clonal isolates with unusual phenotypes for whole genome sequencing (WGS). Six classes of antimicrobials were assessed with disk diffusion and colistin with minimum inhibitory concentration (MIC) by broth microdilution. In order to confirm the discrepant phenotypes, MIC by agar dilution was performed for the beta-lactams aztreonam, ceftazidime, cefepime and the aminoglycoside neomycin. The genus Pseudomonas was confirmed by matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF) and the clonal relationships were examined using repetitive extragenic palindromic polymerase chain reaction (BOX-PCR), from which 14 strains were selected for WGS. Antimicrobial susceptibility testing revealed that all strains were susceptible to neomycin and exhibited varying degrees of intermediate or full resistance to aztreonam and colistin. Additionally, 11 strains demonstrated intermediate resistance to ceftazidime, and six were resistant to cefepime. The genomic analysis identified various efflux pumps, predominantly from the ABC transporter and resistance-nodulation-division families. Resistance genes were detected against eight classes of antimicrobials, listed by prevalence: beta-lactams, tetracyclines, polymyxins, aminoglycosides, fosmidomycin, fosfomycin, quinolones, and chloramphenicol. Genes associated with heavy-metal resistance, prophages, and adaptations to extreme environments were also investigated. One notable isolate exhibited not only the highest number of pathogenicity and resistance islands, but also presented a carbapenemase-encoding gene (bla PFM-2) in its genome. Overall, one plasmid was identified in a distinct isolate, which did not exhibit antimicrobial resistance determinants. The genotypic and phenotypic findings are consistent, suggesting that efflux pumps play a critical role in antimicrobial extrusion. This study offers valuable insight into the evolution of antimicrobial resistance in P. fluorescens, particularly in extreme environments, such as Antarctica. By exploring the antimicrobial resistance mechanisms in P. fluorescens, the study sheds light on how isolated ecosystems drive the natural evolution of resistance genes.}, }
@article {pmid40098226, year = {2025}, author = {Frühe, L and Klein, SG and Angulo-Preckler, C and Martynova, A and Alamoudi, T and García, JVA and Arossa, S and Breavington, J and Frappi, S and Laiolo, E and Lim, KK and Parry, AJ and Re, E and Rosas, DER and Rodrigue, M and Steckbauer, A and Pieribone, VA and Qurban, MA and Duarte, CM}, title = {Particle-Associated Bacterioplankton Communities Across the Red Sea.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70075}, pmid = {40098226}, issn = {1462-2920}, support = {//National Center of Wildlife/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {Indian Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Plankton/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Saudi Arabia ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.}, }
@article {pmid40097839, year = {2025}, author = {Blanco, S and Viso, R and Borrego-Ramos, M and López-Flores, R and Mota-Echeandía, D and Tierra, M and Herrero, J and C Castañeda, }, title = {The Ecology of Benthic Diatom Assemblages in Saline Wetlands of the Ebro Basin, NE Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {16}, pmid = {40097839}, issn = {1432-184X}, support = {TED2021-130303B-I00//MCIN/AEI/ ; }, mesh = {*Diatoms/classification/physiology ; *Wetlands ; Spain ; Biodiversity ; Ecosystem ; Salinity ; Electric Conductivity ; }, abstract = {Benthic diatoms play a crucial role in aquatic ecosystems as indicators of environmental conditions and contributors to primary productivity. This study explores the ecology of benthic diatom assemblages in saline wetlands in NE Spain, focusing on the relationships between community parameters, species distributions, and environmental factors, particularly conductivity. Samples were collected from several wetlands representing a range of conductivity and trophic state. A total of 25 diatom taxa were identified, with assemblages dominated by halophilous species. Non-metric multidimensional scaling analysis revealed electrical conductivity (EC) as a primary factor shaping diatom communities, with nutrient levels as a secondary influence. Species exhibited varying responses to the EC gradient, with some showing overlapping niches and others clearly separated. The study found strong correlations between species abundance, occupancy, and their contribution to dissimilarity between sampling sites. More abundant and widespread species were key drivers of community structure and differentiation. Additionally, a significant relationship was observed between taxa occurrence and niche breadth, measured as EC tolerance. Species with broader tolerances tended to have higher occupancy rates, supporting ecological theories about generalist strategies in variable environments. Contrary to some previous research, rare taxa (3-5% in relative abundance) had a negligible effect on assemblage segregation among habitats. The findings suggest that both environmental filtering based on EC tolerance and species' inherent characteristics play important roles in shaping diatom community composition across these saline wetlands. This study contributes to our understanding of diatom ecology in saline habitats and highlights the importance of considering both local abundance and environmental tolerance in ecological studies of these communities. The insights gained can inform more accurate ecological models and improve our understanding of species distribution and community dynamics in saline aquatic ecosystems.}, }
@article {pmid40097820, year = {2025}, author = {Blanchette, RA and Rajtar, NN and Lochridge, AG and Held, BW}, title = {Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9142}, pmid = {40097820}, issn = {2045-2322}, support = {no number//Minnesota Invasive Terrestrial Plants and Pests Center, University of Minnesota/ ; }, mesh = {*Wood/microbiology ; *Fungi/isolation &amp; purification/genetics/classification ; Plant Diseases/microbiology ; United States ; Introduced Species ; }, abstract = {The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.}, }
@article {pmid40097298, year = {2025}, author = {Morin, C and Alfahl, Z}, title = {A systematic review on the utility of wastewater surveillance for monitoring yellow fever virus and other arboviruses.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf066}, pmid = {40097298}, issn = {1365-2672}, support = {02-303952//Applied Microbiology International Summer Studentship/ ; }, mesh = {*Wastewater/virology ; *Yellow fever virus/isolation &amp; purification/genetics ; *Arboviruses/isolation &amp; purification/genetics ; Humans ; *Environmental Monitoring/methods ; Yellow Fever/virology ; }, abstract = {AIMS: This review aims to examine wastewater surveillance for the detection of yellow fever virus (YFV) and related arboviruses, focusing on concentration and extraction methodology, viral decay kinetics, and quantification techniques.<br><br>METHODS: A literature search was conducted across 5 databases: PubMed, Science Direct, Web of Science, Embase, and Google Scholar following the PRISMA guidelines. Studies included were original scientific articles published between April 2014 and April 2024. Human research studies investigating wastewater surveillance and YFV or other arboviruses/flaviviruses were assessed.<br><br>RESULTS: A total of 17 studies were included in this review. YFV was not detected in population-based wastewater samples; however, successful detection of similar viruses suggests potential for YFV monitoring with wastewater surveillance. YFV-spiked wastewater studies reveal similar concentration efficiency and decay rates between arboviruses. Effective concentration methods for YFV likely include centrifugation ultrafiltration and solid pellet extraction. YFV and arboviruses decay faster at higher temperatures, though YFV remains detectable for several days at these temperatures.<br><br>CONCLUSIONS: Wastewater surveillance presents a promising approach for monitoring YFV and other arboviruses. However, further research is needed to overcome existing limitations and enhance its effectiveness.}, }
@article {pmid40092580, year = {2025}, author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ}, title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf015}, pmid = {40092580}, issn = {2730-6151}, abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.}, }
@article {pmid40090302, year = {2025}, author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM}, title = {An efficient strategy for BDD electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137915}, doi = {10.1016/j.jhazmat.2025.137915}, pmid = {40090302}, issn = {1873-3336}, mesh = {Electrodes ; *Anti-Bacterial Agents/chemistry ; Electron Transport ; *Water Pollutants, Chemical/chemistry ; Genes, Bacterial ; Electrochemical Techniques ; Catalysis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.}, }
@article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14099}, doi = {10.1111/1755-0998.14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, }
@article {pmid40086056, year = {2025}, author = {Liang, L and Dang, B and Ouyang, X and Zhao, X and Huang, Y and Lin, Y and Cheng, X and Xie, G and Lin, J and Mi, P and Ye, Z and Guleng, B and Cheng, SC}, title = {Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis.}, journal = {International immunopharmacology}, volume = {152}, number = {}, pages = {114408}, doi = {10.1016/j.intimp.2025.114408}, pmid = {40086056}, issn = {1878-1705}, mesh = {Animals ; *Succinic Acid/therapeutic use/pharmacology ; *Colitis/chemically induced/immunology/drug therapy ; Dextran Sulfate ; Mice ; *Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Mice, Inbred C57BL ; Dietary Supplements ; Mice, Knockout ; Monocytes/immunology ; Colon/immunology/drug effects/pathology ; Male ; Disease Models, Animal ; Humans ; Signal Transduction ; Cytokines/metabolism ; Interleukin-4 Receptor alpha Subunit ; }, abstract = {Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2[-/-] mice, confirming the role of monocyte recruitment, but persisted in Rag1[-/-] mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.}, }
@article {pmid40085655, year = {2025}, author = {Muratore, D and Gilbert, NE and LeCleir, GR and Wilhelm, SW and Weitz, JS}, title = {Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {11}, pages = {e2410268122}, pmid = {40085655}, issn = {1091-6490}, support = {OCE-1829641//National Science Foundation (NSF)/ ; OCE-1829636//National Science Foundation (NSF)/ ; 721231//Simons Foundation (SF)/ ; }, mesh = {*Phosphorus/metabolism ; *Phytoplankton/metabolism/genetics ; *Seawater/microbiology ; *Cyanobacteria/metabolism/genetics ; Nitrogen/metabolism ; Ecosystem ; *Bacteria/metabolism/genetics ; Oceans and Seas ; Pacific Ocean ; }, abstract = {The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.}, }
@article {pmid40085287, year = {2025}, author = {Micciulla, JL and Baubin, C and Fierer, N}, title = {Effects of Geosmin on the Behavior of Soil Protists.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {14}, pmid = {40085287}, issn = {1432-184X}, support = {2126106//National Science Foundation/ ; }, mesh = {*Soil/parasitology/chemistry ; *Soil Microbiology ; *Naphthols/metabolism/pharmacology ; *Acanthamoeba castellanii/physiology/drug effects ; *Ciliophora/physiology/drug effects ; Bacteria/metabolism ; Cercozoa/physiology/drug effects ; }, abstract = {Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic "earthy" scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing (Streptomyces coelicolor M145) and non-producing (S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists (Cercomonas sp. and A. castellanii) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.}, }
@article {pmid40085262, year = {2025}, author = {Castelli, M and Petroni, G}, title = {An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {15}, pmid = {40085262}, issn = {1432-184X}, mesh = {Phylogeny ; *Biological Evolution ; Animals ; *Alphaproteobacteria/classification/genetics/physiology ; *Biodiversity ; *Host Microbial Interactions ; }, abstract = {The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.}, }
@article {pmid40084873, year = {2025}, author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H}, title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0198924}, pmid = {40084873}, issn = {2165-0497}, abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.<br><br>IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.}, }
@article {pmid40084850, year = {2025}, author = {Machushynets, NV and Lysenko, V and Du, C and Slingerland, CJ and Elsayed, SS and Liles, MR and Martin, NI and van Wezel, GP}, title = {Exploring the Chemical Space of Paenibacillus NRPs and Discovery of Paenilipoheptin B.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2821-2825}, pmid = {40084850}, issn = {1523-7052}, mesh = {*Paenibacillus/chemistry/metabolism ; Molecular Structure ; *Lipopeptides/chemistry ; Peptide Synthases/metabolism/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; }, abstract = {A combination of genomic and metabolomic analyses paired with molecular networking was applied to a collection of Paenibacillus spp. to identify the producers of a little-studied class of lipopeptides known as paenilipoheptins. Mass spectrometry and NMR spectroscopy allowed revision of the structure of previously reported paenilipoheptin A and elucidation of the structure of novel paenilipoheptin B.}, }
@article {pmid40083115, year = {2025}, author = {Dodds, IL and Watts, EC and Schuster, M and Buscaill, P and Tumas, Y and Holton, NJ and Song, S and Stuttmann, J and Joosten, MHAJ and Bozkurt, T and van der Hoorn, RAL}, title = {Immunity gene silencing increases transient protein expression in Nicotiana benthamiana.}, journal = {Plant biotechnology journal}, volume = {23}, number = {5}, pages = {1768-1770}, pmid = {40083115}, issn = {1467-7652}, support = {BB/R017913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S003193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00230/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101019324/ERC_/European Research Council/International ; }, }
@article {pmid40082592, year = {2025}, author = {Thomas, PW and Kothamasi, D}, title = {Hunting dog behaviour is a key driver impacting harvest quantity and quality of truffles.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8662}, pmid = {40082592}, issn = {2045-2322}, mesh = {Animals ; Humans ; Dogs ; *Ascomycota/physiology/growth &amp; development ; *Hunting ; *Behavior, Animal ; Seasons ; }, abstract = {Truffles are an iconic food that have long held high regard. Here we explore the seasonality and eco-physiological interactions affecting truffle quality and quantity across time and space. Collaborating with professional truffle hunters working eight different locations, detailed metrics of 3180 recovered truffles from 236 hunt events and spanning a full fruiting period, were recorded. Contrary to expectations, truffle weight showed no correlation with climate variables, suggesting a limited influence of environmental factors such as temperature and precipitation on truffle size. We also found that truffle maturity and damage from mycophagy were strongly linked, with deeper truffles being more mature but also more susceptible to damage. Finally, we observe that scent-dog behaviour significantly impacts the quantity and quality of recovered truffles, and we address the necessity of considering this in truffle ecophysiology studies. Alongside advances in our biological understanding, we make recommendations of how training methods can be improved to lead to greater detection and quality targeting with immediate socioeconomic impact. These findings highlight the complex interplay between truffle physiology, environmental factors, and human and animal behaviours, emphasizing the need for further considered research to enhance our understanding of truffle biology and to improve truffle cultivation practices.}, }
@article {pmid40080573, year = {2025}, author = {Shumilova, O and Sukhodolov, A and Osadcha, N and Oreshchenko, A and Constantinescu, G and Afanasyev, S and Koken, M and Osadchyi, V and Rhoads, B and Tockner, K and Monaghan, MT and Schröder, B and Nabyvanets, J and Wolter, C and Lietytska, O and van de Koppel, J and Magas, N and Jähnig, SC and Lakisova, V and Trokhymenko, G and Venohr, M and Komorin, V and Stepanenko, S and Khilchevskyi, V and Domisch, S and Blettler, M and Gleick, P and De Meester, L and Grossart, HP}, title = {Environmental effects of the Kakhovka Dam destruction by warfare in Ukraine.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6739}, pages = {1181-1186}, doi = {10.1126/science.adn8655}, pmid = {40080573}, issn = {1095-9203}, mesh = {Humans ; *Ecosystem ; Geologic Sediments/chemistry ; Ukraine ; *Warfare ; *Disasters ; }, abstract = {The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster's spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.}, }
@article {pmid40080167, year = {2025}, author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C}, title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {13}, pmid = {40080167}, issn = {1432-184X}, support = {(PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; }, mesh = {*Soil Microbiology ; *Hevea/growth &amp; development ; Cote d'Ivoire ; Soil/chemistry ; Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; Trees ; }, abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.}, }
@article {pmid40078544, year = {2025}, author = {Acciardo, AS and Arnet, M and Gholizadeh Doonechaly, N and Ceccato, A and Rodriguez, P and Tran, HNH and Wenning, Q and Zimmerman, E and Hertrich, M and Brixel, B and Magnabosco, C}, title = {Spatial and temporal groundwater biogeochemical variability help inform subsurface connectivity within a high-altitude Alpine catchment (Riale di Ronco, Switzerland).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522714}, pmid = {40078544}, issn = {1664-302X}, abstract = {Accessing the deep terrestrial subsurface (greater than 1 km below the surface) presents significant practical challenges, leaving these ecosystems largely uncharacterized despite their extensive presence beneath Earth's landmasses. In this study, we introduce the BedrettoLab Deep Life Observatory (DELOS), a new underground laboratory to study the biogeochemical diversity of groundwater in a high-altitude Alpine catchment tens of meters to 1.6 km underground. Biogeochemical monitoring of DELOS over spatial and temporal scales highlight three dominant ecotypes throughout DELOS: (1) Shallow groundwater with low electrical conductivity enriched in Leptospirillia; (2) High-inflow fault zones enriched in ultra-small bacteria and archaea; (3) Bicarbonate-enriched waters that are enriched in Candidatus Kryptonia and Spirochaetota. Despite a consistent lithology throughout DELOS, groundwater from fractures that are spatially near each other are not always represented by the same ecotype and can be more similar to groundwater emitted from fractures thousands of meters away. Despite this heterogeneity, the biological and hydrochemical compositions of the groundwater of individual fractures remained relatively stable throughout the course of a 1-year monitoring period. An exception to this trend occurred after a series of seismic events near one groundwater-bearing fracture. Here, the microbial community and hydrochemical composition of the groundwater changed after the seismic events but returned to the site's "baseline" composition within 3 weeks. Taken together, these findings provide new insights into the spatial and temporal heterogeneity of deep subsurface ecosystems and the subsurface connectivity of an Alpine subsurface environment.}, }
@article {pmid40077554, year = {2025}, author = {Smirani, N and Bouazizi, S and Bettaieb, E and Torkhani, R and Hamdi, M}, title = {Effect of Environmentally Friendly Betalain Extraction Methods on Antioxidant Compounds of Tunisian Opuntia stricta Fruit.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40077554}, issn = {2304-8158}, abstract = {This study focuses on the extraction of betalain compounds from Opuntia stricta as a natural alternative to synthetic colorants and sustainable environmentally friendly technology solutions. Non-conventional extraction technologies including microwave (MW) and ultrasound (US) were used alone or in combination. The extraction process was conducted for both undried Opuntia stricta (OS) and dried Opuntia stricta (DOS) plant material at two distinct drying temperatures, 40 °C and 60 °C, to assess the stability of betalain molecules. The colorant's potential was evaluated by determining the betalain content, total phenolic content, and antioxidant activity. The MW (2 min) and MW (2 min) + US (10 min) extraction processes yielded the greatest betalain content in OS fresh weight (FW), with 48.54 ± 0.29 mg/100 g FW and 51.01 ± 0.16 mg/100 g FW, respectively. Furthermore, the results showed a considerable drop in betalain content when the plant material was dried at 40 °C and 60 °C, with reduction rates of 53.75% and 24.82%, respectively, compared to the betalain content before the drying process. The LC-DAD-ESI-MS analysis supported this result, revealing the presence of 17-decarboxy betanin, 17-decarboxy neobetanin, and Cyclo-dopa5-O-βglucoside in DOS at 40 °C. This study highlights the potential future in the sustainable green extraction of betalain compounds with less heat degradation to offer a stable natural colorant.}, }
@article {pmid40072629, year = {2025}, author = {Dyczko, D and Szymański, DM and Szymański, D and Kupczak, M and Kolenda, K}, title = {First European record of Rickettsia bellii in Amblyomma rotundatum from Rhinella marina imported to Poland.}, journal = {Experimental &amp; applied acarology}, volume = {94}, number = {3}, pages = {43}, pmid = {40072629}, issn = {1572-9702}, mesh = {Animals ; Poland ; *Amblyomma/microbiology ; *Rickettsia/isolation &amp; purification/genetics ; Female ; *Tick Infestations/veterinary/parasitology ; }, abstract = {This study reports on the first documented case of Amblyomma rotundatum ticks, a species typically found in the Americas, parasitising an imported toad in Poland. A total of 12 ticks were collected from a single Rhinella marina toad. These ticks were identified as female specimens of A. rotundatum using an examination of morphological characteristics and a molecular analysis. Polymerase chain reaction testing revealed that 75.0% (9/12) of these females were positive for Rickettsia spp. Sequencing of positive samples confirmed the presence of R. bellii. However, no DNA evidence of Borrelia spp. and Anaplasma spp. was detected in the tested ticks. Nevertheless, given the limited number of tick specimens collected from a single host, further research is required to elucidate the pathogen profile of a tick species. This finding represents the second European report of A. rotundatum associated with exported animals, underscoring the importance of vigilance in monitoring the potential spread of ticks and tick-borne pathogens through the global wildlife trade.}, }
@article {pmid40072582, year = {2025}, author = {Barjau-Aguilar, M and Reyes-Hernández, AMJ and Merino-Ibarra, M and Vilaclara, G and Ramírez-Zierold, JA and Alcántara-Hernández, RJ}, title = {Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {12}, pmid = {40072582}, issn = {1432-184X}, support = {CVU: 747276//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 1249011//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CF-2023-G-155//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 41120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UNAM, PAPIIT-IN207702//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; UNAM-PAPIIT IN217622//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Nitrogen/analysis ; Phosphorus/analysis ; *Fresh Water/microbiology/chemistry ; Tropical Climate ; Oxygen/analysis ; Phylogeny ; *Microbiota ; Water Microbiology ; Eutrophication ; }, abstract = {Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3[-] concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.}, }
@article {pmid40070274, year = {2025}, author = {Cidan, Y and Wang, J and Wang, H and Xu, C and Zhu, Y and Khan, MK and Basang, W and Li, K}, title = {Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2476539}, doi = {10.1080/10495398.2025.2476539}, pmid = {40070274}, issn = {1532-2378}, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Mycobiome ; *Gastrointestinal Microbiome ; }, abstract = {This study aimed to explore the diversity and functions of rumen mycobiota in 14‑ (PLf) and 15‑rib (DLf) Jiani yaks using ITS sequencing. A total of 1,079,105 and 1,086,799 filtered sequences were obtained for the PLf and DLf groups, respectively, with 491 ASVs common to both. No significant difference regarding the α‑diversity of mycobiota within the two groups was observed. While β‑diversity analysis indicated that the abundance of fifteen (15) genera in the PLf group and two (2) genera in the DLf group was found to be significantly different (p < 0.05). 16S rRNA sequencing results indicated that at the phylum level, in 14 ribs yaks Ascomycota, Basidiomycota, and Olpidiomycota, while in 15 rib yaks, Neocallimastigomycota, Mortierellomycota, and Rozellomycota were found to be significantly different (p < 0.05). At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. This study sheds novel insights into how genetic variations influence gut mycobiota in Jiani yak.}, }
@article {pmid40068413, year = {2025}, author = {Yang, H and Cappitelli, F and Li, X}, title = {Pollution gradients shape structure and functions of stone heritage bacterial communities at global scale.}, journal = {The Science of the total environment}, volume = {971}, number = {}, pages = {179087}, doi = {10.1016/j.scitotenv.2025.179087}, pmid = {40068413}, issn = {1879-1026}, mesh = {*Bacteria/classification ; *Microbiota/drug effects ; *Environmental Monitoring ; Particulate Matter/analysis ; Biodiversity ; }, abstract = {Previous studies mainly focused on the impact of climatic conditions on stone heritage microbial communities, while ignoring a global ecological perspective of pollution on heritage microorganisms. In particular, there is a lack of detailed analysis of the impact of pollution levels on microbial metabolic function. In this study, >6000 bacterial OTUs from 17 world cultural heritage sites were considered. The microbial diversity indexes and potential functions under different pollution levels were analyzed. The results show that particulate matter pollution, such as PM2.5, has an effect on the microbial community in heritage sites comparable to that of temperature and precipitation. High concentrations of particulate matter increased bacterial richness and facilitated the introduction of unique species. Among them, phototrophic bacteria (e.g., Cyanobacteria) and some heterotrophic bacteria (e.g., Actinobacteria and Proteobacteria) formed the core of the microbial community. However, high concentrations of particulate matter reduced the complexity and stability of microbial ecological networks, favoring pollution-tolerant species. Furthermore, elevated particulate concentrations partially suppressed the expression of certain metabolic pathways, particularly genes related to denitrification (e.g., nosZ and nirS). This study reveals the long-term impact of polluted environments on the diversity and potential functions of microbial communities, providing a theoretical basis for developing sustainable strategies for cultural heritage conservation.}, }
@article {pmid40066860, year = {2025}, author = {Defoirdt, T}, title = {Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476582}, pmid = {40066860}, issn = {1949-0984}, mesh = {*Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; *Bacteria/drug effects ; *Bacterial Infections/microbiology/drug therapy ; Animals ; }, abstract = {Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.}, }
@article {pmid40065660, year = {2025}, author = {Guislain, ALN and Nejstgaard, JC and Köhler, J and Sperfeld, E and Mischke, U and Skjelbred, B and Grossart, HP and Lyche Solheim, A and Gessner, MO and Berger, SA}, title = {Cell size explains shift in phytoplankton community structure following storm-induced changes in light and nutrients.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70043}, pmid = {40065660}, issn = {1939-9170}, support = {731065//European Commission/ ; 871081//European Commission/ ; 01LC1501//German Federal Ministry of Education and Research (BMBF)/ ; GE 1775/2-1//German Research Foundation (DFG)/ ; 603378//the European Commission under its 7th Framework Programme/ ; SAW-2015-IGB-1//Leibniz Association/ ; K45/2017//Leibniz Association/ ; 033L041B//BMBF Infrastructure/ ; }, mesh = {*Phytoplankton/physiology/cytology ; *Light ; *Ecosystem ; Nutrients ; }, abstract = {Understanding the mechanisms driving community structure and dynamics is crucial in the face of escalating climate change, including increasing incidences of extreme weather. Cell size is a master trait of small organisms that is subject to a trade-off between resistance to grazing and competition for resources, and thus holds potential to explain and predict community dynamics in response to disturbances. Here, we aimed at determining whether cell size can explain shifts in phytoplankton communities following changes in nutrient and light conditions resulting from storm-induced inputs of nutrients and colored dissolved organic matter (cDOM) to deep clearwater lakes. To ensure realistic environmental conditions, we used a crossed gradient design to conduct a large-scale enclosure experiment over 6 weeks. Cell size explained phytoplankton community structure when light availability declined as a result of cDOM supply. Initially unimodal, with small-celled species accounting for up to 60% of the total community biovolume, the cell-size distribution gradually shifted toward large-celled species as light levels declined following cDOM addition. Neither nutrients nor mesozooplankton affected the shift in cell-size distribution. These results suggest a distinct competitive advantage of larger over smaller species at reduced light levels following cDOM inputs during storm events. Importantly, the clustering of species in two distinct size classes implies that interspecific size differences matter as much as cell size per se to understand community dynamics. Given that shifts in cell-size distribution have strong implications for food-web structure and biogeochemical cycles, our results point to the importance of analyzing cell-size distributions of small organisms as an essential element to forecast community and ecosystem dynamics in response to environmental change.}, }
@article {pmid40064943, year = {2025}, author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC}, title = {GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8214}, pmid = {40064943}, issn = {2045-2322}, support = {3G062519//Fonds Wetenschappelijk Onderzoek/ ; 1S51925N//Fonds Wetenschappelijk Onderzoek/ ; 40007505//Excellence Of Science (F.W.O.-F.R.S.-FNRS.)/ ; }, mesh = {Humans ; *Tissue Scaffolds/chemistry ; Caco-2 Cells ; *Epithelial Cells/cytology/metabolism ; Hydrogels/chemistry ; *Intestine, Small/cytology ; *Gelatin/chemistry ; Cell Survival/drug effects ; Permeability ; *Cellular Microenvironment ; Biocompatible Materials/chemistry ; Intestinal Mucosa ; Cell Adhesion ; Coculture Techniques ; }, abstract = {Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.}, }
@article {pmid40062895, year = {2025}, author = {McDonald, MD and Lewis, KL and Gentry, TJ}, title = {No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0018425}, pmid = {40062895}, issn = {1098-5336}, support = {//Texas A&amp;M AgriLife Research Air Quality Initiative/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Photosynthesis/genetics ; *Soil/chemistry ; *Agriculture/methods ; *Bacteria/genetics/metabolism ; Triticum/growth &amp; development ; Crops, Agricultural/growth &amp; development ; }, abstract = {Managing soils in semi-arid agricultural croplands generally focuses on reducing wind erosion, increasing fertility, and storing carbon. Thus, converting conventionally tilled systems to no-tillage and cover-cropped systems are often the first steps towards a conservation management approach across the growing area of semi-arid croplands. From a soil biological perspective, introducing cover crops to semi-arid soils has been shown to alter microbial community structure, which may lead to changes in the biogeochemical pathways expressed in these soils. In this study, we examined the impact of single-species wheat cover cropping and no-tillage on microbial gene expression after 4 and 5 years of implementation. We sequenced the metatranscriptomes of three production systems with varying levels of conservation management: conventional tillage winter fallow, no-tillage winter fallow, and no-tillage with a winter wheat cover crop. Removing tillage was the biggest factor altering microbial gene expression in this study, specifically resulting in upregulation of several photosystem-associated functions. These functions were taxonomically linked to organisms that make up the early stages of biological soil crusts, which may introduce additional benefits to these semi-arid agricultural systems beyond a reduction in wind erosion. Implementing a cover crop did not clearly alter gene expression beyond the effect of tillage removal; however, it did indicate a potential to reduce fungal disease incidence in 1 year of the study. These alterations of microbial activities and selection for potentially beneficial functions should be considered and further studied to aid in maintaining sustainable croplands for our changing climate.IMPORTANCEEliminating tillage from semi-arid agricultural soils has the potential to significantly alter the activities of the soil bacterial community compared with conventionally tilled soils. A major driver of this change was the activities of biological soil crust forming organisms that can provide several environmental benefits to the soil ecosystem beyond the typically associated benefits of conservation management. Furthermore, this study revealed that the implementation of a cover crop regime on no-tillage soils does not confer a major change in the function of the organisms present. Overall, the study reported here reveals that soil management practices aimed at reducing wind erosion and improving sustainability will positively impact the function of the microbial community and suggests that future investigations into the consequences of these functional changes may provide valuable services to these agricultural ecosystems.}, }
@article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0298924}, pmid = {40062772}, issn = {2150-7511}, support = {T32 GM007491/GM/NIGMS NIH HHS/United States ; 5T32GM007491-46//HHS | National Institutes of Health (NIH)/ ; //Elsa U. Pardee Foundation (EUPF)/ ; }, mesh = {*Fusobacterium nucleatum/genetics/isolation &amp; purification/classification/physiology ; Humans ; *Colorectal Neoplasms/microbiology ; Female ; Male ; *Fusobacterium Infections/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Gingiva/microbiology ; Genome, Bacterial ; }, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, }
@article {pmid40062764, year = {2025}, author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K}, title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.}, journal = {Journal of women's health (2002)}, volume = {34}, number = {5}, pages = {644-652}, doi = {10.1089/jwh.2024.0583}, pmid = {40062764}, issn = {1931-843X}, mesh = {Humans ; *Vaginosis, Bacterial/epidemiology/microbiology/ethnology ; Female ; United States/epidemiology ; Prevalence ; Vagina/microbiology ; Risk Factors ; Microbiota ; Black or African American/statistics &amp; numerical data ; White ; }, abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.}, }
@article {pmid40062709, year = {2025}, author = {Jeong, IJ and Hong, JK and Bae, YJ and Lee, TK}, title = {Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {107}, number = {3}, pages = {203-213}, doi = {10.1002/cyto.a.24923}, pmid = {40062709}, issn = {1552-4930}, support = {2020R1C1C100624912//National Research Foundation of Korea/ ; }, mesh = {*Flow Cytometry/methods ; *Machine Learning ; *Bacteria/classification/isolation &amp; purification ; Phenotype ; Escherichia coli ; }, abstract = {Although flow cytometry produces reliable results, the data processing from gating to fingerprinting is prone to subjective bias. Here, we integrated autogating with Automated Machine Learning in flow cytometry to enhance the classification of bacterial phenotypes. We analyzed six bacterial strains prevalent in the soil and groundwater- Bacillus subtilis , Burkholderia thailandensis , Corynebacterium glutamicum , Escherichia coli , Pseudomonas putida , and Pseudomonas stutzeri . Using the H2O-AutoML framework, we applied gradient-boosting machine (GBM) models to classify bacteria across different metabolic phases. Our results demonstrated an overall classification accuracy of 82.34% for GBM. Notably, accuracy varied across metabolic phases, with the highest observed during the late log (88.06%), lag (88.43%), and early log phases (89.37%), whereas the stationary phase showed a slightly lower accuracy of 80.73%. P. stutzeri exhibited consistently high sensitivity and specificity across all the phases, which indicated that it was the most distinctly identifiable strain. In contrast, E. coli showed low sensitivity, particularly in the stationary phase, which indicated challenges in its classification. Overall, this study with incorporating autogating and the AutoML framework, substantially reduces subjective biases and enhances the reproducibility and accuracy of microbial classification. Our methodology offers a robust framework for microbial classification in flow cytometric analysis, paving the way for more precise and comprehensive analyses of microbial ecology.}, }
@article {pmid40060716, year = {2025}, author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y}, title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70994}, pmid = {40060716}, issn = {2045-7758}, abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.}, }
@article {pmid40060289, year = {2025}, author = {Sarkar, A and Bhattacharjee, S}, title = {Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {78}, pmid = {40060289}, issn = {2190-572X}, abstract = {Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.}, }
@article {pmid40060287, year = {2025}, author = {Maity, A and Das, A and Roy, R and Malik, M and Das, S and Paul, P and Sarker, RK and Sarkar, S and Dasgupta, A and Chakraborty, P and Tribedi, P}, title = {Development of novel strategies against the threats of drug-resistant Escherichia coli: an in silico and in vitro investigation.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {77}, pmid = {40060287}, issn = {2190-572X}, abstract = {UNLABELLED: Escherichia coli (E. coli) biofilms pose alarming threats in healthcare due to their invulnerability to drug therapy. Stand-alone therapies of antimicrobial compounds/antibiotics are not particularly effective against those resistant strains. However, combination therapy of compounds could be used to deal with such threats. Towards this direction, the natural compound cuminaldehyde was employed in combination with the aminoglycoside antibiotic tobramycin to target the biofilm-forming multidrug-resistant (MDR) clinical strains of E. coli, which were isolated from urine samples of patient's at Suraksha Diagnostic Private Limited (Kolkata, India). At first, an integrated in silico approach (PASS online, Swiss ADME, PROTOX 3.0, and OSIRIS) was explored to predict the potential biological activities, and other relevant pharmacokinetic parameters of cuminaldehyde and tobramycin. The in silico analysis suggested that tobramycin might not be bioavailable orally due to its molecular size, polarity, and poor GI absorption. However, cuminaldehyde was well absorbed in the GI but could cause irritation if swallowed in LD50 amounts. Further, in vitro assessments were performed to analyse the antimicrobial and antibiofilm activity of both compounds, alone and in combination, against clinical strains of E. coli. The results suggested that cuminaldehyde and tobramycin together could show an additive effect against the clinical strains of E. coli. The combination of the compounds showed a substantial decrease in minimum inhibitory concentration (MIC) and biofilm formation compared to individual application. The present study indicates that combinatorial application involving cuminaldehyde and tobramycin could inhibit the formation of biofilms in E. coli, potentially aiding in the management of microbial infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04246-0.}, }
@article {pmid40058043, year = {2025}, author = {Zhong, Q and Santás-Miguel, V and Cruz-Paredes, C and Rousk, J}, title = {Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124883}, doi = {10.1016/j.jenvman.2025.124883}, pmid = {40058043}, issn = {1095-8630}, mesh = {*Metals, Heavy ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; *Soil Pollutants ; Soil/chemistry ; Agriculture ; Forests ; Tetracycline ; Copper ; Bacteria/drug effects ; }, abstract = {The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg[-1] Cu and 6000 mg kg[-1] tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.}, }
@article {pmid40052378, year = {2025}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf055}, pmid = {40052378}, issn = {1365-2672}, support = {JPNP18016//New Energy and Industrial Technology Development Organization/ ; JPMJMI20E5//JST-Mirai Program/ ; }, mesh = {*Soil Microbiology ; *Nitrous Oxide/metabolism ; RNA, Ribosomal, 16S/genetics ; *Oxidoreductases/genetics/metabolism ; *Betaproteobacteria/genetics/metabolism/classification/enzymology ; Soil/chemistry ; Phylogeny ; Oryza ; }, abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.}, }
@article {pmid40049093, year = {2025}, author = {Fonvielle, J and Thuile Bistarelli, L and Tao, Y and Woodhouse, JN and Shatwell, T and Villalba, LA and Berger, SA and Kyba, CCM and Nejstgaard, JC and Jechow, A and Kupprat, F and Stephan, S and Walles, TJW and Wollrab, S and Hölker, F and Dittmar, T and Gessner, MO and Singer, GA and Grossart, HP}, title = {Skyglow increases cyanobacteria abundance and organic matter cycling in lakes.}, journal = {Water research}, volume = {278}, number = {}, pages = {123315}, doi = {10.1016/j.watres.2025.123315}, pmid = {40049093}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Cyanobacteria ; Ecosystem ; Light ; Carbon Cycle ; }, abstract = {Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.}, }
@article {pmid40048904, year = {2025}, author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y}, title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.}, journal = {Water research}, volume = {279}, number = {}, pages = {123419}, doi = {10.1016/j.watres.2025.123419}, pmid = {40048904}, issn = {1879-2448}, mesh = {*Microbiota ; Anaerobiosis ; Bioreactors/microbiology ; }, abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.}, }
@article {pmid40047954, year = {2025}, author = {Sobhy, IS and Goelen, T and Wäckers, F and Verstrepen, KJ and Wenseleers, T and Jacquemyn, H and Lievens, B}, title = {Impact of Nectar Composition and Nectar Yeasts on Volatile Emissions and Parasitoid Behavior.}, journal = {Journal of chemical ecology}, volume = {51}, number = {2}, pages = {29}, pmid = {40047954}, issn = {1573-1561}, support = {C3 grant (IOF-C32/15/020)//KU Leuven/ ; }, mesh = {Animals ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Plant Nectar/chemistry/metabolism ; Female ; *Wasps/physiology ; *Metschnikowia/metabolism/physiology ; Fermentation ; *Aphids/parasitology/physiology ; Amino Acids/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Yeasts ; }, abstract = {Nectar yeasts can significantly influence the scent of floral nectar and therefore the foraging behavior of flower-visiting insects. While these effects likely depend on nectar chemistry and yeast species, their joint impact on nectar volatile profiles and associated insect responses remain poorly understood. Here, we used four synthetic nectar types varying in sugar and amino acid concentration and two specialist nectar yeasts (Metschnikowia gruessii and Metschnikowia reukaufii) to investigate how nectar composition and yeast species affect volatile profiles and the olfactory responses of the generalist aphid parasitoid Aphidius ervi. Olfactometer assays showed that A. ervi females significantly preferred fermented nectars with high amino acid-low sugar content (HL) and low amino acid-high sugar (LH) content, regardless being fermented by M. gruessii or M. reukaufii, over non-inoculated nectars. This effect was not observed for nectars with low amino acid-low sugar (LL) and high amino acid-high sugar (HH) content. Moreover, LL nectar fermented with M. gruessii became even repellent to the parasitoids. GC-MS analysis of volatile organic compounds (VOCs) revealed that VOC profiles of fermented nectars depended significantly on nectar type (i.e., chemical composition), yeast species, and their interaction. Whereas propyl acetate, isobutyl acetate, styrene, α-guaiene and pentyl-octanoate were associated with the LH fermented nectars, ethyl acetate and E-methyl isoeugenol were mainly associated with the HL fermented nectars, suggesting possible involvement in A. ervi attraction to these nectars. In contrast, isopropyl-hexadecanoate was associated with the non-attractive or repellent LL fermented nectars. Altogether, our results indicate that nectar composition has a strong impact on nectar scent when fermented by specialist nectar yeasts and subsequently on insect foraging behavior.}, }
@article {pmid40046987, year = {2025}, author = {Scott, WT and Rockx, S and Mariën, Q and Regueira, A and Candry, P and Ganigué, R and Koehorst, JJ and Schaap, PJ}, title = {Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {649-660}, pmid = {40046987}, issn = {2001-0370}, abstract = {Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of Clostridia species, such as Clostridium kluyveri, Clostridium autoethanogenum, and Clostridium ljungdahlii. Clostridium luticellarii, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create iSJ444, a constraint-based metabolic model of C. luticellarii using iHN637 of a close relative C. ljungdahlii as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that C. luticellarii maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that C. luticellarii might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of C. luticellarii as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of C. luticellarii to enhance syngas fermentation platforms.}, }
@article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, }
@article {pmid40044467, year = {2025}, author = {Sharma, P and Reitz, T and Singh, SP and Worrich, A and Muehe, EM}, title = {Going beyond improving soil health: cover plants as contaminant removers in agriculture.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {539-552}, doi = {10.1016/j.tplants.2025.01.009}, pmid = {40044467}, issn = {1878-4372}, mesh = {*Agriculture/methods ; *Soil/chemistry ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Plants/metabolism ; }, abstract = {Agriculture faces the increasing demands of a growing global population amid simultaneous challenges to soils from climate change and human-induced contamination. Cover plants are vital in sustainable agriculture, contributing to soil health improvement, erosion prevention, and enhanced climate resilience, but their role in contaminant management is underexplored. Herein we review the utilization of cover plants for remediating contaminants such as metals, organic pollutants, nitrate, antibiotics, antimicrobial resistance genes, plastics, and salts. We explore phytoremediation strategies - including phytoextraction, phytodegradation, and phytostabilization - in cover plant management. We highlight the challenges of selecting effective cover plants and the need for biomass removal of non-biodegradable contaminants, and we advocate incorporating phytoremediation concepts into sustainable agricultural management practices beyond nutrient cycling and climate resilience.}, }
@article {pmid40042720, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {14}, pmid = {40042720}, issn = {2197-4365}, abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.}, }
@article {pmid40042690, year = {2025}, author = {Zhang, T and Wang, XL and Zhou, J and Zhou, W and Zhou, SQ}, title = {Construction of Phosphate-Solubilizing Microbial Consortium and Its Effect on the Remediation of Saline-Alkali Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {11}, pmid = {40042690}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Phosphates/metabolism ; Phosphorus/metabolism ; *Microbial Consortia ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Arachis/growth &amp; development ; Alkalies/metabolism ; Calcium Sulfate/metabolism ; Salinity ; Nitrogen/analysis/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {In this study, phosphate solubilizing bacteria (PSB) with good phosphate-solubilizing capability were isolated from phosphogypsum (PG) storage yard, and phosphate-solubilizing bacteria without antagonistic effect were selected to construct phosphate solubilizing microbial consortium (PSMC), and the synergistic effect of PSMC and PG on the physical and chemical properties of saline-alkali soil, soil enzyme activity, soil bacterial diversity, and the growth index and biomass of peanut plants were explored. The results showed that the effect of phosphorus containing soil amendment on saline-alkali soil was better than that of single PSMC or PG. In the T6 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (6.0 g)), the pH of saline-alkali soil decreased from 8.54 to 7.03, the content of organic matter increased by 6.64%, the content of alkali hydrolyzable nitrogen, available phosphorus and available potassium increased by 81.68%, 60.31%, and 42.03%, respectively, and the activity of alkaline phosphatase increased by 94.95%. In addition, the electrical conductivity value in T4 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (3.0g)) decreased significantly by 20.21%. The diversity and richness of bacterial community in T4 group were the highest, and the growth of peanut plants was the best. The fresh weight of roots and stems increased by 73.34% and 116.6%, respectively. In conclusion, the phosphorus containing soil conditioner prepared by PSMC and PG can effectively improve the soil environment of saline-alkali soil and promote the resource utilization of saline alkali soil.}, }
@article {pmid40042528, year = {2025}, author = {Zaki, H and Hussein, MA and El-Dawy, EGAM}, title = {Diversity and Symbiotic Associations of Endophytic Fungi in Calotropis procera (Aiton) W.T. Aiton (Asclepiadaceae) Across Three Egyptian Regions: Phenotypic Characterization and Mitotic Activity.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {10}, pmid = {40042528}, issn = {1432-184X}, mesh = {*Endophytes/physiology/classification/isolation &amp; purification/genetics ; Egypt ; *Fungi/classification/physiology/isolation &amp; purification/genetics ; *Symbiosis ; *Biodiversity ; Soil Microbiology ; *Calotropis/microbiology/physiology ; Mitosis ; Phenotype ; }, abstract = {Endophytic fungi are essential contributors to fungal biodiversity, playing key roles in plant defense against pathogens, alleviation of abiotic stress, and promotion of growth. This study conducted a comprehensive survey of the phenotypic characterization of Calotropis procera and its associated endophytic fungi across three regions in Egypt: Qena-Safaga, Qena, and Qena-Kosseir. Positive and significant Pearson correlations among plant morphological traits suggest intrinsic connections. Fungal species diversity exhibited significant variation across the three regions examined. Particularly, the Qena-Kosseir region demonstrated the highest fungal species richness both in soil samples and endophytic fungi. Unique to this region, Allocanariomyces tritici, Aspergillus terreus, Chaetomium globosum, C. murorum, Cladosporium cladosporioides, C. sphaerospermum, Fusarium proliferatum, Penicillium crustosum, P. granulatum, P. spinuloseum, and Roussoella intermedia were identified as endophytes. Additionally, compared to other regions, the Qena-Kosseir area exhibited the presence of Aspergillus fumigatus, A. ochraceus, A. ornatus, A. sclerotiocabonarus, Drechslera halodes, Emericella echinulata, Fusarium oxysporum, and Macrophomina phaseolina in soil samples, underscoring its distinct fungal community composition. Furthermore, antimitotic assays using the Allium cepa test revealed distinct effects of endophytic extracts on various mitotic stages. Of the 33 treatments, 11 showed an increase in the mitotic index (MI), indicating a potential positive effect on plant growth and cell division. This study offers valuable insights into the diversity and functional roles of endophytic fungi associated with C. procera, highlighting their promising applications in sustainable agriculture and plant health management.}, }
@article {pmid40042412, year = {2025}, author = {Hicks, LC and Leizeaga, A and Cruz Paredes, C and Brangarí, AC and Tájmel, D and Wondie, M and Sandén, H and Rousk, J}, title = {Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests.}, journal = {Global change biology}, volume = {31}, number = {3}, pages = {e70065}, pmid = {40042412}, issn = {1365-2486}, support = {2016-06327//Vetenskapsr&#xe5;det/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; CTS 22:2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 2022-00672//Svenska Forskningsr&#xe5;det Formas/ ; 2023-02438//Svenska Forskningsr&#xe5;det Formas/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; }, mesh = {*Climate Change ; *Droughts ; Ethiopia ; *Forests ; *Soil Microbiology ; Fungi/growth &amp; development ; *Microbiota ; Soil/chemistry ; Bacteria/growth &amp; development ; Crops, Agricultural ; }, abstract = {Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.}, }
@article {pmid40042334, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM}, title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0156124}, pmid = {40042334}, issn = {2165-0497}, support = {2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; DEB 1952687//National Science Foundation (NSF)/ ; 2015/13546-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2018/14974-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 133769/2015-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; DEB 1442214//National Science Foundation (NSF)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 2109481//National Science Foundation (NSF)/ ; //Stanford Doerr School of Sustainability Discovery grant/ ; }, mesh = {*Soil Microbiology ; Brazil ; Forests ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; Genome, Bacterial ; Phylogeny ; Soil/chemistry ; Base Composition ; Genome, Archaeal ; Genomics ; }, abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.}, }
@article {pmid40041707, year = {2025}, author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q}, title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf025}, pmid = {40041707}, issn = {2730-6151}, abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.}, }
@article {pmid40041702, year = {2025}, author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H}, title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf002}, pmid = {40041702}, issn = {2730-6151}, abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.}, }
@article {pmid40041671, year = {2025}, author = {Zernadji, W and Rahmani, F and Jebri, S and Hamdi, M and Khammassi, M and Dhib, S and Hmaied, F}, title = {Distribution of Microbial Contaminants of Minimally Processed Salads Produced in Tunisia: Need to Strengthen Good Hygiene Practices.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {9570620}, pmid = {40041671}, issn = {2314-5765}, abstract = {The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 10[6] CFU/g) and total coliforms (> 10[4] CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81 ± 0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.}, }
@article {pmid40037241, year = {2025}, author = {Lu, Z and Zeng, J and Wang, L and Zhu, D and Cheng, X and Huang, D and Zhang, J and Yuan, L}, title = {The influence of turbulence caused by hydraulic structures on the community assembly of epilithic biofilms in rivers.}, journal = {Journal of environmental management}, volume = {378}, number = {}, pages = {124645}, doi = {10.1016/j.jenvman.2025.124645}, pmid = {40037241}, issn = {1095-8630}, mesh = {*Biofilms ; *Rivers/microbiology ; Ecosystem ; Hydrodynamics ; }, abstract = {The assembly mechanisms of riverine biofilm communities in river systems represent a central question in aquatic microbial ecology. However, the influence of turbulence on the assembly of generalists and specialists within biofilms remains poorly understood. This study aimed to address this gap by examining a river with multiple spur dikes, using high-throughput sequencing, ecological network analysis, and partial least squares path modeling to explore the assembly process and community structure of biofilms. The results revealed that turbulence intensity (0.029 m/s) and kinetic energy (0.0018 m[2]/s[2]) were significantly higher at the heads of spur dikes compared to the tails. Notably, hydrodynamic parameters explained 6.50% of biofilm community variance, highlighting their underappreciated role as deterministic drivers of microbial assembly. Habitat specialists exhibited heightened sensitivity to hydrodynamic fluctuations, occupying central positions in co-occurrence networks. Additionally, turbulence intensity and kinetic energy emerged as the primary drivers of community assembly, influencing critical ecological processes such as homogeneous selection, drift and dispersal limitation. At the head of spur dikes, a high turbulence region, the weakened impact of homogeneous selection, combined with an increase in dispersal limitation, created conditions that particularly favored habitat generalists. Conversely, low turbulence dike tails supported specialist proliferation via strengthened deterministic selection and nutrient-driven niche partitioning. Furthermore, the partial least squares path modeling confirmed that turbulence dominates the assembly process of microbial specialists and generalists. This study revealed the pivotal role of turbulence in shaping biofilm assembly and driving the spatial differentiation of generalists and specialists, offering fresh insights into the complex interplay between hydrodynamics and microbial ecology in rivers impacted by hydraulic structures. These findings significantly enhance the understanding of biofilm assembly mechanisms and their broader implications for effective river ecosystem management.}, }
@article {pmid40036370, year = {2025}, author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M}, title = {A specific blend of prebiotics and postbiotics improved the gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, pmid = {40036370}, issn = {1525-3163}, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Prebiotics/administration &amp; dosage ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/classification ; Male ; }, abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of the long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After 2 d of stabilization, the 8-d parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites such as propionate (donor-dependent), acetate, and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with the test product compared to control. Repeated supplementation with the test product was therefore able to induce-in vitro-a positive modulation of the microbiome originated from dogs with soft stools.}, }
@article {pmid40035794, year = {2025}, author = {Vieira, AR and Camacho, F and Sousa, ML and Luelmo, S and Santarém, N and Cordeiro-da-Silva, A and Leão, PN}, title = {The Cyanobacterial Oxadiazine Nocuolin A Shows Broad-Spectrum Toxicity Against Protozoans and the Nematode C. elegans.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {9}, pmid = {40035794}, issn = {1432-184X}, support = {2022.04572.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.04285.CEECIND/CP1663/CT0004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 952374//Horizon 2020/ ; }, mesh = {Animals ; *Cyanobacteria/chemistry/metabolism ; *Caenorhabditis elegans/drug effects ; *Dictyostelium/drug effects ; }, abstract = {Cyanobacteria, known to be rich sources of valuable natural products (NPs) with relevant biological properties, are a unique subject to study the interplay between chemistry and ecology. Cultivation of cyanobacteria as isolated strains may only reveal a small fraction of their NPs. In contrast, investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Cyanobacteria and amoebae are known to co-exist in diverse environments, but the interaction between these organisms has been poorly investigated. Defense strategies against grazer organisms may rely on morphological changes including biofilm formation or increased motility; however, secretion of toxic metabolites seems to be more effective on this regard. Among the most structurally unique cyanobacterial secondary metabolites is nocuolin A, an 1,2,3-oxadiazine metabolite isolated from the cyanobacterial strain Nodularia sp. LEGE 06071 that exhibits potent anti-proliferative activity against several human cancer lines, associated with impairment of mitochondrial oxidative phosphorylation. In this work, we show that nocuolin A is toxic against two well-known model amoebae, Acanthamoeba and Dictyostelium, leading to amoebae encystation and decrease in viability. In addition, in lawn grazing assays, we observed that Nodularia sp. LEGE 06071, the producer strain of nocuolin A, was not grazed by amoeba, while a related strain, which does not produce detectable levels of nocuolin A, was. These results support the possible involvement of nocuolin A as a chemical mediator during the interaction between these organisms. Furthermore, we show that this cyanobacterial metabolite also exhibits potent toxicity against other protozoan organisms and a free-living nematode, making it an interesting broad-spectrum scaffold for the development of antiprotozoal or anti-helminthic drugs.}, }
@article {pmid40034844, year = {2024}, author = {Thompson, MA and Valentine, DL and Peng, X}, title = {Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtae028}, pmid = {40034844}, issn = {2633-6685}, abstract = {Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.}, }
@article {pmid40033656, year = {2025}, author = {Orr, JA and Armitage, DW and Letten, AD}, title = {Coexistence Theory for Microbial Ecology, and Vice Versa.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70072}, pmid = {40033656}, issn = {1462-2920}, support = {DE230100373//Australian Research Council/ ; DP220103350//Australian Research Council/ ; DE250100656//Australian Research Council/ ; }, mesh = {*Ecology/methods ; *Microbiota ; Ecosystem ; Models, Biological ; Bacteria ; }, abstract = {Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory can be used to disentangle the contributions different mechanisms (e.g., resource partitioning, environmental variability) make to species coexistence. We begin with a short primer on the fundamental concepts of coexistence theory, with an emphasis on the relevance to microbial communities. We next present a systematic review, which highlights the paucity of empirical applications of coexistence theory in microbial systems. In light of this gap, we then identify and discuss ways in which: (i) coexistence theory can help to answer fundamental and applied questions in microbial ecology, particularly in spatio-temporally heterogeneous environments, and (ii) experimental microbial systems can be leveraged to validate and advance coexistence theory. Finally, we address several unique but often surmountable empirical challenges posed by microbial systems, as well as some conceptual limitations. Nevertheless, thoughtful integration of coexistence theory into microbial ecology presents a wealth of opportunities for the advancement of both theoretical and microbial ecology.}, }
@article {pmid40028056, year = {2025}, author = {Vignolle, A and Zehl, M and Kirkegaard, RH and Vignolle, GA and Zotchev, SB}, title = {Secondary Metabolite Biosynthesis Potential of Streptomyces Spp. from the Rhizosphere of Leontopodium nivale Subsp. alpinum.}, journal = {ACS omega}, volume = {10}, number = {7}, pages = {7163-7171}, pmid = {40028056}, issn = {2470-1343}, abstract = {Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeutics. With high rediscovery rates, the attention has shifted to Streptomyces from unique ecological niches for the discovery of new SMs. The plant rhizosphere is one such niche, characterized by complex chemical interactions between the plant and its rhizobiome, which can elicit the production of SMs in Streptomyces. In the present study, 18 Streptomyces strains were previously isolated from the rhizosphere of the rare alpine medicinal plant Leontopodium nivale subsp. alpinum were investigated for their capacity to produce secondary metabolites. Genomes of these strains were analyzed for the presence of SM biosynthetic gene clusters (BGCs). In total, 551 BGCs were detected, of which 217 could not be linked to known SMs. These isolates were cultivated in different media known to support the production of SMs, and 15 out of the 54 methanolic extracts from these cultures exhibited antimicrobial activities. Subsequent liquid chromatography-mass spectrometry analyses of the bioactive extracts led to a putative identification of 69 known SMs as well as 16 potentially new molecules. The results of this study may provide a basis for the discovery of unique molecules with the potential to be developed as drugs against a variety of human diseases.}, }
@article {pmid40025674, year = {2025}, author = {Abdolahpur Monikh, F and Quik, JTK and Wiesner, MR and Tapparo, A and Pastore, P and Grossart, HP and Akkanen, J and Kortet, R and Kukkonen, JVK}, title = {Importance of Attachment Efficiency in Determining the Fate of PS and PVC Nanoplastic Heteroaggregation with Natural Colloids Using a Multimedia Model.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {9}, pages = {4674-4683}, pmid = {40025674}, issn = {1520-5851}, mesh = {*Polyvinyl Chloride/chemistry ; Colloids/chemistry ; *Polystyrenes/chemistry ; Silicon Dioxide/chemistry ; Calcium Chloride/chemistry ; Models, Chemical ; Nanoparticles ; }, abstract = {Here, we assessed the heteroaggregation of polystyrene (PS) and poly(vinyl chloride) (PVC) nanoplastics with SiO2 as a model of natural colloids. Homoaggregation and heteroaggregation were evaluated as a function of CaCl2 (0-100 mM) and natural organic matter (NOM) (50 mg L[-1]) at a designated concentration of nanoplastics (200 μg L[-1]). Critical coagulation concentrations (CCC) of nanoplastics were determined in homoaggregation and heteroaggregation experiments with SiO2 and CaCl2. The attachment efficiency (α) was calculated by quantifying the number of nanoplastics in the presence of CaCl2, NOM, and SiO2 using single-particle inductively coupled plasma mass spectrometry (spICP-MS) and pseudo-first-order kinetics. The calculated α was fed into the SimpleBox4Plastics model to predict the fate of nanoplastics across air, water, soil, and sediment compartments. Nanoplastics exhibited high stability against homoaggregation, while significant heteroaggregation with SiO2 occurred at CaCl2 concentrations above 100 mM. The influence of NOM was also evaluated, showing a reduction in heteroaggregation with SiO2 for both nanoplastic types. Sensitivity analysis indicated that the degradation half-life of the tested nanoplastics had a more significant impact on persistence than did α. The results emphasize the environmental stability of nanoplastics, particularly in freshwater and soil compartments, and the critical role of NOM and emission pathways in determining their fate.}, }
@article {pmid40024538, year = {2025}, author = {Sliti, A and Kim, RH and Lee, D and Shin, JH}, title = {Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules.}, journal = {Microbial pathogenesis}, volume = {202}, number = {}, pages = {107405}, doi = {10.1016/j.micpath.2025.107405}, pmid = {40024538}, issn = {1096-1208}, mesh = {*Probiotics/adverse effects ; *Whole Genome Sequencing ; Genome, Bacterial ; *Fecal Microbiota Transplantation ; Humans ; *Lacticaseibacillus paracasei/genetics/isolation &amp; purification/classification ; Phylogeny ; Computer Simulation ; Virulence Factors/genetics ; Feces/microbiology ; Capsules ; Plasmids/genetics ; Prophages/genetics ; Multigene Family ; Gastrointestinal Microbiome ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.}, }
@article {pmid40022977, year = {2025}, author = {Noiset, P and Héger, M and Salmon, C and Kwapong, P and Combey, R and Thevan, K and Warrit, N and Rojas-Oropeza, M and Cabirol, N and Zaragoza-Trello, C and Rasmussen, C and Nkoba, K and Vereecken, NJ}, title = {Ecological and evolutionary drivers of stingless bee honey variation at the global scale.}, journal = {The Science of the total environment}, volume = {969}, number = {}, pages = {178945}, doi = {10.1016/j.scitotenv.2025.178945}, pmid = {40022977}, issn = {1879-1026}, mesh = {*Honey/analysis ; Bees ; Animals ; Biological Evolution ; }, abstract = {Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.}, }
@article {pmid40022770, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {277}, number = {}, pages = {123328}, doi = {10.1016/j.watres.2025.123328}, pmid = {40022770}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; *Water Purification/methods ; *Filtration/methods ; *Sand/chemistry ; Netherlands ; Water Microbiology ; }, abstract = {Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.}, }
@article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Soil Microbiology ; Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, }
@article {pmid40012773, year = {2025}, author = {Sun, P and Wu, Y and Zhu, P and Wang, J and Yu, X and Guo, W}, title = {Spartina alterniflora invasion significantly alters the assembly and structure of soil bacterial communities in the Yellow River Delta.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525632}, pmid = {40012773}, issn = {1664-302X}, abstract = {Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.}, }
@article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, }
@article {pmid40005728, year = {2025}, author = {Yi, S and Wu, H and Lin, Y and Cha, X and Shang, Y}, title = {Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005728}, issn = {2076-2607}, support = {R21 AG050009/AG/NIA NIH HHS/United States ; 32260624//the National Natural Science Foundation of China/ ; 202202AG050009//Yunnan Major Scientific and Technological Projects/ ; }, abstract = {The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide sul1 gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide sul2 and sul3 genes, both at 1.79%. Among six tetracycline resistance genes, only tetK and tetM were detected. For β-lactam antibiotics, blaTEM, blaVIM, and blaSHV genes were present, while blaOXA was absent. In aminoglycoside resistance genes, aadB was not detected, while detection rates for aac(3')-IIa, acrB, and aadA1 were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol Cat gene was detected at a rate of 14.29%, whereas floR was absent. For polypeptide resistance, VanC was detected at 3.57%, with EmgrB not detected. All three quinolone genes were detected, with detection rates of 8.92% for GyrA, 39.29% for GyrB, and 37.5% for ParC. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security.}, }
@article {pmid40005607, year = {2025}, author = {Li, S and Zhuang, W and Feng, X and Warren, A and Gong, J}, title = {Morphology and Molecular Phylogeny of Four Anaerobic Ciliates (Protista, Ciliophora, Armophorea), with Report of a New Species and a Unique Arrangement Pattern of Dikinetids in Family Metopidae.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005607}, issn = {2076-2607}, support = {41976086, 42276094//National Natural Science Foundation of China/ ; }, abstract = {The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130-190 × 90-120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87-107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively.}, }
@article {pmid40005589, year = {2025}, author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM}, title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005589}, issn = {2076-2607}, support = {Merck Future Insight Prize//Merck KGaA/ ; }, abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.}, }
@article {pmid40003826, year = {2025}, author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ}, title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003826}, issn = {2075-4450}, support = {57545//Universidad Nacional de Colombia/ ; }, abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.}, }
@article {pmid40003751, year = {2025}, author = {Rampanti, G and Cardinali, F and Ferrocino, I and Milanović, V and Garofalo, C and Osimani, A and Aquilanti, L}, title = {Deciphering the Microbiota of Edible Insects Sold by Street Vendors in Thailand Using Metataxonomic Analysis.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003751}, issn = {2075-4450}, abstract = {The aim of the present study was to investigate the microbiota of processed ready-to-eat (fried or boiled) edible insects sold by street vendors at local green markets in Thailand (Bangkok and Koh Samui). To this end, samples of 4 insect species (rhino beetle adults, silkworm pupae, giant waterbugs adults, and black scorpions) were collected and analyzed through viable counting and metataxonomic analysis. Enterobacteriaceae showed counts below 1 log cfu g[-1] in all samples, except for black scorpions, which showed elevated counts reaching up to 4 log cfu g[-1]. Total mesophilic aerobes counts were up to 8 log cfu g[-1] in all the analyzed samples. Counts below 1 log cfu g[-1] were observed for Escherichia coli, Staphylococcus aureus, sulfite-reducing clostridia viable cells and spores, and Bacillus cereus. All the samples showed the absence of Listeria monocytogenes and Salmonella spp. According to metataxonomic analysis, 14 taxa were consistently present across all insect samples, including Dellaglioa algida, Latilactobacillus curvatus, Latilactobacillus sakei, Acetobacteraceae, Apilactobacillus kunkeei, Bombilactobacillus spp., Enterobacteriaceae, Gilliamella spp., Lactobacillus spp., Lactobacillus apis, Streptococcus thermophilus, Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Weissella spp. Minority taxa included Alcaligenes spp., Brochothrix thermosphacta, Psychrobacter spp., Staphylococcus saprophyticus, Lactobacillus melliventris, Pediococcus spp., Levilactobacillus brevis, and Snodgrassella alvi.}, }
@article {pmid39998093, year = {2025}, author = {Varini, C and Manganelli, M and Scardala, S and Antonelli, P and Losasso, C and Testai, E}, title = {An Update of Tetrodotoxins Toxicity and Risk Assessment Associated to Contaminated Seafood Consumption in Europe: A Systematic Review.}, journal = {Toxins}, volume = {17}, number = {2}, pages = {}, pmid = {39998093}, issn = {2072-6651}, support = {project n. RF-2021-12373885//Ministry of Health of Italy/ ; }, mesh = {Risk Assessment ; Europe ; *Food Contamination/analysis ; *Seafood/analysis ; Humans ; Animals ; *Tetrodotoxin/toxicity/analysis ; }, abstract = {Following the occurrence of Tetrodotoxins (TTXs) in Europe-a group of neurotoxins identified in Asia, where fatalities occurred after the ingestion of contaminated pufferfish-the EFSA proposed a limit of 44 µg of TTX/kg of shellfish meat in mollusks in 2017, to protect heavy consumers. The limit was based on an acute reference dose (ARfD) derived from the few available data on TTX toxicity. TTX is expected to increase with sea-surface warming; indeed, it has been found in spring/summer in mollusks in Europe, with concentrations often exceeding this limit. Due to the numerous uncertainties of the EFSA's ARfD, we conducted a systematic review to provide an update on TTX toxicity. Out of 12,741 articles retrieved from PubMed, Science Direct, and Scopus since 2017, only 17 were eligible for data extraction. Our results show that they are not sufficient to modify the EFSA's conclusions. Furthermore, our analysis of occurrence data in European seafood, to assess the current risk of exposure to TTX, reveals several gaps, such as different LODs/LOQs and seasonal monitoring not allowing comparisons between areas and too few analyzed sites. However, the presence of positive samples exceeding the EFSA limit indicates a potential risk even for general consumers, highlighting the urgency to address these knowledge gaps.}, }
@article {pmid39996333, year = {2025}, author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L}, title = {Antarctic bacterial natural products: from genomic insights to drug discovery.}, journal = {Natural product reports}, volume = {42}, number = {5}, pages = {774-787}, doi = {10.1039/d4np00045e}, pmid = {39996333}, issn = {1460-4752}, mesh = {*Biological Products/chemistry/pharmacology/metabolism ; Antarctic Regions ; *Drug Discovery ; *Bacteria/genetics/chemistry/metabolism ; Genomics ; Molecular Structure ; }, abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.}, }
@article {pmid39992142, year = {2025}, author = {Sun, L and Wang, Q and Huang, J and Wang, H and Yu, Z}, title = {Disrupting the balance: how acne duration impacts skin microbiota assembly processes.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0260324}, pmid = {39992142}, issn = {2165-0497}, support = {32000054, 32170071//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; *Acne Vulgaris/microbiology ; *Skin/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Adult ; Young Adult ; Skin Microbiome ; }, abstract = {Growing interest in the impact of microbial balance on health has driven studies on the ecological processes shaping the skin microbiota. Skin diseases, which alter the skin's local environment, can disrupt the microbial structure and interact with the disease itself. However, research on microbial assembly in diseased skin remains limited. In this study, we applied ecological models to characterize the processes shaping the skin microbiota in acne patients, considering the impact of disease duration on both skin pores and surfaces using bacterial amplicon sequencing. Our results revealed a significant shift in microbial diversity on the skin surface of patients with long-term acne. Further microbial community analyses showed a transition in ecological processes from healthy to diseased skin. Microbial communities on the skin surfaces of healthy controls and individuals with short-duration acne were primarily driven by heterogeneous selection, whereas microbial drift dominated the assembly process in the long-duration groups. Using the Sloan neutral model, we classified amplicon sequence variants (ASVs) into high-effect and low-effect groups based on relative abundance and sample occurrence. High-effect ASVs, likely exerting a greater ecological influence, were predominantly represented by Cutibacterium across all acne-affected skin groups, while Staphylococcus became enriched among high-effect ASVs in patients with long-term acne. Functional profiling further demonstrated that high-effect ASVs were significantly enriched in motility-related pathways. Additionally, we observed a reduction in microbial network complexity on skin surfaces as disease duration increased. Overall, the ecological dynamics of skin microbial communities may offer valuable insights into the mechanisms underlying disease onset and persistence.IMPORTANCEThe skin microbiota plays a critical role in acne development, yet the processes governing microbial assembly during acne progression remain poorly understood. Previous studies predominantly focused on factors such as acne severity, location, and duration in relation to skin microbial structure, with little attention given to the ecological mechanisms shaping the communities. In this study, we applied ecological models to investigate the processes influencing microbial assembly of skin microbiota in acne patients with varying disease durations and examined functions of ecologically important non-neutral amplicon sequence variants (ASVs). Our findings reveal a transition in ecological processes from deterministic to neutral processes as acne duration increased, with non-neutral ASVs potentially contributing to acne pathogenicity and persistence. These insights contribute to a deeper understanding of the ecological dynamics underlying acne and indicate that targeting these non-neutral ASVs or their associated functions may serve as the basis for future therapeutic strategies.}, }
@article {pmid39992122, year = {2025}, author = {Li, X and Wang, H and Zang, Y and Xue, S and Xin, J and Liu, L and Tang, X and Chen, J}, title = {Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0243724}, pmid = {39992122}, issn = {1098-5336}, support = {42176154,42206117//MOST | National Natural Science Foundation of China (NSFC)/ ; U1806213//MOST | NSFC | National Natural Science Foundation of China-Shandong Joint Fund (-)/ ; 2019YFD0901204//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2024QD017//| Natural Science Foundation of Shandong Province ()/ ; }, mesh = {*Rhizosphere ; *Zosteraceae/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; *Soil Microbiology ; Ecosystem ; }, abstract = {Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.}, }
@article {pmid39991271, year = {2025}, author = {Morales, SE and Tobias-Hünefeldt, SP and Armstrong, E and Pearman, WS and Bogdanov, K}, title = {Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf001}, pmid = {39991271}, issn = {2730-6151}, abstract = {Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.}, }
@article {pmid39988434, year = {2025}, author = {Howells, G and Sezmis, AL and Blake, C and McDonald, MJ}, title = {Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70061}, pmid = {39988434}, issn = {1462-2920}, support = {APP1186140//National Health and Medical Research Council/ ; DP220103548//Australian Research Council/ ; }, mesh = {*Pseudomonas fluorescens/genetics/growth &amp; development/physiology ; *Escherichia coli/genetics/growth &amp; development/physiology ; Coculture Techniques ; Adaptation, Physiological ; Genome, Bacterial ; Whole Genome Sequencing ; }, abstract = {Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co-culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.}, }
@article {pmid39987915, year = {2025}, author = {De Luca, G and Barakat, M and Verméglio, A and Achouak, W and Heulin, T}, title = {The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70059}, pmid = {39987915}, issn = {1462-2920}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Adaptation, Physiological/genetics ; Genome, Bacterial ; Soil Microbiology ; *Burkholderiaceae/genetics/physiology/classification ; }, abstract = {Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.}, }
@article {pmid39987257, year = {2025}, author = {Zhang, X and Ta, N and Yi, S and Xiong, H}, title = {Intolerance of uncertainty and mental health in patients with IBD: the mediating role of maladaptive coping.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6464}, pmid = {39987257}, issn = {2045-2322}, mesh = {Humans ; *Adaptation, Psychological ; Female ; Male ; *Inflammatory Bowel Diseases/psychology ; Uncertainty ; Adult ; *Mental Health ; Middle Aged ; Anxiety/psychology ; Surveys and Questionnaires ; Depression/psychology ; Young Adult ; }, abstract = {The aim of this study was to investigate the relationship between intolerance of uncertainty (IU) and mental health in patients with Inflammatory Bowel Disease (IBD), and to explore the mediating role of coping styles. A questionnaire was administered to adult patients with IBD, which included general demographic information, the Intolerance of Uncertainty Scale, the Generalized Anxiety Disorder-7, and the Patient Health Questionnaire-9. The study ultimately included validated questionnaires from 163 IBD patients. Intolerance of uncertainty was significantly and positively correlated with anxiety (r = 0.738, p < 0.01) and depression (r = 0.683, p < 0.01). The mediating effect of adaptive coping style was not significant. The maladaptive coping style partially mediated the relationship between IU and anxiety, as well as between IU and depression, with the mediating effect size of 25.5% and 34.2%, respectively. Our findings emphasize the impact of the inability to tolerate uncertainty on the mental health of patients with IBD. It suggests that interventions can be implemented to enhance IBD patients' tolerance of uncertainty and to modify their maladaptive coping styles to promote mental health. This offers a valuable framework for psychological interventions for IBD patients.}, }
@article {pmid39985718, year = {2025}, author = {Gufwan, LA and Peng, L and Gufwan, NM and Lan, S and Wu, L}, title = {Enhancing Soil Health Through Biocrusts: A Microbial Ecosystem Approach for Degradation Control and Restoration.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {8}, pmid = {39985718}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Fungi/metabolism ; *Environmental Restoration and Remediation/methods ; Biodiversity ; Lichens ; Cyanobacteria ; Microbiota ; Bryophyta ; Biodegradation, Environmental ; }, abstract = {Escalating global concerns about soil degradation, driven by erosion, salinization, compaction, pollution, and organic matter loss, highlights the critical need for sustainable remediation. Biocrusts-complex communities of cyanobacteria, algae, lichens, bryophytes, and fungi-play a pivotal role in soil stabilization, erosion prevention, and nutrient cycling. This study presents recent advancements in biocrust application for soil management and restoration, focusing on artificial biocrusts as a nature-based solution biotechnology. It emphasizes their effectiveness in enhancing soil quality, biodiversity, and ecosystem functionality. Researchers are leveraging these microbial communities to develop strategies that improve soil health and rehabilitate degraded landscapes. The review concludes that biocrusts are a viable strategy for boosting soil resilience and enhancing soil health against environmental stressors. It recommends future research on their long-term ecological impacts and methods to enhance their functionality.}, }
@article {pmid39978646, year = {2025}, author = {Kij, A and Kieronska-Rudek, A and Bar, A and Czyzynska-Cichon, I and Strus, M and Kozien, L and Wiecek, G and Zeber-Lubecka, N and Kulecka, M and Kwiatkowski, G and Przyborowski, K and Mohaissen, T and Sternak, M and Buczek, E and Zakrzewska, A and Proniewski, B and Kus, K and Franczyk-Zarow, M and Kostogrys, RB and Pieterman, EJ and Princen, HMG and Chlopicki, S}, title = {Low phylloquinone intake deteriorates endothelial function in normolipidemic and dyslipidaemic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {140}, number = {}, pages = {109867}, doi = {10.1016/j.jnutbio.2025.109867}, pmid = {39978646}, issn = {1873-4847}, mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Endothelium, Vascular/physiopathology/drug effects/metabolism ; *Vitamin K 1/administration &amp; dosage/blood ; *Dyslipidemias/physiopathology/metabolism ; Mice ; Vitamin K 2/analogs &amp; derivatives/metabolism ; Liver/metabolism ; Vasodilation/drug effects ; Aorta/metabolism ; Gastrointestinal Microbiome ; Dietary Supplements ; }, abstract = {While the plasma phylloquinone (PK) concentration is inversely correlated with cardiovascular risk, the involvement of PK in regulating endothelial function has not been directly investigated. Therefore, in this study we assessed the effects of short-term treatment with PK-deficient diets (5-10 weeks) on endothelial function in normolipidemic 14-week-old male C57BL/6JCmd mice and age-matched dyslipidaemic male E3L.CETP mice. Our results show that in normolipidemic mice dietary PK deficiency was associated with a marked reduction of PK levels in the plasma and liver (liquid chromatography-mass spectrometry measurements) and with impaired endothelium-dependent vasodilation assessed in vivo by magnetic resonance imaging (MRI). Dietary PK deficiency-induced endothelial dysfunction was fully reversed by PK supplementation. In dyslipidaemic E3L.CETP mice, dietary PK deficiency exacerbated preexisting endothelial dysfunction. Furthermore, dietary PK deficiency decreased menaquinone-4 (MK-4) levels in the aorta but did not affect blood coagulation (calibrated automated thrombography), microbiota composition (culturing and next-generation sequencing), and gut menaquinone production. In conclusion, our study demonstrated for the first time that sufficient dietary PK intake supports endothelial function in normolipidemic and dyslipidaemic mice indicating nutritional significance of dietary PK in the maintenance of endothelial function in humans.}, }
@article {pmid39976768, year = {2025}, author = {Kauserud, H and Martin-Sanchez, PM and Estensmo, EL and Botnen, S and Morgado, L and Maurice, S and Høiland, K and Skrede, I}, title = {Yeasts Prefer Daycares and Molds Prefer Private Homes.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {7}, pmid = {39976768}, issn = {1432-184X}, support = {741332//Horizon 2020/ ; PID2021-123184OA-I00//MICIN/AEI, Spain/ ; }, mesh = {*Fungi/classification/isolation &amp; purification/genetics ; *Yeasts/isolation &amp; purification/classification/genetics ; Humans ; Dust/analysis ; *Air Pollution, Indoor/analysis ; *Child Day Care Centers ; *Mycobiome ; Norway ; *Air Microbiology ; *Housing ; DNA, Fungal/genetics ; Child ; Child, Preschool ; }, abstract = {Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children's daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.}, }
@article {pmid39972634, year = {2025}, author = {de Sousa, T and Silva, C and Igrejas, G and Hébraud, M and Poeta, P}, title = {The Interactive Dynamics of Pseudomonas aeruginosa in Global Ecology.}, journal = {Journal of basic microbiology}, volume = {65}, number = {4}, pages = {e70004}, doi = {10.1002/jobm.70004}, pmid = {39972634}, issn = {1521-4028}, support = {//This work was supported by grant 2020.05332.BD, and the projects UI/00772 and LA/P/0059/2020 funded by the Portuguese Foundation for Science and Technology (FCT)./ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/physiology ; Humans ; Ecosystem ; *Pseudomonas Infections/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Biodiversity ; Ecology ; }, abstract = {Pseudomonas aeruginosa is an opportunistic bacterium widely distributed in both natural and urban environments, playing a crucial role in global microbial ecology. This article reviews the interactive dynamics of P. aeruginosa across different ecosystems, highlighting its capacity for adaptation and resistance in response to environmental and therapeutic pressures. We analyze the mechanisms of antibiotic resistance, including the presence of resistance genes and efflux systems, which contribute to its persistence in both clinical and nonclinical settings. The interconnection between human, animal, and environmental health, within the context of the One Health concept, is discussed, emphasizing the importance of monitoring and sustainable management practices to mitigate the spread of resistance. Through a holistic approach, this work offers insights into the influence of P. aeruginosa on public health and biodiversity.}, }
@article {pmid39971349, year = {2025}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.}, journal = {Annual review of biophysics}, volume = {54}, number = {1}, pages = {401-426}, pmid = {39971349}, issn = {1936-1238}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, mesh = {*Models, Biological ; Animals ; Humans ; }, abstract = {All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework-soft modes-to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39970705, year = {2025}, author = {Yuan, K and Xu, H and Li, S and Coker, OO and Liu, W and Wang, L and Zhang, X and Yu, J}, title = {Intraneoplastic fungal dysbiosis is associated with colorectal cancer progression and host gene mutation.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105608}, pmid = {39970705}, issn = {2352-3964}, mesh = {Humans ; *Colorectal Neoplasms/pathology/genetics/microbiology/etiology ; *Dysbiosis/microbiology ; *Mutation ; Disease Progression ; Female ; Male ; Middle Aged ; *Fungi/genetics/classification ; Microsatellite Instability ; Aged ; Adenoma/microbiology/genetics/pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; }, abstract = {BACKGROUND: The relationship between intraneoplastic fungi and colorectal cancer (CRC) progression remains largely unclear. Here, we investigated fungal community changes in adenoma and CRC and their correlation with host genetic mutations.<br><br>METHODS: We obtained 261 tissue biopsies from two geographically distinct cohorts of CRC and adenoma patients, with each individual contributing 2-5 biopsies from lesions and 2 from adjacent normal tissues. 18S ribosomal RNA gene sequencing was used for microbial profiling. Host genetic alterations including KRAS mutations and microsatellite instability (MSI) were detected concurrently.<br><br>FINDINGS: Intra-neoplastic fungal composition significantly differed between CRC and adenoma in two independent cohorts, with enrichment of highly variable fungi (HVF) in CRC. Six HVFs exhibited higher abundances in adenoma and CRC compared to adjacent normal tissues with Malassezia showing a progressive increase from adenoma to CRC. Fungi intratumoral heterogeneity index also increased from adenoma through stages I to IV of CRC. Intra-tumoral fungi-fungi co-abundance analysis indicated stronger positive interactions in CRC than in adenoma, with increasingly robust links among intra-tumoral fungi along adenoma-CRC progression, primarily driven by Malassezia and Aspergillus. Furthermore, fungal heterogeneity was significantly correlated with host genetic mutations, with higher risk indices in CRC tissues harboring KRAS and MSI mutations. Thirteen fungi stratified CRC samples with KRAS mutations, achieving an area under the curve (AUC) of 0.86, while those associated with MSI status showed an AUC of 0.89.<br><br>INTERPRETATION: This study demonstrates that intraneoplastic fungal community alterations occur between adenoma and CRC, with increasing heterogeneity associated with host genetic mutations, emphasizing the role of fungal dysbiosis in CRC.<br><br>FUNDING: This work was supported by RGC Research Impact Fund Hong Kong (R4032-21F); RGC-CRF (C4008-23W); Strategic Seed Funding Collaboration Research Scheme CUHK (3133344); Strategic Impact Enhancement Fund CUHK (3135509); Impact case for RAE CUHK (3134277).}, }
@article {pmid39970561, year = {2025}, author = {Gullì, M and Cangioli, L and Frusciante, S and Graziano, S and Caldara, M and Fiore, A and Klonowski, AM and Maestri, E and Brunori, A and Mengoni, A and Pihlanto, A and Diretto, G and Marmiroli, N and Bevivino, A}, title = {The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178872}, doi = {10.1016/j.scitotenv.2025.178872}, pmid = {39970561}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development/physiology ; *Charcoal ; Fertilizers ; *Agriculture/methods ; *Soil Microbiology ; Soil/chemistry ; Mycorrhizae ; Microbiota ; }, abstract = {Adoption of sustainable maize cropping practices is urgently needed. Synthetic microbial communities (SynComs) made of plant growth-promoting microorganisms (PGPMs), coupled with biochar from residual biomass, offer an environmentally compatible alternative to inorganic fertilizers and may improve soil fertility. This article extends in a two-year field trial with preliminary results obtained in previous pot experiments, monitoring plant physiology, soil biology and chemistry, and kernel metabolomics. Here, we report the synergistic effect of the co-application of biochar, SynComs, and arbuscular mycorrhizal fungi on the soil microbiome, maize growth, and kernel metabolomic profile. SynComs application did not affect the diversity and richness of soil microbial communities; therefore, it posed a low risk of long-term effects on soil microbial ecology. With SynComs and biochar co-application to the soil, the physiology of maize plants was characterized by higher chlorophyll content, ear weight, and kernel weight. The combination of SynComs and biochar also affected the kernel metabolome, resulting in enriched health-beneficial and anti-stress metabolites. Since the preliminary evidence on the environmental and economic impact of these new associations was more favorable than that of conventional fertilizers, it seems reasonable that their large-scale implementation can eventually favor the transition to more sustainable agriculture.}, }
@article {pmid39970001, year = {2025}, author = {Vo, L and Avgidis, F and Mattingly, HH and Edmonds, K and Burger, I and Balasubramanian, R and Shimizu, TS and Kazmierczak, BI and Emonet, T}, title = {Nongenetic adaptation by collective migration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {8}, pages = {e2423774122}, pmid = {39970001}, issn = {1091-6490}, support = {R01 GM138533/GM/NIGMS NIH HHS/United States ; R01 GM106189/GM/NIGMS NIH HHS/United States ; R01GM138533//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM106189//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31 GM149174/GM/NIGMS NIH HHS/United States ; F31GM149174-01//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Escherichia coli/physiology/genetics ; *Adaptation, Physiological ; *Chemotaxis/physiology ; Phenotype ; Escherichia coli Proteins/metabolism/genetics ; }, abstract = {Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.}, }
@article {pmid39963424, year = {2024}, author = {Höner Zu Siederdissen, C and Spangenberg, J and Bisdorf, K and Krautwurst, S and Srivastava, A and Marz, M and Taubert, M}, title = {Nanopore sequencing enables novel detection of deuterium incorporation in DNA.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3584-3594}, pmid = {39963424}, issn = {2001-0370}, abstract = {Identifying active microbes is crucial to understand their role in ecosystem functions. Metabolic labeling with heavy, non-radioactive isotopes, i.e., stable isotope probing (SIP), can track active microbes by detecting heavy isotope incorporation in biomolecules such as DNA. However, the detection of heavy isotope-labeled nucleotides directly during sequencing has, to date, not been achieved. In this study, Oxford nanopore sequencing was utilized to detect heavy isotopes incorporation in DNA molecules. Two isotopes widely used in SIP experiments were employed to label a bacterial isolate: deuterium (D, as D2O) and carbon-13 ([13]C, as glucose). We hypothesize that labeled DNA is distinguishable from unlabeled DNA by changes in the nanopore signal. To verify this distinction, we employed a Bayesian classifier trained on signal distributions of short oligonucleotides (k-mers) from labeled and unlabeled sequencing reads. Our results show a clear distinction between D-labeled and unlabeled reads, based on changes in median and median absolute deviation (MAD) of the nanopore signals for different k-mers. In contrast, [13]C-labeled DNA cannot be distinguished from unlabeled DNA. For D, the model employed correctly predicted more than 85% of the reads. Even when metabolic labeling was conducted with only 30% D2O, 80% of the obtained reads were correctly classified with a 5% false discovery rate. Our work demonstrates the feasibility of direct detection of deuterium incorporation in DNA molecules during Oxford nanopore sequencing. This finding represents a first step in establishing the combined use of nanopore sequencing and SIP for tracking active organisms in microbial ecology.}, }
@article {pmid39962695, year = {2025}, author = {Peng, SW and Zhang, GY and Jiao, YY}, title = {[Microbial Ecology in the Mask-derived Plastisphere in a Water Environment].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {2}, pages = {1193-1202}, doi = {10.13227/j.hjkx.202402057}, pmid = {39962695}, issn = {0250-3301}, mesh = {*Masks/microbiology ; *Microplastics/analysis ; *Water Microbiology ; COVID-19/prevention &amp; control ; *Microbiota ; *Ecosystem ; }, abstract = {As a result of the impact of COVID-19 and other respiratory diseases, the regular use of medical masks and the associated risk that the mask waste enters the water environment have increased, and the mask-derived microplastics are finally posing a potential impact on the aquatic ecological environment. This study explored the microbial diversity, function, assembly mechanism, and ecological network in the plastisphere derived from different layers of masks. The results indicated that the plastisphere in each layer had a unique microbial community, and the community richness gradually increased over time. The functions of microbial communities in the plastisphere, including pathogenicity, phototrophy, compound degradation, and the functions related to the cycling of carbon, nitrogen, and sulfur, changed significantly over time. As to the microbial assembly mechanism in the plastisphere, stochastic processes were more dominant （NST>0.5）, but the influence of deterministic processes gradually grew. The ecological network results indicated that all the plastispheres exhibited a high number of modules and high modularity, and the complexity of the microbial community gradually decreased with colonization time. This study indicates that the mask-derived plastisphere has a unique ecological process, which strengthens our understanding of the ecological effects and microbial colonization processes of the mask-derived plastisphere.}, }
@article {pmid39961999, year = {2025}, author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1291-1302}, pmid = {39961999}, issn = {1678-4405}, support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Animals, Zoo/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Animals, Wild/microbiology ; *Chiroptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Russia ; Panama ; }, abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.}, }
@article {pmid39961275, year = {2025}, author = {Wang, A and Bong, CW and Tao, S and Ye, X and Liu, B and Liang, H and Zheng, X and Wong, YY and Loh, KH and Li, H and Chen, K and Lim, SH and Lee, CW}, title = {Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.}, journal = {Marine environmental research}, volume = {205}, number = {}, pages = {107017}, doi = {10.1016/j.marenvres.2025.107017}, pmid = {39961275}, issn = {1879-0291}, mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; *Geologic Sediments/chemistry ; *Rivers/chemistry ; *Environmental Monitoring ; Malaysia ; *Estuaries ; Risk Assessment ; }, abstract = {As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.}, }
@article {pmid39961017, year = {2025}, author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES}, title = {Microbial ecology of serpentinite-hosted ecosystems.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39961017}, issn = {1751-7370}, support = {80NSSC21K0489//NASA Exobiology and Evolutionary Biology program/ ; }, mesh = {*Ecosystem ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.}, }
@article {pmid39960660, year = {2025}, author = {Gomi, R and Adachi, F}, title = {Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {6}, pmid = {39960660}, issn = {1432-184X}, support = {JP22K18038//JSPS KAKENHI/ ; 22B006//Kurita Water and Environment Foundation, Japan/ ; 2230113//Sumitomo Foundation, Japan/ ; JPMEERF20235R01//Environment Research and Technology Development Fund/ ; }, mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Quinolones/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Proteins/genetics ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Genomics ; Plasmids/genetics ; }, abstract = {Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.}, }
@article {pmid39954521, year = {2025}, author = {Hernández-Villamor, D and Li, P and Aydogan, M and Verhelst, M and Van de Wiele, T and Rabaey, K and Prévoteau, A}, title = {Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.}, journal = {Biosensors &amp; bioelectronics}, volume = {276}, number = {}, pages = {117232}, doi = {10.1016/j.bios.2025.117232}, pmid = {39954521}, issn = {1873-4235}, mesh = {*Geobacter/physiology/growth &amp; development/metabolism ; *Biofilms/growth &amp; development ; Electrodes ; *Bioelectric Energy Sources/microbiology ; Electron Transport ; *Biosensing Techniques ; Oxidation-Reduction ; }, abstract = {The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.}, }
@article {pmid39954444, year = {2025}, author = {He, M and Tang, R and Guan, F and Peng, W and Lu, J and Li, K and Zhou, L and Wang, Y and Yuan, Y}, title = {Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137608}, doi = {10.1016/j.jhazmat.2025.137608}, pmid = {39954444}, issn = {1873-3336}, mesh = {*Zinc Oxide/toxicity/chemistry ; *Soil Microbiology ; *Methane/biosynthesis ; Soil/chemistry ; *Soil Pollutants/toxicity ; *Metal Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; Oryza ; *Sulfides/toxicity ; *Nanoparticles/toxicity ; }, abstract = {The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.}, }
@article {pmid39954056, year = {2025}, author = {Ren, Z and Gao, H and Martyniuk, N and Ren, H and Xiong, X and Luo, W}, title = {Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {5}, pmid = {39954056}, issn = {1432-184X}, support = {2023YFF1303700//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Rivers/microbiology ; China ; Ecosystem ; Biodiversity ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.}, }
@article {pmid39953673, year = {2025}, author = {Kotsakis, GA and Ganesan, SM}, title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.}, journal = {Journal of dental research}, volume = {104}, number = {5}, pages = {473-480}, doi = {10.1177/00220345241307939}, pmid = {39953673}, issn = {1544-0591}, mesh = {Humans ; *Peri-Implantitis/microbiology/immunology/etiology ; *Dysbiosis/microbiology/immunology ; *Titanium/adverse effects ; *Dental Implants/adverse effects/microbiology ; Microbiota ; }, abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.}, }
@article {pmid39952886, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {451-453}, doi = {10.1016/j.tplants.2025.01.011}, pmid = {39952886}, issn = {1878-4372}, mesh = {*Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Plant Leaves/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.}, }
@article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Vegetables/virology/microbiology ; Metagenomics ; Fermentation ; *Fermented Foods/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Brassica/virology/microbiology ; Microbiota ; *Viruses/classification/genetics/isolation &amp; purification ; Food Microbiology ; Biodiversity ; RNA Viruses/genetics/classification/isolation &amp; purification ; Virome ; DNA Viruses/genetics/classification/isolation &amp; purification ; Daucus carota/virology/microbiology ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, }
@article {pmid39952743, year = {2025}, author = {Wu, Y and Ma, F and Tan, S and Niu, A and Chen, Y and Liu, Y and Qiu, W and Wang, G}, title = {The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104708}, doi = {10.1016/j.fm.2024.104708}, pmid = {39952743}, issn = {1095-9998}, mesh = {*Bacterial Proteins/genetics/metabolism ; Chickens/microbiology ; Animals ; *Pseudomonas fragi/genetics/growth &amp; development/metabolism ; *Meat/microbiology ; Biofilms/growth &amp; development ; Mutation ; Food Microbiology ; Pseudomonas/genetics ; }, abstract = {Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.}, }
@article {pmid39951503, year = {2025}, author = {Bauermann, J and Benzi, R and Nelson, DR and Shankar, S and Toschi, F}, title = {Turbulent mixing controls fixation of growing antagonistic populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2417075122}, pmid = {39951503}, issn = {1091-6490}, mesh = {*Models, Biological ; *Saccharomyces cerevisiae/growth &amp; development/physiology ; Population Dynamics ; *Antibiosis/physiology ; Computer Simulation ; *Bacteria/growth &amp; development ; }, abstract = {Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.}, }
@article {pmid39950593, year = {2025}, author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME}, title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {35}, number = {1}, pages = {e70007}, pmid = {39950593}, issn = {1939-5582}, support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; }, mesh = {*Soil Microbiology ; *Trees/growth &amp; development/microbiology ; *Fungi/physiology/classification ; *Microbiota ; *Conservation of Natural Resources ; *Environmental Restoration and Remediation ; }, abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.}, }
@article {pmid39945937, year = {2025}, author = {Gharbi, D and Neumann, FH and Staats, J and McDonald, M and Linde, JH and Mmatladi, T and Podile, K and Piketh, S and Burger, R and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {3}, pages = {287}, pmid = {39945937}, issn = {1573-2959}, support = {ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; }, mesh = {South Africa/epidemiology ; Humans ; *Allergens/analysis/immunology ; Male ; Adult ; Female ; Pilot Projects ; Adolescent ; Prevalence ; Middle Aged ; Young Adult ; *Air Pollutants/analysis ; *Hypersensitivity/epidemiology ; *Air Pollution/statistics &amp; numerical data ; Pollen ; *Environmental Exposure/statistics &amp; numerical data ; Skin Tests ; }, abstract = {This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.}, }
@article {pmid39945839, year = {2025}, author = {Márquez-Sanz, R and Garrido-Benavent, I and Durán, J and de Los Ríos, A}, title = {The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {4}, pmid = {39945839}, issn = {1432-184X}, support = {PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigaci&#xf3;n/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; *Chlorophyta/growth &amp; development/physiology/classification ; *Microbiota ; Nitrogen/analysis ; Ecosystem ; }, abstract = {Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.}, }
@article {pmid39943131, year = {2025}, author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL}, title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, pmid = {39943131}, issn = {2076-2615}, abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.}, }
@article {pmid39942291, year = {2025}, author = {Santás-Miguel, V and Lalín-Pousa, V and Conde-Cid, M and Rodríguez-Seijo, A and Pérez-Rodríguez, P}, title = {Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {3}, pages = {}, pmid = {39942291}, issn = {1996-1944}, support = {ED481D-2021/016//Conseller&#xed;a de Cultura, Educaci&#xf3;n e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 101112754//MRV4SOC project/ ; ED481B-2022-081//Xunta de Galicia/ ; }, abstract = {This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.}, }
@article {pmid39942061, year = {2025}, author = {Di Biase, M and Scicchitano, D and Valerio, F and Lonigro, SL and Cifarelli, V and Ostante, G and D'Antuono, I and Candela, M and Ferrara, M}, title = {Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {39942061}, issn = {2304-8158}, support = {MicroBHE Project//IBISBA - IT/ ; DAB.AD005.225//FOE - 2021/ ; }, abstract = {Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.}, }
@article {pmid39937305, year = {2025}, author = {Argentino, ICV and Godoy, MG and Seldin, L and Jurelevicius, D}, title = {Distribution of Bacillota in Water and Sediments from Aquatic Environments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {3}, pmid = {39937305}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Brazil ; Microbiota ; Phylogeny ; *Water Microbiology ; *Seawater/microbiology ; *Fresh Water/microbiology ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.}, }
@article {pmid39936183, year = {2025}, author = {Brait, N and Hackl, T and Lequime, S}, title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14083}, pmid = {39936183}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; }, abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.}, }
@article {pmid39935057, year = {2025}, author = {Ruiz-Ruiz, P and Mohedano-Caballero, P and De Vrieze, J}, title = {Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124223}, doi = {10.1016/j.jenvman.2025.124223}, pmid = {39935057}, issn = {1095-8630}, mesh = {*Biofuels ; *Microalgae/metabolism ; Methane/metabolism ; *Amino Acids, Diamino/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.}, }
@article {pmid39934529, year = {2025}, author = {Roy, R and Das, A and Ganguly, D and Chakraborty, P and Paul, P and Das, S and Maity, A and Malik, M and Tribedi, P}, title = {Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1033-1048}, pmid = {39934529}, issn = {1678-4405}, support = {TNU/R&amp;D/M/11//The Neotia University/ ; }, mesh = {*Biofilms/drug effects ; *Gentamicins/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; Drug Synergism ; Microbial Sensitivity Tests ; Humans ; Staphylococcal Infections/microbiology/drug therapy ; *Benzaldehydes/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.}, }
@article {pmid39933594, year = {2025}, author = {Verdon, N and Popescu, O and Titmuss, S and Allen, RJ}, title = {Habitat fragmentation enhances microbial collective defence.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {223}, pages = {20240611}, pmid = {39933594}, issn = {1742-5662}, support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; }, mesh = {*Ecosystem ; *Models, Biological ; *Bacteria ; }, abstract = {Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.}, }
@article {pmid39928396, year = {2025}, author = {Nakajima, M and Nakai, R and Hirakata, Y and Kubota, K and Satoh, H and Nobu, MK and Narihiro, T and Kuroda, K}, title = {Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.006668}, pmid = {39928396}, issn = {1466-5034}, mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Base Composition ; Methanospirillum/growth &amp; development ; Symbiosis ; DNA, Archaeal/genetics ; Fatty Acids/chemistry/analysis ; }, abstract = {In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.}, }
@article {pmid39924526, year = {2025}, author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C}, title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {40}, pmid = {39924526}, issn = {1741-7007}, support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Microbiota ; *Odorants/analysis ; Volatile Organic Compounds/analysis ; Humans ; *Clothing ; *Laundering ; Skin/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.<br><br>RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.<br><br>CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.}, }
@article {pmid39915510, year = {2025}, author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ}, title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4459}, pmid = {39915510}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Malaysia ; *Microbiota ; Biodiversity ; Symbiosis ; Coral Reefs ; Bacteria/genetics/classification ; Climate Change ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.}, }
@article {pmid39914458, year = {2025}, author = {Wenger, A and Bakkeren, E and Granato, E and Tecon, R and Mitri, S and Möbius, W}, title = {MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, pmid = {39914458}, issn = {1574-6968}, support = {51NF40_180575/SNSF_/Swiss National Science Foundation/Switzerland ; BB/V004328/1//BBSRC/ ; 51NF40_180575//NCCR Microbiomes/ ; }, mesh = {*Congresses as Topic ; Humans ; *Ecology ; *Biological Evolution ; *Microbiology ; Europe ; }, abstract = {Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this 3-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical, and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement, such as hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.}, }
@article {pmid39914213, year = {2025}, author = {Ma, R and Huang, Z and Jiang, Y and Zhao, A and Yu, G and Lin, C and Zhu, L and Zhang, X and Li, X and Wang, C}, title = {Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124382}, doi = {10.1016/j.jenvman.2025.124382}, pmid = {39914213}, issn = {1095-8630}, mesh = {Fermentation ; *Quorum Sensing ; *Ethanol/metabolism ; Anaerobiosis ; Phenylethyl Alcohol/analogs &amp; derivatives ; Food Loss and Waste ; }, abstract = {Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.}, }
@article {pmid39913585, year = {2025}, author = {Pertierra, LR and Convey, P and Barbosa, A and Biersma, EM and Cowan, D and Diniz-Filho, JAF and de Los Ríos, A and Escribano-Álvarez, P and Fraser, CI and Fontaneto, D and Greve, M and Griffiths, HJ and Harris, M and Hughes, KA and Lynch, HJ and Ladle, RJ and Liu, XP and le Roux, PC and Majewska, R and Molina-Montenegro, MA and Peck, LS and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, LG and Terauds, A and Varliero, G and Vianna, JA and Wilmotte, A and Chown, SL and Olalla-Tárraga, M&#xc1; and Hortal, J}, title = {Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6734}, pages = {609-615}, doi = {10.1126/science.adk2118}, pmid = {39913585}, issn = {1095-9203}, mesh = {Antarctic Regions ; *Biodiversity ; Animals ; *Fresh Water ; Invertebrates/physiology ; Vertebrates ; }, abstract = {Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.}, }
@article {pmid39912641, year = {2025}, author = {Hamovit, N and RoyChowdhury, T and Akob, DM and Zhang, X and McCarty, G and Yarwood, S}, title = {Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0216124}, pmid = {39912641}, issn = {1098-5336}, support = {2017-67003-26484//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; Carbon Isotopes/analysis ; *Archaea/metabolism/genetics/classification ; Oxidation-Reduction ; Maryland ; Microbiota ; }, abstract = {Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.}, }
@article {pmid39912591, year = {2025}, author = {Porras-Socias, P and Mattiussi, R and Silveira, KA and O'Flaherty, V}, title = {Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0011624}, pmid = {39912591}, issn = {1935-7877}, abstract = {In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.}, }
@article {pmid39911734, year = {2025}, author = {Jia, C and Li, J and Li, Z and Zhang, L}, title = {Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.}, journal = {Water research X}, volume = {27}, number = {}, pages = {100304}, pmid = {39911734}, issn = {2589-9147}, abstract = {Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.}, }
@article {pmid39911603, year = {2025}, author = {Sikombe, TW and Linnemann, AR and Moonga, HB and Quilitz, S and Schoustra, SE and Smid, EJ and Alekseeva, A}, title = {Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {100976}, pmid = {39911603}, issn = {2665-9271}, abstract = {Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.}, }
@article {pmid39911488, year = {2024}, author = {Vaselek, S and Alten, B}, title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1522917}, pmid = {39911488}, issn = {2297-1769}, abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.}, }
@article {pmid39909903, year = {2025}, author = {Panico, SC and Alberti, G and Foscari, A and Sciabbarrasi, GL and Tomao, A and Incerti, G}, title = {Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {2}, pmid = {39909903}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil/chemistry ; *Fungi/classification/genetics/isolation &amp; purification ; Italy ; Biodiversity ; Grassland ; Nitrogen/analysis ; Forests ; Carbon/analysis ; Phosphorus/analysis ; Microbiota ; *Mycobiome ; }, abstract = {Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.}, }
@article {pmid39907926, year = {2025}, author = {Breedt, G and Korsten, L and Gokul, JK}, title = {Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39907926}, issn = {1874-9356}, abstract = {In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.}, }
@article {pmid39905550, year = {2025}, author = {Martínez Rendón, C and Braun, C and Kappelsberger, M and Boy, J and Casanova-Katny, A and Glaser, K and Dumack, K}, title = {Enhancing microbial predator-prey detection with network and trait-based analyses.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {37}, pmid = {39905550}, issn = {2049-2618}, mesh = {*Food Chain ; Antarctic Regions ; *Microbiota ; Animals ; Predatory Behavior ; Bacteria/classification/genetics ; Eukaryota ; }, abstract = {BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.<br><br>RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.<br><br>CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.}, }
@article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, mesh = {*Camellia sinensis/microbiology/metabolism ; *Flavonoids/biosynthesis ; *Plant Roots/microbiology ; *Mycorrhizae/growth &amp; development ; Soil Microbiology ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; *Trichoderma/physiology/growth &amp; development ; India ; Symbiosis ; Plant Leaves/microbiology/metabolism ; Tea/microbiology ; Phylogeny ; }, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, }
@article {pmid39902955, year = {2025}, author = {Li, Q and Marietou, A and Andersen, FF and Hosek, J and Scavenius, C and Zhang, J and Schwab, C}, title = {In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0219324}, pmid = {39902955}, issn = {2165-0497}, support = {00//M&#xe6;lkeafgiftsfonden (Milk Tax Fund)/ ; 00//Brodrene Hartmann Fonden/ ; }, mesh = {*Feces/microbiology ; Fermentation ; Lactose/metabolism ; *Gastrointestinal Microbiome ; Humans ; beta-Galactosidase/genetics/metabolism ; Streptococcus thermophilus/metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; *Cultured Milk Products/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Butyrates/metabolism ; *Dairy Products/microbiology ; }, abstract = {UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.<br><br>IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.}, }
@article {pmid39897492, year = {2025}, author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C}, title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18807}, pmid = {39897492}, issn = {2167-8359}, mesh = {*Porifera/microbiology ; Animals ; *Microbiota ; *Fresh Water/microbiology ; North Carolina ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; }, abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.}, }
@article {pmid39890664, year = {2025}, author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L}, title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {1}, pmid = {39890664}, issn = {1432-184X}, support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; }, mesh = {*Capsicum/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Diseases/microbiology ; Fungi/classification/isolation &amp; purification/genetics ; Endophytes/classification/genetics/physiology/isolation &amp; purification ; Plant Roots/microbiology ; Biodiversity ; }, abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.}, }
@article {pmid39890294, year = {2025}, author = {Baker, JM and Dickson, RP}, title = {The Microbiome and Pulmonary Immune Function.}, journal = {Clinics in chest medicine}, volume = {46}, number = {1}, pages = {77-91}, doi = {10.1016/j.ccm.2024.10.006}, pmid = {39890294}, issn = {1557-8216}, mesh = {Humans ; *Microbiota/immunology ; *Lung/immunology/microbiology ; *Lung Diseases/immunology/microbiology ; }, abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.}, }
@article {pmid39889603, year = {2025}, author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P}, title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137399}, doi = {10.1016/j.jhazmat.2025.137399}, pmid = {39889603}, issn = {1873-3336}, mesh = {Animals ; China ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Mytilus/microbiology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Oceans and Seas ; Microbiota ; Aquaculture ; }, abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.}, }
@article {pmid39885242, year = {2025}, author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N}, title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3796}, doi = {10.1038/s41598-025-87051-2}, pmid = {39885242}, issn = {2045-2322}, }
@article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Desert Climate ; Phylogeny ; Plant Roots/microbiology ; *Microbiota ; *Plants/microbiology ; Namibia ; DNA, Bacterial/genetics ; Soil/chemistry ; Biodiversity ; }, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, }
@article {pmid39883228, year = {2024}, author = {Han, JR and Li, S and Li, WJ and Dong, L}, title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.}, journal = {Advanced biotechnology}, volume = {2}, number = {3}, pages = {26}, pmid = {39883228}, issn = {2948-2801}, support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; }, abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.}, }
@article {pmid39883081, year = {2025}, author = {Shin, GY and Asselin, JA and Smith, A and Aegerter, B and Coutinho, T and Zhao, M and Dutta, B and Mazzone, J and Neupane, R and Gugino, B and Hoepting, C and Khanal, M and Malla, S and Nischwitz, C and Sidhu, J and Burke, AM and Davey, J and Uchanski, M and Derie, ML and du Toit, LJ and Stresow-Cortez, S and Bonasera, JM and Stodghill, P and Kvitko, B}, title = {Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39883081}, issn = {1751-7370}, support = {2019-51181-30013//Specialty Crops Research Initiative Award/ ; //National Institute of Food and Agriculture/ ; //U.S. Department of Agriculture/ ; }, mesh = {*Onions/microbiology ; *Pantoea/genetics/pathogenicity ; *Plasmids/genetics ; *Plant Diseases/microbiology ; Phylogeny ; Genome, Bacterial ; Virulence ; Multigene Family ; Virulence Factors/genetics ; }, abstract = {Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.}, }
@article {pmid39882875, year = {2025}, author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL}, title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0236824}, pmid = {39882875}, issn = {1098-5336}, support = {IOS 2312818//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Phylogeny ; Diet ; }, abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.<br><br>IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.}, }
@article {pmid39882867, year = {2025}, author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR}, title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0220924}, pmid = {39882867}, issn = {2165-0497}, mesh = {Animals ; *Microbiota/genetics ; Swine ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Red Meat/microbiology ; *Pork Meat/microbiology ; Salmonella/isolation &amp; purification/genetics/classification ; *Meat/microbiology ; Food Handling ; }, abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.}, }
@article {pmid39880965, year = {2025}, author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A}, title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {181}, pmid = {39880965}, issn = {1432-184X}, support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Agave/microbiology/growth &amp; development ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Agriculture/methods ; RNA, Ribosomal, 16S/genetics ; *Alcoholic Beverages/microbiology ; Mexico ; Rhizosphere ; Biodiversity ; }, abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.}, }
@article {pmid39880083, year = {2025}, author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T}, title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {24}, number = {3}, pages = {100918}, pmid = {39880083}, issn = {1535-9484}, mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; }, abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.}, }
@article {pmid39878512, year = {2025}, author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC}, title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.}, journal = {mBio}, volume = {16}, number = {3}, pages = {e0392824}, pmid = {39878512}, issn = {2150-7511}, support = {ZK-57//Austrian Science Fund (FWF)/ ; }, mesh = {*MicroRNAs/genetics/metabolism ; Humans ; *Tryptophan/biosynthesis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides thetaiotaomicron/metabolism/genetics ; Feces/microbiology ; Irritable Bowel Syndrome/microbiology ; Gene Expression Regulation, Bacterial ; Indoles ; }, abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.<br><br>IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.}, }
@article {pmid39878482, year = {2025}, author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J}, title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0005624}, pmid = {39878482}, issn = {1935-7877}, abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.}, }
@article {pmid39876091, year = {2025}, author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI}, title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.}, journal = {Clinical implant dentistry and related research}, volume = {27}, number = {1}, pages = {e13423}, doi = {10.1111/cid.13423}, pmid = {39876091}, issn = {1708-8208}, support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Male ; Middle Aged ; Female ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S ; Adult ; Aged ; }, abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.<br><br>METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.<br><br>RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p&#x2009;<&#x2009;0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.<br><br>CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.}, }
@article {pmid39874167, year = {2025}, author = {Zhang, F and Zhang, S and Wu, Y and Liu, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-12-24-2632-PDN}, pmid = {39874167}, issn = {0191-2917}, abstract = {Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.}, }
@article {pmid39873755, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {180}, doi = {10.1007/s00248-025-02498-0}, pmid = {39873755}, issn = {1432-184X}, }
@article {pmid39871445, year = {2025}, author = {Zahir, Z and Khan, F and Hall, BD}, title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70069}, pmid = {39871445}, issn = {1758-2229}, support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; }, mesh = {*Wetlands ; *Sulfates/analysis ; *Ponds/microbiology/chemistry ; *Carbon/analysis/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; *Microbiota ; Geologic Sediments/microbiology/chemistry ; }, abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.}, }
@article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, }
@article {pmid39871020, year = {2025}, author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J}, title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {177}, pmid = {39871020}, issn = {1432-184X}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Carbon/metabolism ; *Soil/chemistry ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification ; Ecosystem ; Microbial Interactions ; }, abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.}, }
@article {pmid39870904, year = {2025}, author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P}, title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {179}, pmid = {39870904}, issn = {1432-184X}, mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Reunion ; Fungi/classification/isolation &amp; purification/genetics ; *Seawater/microbiology ; *Environmental Monitoring/methods ; Geologic Sediments/microbiology ; Biodiversity ; Seasons ; Microalgae/classification/isolation &amp; purification/genetics ; Biomarkers/analysis ; }, abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.}, }
@article {pmid39870843, year = {2025}, author = {Li, Q and Shao, H}, title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {178}, pmid = {39870843}, issn = {1432-184X}, support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; Soil Microbiology ; Host-Pathogen Interactions ; }, abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.}, }
@article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.}, }
@article {pmid39868180, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868180}, issn = {2692-8205}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; }, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.}, }
@article {pmid39862387, year = {2025}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {2}, pages = {}, pmid = {39862387}, issn = {1367-4811}, support = {/ERC_/European Research Council/International ; 833522//European Union's Horizon 2020 research and innovation program/ ; }, mesh = {*Software ; *Gene Duplication ; *Genome ; *Genomics/methods ; }, abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.<br><br>doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.}, }
@article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39861970}, issn = {1751-7370}, support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y Le&#xf3;n/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andaluc&#xed;a/ ; //V Plan Propio de investigaci&#xf3;n of the University Pablo de Olavide/ ; }, mesh = {*Microbial Consortia/genetics ; Biodegradation, Environmental ; Plasmids/genetics ; *Ibuprofen/metabolism ; *Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Phylogeny ; }, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, }
@article {pmid39857259, year = {2025}, author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH}, title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857259}, issn = {2079-7737}, support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; }, abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.}, }
@article {pmid39856188, year = {2025}, author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D}, title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3152}, pmid = {39856188}, issn = {2045-2322}, support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; }, mesh = {*Microcystis/virology/growth &amp; development ; *Bacteriophages/physiology ; Fresh Water/microbiology ; *Cyanobacteria/virology ; Photosynthesis ; Eutrophication ; }, abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.}, }
@article {pmid39855017, year = {2025}, author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J}, title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.}, journal = {Water research}, volume = {275}, number = {}, pages = {123138}, doi = {10.1016/j.watres.2025.123138}, pmid = {39855017}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Harmful Algal Bloom ; Temperature ; Cyanobacteria ; Climate Change ; Nutrients ; Eutrophication ; Phosphorus ; }, abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.}, }
@article {pmid39854900, year = {2025}, author = {Reid, CJ and Farrell, M and Kirby, JK}, title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124203}, doi = {10.1016/j.jenvman.2025.124203}, pmid = {39854900}, issn = {1095-8630}, mesh = {*Soil Microbiology ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; *Sewage/microbiology ; Microbiota ; }, abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.}, }
@article {pmid39853499, year = {2025}, author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC}, title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {176}, pmid = {39853499}, issn = {1432-184X}, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Italy ; Batrachochytrium/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Wetlands ; Temperature ; Biodiversity ; Hydrogen-Ion Concentration ; Skin Microbiome ; }, abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.}, }
@article {pmid39849986, year = {2025}, author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z}, title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39849986}, issn = {1751-7370}, support = {SDCX-ZG-202203032//Postdoctoral Innovation Project of Shandong Province/ ; BK20230248//Natural Science Foundation of Jiangsu Province/ ; ZR2022QC001//Science Foundation for Youths of Shandong Province/ ; 32070030//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; *Bacteria/classification/metabolism/drug effects/genetics ; *Anti-Infective Agents/metabolism ; *Toxins, Biological ; *Microbiota ; }, abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.}, }
@article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, }
@article {pmid39848193, year = {2025}, author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F}, title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124191}, doi = {10.1016/j.jenvman.2025.124191}, pmid = {39848193}, issn = {1095-8630}, mesh = {*Manure ; Chickens ; Animals ; Anaerobiosis ; Water ; Carbon/chemistry ; Methane ; }, abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.}, }
@article {pmid39847340, year = {2025}, author = {Ganley, JG and Seyedsayamdost, MR}, title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {4}, pages = {e2414434122}, pmid = {39847340}, issn = {1091-6490}, support = {R35 GM152049/GM/NIGMS NIH HHS/United States ; Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; }, mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Symbiosis ; *Cell Membrane/metabolism ; Metabolome ; }, abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.}, }
@article {pmid39845484, year = {2024}, author = {Tóth, VR}, title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1476142}, pmid = {39845484}, issn = {1664-462X}, abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.}, }
@article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/growth &amp; development/microbiology ; *Soil Microbiology ; *Bacillus thuringiensis/physiology ; Soil/chemistry ; *Rhizobium/physiology ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, }
@article {pmid39844346, year = {2025}, author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A}, title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844346}, issn = {1574-6941}, support = {DFG SO 428/17-1//German Research Foundation/ ; //Ulm University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Chiroptera/microbiology/physiology ; *Circadian Rhythm ; Feces/microbiology ; *Feeding Behavior ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the faecal microbiota and gut pH every 2 h. We detected strong diurnal rhythms in both microbial alpha diversity and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed-feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.}, }
@article {pmid39843903, year = {2025}, author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA}, title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {133}, pmid = {39843903}, issn = {2052-4463}, support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.}, }
@article {pmid39840338, year = {2024}, author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C}, title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1420282}, pmid = {39840338}, issn = {2297-1769}, abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.<br><br>METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.<br><br>RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.<br><br>DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.}, }
@article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Viral Proteins/genetics/metabolism/chemistry ; *Molecular Sequence Annotation/methods ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, }
@article {pmid39838210, year = {2025}, author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B}, title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2638}, pmid = {39838210}, issn = {2045-2322}, support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; }, mesh = {Humans ; *Crohn Disease/genetics/pathology ; Male ; Female ; *Mutation ; *Epithelial Cells/metabolism/pathology ; Apoptosis/genetics ; Adult ; Exome Sequencing ; *Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation/genetics ; *Serpins/genetics ; Cell Movement/genetics ; }, abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.}, }
@article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garant&#xed;a Juvenil (Fondo Social Europeo, Gobierno de Espa&#xf1;a/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andaluc&#xed;a 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/biosynthesis/metabolism ; *Enterococcus/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; Biodiversity ; Microbiota ; Animals ; Milk/microbiology ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, }
@article {pmid39836327, year = {2025}, author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C}, title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {174}, pmid = {39836327}, issn = {1432-184X}, mesh = {*Zea mays/growth &amp; development/microbiology ; *Soil Microbiology ; *Asparagus Plant/microbiology/growth &amp; development ; Plant Roots/microbiology/growth &amp; development ; Rhizosphere ; Peru ; *Bacteria/isolation &amp; purification/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Salt Tolerance ; Soil/chemistry ; }, abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.}, }
@article {pmid39833680, year = {2025}, author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M}, title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {51}, pmid = {39833680}, issn = {1471-2164}, mesh = {*Extreme Environments ; Phylogeny ; Genome, Bacterial ; Soil Microbiology ; Genomics ; Stress, Physiological ; Metals, Heavy ; }, abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.<br><br>RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.<br><br>CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.}, }
@article {pmid39830292, year = {2024}, author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 1697-1780.}, journal = {Fungal systematics and evolution}, volume = {14}, number = {}, pages = {325-577}, pmid = {39830292}, issn = {2589-3831}, support = {P01 CA125066/CA/NCI NIH HHS/United States ; }, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.}, }
@article {pmid39828718, year = {2025}, author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X}, title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {173}, pmid = {39828718}, issn = {1432-184X}, support = {41976131//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; Metals, Heavy/analysis ; }, abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.}, }
@article {pmid39826456, year = {2025}, author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T}, title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137241}, doi = {10.1016/j.jhazmat.2025.137241}, pmid = {39826456}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/drug effects/genetics ; *Plastics/toxicity ; Tibet ; Biodiversity ; Soil/chemistry ; China ; *Microplastics/toxicity ; }, abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.}, }
@article {pmid39826104, year = {2025}, author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P}, title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2452277}, doi = {10.1080/19490976.2025.2452277}, pmid = {39826104}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/immunology/microbiology ; Animals ; Tumor Microenvironment ; Immunotherapy/methods ; Treatment Outcome ; }, abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.}, }
@article {pmid39825576, year = {2025}, author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA}, title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70022}, pmid = {39825576}, issn = {1462-2920}, mesh = {Animals ; *Soil Microbiology ; *Microbiota ; *Herbivory ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Grassland ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.}, }
@article {pmid39825218, year = {2025}, author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM}, title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {27}, pmid = {39825218}, issn = {1471-2180}, support = {2021/10626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/05561-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.}, }
@article {pmid39821365, year = {2025}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.}, journal = {Drug development research}, volume = {86}, number = {1}, pages = {e70045}, doi = {10.1002/ddr.70045}, pmid = {39821365}, issn = {1098-2299}, support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; }, mesh = {Humans ; *Pharmacovigilance ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; *Histamine H2 Antagonists/adverse effects/administration &amp; dosage ; United States ; United States Food and Drug Administration ; *Famotidine/adverse effects/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adult ; Aged ; Young Adult ; Adolescent ; Databases, Factual ; Child ; }, abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.}, }
@article {pmid39820572, year = {2025}, author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I}, title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {171}, pmid = {39820572}, issn = {1432-184X}, support = {US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; }, mesh = {Spain ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Salinity ; *Biodiversity ; Phylogeny ; *Natural Springs/microbiology ; *Saline Waters ; DNA, Bacterial/genetics ; Rivers/microbiology ; Water Microbiology ; DNA, Archaeal/genetics ; }, abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.}, }
@article {pmid39820498, year = {2025}, author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z}, title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {172}, pmid = {39820498}, issn = {1432-184X}, support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; }, mesh = {*Wetlands ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Estuaries ; Soil Microbiology ; Geologic Sediments/microbiology ; Ecosystem ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; *Drug Resistance, Microbial/genetics ; Microbiota ; }, abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.}, }
@article {pmid39820407, year = {2025}, author = {Hahn, MW and Kisand, V}, title = {Editorial: FEMS EC Thematic Issue "Aquatic Microbial Ecology".}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39820407}, issn = {1574-6941}, abstract = {High relative abundance of yeast (Vishniacozyma, Papiliotrema, and Filobasidium) and bacterial (Massilia) genera found in spinach seeds correlates with suppression of Globisporangium ultimum damping-off infection.}, }
@article {pmid39817738, year = {2025}, author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL}, title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0206924}, pmid = {39817738}, issn = {1098-5336}, support = {847693//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Sk&#x142;odowska-Curie Actions (MSCA)/ ; }, mesh = {*Oligochaeta/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Fatty Acids, Unsaturated/metabolism/biosynthesis ; Composting ; *Soil Microbiology ; *Shewanella/metabolism/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Soil/chemistry ; Phylogeny ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.}, }
@article {pmid39813101, year = {2025}, author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y}, title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {3}, pages = {1683-1692}, doi = {10.1021/acs.est.4c07954}, pmid = {39813101}, issn = {1520-5851}, mesh = {Bacteria ; Kinetics ; Porosity ; Soil ; *Soil Microbiology ; }, abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.}, }
@article {pmid39811355, year = {2025}, author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS}, title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.}, journal = {Heliyon}, volume = {11}, number = {1}, pages = {e41400}, pmid = {39811355}, issn = {2405-8440}, abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.}, }
@article {pmid39808188, year = {2025}, author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM}, title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39808188}, issn = {1574-6941}, support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; }, mesh = {*Vaccinium myrtillus/microbiology/growth &amp; development/chemistry ; *Phenols/metabolism/analysis ; *Fruit/microbiology/growth &amp; development/chemistry ; *Endophytes/genetics/classification/physiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Mycobiome ; }, abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.}, }
@article {pmid39807875, year = {2025}, author = {Schloss, PD}, title = {phylotypr: an R package for classifying DNA sequences.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0114424}, pmid = {39807875}, issn = {2576-098X}, abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.}, }
@article {pmid39806487, year = {2025}, author = {Dieppa-Colón, E and Martin, C and Kosmopoulos, JC and Anantharaman, K}, title = {Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {5}, pmid = {39806487}, issn = {2524-6372}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; T32GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39805038, year = {2025}, author = {Wei, L and Van Beeck, W and Hanlon, M and DiCaprio, E and Marco, ML}, title = {Lacto-Fermented Fruits and Vegetables: Bioactive Components and Effects on Human Health.}, journal = {Annual review of food science and technology}, volume = {16}, number = {1}, pages = {289-314}, doi = {10.1146/annurev-food-052924-070656}, pmid = {39805038}, issn = {1941-1421}, mesh = {Humans ; *Fruit/chemistry/microbiology ; *Vegetables/chemistry/microbiology ; Fermentation ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; }, abstract = {Lacto-fermented fruits and vegetables (FVs) such as kimchi, sauerkraut, and fermented olives and nonalcoholic juices have a long history as dietary staples. Herein, the production steps and microbial ecology of lacto-fermented FVs are discussed alongside findings from human and laboratory studies investigating the health benefits of these foods. Lacto-fermented FVs are enriched in beneficial live microbes and bioactive compounds, including lactic and acetic acids, phenolic compounds, bacteriocins, and amino acid derivatives such as indole-3-lactic acid, phenyl-lactic acid, and γ-aminobutyric acid. At least 11 human studies have been performed on kimchi, whereas others have been investigated in only one or two trials. Besides exploring the health benefits, it is imperative to ensure that these foods made either commercially or at home have minimal risk for foodborne illness and exposure to undesired compounds like biogenic amines. Development of starter-culture strains and production protocols can lead to lacto-fermented FVs designed for specific health benefits.}, }
@article {pmid39804671, year = {2025}, author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV}, title = {Long-term climate establishes functional legacies by altering microbial traits.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39804671}, issn = {1751-7370}, mesh = {*Soil Microbiology ; Metagenomics ; *Climate ; Carbon Cycle ; Soil/chemistry ; Droughts ; *Bacteria/genetics/classification/metabolism ; }, abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.}, }
@article {pmid39799671, year = {2025}, author = {Mo, Y and Abdolahpur Monikh, F and Jaffer, YD and Mugani, R and Ionescu, D and Chen, G and Yang, J and Grossart, HP}, title = {Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137062}, doi = {10.1016/j.jhazmat.2024.137062}, pmid = {39799671}, issn = {1873-3336}, mesh = {*Bacteria/drug effects ; *Fungi/drug effects ; *Fresh Water/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; *Water Microbiology ; }, abstract = {Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water and sediment without and with TWPs addition in a rural vs. urban lake system. Our results revealed the degree of change in microbial community diversity in water is higher than that in sediment following TWPs addition. For bacterial communities, TWPs addition changed their composition in the water, but only little in the sediment. For fungal communities, TWPs addition changed their composition both in water and sediments. Furthermore, in water, TWPs addition increased network complexity between bacteria-bacteria, fungi-fungi and bacteria-fungi in the urban system but reduced it in the rural one. In contrast, TWPs presence did not significantly change network complexity among microbial communities in the sediment of both lakes. Isotope labeling analysis uncovered that based on a short-term (6 hours) incubation experiment, TWPs addition did not significantly change carbon nor nitrogen cycling in the water. Yet, certain changes could be observed, especially in the long-term experiment (1 month), indicating that TWPs pollution has the potential to impact elemental cycling and thus ecosystem functions by altering microbial communities. Our results provide new insights into TWPs-induced ecological effects on microorganisms and potential biogeochemical consequences in a rural vs. urban lakes.}, }
@article {pmid39798462, year = {2025}, author = {Kovarova, A and Prole, G and Farrell, ML and Maguire, M and Murphy, LC and Chueiri, A and O'Connor, L and Miliotis, G and Morris, D and Burke, LP}, title = {Antimicrobial resistant Enterobacterales of clinical importance in mute swans.}, journal = {The Science of the total environment}, volume = {961}, number = {}, pages = {178400}, doi = {10.1016/j.scitotenv.2025.178400}, pmid = {39798462}, issn = {1879-1026}, mesh = {*Enterobacteriaceae/drug effects ; Animals ; *Drug Resistance, Bacterial/genetics ; Ireland ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Feces/microbiology ; Clinical Relevance ; }, abstract = {Urban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates. Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.}, }
@article {pmid39798088, year = {2025}, author = {Stefanic, P and Stare, E and Floccari, VA and Kovac, J and Hertel, R and Rocha, U and Kovács, &#xc1;T and Mandić-Mulec, I and Strube, ML and Dragoš, A}, title = {Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.}, journal = {Cell reports}, volume = {44}, number = {1}, pages = {115197}, doi = {10.1016/j.celrep.2024.115197}, pmid = {39798088}, issn = {2211-1247}, mesh = {*Bacillus subtilis/virology/genetics ; *Prophages/genetics ; Phylogeny ; Genome, Bacterial/genetics ; }, abstract = {Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.}, }
@article {pmid39797436, year = {2025}, author = {Shopen Gochev, C and Demory, D and Lopes Dos Santos, A and Carlson, MCG and Gutiérrez-Rodríguez, A and Weitz, JS and Lindell, D}, title = {Cold Surface Waters of the Sub-Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70031}, pmid = {39797436}, issn = {1462-2920}, support = {2679/20//Israel Science Foundation/ ; 639682//Simons Foundation/ ; 721231//Simons Foundation/ ; 721254//Simons Foundation/ ; }, mesh = {*Cyanobacteria/classification/virology ; Pacific Ocean ; *Seawater/chemistry/microbiology/virology ; Bacteriophages ; Cold Temperature ; Iron/analysis ; }, abstract = {Cyanobacterial distributions are shaped by abiotic factors including temperature, light and nutrient availability as well as biotic factors such as grazing and viral infection. In this study, we investigated the abundances of T4-like and T7-like cyanophages and the extent of picocyanobacterial infection in the cold, high-nutrient-low-chlorophyll, sub-Antarctic waters of the southwest Pacific Ocean during austral spring. Synechococcus was the dominant picocyanobacterium, ranging from 4.7 × 10[3] to 1.2 × 10[5] cells∙mL[-1], while Prochlorococcus abundances were relatively low overall, ranging from 1.0 × 10[3] to 3.9 × 10[4] cells∙mL[-1]. Using taxon-specific, single-virus and single-cell polony methods, we found that cyanophages were on average 15-fold, and up to 50-fold, more abundant than cyanobacteria in these waters. T4-like cyanophages (ranging from 1.7 × 10[5] to 6.5 × 10[5] phage·mL[-1]) were 2.7-fold more abundant than T7-like cyanophages (ranging from 3.1 × 10[4] to 2.8 × 10[5] phage·mL[-1]). Picocyanobacteria were primarily infected by T4-like cyanophages with more Synechococcus (4.8%-12.1%) infected than Prochlorococcus (2.5%-6.2%), whereas T7-like cyanophages infected less than 1% of both genera. These infection levels translated to daily mortality in the range of 5.7%-26.2% and 2.9%-14.3% of the standing stock of Synechococcus and Prochlorococcus, respectively. Our findings suggest that T4-like cyanophages are significant agents of cyanobacterial mortality in the cold, low-iron, sub-Antarctic waters of the South Pacific Ocean.}, }
@article {pmid39794865, year = {2025}, author = {Passarelli-Araujo, H and Venancio, TM and Hanage, WP}, title = {Relating ecological diversity to genetic discontinuity across bacterial species.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {8}, pmid = {39794865}, issn = {1474-760X}, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Genetic Variation ; Phylogeny ; Mycobacterium tuberculosis/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity (δ) and investigate how this metric is related to ecology.<br><br>RESULTS: We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.<br><br>CONCLUSIONS: Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.}, }
@article {pmid39794276, year = {2025}, author = {Tang, L and Manefield, M}, title = {Aeration promotes Proteobacteria over Firmicutes in macerated food waste, resulting in superior anaerobic digestion efficiency.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf001}, pmid = {39794276}, issn = {1574-6968}, support = {//Department of Planning, Industry and Environment/ ; }, mesh = {Anaerobiosis ; *Proteobacteria/metabolism/genetics ; *Firmicutes/metabolism ; Biofuels ; Food ; Aerobiosis ; Food Loss and Waste ; }, abstract = {Aeration is a common pretreatment method to enhance biogas production via anaerobic digestion of waste organic feedstocks such as unused food. While impacts on downstream anaerobic digestion have been intensively investigated, the consequence of aeration on the microbial community in food waste has not been characterized. Food waste has a low pH resulting from the dominance of lactic acid bacteria within the Firmicutes phylum. This excludes other phylotypes with a higher potential to hydrolyse complex biopolymers in food waste. In this study, we reveal that aeration of macerated food waste results in a dramatic shift away from Firmicutes towards dominance of Proteobacteria that are better known for extracellular enzyme production. Given that hydrolysis is the rate limiting step in anaerobic digestion, this explains why aeration improves the efficiency of biogas production from food waste. The discovery that Proteobacteria dominate microbial communities in aerated food waste opens up opportunities to manipulate extracellular enzyme production through gene expression mechanisms common among Proteobacteria such as quorum sensing.}, }
@article {pmid39792461, year = {2025}, author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , }, title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.}, journal = {Astrobiology}, volume = {25}, number = {1}, pages = {72-81}, doi = {10.1089/ast.2023.0124}, pmid = {39792461}, issn = {1557-8070}, mesh = {*Mars ; Iceland ; *Extraterrestrial Environment ; *Microbiota/genetics ; Phylogeny ; Exobiology ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.}, }
@article {pmid39792290, year = {2025}, author = {Foffi, R and Brumley, DR and Peaudecerf, FJ and Stocker, R and Słomka, J}, title = {Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2411074122}, pmid = {39792290}, issn = {1091-6490}, support = {PZ00P2_202188//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0015-01//Agence Nationale de la Recherche (ANR)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Phytoplankton/physiology ; *Chemotaxis/physiology ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Models, Biological ; }, abstract = {Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial phenotypes and phytoplankton size: large phytoplankton produce spatially extended but shallow gradients, whereas small phytoplankton produce steeper but spatially more confined gradients. To date, it has remained unclear how phytoplankton size and bacterial swimming speed affect bacteria's gradient detection ability and search times for phytoplankton. Here, we compute an upper bound on the increase in bacterial encounter rate with phytoplankton due to chemotaxis over random motility alone. We find that chemotaxis can substantially decrease search times for small phytoplankton, but this advantage is highly sensitive to variations in bacterial phenotypes or phytoplankton leakage rates. By contrast, chemotaxis toward large phytoplankton cells reduces the search time more modestly, but this benefit is more robust to variations in search or environmental parameters. Applying our findings to marine phytoplankton communities, we find that, in productive waters, chemotaxis toward phytoplankton smaller than 2 μm provides little to no benefit, but can decrease average search times for large phytoplankton (∼20 μm) from 2 wk to 2 d, an advantage that is robust to variations and favors bacteria with higher swimming speeds. By contrast, in oligotrophic waters, chemotaxis can reduce search times for picophytoplankton (∼1 μm) up to 10-fold, from a week to half a day, but only for bacteria with low swimming speeds and long sensory timescales. This asymmetry may promote the coexistence of diverse search phenotypes in marine bacterial populations.}, }
@article {pmid39789151, year = {2025}, author = {Frasca, S and Alabiso, A and D'Andrea, MM and Migliore, L}, title = {Uncovering the Fungal Community Composition of Alive and Dead Posidonia oceanica Matte.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {170}, pmid = {39789151}, issn = {1432-184X}, mesh = {*Alismatales/microbiology ; Ascomycota/genetics/classification/metabolism/growth &amp; development ; Mycobiome ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; DNA, Fungal/genetics ; Seawater/microbiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions.}, }
@article {pmid39788196, year = {2025}, author = {Kim, YT and Huang, YP and Ozturk, G and Hahn, J and Taha, AY and Wang, A and Barile, D and Mills, DA}, title = {Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate.}, journal = {Journal of dairy science}, volume = {108}, number = {4}, pages = {3366-3381}, doi = {10.3168/jds.2024-25885}, pmid = {39788196}, issn = {1525-3198}, mesh = {*Bifidobacterium bifidum/metabolism/growth &amp; development ; *Whey Proteins ; Humans ; *Phospholipids/metabolism ; Milk, Human/chemistry ; Animals ; Oligosaccharides/metabolism ; }, abstract = {Whey protein phospholipid concentrate (WPPC) is a co-product generated during the manufacture of whey protein isolate. Whey protein phospholipid concentrate is depleted of simple sugars but contains numerous glycoconjugates embedded in the milk fat globule membrane, suggesting this fraction may serve as a carbon source for growth of bifidobacteria commonly enriched in breastfed infants. In this work, we demonstrate that WPPC can serve as a sole carbon source for the growth of Bifidobacterium bifidum, a species common to the breastfed infant and routinely used as a probiotic. Growth on WPPC fractions resulted in expression of key extracellular glycosyl hydrolases in B. bifidum associated with the catabolism of glycoproteins. Interestingly, this included induction of fucosidase genes in B. bifidum linked to catabolism of fucosylated human milk oligosaccharides even though the WPPC glycan possesses little fucose. Additional growth studies revealed that WPPC-glycan components N-acetylglucosamine or N-acetylgalactosamine were required for pre-activation of B. bifidum toward rapid growth on fucosylated human milk oligosaccharides. Growth on WPPC fractions also resulted in expression of extracellular sialidases in B. bifidum which promoted a consistent release of sialic acid, a well-known component of bovine milk oligosaccharides and glycoconjugates with potential effects on gut microbial ecology and host cognition. These studies suggest WPPC may serve as a promising bioactive component to facilitate probiotic activity for use in infant formulas and other synbiotic applications.}, }
@article {pmid39787750, year = {2025}, author = {Zhang, S and Wang, J and Liu, Z and Xia, X and Wu, X and Li, X and Liu, Y and Xu, Z and Marzadri, A and McDowell, WH and Cai, Y and Yang, Z}, title = {Temperature has an enhanced role in sediment N2O and N2 fluxes in wider rivers.}, journal = {Water research}, volume = {273}, number = {}, pages = {123095}, doi = {10.1016/j.watres.2025.123095}, pmid = {39787750}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Geologic Sediments/chemistry ; *Nitrogen ; *Temperature ; *Nitrous Oxide ; China ; Denitrification ; Nitrates ; Bacteria/metabolism ; }, abstract = {Riverine N2O and N2 fluxes, key components of the global nitrogen budget, are known to be influenced by river size (often represented by average river width), yet the specific mechanisms behind these effects remain unclear. This study examined how environmental and microbial factors influenced sediment N2O and N2 fluxes across rivers with varying widths (2.8 to 2,000 m) in China. Sediment acted as sources of both N2O and N2 emissions, with both N2 (0.2 to 20.8 mmol m[-2] d[-1]) and N2O fluxes (0.7-54.2 μmol m[-2] d[-1]) decreasing significantly as river width increased. N2 fluxes were positively correlated with denitrifying bacterial abundance, whereas N2O fluxes, when normalized by the abundance of denitrifying bacteria, were negatively correlated with the abundance of N2O-reducing microbes. Water physicochemical factors, particularly temperature and nitrate, were more important drivers of these fluxes than sediment factors. Nitrate significantly increased denitrifying bacterial abundance, whereas higher temperatures enhanced cell-specific activity. Lower N2O and N2 emissions in wider rivers were attributed to decreased denitrifying microbial abundance and lower denitrification rates, in addition to the commonly assumed reduction in exogenous N2O and N2 inputs. Rolling regression analysis showed that nitrate concentration had a stronger effect on sediment N2O and N2 fluxes in narrower rivers, whereas temperature was more influential in wider rivers. This difference is attributed to more stable nitrate concentrations and decreased nitrogen removal efficiency in wider rivers, while temperature variation remained consistent across all river widths. Beyond sediments, temperature had a greater effect on excess N2O concentrations than nitrate in the overlying water of wider rivers (>165 m), highlighting its broader impact. This study provides new biogeochemical insights into how river width influences sediment N2O and N2 fluxes and highlights the importance of incorporating temperature into flux predictions, particularly for wider rivers.}, }
@article {pmid39786593, year = {2025}, author = {Xu, Y and Liang, J and Qin, L and Niu, T and Liang, Z and Li, Z and Chen, B and Zhou, J and Yu, K}, title = {The Dynamics of Symbiodiniaceae and Photosynthetic Bacteria Under High-Temperature Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {169}, pmid = {39786593}, issn = {1432-184X}, support = {42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; }, mesh = {*Photosynthesis ; *Symbiosis ; *Anthozoa/microbiology/physiology ; China ; *Hot Temperature ; *Dinoflagellida/physiology ; Animals ; *Seasons ; Bacteria/classification/metabolism/genetics ; Cyanobacteria/physiology ; Chlorophyll A/metabolism ; }, abstract = {Coral thermal tolerance is intimately linked to their symbiotic relationships with photosynthetic microorganisms. However, the potential compensatory role of symbiotic photosynthetic bacteria in supporting Symbiodiniaceae photosynthesis under extreme summer temperatures remains largely unexplored. Here, we examined the seasonal variations in Symbiodiniaceae and photosynthetic bacterial community structures in Pavona decussata corals from Weizhou Island, Beibu Gulf, China, with particular emphasis on the role of photosynthetic bacteria under elevated temperature conditions. Our results revealed that Symbiodiniaceae density and Chlorophyll a concentration were lowest during the summer and highest in the winter. Notably, the summer bacterial community was predominately composed of the proteorhodopsin bacterium BD 1-7 _clade, alongside a significant increase in Cyanobacteria, particularly Synechococcus_CC9902 and Cyanobium_PCC-6307, which represented 61.85% and 31.48% of the total Cyanobacterial community, respectively. In vitro experiments demonstrated that Cyanobacteria significantly enhanced Symbiodiniaceae photosynthetic efficiency under high-temperature conditions. These findings suggest that the increased abundance of photosynthetic bacteria during summer may mitigate the adverse physiological effects of reduced Symbiodiniaceae density, thereby contributing to coral stability. Our study highlights a potential synergistic interaction between Symbiodiniaceae and photosynthetic bacteria, emphasizing the importance of understanding these dynamic interactions in sustaining coral resilience against environmental stress, although further research is necessary to establish their role in preventing coral bleaching.}, }
@article {pmid39786575, year = {2025}, author = {McNeal, R and Wells, JD and Tomberlin, JK}, title = {Bernard Greenberg: a legacy in medical, veterinary, and forensic entomology.}, journal = {Journal of medical entomology}, volume = {62}, number = {2}, pages = {231-235}, doi = {10.1093/jme/tjae158}, pmid = {39786575}, issn = {1938-2928}, mesh = {Animals ; History, 20th Century ; *Entomology/history ; *Forensic Entomology/history ; *Diptera/microbiology ; History, 21st Century ; Humans ; United States ; Veterinary Medicine/history ; }, abstract = {Bernard Greenberg was a ground-breaking scientist in the worlds of medical-veterinary and forensic entomology, studying the ability of flies to serve as a vector of human and other vertebrate pathogens. His work also extended beyond these topics, creating key studies on flies and their associated microbial ecology. These efforts led to numerous research publications and two books on flies and their associated microorganisms. Greenberg served a pioneering role in establishing the field of forensic entomology in the USA later in his career, publishing key papers and a book that are highly cited to this day. We present a review of Dr Greenberg's scientific contributions concerning flies and disease, insect/microbe interactions, and insects as forensic indicators.}, }
@article {pmid39779689, year = {2025}, author = {Cottin, A and Dequiedt, S and Djemiel, C and Prévost-Bouré, NC and Tripied, J and Lelièvre, M and Terreau, L and Régnier, T and Karimi, B and Jolivet, C and Bispo, A and Saby, N and Maron, PA and Ranjard, L and Terrat, S}, title = {Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {34}, pmid = {39779689}, issn = {2052-4463}, support = {2021PRE00370//Conseil r&#xe9;gional de Bourgogne-Franche-Comt&#xe9; (Regional Council of Burgundy)/ ; }, mesh = {*Soil Microbiology ; France ; *Fungi/genetics ; *Archaea/genetics ; *Bacteria/genetics/classification ; Environmental Monitoring ; Soil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).}, }
@article {pmid39779584, year = {2025}, author = {Roy, A and Ray, S}, title = {Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39779584}, issn = {1559-0305}, abstract = {Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.}, }
@article {pmid39779304, year = {2025}, author = {Diakaki, M and Andreo Jimenez, B and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J}, title = {Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39779304}, issn = {1574-6941}, support = {//Ministry of Agriculture/ ; }, mesh = {*Spinacia oleracea/microbiology ; *Seeds/microbiology ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Pythium/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.}, }
@article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, }
@article {pmid39777152, year = {2024}, author = {Liao, H and Wang, X and Wang, X and Zhang, M and Zhang, Y and Huang, S and Wang, H and Jin, H and Wang, J and Li, X and Yan, J and Schubert, T and Löffler, FE and Yang, Y}, title = {Organohalide respiration: retrospective and perspective through bibliometrics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1490849}, pmid = {39777152}, issn = {1664-302X}, abstract = {Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.}, }
@article {pmid39775407, year = {2025}, author = {Sun, X and Armstrong, M and Moradi, A and Bhattacharya, R and Antão-Geraldes, AM and Munthali, E and Grossart, HP and Matsuzaki, SS and Kangur, K and Dunalska, JA and Stockwell, JD and Borre, L}, title = {Impacts of climate-induced drought on lake and reservoir biodiversity and ecosystem services: A review.}, journal = {Ambio}, volume = {54}, number = {3}, pages = {488-504}, pmid = {39775407}, issn = {1654-7209}, support = {RGPIN-2019-04315//Natural Sciences and Engineering Research Council of Canada/ ; 1638679//U.S. National Science Foundation (NSF) Macrosystems Biology Program/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; LA/P/0007/2020//SusTEC/ ; PRG 1266//Estonian Research Council/ ; JPMEERF20232002//Environmental Restoration and Conservation Agency/ ; 1702991//National Science Foundation/ ; UIDB/00690/2020//CIMO/ ; UIDP/00690/2020//CIMO/ ; PIDDAC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Droughts ; *Biodiversity ; *Lakes ; *Ecosystem ; *Climate Change ; Conservation of Natural Resources ; }, abstract = {Intensifying extreme droughts are altering lentic ecosystems and disrupting services provisioning. Unfortunately, drought research often lacks a holistic and intersectoral consideration of drought impacts, which can limit relevance of the insights for adaptive management. This literature review evaluated the current state of lake and reservoir extreme drought research in relation to biodiversity and three ecosystem services. The study findings demonstrated that few articles linked or discussed drought implications with one or more ecosystem services, instead focusing primarily on biodiversity. Drought effects on biodiversity varied among species and taxonomic groups. In the limited literature that included ecosystem service provisioning, droughts had a general negative effect. Drinking water supply can decrease and become more costly. Decreasing water flow and volume can reduce hydropower generation. Degraded water quality can also impact recreation. Future intersectoral collaborations and research on intensifying droughts should support adaptive management efforts in mitigating drought impacts.}, }
@article {pmid39774713, year = {2025}, author = {Dobrzyński, J and Kulkova, I and Jakubowska, Z and Wróbel, B}, title = {Non-native PGPB Consortium Altered the Rhizobacterial Community and Slightly Stimulated the Growth of Winter Oilseed Rape (Brassica napus L.) Under Field Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {168}, pmid = {39774713}, issn = {1432-184X}, support = {DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; }, mesh = {*Brassica napus/microbiology/growth &amp; development ; *Soil Microbiology ; Pseudomonas/growth &amp; development/metabolism ; Plant Roots/microbiology/growth &amp; development ; Phosphorus/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Nitrogen/metabolism ; Rhizosphere ; Microbial Consortia ; Indoleacetic Acids/metabolism ; Microbiota ; Azotobacter/growth &amp; development/metabolism ; }, abstract = {Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH4 and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH4. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH4 and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.}, }
@article {pmid39774673, year = {2025}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {453}, doi = {10.1038/s41467-024-55458-6}, pmid = {39774673}, issn = {2041-1723}, }
@article {pmid39772705, year = {2025}, author = {Zhou, J and Liu, Z and Wang, S and Li, J and Zhang, L and Liao, Z}, title = {A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0419223}, pmid = {39772705}, issn = {2165-0497}, support = {20190ZKK0303//The Second Tibetan Plateau Scientific Expedition and Research Program/ ; 32201424//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Symbiosis ; *Microbiota/genetics ; *Amphibians/microbiology ; Altitude ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {UNLABELLED: Existing analytical frameworks for community assembly have a noticeable knowledge gap, lacking a comprehensive assessment of the relative contributions of individual or grouped microbial distinct sampling units (DSUs) and distinct taxonomic units (DTUs) to each mechanism. Here, we propose a comprehensive framework for identifying DTUs/DSUs that remarkably contribute to the various mechanisms sustaining microbial community structure. Amphibian symbiotic microbes along an altitudinal gradient from Sichuan Province, China, were employed to examine the proposed statistical framework. In different altitude groups, we found that heterogeneous selection governed the community structure of symbiotic microbes across DSUs, while stochastic processes tended to increase with altitude. For DTUs at phylum and family levels, drift emerged as the dominant mechanism driving the community structure in the most symbiotic microbial taxa, while heterogeneous selection governs the most dominant or indicator taxa. Notably, the relative contribution of heterogeneous selection was significantly positively correlated with the relative abundance and niche breadth of taxa, and negatively correlated with drift. We also detected that community assembly processes remarkably regulate the structure of symbiotic microbial communities and their correlation with environmental variables. Altogether, our modeling framework is a robust and valuable tool that further enlarges our insight into microbiota community assembly.<br><br>IMPORTANCE: Distinguishing the drivers regulating microbial community assembly is essential in microbial ecology. We propose a novel modeling framework to partition the relative contributions of each individual or group of microbial DSUs and DTUs into different underpinning mechanisms. An empirical study on amphibian symbiotic microbes notably enlarges insight into community assembly patterns in the herpetological symbiotic ecosystem and demonstrates that the proposed statistical framework is an informative and sturdy tool to quantify microbial assembly processes at both levels of DSUs and DTUs. More importantly, our proposed modeling framework can provide in-depth insights into microbiota community assembly within the intricate tripartite host-environment-microbe relationship.}, }
@article {pmid39772204, year = {2024}, author = {Obong'o, BO and Ogutu, FO and Hurley, SK and Okiko, GM and Mahony, J}, title = {Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety.}, journal = {Viruses}, volume = {16}, number = {12}, pages = {}, pmid = {39772204}, issn = {1999-4915}, mesh = {Africa South of the Sahara ; *Bacteriophages/physiology ; *Water Quality ; *Water Microbiology ; *Water Purification/methods ; Bacteria/virology ; Humans ; Food Safety/methods ; Biodegradation, Environmental ; }, abstract = {Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.}, }
@article {pmid39771075, year = {2024}, author = {Tapia, Y and Salazar, O and Seguel, O and Suazo-Hernández, J and Urdiales-Flores, D and Aponte, H and Urdiales, C}, title = {Optimizing Heavy Metal Uptake in Carpobrotus aequilaterus Through Electrokinetic Treatment: A Comprehensive Study on Phytoremediation from Mine Tailings.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771075}, issn = {2305-6304}, support = {3220201//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Copper mining drives economic growth, with the global demand expected to reach 120 million metric tons annually by 2050. However, mining produces tailings containing heavy metals (HMs), which poses environmental risks. This study investigated the efficacy of phytoremediation (Phy) combined with electrokinetic treatment (EKT) to increase metal uptake in Carpobrotus aequilaterus grown in tailings from the Metropolitan Region of Chile. The plants were exposed to varying voltages and treatment durations. In the control (no EKT), the root metal contents were Fe (1008.41 mg/kg) > Cu (176.38 mg/kg) > Mn (103.73 mg/kg) > Zn (30.26 mg/kg), whereas in the shoots, the order was Mn (48.69 mg/kg) > Cu (21.14 mg/kg) > Zn (17.67 mg/kg) > Fe (27.32 mg/kg). The optimal EKT (15 V for 8 h) significantly increased metal uptake, with roots accumulating Fe (5997.24 mg kg[-1]) > Mn (672 mg kg[-1]) > Cu (547.68 mg kg[-1]) > Zn (90.99 mg kg[-1]), whereas shoots contained Fe (1717.95 mg kg[-1]) > Mn (930 mg kg[-1]) > Cu (219.47 mg kg[-1]) > Zn (58.48 mg kg[-1]). Although EKT enhanced plant growth and biomass, higher voltages stressed the plants. Longer treatments were more effective, suggesting that EK-Phy is a promising method for remediating metal-contaminated tailings.}, }
@article {pmid39770685, year = {2024}, author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F}, title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770685}, issn = {2076-2607}, support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; }, abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.}, }
@article {pmid39770645, year = {2024}, author = {Neviani, E}, title = {The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770645}, issn = {2076-2607}, abstract = {Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.}, }
@article {pmid39770585, year = {2024}, author = {Heczko, PB and Giemza, M and Ponikiewska, W and Strus, M}, title = {Importance of Lactobacilli for Human Health.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770585}, issn = {2076-2607}, support = {RPMP.01.02.01-12-0413/17.//The National Centre for Research and Development/ ; }, abstract = {As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include "Lactobacillus" in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.}, }
@article {pmid39770454, year = {2024}, author = {Atazhanova, GA and Levaya, YK and Badekova, KZ and Ishmuratova, MY and Smagulov, MK and Ospanova, ZO and Smagulova, EM}, title = {Inhibition of the Biofilm Formation of Plant Streptococcus mutans.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {12}, pages = {}, pmid = {39770454}, issn = {1424-8247}, support = {&#x410;&#x420;23488250//MINISTRY OF SCIENCE AND HIGHER EDUCATION OF REPUBLIC OF KAZAKHSTAN/ ; }, abstract = {This review is devoted to a systematic analysis of studies aimed at investigating plant extracts, essential oils and phytochemical compounds capable of inhibiting Streptococcus mutans biofilm formation. This paper investigates the effect of extracts, essential oils and individual plant compounds on inhibiting the biofilm formation of Streptococcus mutans, one of the major pathogens responsible for the development of dental caries. Using cultural microbiology and molecular biology techniques, the authors describe the mechanisms by which plant samples reduce Streptococcus mutans adhesion and growth. The results show that several plant components have antibacterial properties, contributing to the reduction of Streptococcus mutans colony numbers and inhibiting the synthesis of extract-exopolysaccharide matrices required for biofilm formation. This work highlights the potential of botanicals in inhibiting Streptococcus mutans biofilm formation, which can be applied as natural antimicrobial agents in the prevention and treatment of dental diseases. Views on the use of these plant extracts and their components in dental preparations such as toothpastes, rinses and gels aimed at preventing dental caries are evaluated. The review shows the relevance of the research to optimizing the use of plant extracts, essential oils, individual compounds and their active actions in the control of Streptococcus mutans biofilms.}, }
@article {pmid39769364, year = {2024}, author = {Grzyb, T and Szulc, J}, title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, pmid = {39769364}, issn = {1422-0067}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; }, abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.}, }
@article {pmid39768235, year = {2024}, author = {Riekeles, M and Santos, B and Youssef, SA and Schulze-Makuch, D}, title = {Viability and Motility of Escherichia coli Under Elevated Martian Salt Stresses.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768235}, issn = {2075-1729}, support = {Scholarship for Max Riekeles//Friedrich-Ebert-Stiftung e.V./ ; }, abstract = {This study investigates the effects of three Martian-relevant salts-sodium chlorate, sodium perchlorate, and sodium chloride-on the viability and motility of Escherichia coli, a model organism for understanding microbial responses to environmental stress. These salts are abundant on Mars and play a crucial role in forming brines, one of the few sources of stable liquid water on the planet. We analyze the survivability under different salt concentrations using colony plating. Additionally, we perform a semi-automated motility analysis, analyzing microbial speeds and motility patterns. Our results show that sodium perchlorate is the most toxic, followed by sodium chlorate, with sodium chloride being the least harmful. Both survivability and motility are affected by salt concentration and exposure time. Notably, we observe a short-lived increase in motility at certain concentrations, particularly under sodium chlorate and sodium perchlorate stress, despite rapid declines in cell viability, suggesting a stress response mechanism. Given that motility might enhance an organism's ability to navigate harsh and variable environments, it holds promise as a key biosignature in the search for life on Mars.}, }
@article {pmid39764393, year = {2024}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39764393}, issn = {2331-8422}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, abstract = {All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39762141, year = {2025}, author = {Nguyen, PN and Rehan, SM}, title = {Supporting wild bee development with a bacterial symbiont.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae317}, pmid = {39762141}, issn = {1365-2672}, abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.<br><br>METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.<br><br>CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.}, }
@article {pmid39760916, year = {2025}, author = {García-Bodelón, &#xc1; and Baković, N and Cano, E and Useros, F and Lara, E and González-Miguéns, R}, title = {Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {166}, pmid = {39760916}, issn = {1432-184X}, support = {PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Class: UP/I-612-07/21-48/170, Ref. No.: 517-10-1-1-21-3, 16.07.2021//Croatian Ministry of Economy and Sustainable Development/ ; }, mesh = {Croatia ; Animals ; *Chiroptera/microbiology ; *Caves/microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Chironomidae/genetics ; Feces/microbiology ; Electron Transport Complex IV/genetics/analysis ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Karst caves, formed from the dissolution of soluble rocks, are characterized by the absence of photosynthetic activity and low levels of organic matter. Organisms evolve under these particular conditions, which causes high levels of endemic biodiversity in both macroorganism and microbes. Recent research has highlighted the presence of testate amoebae (Arcellinida) group in cave environments. This study investigates the diversity of Arcellinida in Dinaric karstic caves in Croatia, a global diversity hotspot, focusing on the influence of bat guano on community structure. Sediment samples were collected from two independent hydrosystems, and a metabarcoding approach was used to assess Arcellinida diversity at specific and intraspecific levels, using Arcellinid-specific primers to amplify the mitochondrial cytochrome oxidase subunit I (COI) region. Results reveal a significant impact of guano on both specific and intraspecific diversity of Arcellinida. Communities in guano-rich sites displayed higher diversity, abundance, and the presence of unique OTUs and genetic variants not observed in other habitats, highlighting the crucial role of bats as ecosystem engineers. In contrast, sites without guano hosted communities with low abundance and reduced biodiversity. These differences suggest the existence of guano-associated Arcellinida communities. This study provides new insights into the biodiversity of subterranean ecosystems and the ecological roles of Arcellinida in karstic environments.}, }
@article {pmid39760871, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {165}, pmid = {39760871}, issn = {1432-184X}, mesh = {*Polygalacturonase/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fungi/enzymology/metabolism/isolation &amp; purification/classification/genetics ; Aspergillus/metabolism/enzymology/isolation &amp; purification ; Egypt ; Fungal Proteins/metabolism ; }, abstract = {Microorganisms are preferred as an enzyme source due to their short lifespan, high production rate, affordability, and absence of harmful chemicals in enzymes generated from plant and animal sources. Fungi communities are biological factories for many bioactive compounds such as the important industrial enzyme pectinase. The current study dealt with production, optimization, purification, biocompatibility, and application of fungal pectinase obtained from five plant rhizospheres (banana, jarawa, lemon, tomato, and wheat) at Fayoum Governorate, Egypt. The highest pectinase degrading index (PDI) was scored for FB5, FJ2, and FW1 isolates. Pectinase production was also examined quantitively and the highest output of 1603.67, 1311.22, and 1264.83 U/ml was gained by FB5, FJ1, and FW1 fungal isolates, respectively. The most active pectinase-producing fungi were identified as Aspergillus niveus strain AUMC1624, A. niger strain AUMC16245, and A. brasiliensis strain AUMC16244, respectively. For pectinase production optimization, one factor at a time (OFAT) protocol was applied and revealed that A. niger, A. niveus, and A. brasiliensis reached maximum pectinase levels at 1% pectin after 5, 7, and 7 days, at 40, 45, and 45 °C, respectively. Obtained pectinases were partially purified using ammonium sulfate precipitation (ASP) and organic solvent precipitation (OSP) methods. The highest activity using the ASP method scored at 40-60% saturation with A. niger. The thermostability characterization of A. niger pectinase was reached with relative activities of 61.7, 69.0, 99.9, 91.3, and 90.6% at temperatures ranging between 30 and 70 °C. pH optimized at pH 5-7. The enzyme's molecular weight was approximately 30 kDa. The GC-mass analysis of pectinase end products included acetic acid ethyl ester, hexadecane carbonsaure methylase, and hexadecenoic acid. The biocompatibility was examined using a human skin cell line (HFb-4) for the first time, with a minimal half concentration (IC50) of 151.86 ± 0.76 U/ml. The biocompatible pectinase was applied as a clothes bioscouring agent with different concentrations of 1893.52 U/ml achieving the highest bioscouring with 20.0%.}, }
@article {pmid39760805, year = {2025}, author = {Willemsen, A and Manzano-Marín, A and Horn, M}, title = {Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39760805}, issn = {1759-6653}, support = {//European Union's Horizon 2020 research and innovation programme/ ; 891572//Marie Sklodowska-Curie/ ; 101039843//European Union/ ; //European Research Council Executive Agency/ ; //Austrian Science Fund/ ; }, mesh = {*Giant Viruses/genetics ; *Codon Usage ; *Amoeba/virology/genetics ; Genome, Protozoan ; Host Specificity ; Phylogeny ; Acanthamoeba/virology/genetics ; }, abstract = {The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.}, }
@article {pmid39753761, year = {2025}, author = {Peng, Z and van der Heijden, MGA and Liu, Y and Li, X and Pan, H and An, Y and Gao, H and Qi, J and Gao, J and Qian, X and Tiedje, JM and Wei, G and Jiao, S}, title = {Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems.}, journal = {Nature food}, volume = {6}, number = {4}, pages = {375-388}, pmid = {39753761}, issn = {2662-1355}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; China ; *Climate Change ; Crops, Agricultural/growth &amp; development ; *Ecosystem ; *Microbiota ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.}, }
@article {pmid39752189, year = {2025}, author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE}, title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39752189}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Salmonella/genetics/isolation &amp; purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification/classification ; }, abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.}, }
@article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Microbiota ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Carbon Cycle ; Estuaries ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.<br><br>IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, }
@article {pmid39745058, year = {2025}, author = {Doyle, RT and Grieves, LA and Gerstein, AC}, title = {Microbial ecology and evolution.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-3}, doi = {10.1139/cjm-2024-0192}, pmid = {39745058}, issn = {1480-3275}, }
@article {pmid39744675, year = {2024}, author = {Mathers, AJ and Li, TJX and He, Q and Narendra, S and Stoesser, N and Eyre, DW and Walker, AS and Barry, KE and Castañeda-Barba, S and Huang, FW and Parikh, H and Kotay, S and Crook, DW and Reidys, C}, title = {Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir.}, journal = {npj antimicrobials and resistance}, volume = {2}, number = {1}, pages = {50}, pmid = {39744675}, issn = {2731-8745}, abstract = {Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same bla KPC carbapenemase gene to understand evolution over time in six confined hospital drains over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 bla KPC-carrying plasmids across 16 distinct replicon types. To assess dynamic gene movement, we introduced the 'Composite-Sample Complex', a novel mathematical approach to using probability to capture the directional movement of antimicrobial resistance genes. The Composite Sample Complex accounts for the co-occurrence of both plasmids and chromosomes within an isolate, and highlights likely gene donors and recipients. From the validated model, we demonstrate frequent transposition events of bla KPC from plasmids to other plasmids, as well as integration into the bacterial chromosome within specific drains. We present a novel approach to estimate the directional movement of antimicrobial resistance via gene mobilization.}, }
@article {pmid39744400, year = {2024}, author = {Bradbury, ES and Holland-Moritz, H and Gill, A and Havrilla, CA}, title = {Plant and soil microbial composition legacies following indaziflam herbicide treatment.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450633}, pmid = {39744400}, issn = {1664-302X}, abstract = {Land stewards in dryland ecosystems across the western U.S. face challenges to manage the exotic grass Bromus tectorum (cheatgrass), which is a poor forage, is difficult to remove, and increases risk of catastrophic fire. Managers may consider using indaziflam (Rejuvra™), a relatively new pre-emergent herbicide, which may reduce cheatgrass cover within drylands. However, few studies have explored the effects of indaziflam on non-target organisms. We tested how indaziflam application impacted cover and biomass of native and exotics within the plant community and composition and diversity of the soil microbiome by comparing untreated and treated arid shrubland sites in Boulder County, Colorado, USA. We found that indaziflam application decreased cheatgrass cover by as much as 80% and increased native plant cover by the same amount. Indaziflam application also was associated with increased soil nitrate (NO3 [-]), decreased soil organic matter, and had a significant effect on the composition of the soil microbiome. Microbial community composition was significantly related to soil NO3 [-], soil organic matter, soil pH, and native species and cheatgrass biomass. An indicator species analysis suggested that indaziflam application shifted microbial communities. In untreated sites, ammonia-oxidizing bacteria Nitrosomonadaceae and nitrogen-digesting Opitutaceae and the fungi Articulospora proliferata were found. While in treated sites, ammonia-oxidizing archaea which are associated with intact drylands, Nitrososphaeraceae and toxin digesters and acidic-soil species Sphingomonas and Acidimicrobiia were significantly associated. Overall, these results demonstrate that indaziflam application can increase native plant recruitment, while also affecting soil properties and the soil microbiome. The findings from this study can be used to inform decision-making during dryland restoration planning process as indaziflam use may have benefits and unknown long-term consequences for the biogeochemistry and microbial ecology of the system.}, }
@article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; Phylogeny ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Erwinia/virology ; Genome, Viral ; *Pseudomonas/virology ; DNA, Viral/genetics ; Microbiota ; Plant Leaves/microbiology ; Metagenome ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, }
@article {pmid39742000, year = {2024}, author = {Ford, SE and Slater, GF and Engel, K and Warr, O and Lollar, GS and Brady, A and Neufeld, JD and Lollar, BS}, title = {Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {795}, pmid = {39742000}, issn = {2662-4435}, abstract = {Characterizing deep subsurface microbial communities informs our understanding of Earth's biogeochemistry as well as the search for life beyond the Earth. Here we characterized microbial communities within the Kidd Creek Observatory subsurface fracture water system with mean residence times of hundreds of millions to over one billion years. 16S rRNA analysis revealed that biosamplers well isolated from the mine environment were dominated by a putatively anaerobic and halophilic bacterial species from the Halobacteroidaceae family, Candidatus Frackibacter. Contrastingly, biosamplers and biofilms exposed to the mine environment contained aerobic Sphingomonas taxa. δ[13]C values of phospholipid fatty acids and putative functional predictions derived from 16S rRNA gene profiles, imply Candidatus Frackibacter may use carbon derived from ancient carbon-rich layers common in these systems. These results indicate that Candidatus Frackibacter is not unique to hydraulically fracked sedimentary basins but rather may be indigenous to a wide range of deep, saline groundwaters hosted in carbon-rich rocks.}, }
@article {pmid39741633, year = {2024}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A real-world pharmacovigilance study of Sorafenib based on the FDA Adverse Event Reporting System.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1442765}, pmid = {39741633}, issn = {1663-9812}, abstract = {AIMS: The primary objective of this study was to closely monitor and identify adverse events (AEs) associated with Sorafenib, a pharmacological therapeutic agent used to treat hepatocellular carcinoma, renal cell carcinoma, and thyroid cancer. The ultimate goal was to optimize patient safety and provide evidence-based guidance for the appropriate use of this drug.<br><br>METHODS: Reports from the FDA Adverse Event Reporting System (FAERS) database were comprehensively collected and analyzed, covering the first quarter of 2004 to the first quarter of 2024. Disproportionality analysis was performed using robust algorithms for effective data mining to quantify the signals associated with Sorafenib-related AEs.<br><br>RESULTS: In total, we identifued 18,624 patients (82,857 AEs in the Sorafenib population) from the collected reports and examined, the occurrence of Sorafenib-induced AEs in 26 organ systems. The study results revealed the presence of the expected AEs, including Diarrhoea, Palmar-plantar erythrodysaesthesia syndrome, Hepatocellular carcinoma, Fatigue, and Rash, which was consistent with the information provided in the drug insert. In addition, unexpected significant AEs, such as Gait inability, Palmoplantar keratoderma and Hyperkeratosis were observed at the preferred term (PT) level. These findings suggest the potential occurrence of adverse reactions not currently documented in drug descriptions.<br><br>CONCLUSION: This study successfully detected new and unforeseen signals associated with Sorafenib-related AEs related to Sorafenib administration, providing important insights into the complex correlations between AEs and Sorafenib use. The results of this study emphasize the critical importance of continuous and vigilant surveillance for the timely identification and effective management of AEs to improve the overall patient safety and wellbeing in the context of Sorafenib therapy.}, }
@article {pmid39739109, year = {2024}, author = {Rovira-Alsina, L and Romans-Casas, M and Perona-Vico, E and Ceballos-Escalera, A and Balaguer, MD and Bañeras, L and Puig, S}, title = {Microbial Electrochemical Technologies: Sustainable Solutions for Addressing Environmental Challenges.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39739109}, issn = {0724-6145}, abstract = {Addressing global challenges of waste management demands innovative approaches to turn biowaste into valuable resources. This chapter explores the potential of microbial electrochemical technologies (METs) as an alternative opportunity for biowaste valorisation and resource recovery due to their potential to address limitations associated with traditional methods. METs leverage microbial-driven oxidation and reduction reactions, enabling the conversion of different feedstocks into energy or value-added products. Their versatility spans across gas, food, water and soil streams, offering multiple solutions at different technological readiness levels to advance several sustainable development goals (SDGs) set out in the 2030 Agenda. By critically examining recent studies, this chapter uncovers challenges, optimisation strategies, and future research directions for real-world MET implementations. The integration of economic perspectives with technological developments provides a comprehensive understanding of the opportunities and demands associated with METs in advancing the circular economy agenda, emphasising their pivotal role in waste minimisation, resource efficiency promotion, and closed-loop system renovation.}, }
@article {pmid39738334, year = {2024}, author = {Ahadi, R and Bouket, AC and Alizadeh, A and Masigol, H and Grossart, HP}, title = {Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31701}, pmid = {39738334}, issn = {2045-2322}, mesh = {Iran ; *Phylogeny ; *Pythium/genetics/isolation &amp; purification ; Oomycetes/genetics/classification/isolation &amp; purification ; Cucumis sativus/microbiology ; }, abstract = {During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp. nov., G. mahabadense sp. nov., and Pythium bostanabadense sp. nov. Furthermore, experiments confirmed the pathogenicity of all identified species on cucumber seedlings, suggesting a pathogenic lifestyle also in aquatic systems. Our research contributes to a better understanding of the diversity, host range and distribution of oomycetes genera Globisporangium and Pythium in northwestern Iran. Detailed morphological descriptions and illustrations are provided for all species.}, }
@article {pmid39737770, year = {2025}, author = {Rawstern, AH and Hernandez, DJ and Afkhami, ME}, title = {Central Taxa Are Keystone Microbes During Early Succession.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70031}, pmid = {39737770}, issn = {1461-0248}, support = {DEB-1922521//National Science Foundation/ ; DEB-2030060//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Biodiversity ; Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.}, }
@article {pmid39736538, year = {2024}, author = {Radjasa, OK and Steven, R and Natanael, Y and Nugrahapraja, H and Radjasa, SK and Kristianti, T and Moeis, MR and Trinugroho, JP and Suharya, HB and Rachmatsyah, AO and Dwijayanti, A and Putri, MR and de Fretes, CE and Siallagan, ZL and Fadli, M and Opier, RDA and Farahyah, JD and Rahmawati, V and Rizanti, M and Humaira, Z and Prihatmanto, AS and Hananto, ND and Susanto, RD and Chahyadi, A and Elfahmi,  and Priharto, N and Kamarisima,  and Dwivany, FM}, title = {From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1259}, pmid = {39736538}, issn = {1471-2164}, mesh = {*Lycopene/metabolism ; Indonesia ; *Genome, Bacterial ; Bioprospecting ; Genomics/methods ; Phylogeny ; Multigene Family ; Peptide Synthases/genetics/metabolism ; Whole Genome Sequencing ; Carotenoids/metabolism ; Actinobacteria/genetics/metabolism ; }, abstract = {BACKGROUND: The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods.<br><br>RESULTS: Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4&#xa0;Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (&#x3b1;&#x2009;<&#x2009;1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes.<br><br>CONCLUSIONS: This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.}, }
@article {pmid39736196, year = {2025}, author = {Wong, JWH and Balskus, EP}, title = {Small molecules as modulators of phage-bacteria interactions.}, journal = {Current opinion in chemical biology}, volume = {84}, number = {}, pages = {102566}, doi = {10.1016/j.cbpa.2024.102566}, pmid = {39736196}, issn = {1879-0402}, mesh = {*Bacteriophages/physiology/drug effects ; *Bacteria/virology/metabolism/drug effects ; *Small Molecule Libraries/pharmacology/chemistry ; Lysogeny/drug effects ; }, abstract = {Bacteriophages (phages) play a critical role in microbial ecology and evolution. Their interactions with bacteria are influenced by a complex network of chemical signals derived from a wide range of sources including both endogenous bacterial metabolites and exogenous environmental compounds. In this review, we highlight two areas where small molecules play a pivotal role in modulating phage behaviors. First, we discuss how temperate phages respond to various chemical cues that influence the lysis-lysogeny decision, describing recent advances in our understanding of noncanonical cues. Second, we examine the diverse array of small molecules that disrupt phage infection, potentially serving as bacterial defense strategies against their long-standing competitors. Collectively, this growing body of research highlights the intricate molecular mechanisms governing phage-bacteria dynamics, offering new perspectives on the chemical language shaping microbial communities.}, }
@article {pmid39732620, year = {2025}, author = {Berrios, L and Ansell, TB and Dahlberg, PD and Peay, KG}, title = {Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi.}, journal = {FEMS microbiology reviews}, volume = {49}, number = {}, pages = {}, pmid = {39732620}, issn = {1574-6976}, support = {2109481//National Science Foundation/ ; //Canadian Institute for Advanced Research/ ; 1845544//DEB/ ; }, mesh = {*Mycorrhizae/physiology ; *Bacteria ; Soil Microbiology ; Plant Roots/microbiology ; *Microbial Interactions ; }, abstract = {Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet, we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.}, }
@article {pmid39732444, year = {2025}, author = {Correa, SS and Schultz, J and Zahodnik-Huntington, B and Naschberger, A and Rosado, AS}, title = {Carboxysomes: The next frontier in biotechnology and sustainable solutions.}, journal = {Biotechnology advances}, volume = {79}, number = {}, pages = {108511}, doi = {10.1016/j.biotechadv.2024.108511}, pmid = {39732444}, issn = {1873-1899}, mesh = {*Biotechnology/methods ; *Organelles/metabolism ; Carbon Cycle ; Ribulose-Bisphosphate Carboxylase/metabolism ; *Bacteria/metabolism ; Carbonic Anhydrases/metabolism ; Cyanobacteria/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Some bacteria possess microcompartments that function as protein-based organelles. Bacterial microcompartments (BMCs) sequester enzymes to optimize metabolic reactions. Several BMCs have been characterized to date, including carboxysomes and metabolosomes. Genomic analysis has identified novel BMCs and their loci, often including genes for signature enzymes critical to their function, but further characterization is needed to confirm their roles. Among the various BMCs, carboxysomes, which are found in cyanobacteria and some chemoautotrophic bacteria, and are most extensively investigated. These self-assembling polyhedral proteinaceous BMCs are essential for carbon fixation. Carboxysomes encapsulate the enzymes RuBisCo and carbonic anhydrase, which increase the carbon fixation rate in the cell and decrease the oxygenation rate by RuBisCo. The ability of carboxysomes to concentrate carbon dioxide in crops and industrially relevant microorganisms renders them attractive targets for carbon assimilation bioengineering. Thus, carboxysome characterization is the first step toward developing carboxysome-based applications. Therefore, this review comprehensively explores carboxysome morphology, physiology, and biochemistry. It also discusses recent advances in microscopy and complementary techniques for isolating and characterizing this versatile class of prokaryotic organelles.}, }
@article {pmid39731630, year = {2024}, author = {Fluch, M and Corretto, E and Feldhaar, H and Schuler, H}, title = {Seasonal Changes in the Gut Microbiota of Halyomorpha halys.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {164}, pmid = {39731630}, issn = {1432-184X}, mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Pantoea/isolation &amp; purification/physiology/genetics/classification ; Phylogeny ; }, abstract = {The gut microbiome plays an important role in insect evolution and ecology. Bacteria support the host's nutrition and defense and therefore play an important role in the fitness of the host. Halyomorpha halys is one of the most important invasive pest species in the world. Native to North-Eastern Asia, this Pentatomid bug has recently invaded North America and Europe, causing significant damage to agricultural production. Although an increasing number of studies investigated the biology of this pest species, little is known about the composition of its gut microbiota. Like many other Pentatomid species, H. halys harbors a primary symbiont called "Candidatus Pantoea carbekii," which produces vitamins and essential amino acids for the host. However, information about the presence of other bacteria is currently lacking. Therefore, we investigated the gut microbiota of H. halys individuals, which were collected in the field across the year using a high-throughput 16S rRNA gene metabarcoding approach. Our results revealed 3309 different ASVs associated with H. halys, with Pantoea being the most abundant symbiont, present in almost all individuals. Additionally, many individuals harbor Commensalibacter, a genus of acetic acid bacterial symbionts. Besides these two predominant taxa, we show a high diversity of microorganisms associated with H. halys with seasonal fluctuations, highlighting a dynamic microbiota that might influence the biology of this species.}, }
@article {pmid39730790, year = {2024}, author = {Struniawski, K and Kozera, R and Trzciński, P and Marasek-Ciołakowska, A and Sas-Paszt, L}, title = {Extreme learning machine for identifying soil-dwelling microorganisms cultivated on agar media.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31034}, pmid = {39730790}, issn = {2045-2322}, support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {*Soil Microbiology ; *Machine Learning ; Agar/chemistry ; Soil/chemistry ; Image Processing, Computer-Assisted/methods ; Culture Media ; }, abstract = {The aim of this research is to create an automated system for identifying soil microorganisms at the genera level based on raw microscopic images of monocultural colonies grown in laboratory environment. The examined genera are: Fusarium, Trichoderma, Verticillium, Purpureolicillium and Phytophthora. The proposed pipeline deals with unprocessed microscopic images, avoiding additional sample marking or coloration. The methodology includes several stages: image preprocessing, segmenting images to isolate microorganisms from the background, calculating features related to image color and texture for classification. Using an extensive dataset of 2866 images from the National Institute of Horticultural Research in Skierniewice the Extreme Learning Machine model was trained and validated. The model showcases high accuracy and computational efficiency compared to other Machine Learning state-of-the art methods e.g. CatBoost, Random Forest or Convolutional Neural Networks. Statistical techniques, including Multivariate Analysis of Variance were employed to confirm significant differences among the datasets, enhancing the model's robustness. Nevertheless, Shapley Additive Explanations values provided transparency into the model's decision-making process. This approach has the potential to improve early detection and management of soil pathogens, promoting sustainable agriculture and demonstrating machine learning's potential in environmental monitoring, microbial ecology or industrial microbiology.}, }
@article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology/parasitology/genetics ; *Metagenomics/methods ; Metagenome ; *Deep Learning ; *Databases, Protein ; Rumen/microbiology ; Fungi/genetics/classification ; Computational Biology/methods ; *Eukaryota/genetics/classification ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, }
@article {pmid39730090, year = {2025}, author = {Nguyen, TV and Kim, NK and Lee, SH and Trinh, HP and Park, HD}, title = {Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {144028}, doi = {10.1016/j.chemosphere.2024.144028}, pmid = {39730090}, issn = {1879-1298}, mesh = {Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; Wastewater/microbiology ; *Bacteria/genetics/metabolism ; Bioreactors/microbiology ; }, abstract = {Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.}, }
@article {pmid39726151, year = {2024}, author = {Nieland, MA and Lacy, P and Allison, SD and Bhatnagar, JM and Doroski, DA and Frey, SD and Greaney, K and Hobbie, SE and Kuebbing, SE and Lewis, DB and McDaniel, MD and Perakis, SS and Raciti, SM and Shaw, AN and Sprunger, CD and Strickland, MS and Templer, PH and Vietorisz, C and Ward, EB and Keiser, AD}, title = {Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States.}, journal = {Global change biology}, volume = {30}, number = {12}, pages = {e70016}, doi = {10.1111/gcb.70016}, pmid = {39726151}, issn = {1365-2486}, support = {1831944//Division of Environmental Biology/ ; SC0020382//Biological and Environmental Research/ ; 1845417//National Science Foundation/ ; 2045135//Division of Earth Sciences/ ; //University of Massachusetts Amherst/ ; }, mesh = {*Soil/chemistry ; United States ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Soil Microbiology ; *Nitrification ; Forests ; Biomass ; }, abstract = {Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified (ƒnitrified), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta-glucosidase (BG) and N-acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒnitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒnitrified. The ƒnitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒnitrified, including for high soil C sites predicted to have low ƒnitrified, which decreased the role of soil C as a predictor of ƒnitrified. Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID-19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒnitrified. Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.}, }
@article {pmid39725503, year = {2025}, author = {Belanche, A and Bannink, A and Dijkstra, J and Durmic, Z and Garcia, F and Santos, FG and Huws, S and Jeyanathan, J and Lund, P and Mackie, RI and McAllister, TA and Morgavi, DP and Muetzel, S and Pitta, DW and Yáñez-Ruiz, DR and Ungerfeld, EM}, title = {Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants.}, journal = {Journal of dairy science}, volume = {108}, number = {1}, pages = {375-394}, doi = {10.3168/jds.2024-25046}, pmid = {39725503}, issn = {1525-3198}, mesh = {*Methane ; Animals ; *Animal Feed ; *Ruminants ; *Rumen/metabolism ; Diet/veterinary ; }, abstract = {This publication aims to provide guidelines of the knowledge required and the potential research to be conducted in order to understand the mode of action of antimethanogenic feed additives (AMFA). In the first part of the paper, we classify AMFA into 4 categories according to their mode of action: (1) lowering dihydrogen (H2) production; (2) inhibiting methanogens; (3) promoting alternative H2-incorporating pathways; and (4) oxidizing methane (CH4). The second part of the paper presents questions that guide the research to identify the mode of action of an AMFA on the rumen CH4 production from 5 different perspectives: (1) microbiology; (2) cell and molecular biochemistry; (3) microbial ecology; (4) animal metabolism; and (5) cross-cutting aspects. Recommendations are provided to address various research questions within each perspective, along with examples of how aspects of the mode of action of AMFA have been elucidated before. In summary, this paper offers timely and comprehensive guidelines to better understand and reveal the mode of action of current and emerging AMFA.}, }
@article {pmid39725195, year = {2025}, author = {Xu, W and Lam, C and Wang, Y and Wan, SH and Ho, PH and Myung, J and Yung, CCM}, title = {Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125572}, doi = {10.1016/j.envpol.2024.125572}, pmid = {39725195}, issn = {1873-6424}, mesh = {*Plastics/analysis ; *Seawater/microbiology ; Hong Kong ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Environmental Monitoring ; Bacteria/classification ; *Water Microbiology ; }, abstract = {Marine plastic pollution is a pervasive environmental issue, with microplastics serving as novel substrates for microbial colonization in aquatic ecosystems. This study investigates the succession of plastisphere communities on four common plastic types (polyethylene, polypropylene, polyethylene terephthalate, and polystyrene) in subtropical coastal waters of Hong Kong SAR. Over a 42-day period, we analysed the temporal development of microbial communities using a three-domain universal metabarcoding method. Our results reveal that temporal succession is a stronger driver of community structure than plastic type, with prokaryotic communities converging across different plastics as biofilms mature. Despite this convergence, plastisphere communities remain distinct from planktonic communities throughout the experiment, suggesting that plastics create unique ecological niches in marine environments. We observed differences in diversity patterns and community composition among prokaryotic, eukaryotic, and chloroplastic communities, highlighting the importance of multi-domain analyses in plastisphere research. Functional predictions suggest potential roles of prokaryotic communities in biogeochemical cycling and possible pathogenicity, highlighting the ecological and public health implications of plastisphere formation. This study provides valuable insights into the dynamics of microbial colonization across domains on marine plastics and enhances our understanding of how these anthropogenic substrates influence microbial ecology in marine ecosystems.}, }
@article {pmid39724890, year = {2024}, author = {Kusradze, I and Rcheulishvili, O and Karumidze, N and Rigvava, S and Rcheulishvili, A and Goliadze, R and Kamashidze, L and Chipurupalli, A and Metreveli, N and Goderdzishvili, M}, title = {PHAGE-BACTERIA INTERACTIONS UNDER METAL STRESS: A STUDY OF THE NOVEL STENOTROPHOMONAS MALTOPHILIA PHAGE VB_STM18.}, journal = {Georgian medical news}, volume = {}, number = {355}, pages = {117-122}, pmid = {39724890}, issn = {1512-0112}, mesh = {*Stenotrophomonas maltophilia/virology/drug effects ; *Cadmium/toxicity ; *Bacteriophages ; Biodegradation, Environmental ; Stress, Physiological/drug effects ; }, abstract = {Stenotrophomonas maltophilia is a highly adaptable gram-negative bacteria, demonstrating resilience in metal-contaminated environment, which makes it a key subject for understanding microbial survival under heavy metal stress. This study investigates the effects of cadmium ions (Cd[2+]) on the growth dynamics, cadmium uptake, and bacteriophage vB_Stm18-host interactions, with implications for environmental microbiology and applied biotechnology. Growth analysis revealed that S. maltophilia tolerates Cd[2+] at 0.01 g/L, although exposure prolonged the lag phase by 3 hours. Despite the initial growth inhibition, the bacterium adapted and achieved control-like growth levels by 18 hours. Bioaccumulation assays showed progressive cadmium uptake, reaching 1876 µg/g at 24 hours, highlighting its potential for bioremediation. The influence of Cd[2+] on phage vB_Stm18's life cycle was assessed through adsorption efficiency and burst size measurements. Short-term exposure to Cd[2+] caused minimal reductions in adsorption efficiency (97% vs. 98% in control) but significantly decreased the burst size to 17 particles per infected cell. Prolonged exposure exacerbated these effects, with adsorption efficiency decreasing to 58% and burst size dropping to 6 particles per infected cell, after 18 hours of pre-incubation. These findings suggest that cadmium alters bacterial surface structures, intracellular processes and disrupts phage replication and release. Therefore, this study sheds light on the molecular interplay between environmental pollutants and microbial systems providing valuable insights into microbial ecology in metal-contaminated habitats as well as informing strategies for optimizing phage therapy and bioremediation under heavy metal stress.}, }
@article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, }
@article {pmid39723821, year = {2025}, author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA}, title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0101024}, pmid = {39723821}, issn = {2379-5042}, mesh = {*Acinetobacter/genetics/classification ; *Genome, Bacterial ; *Plant Nectar/metabolism ; Phylogeny ; *Evolution, Molecular ; Ecosystem ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.}, }
@article {pmid39723138, year = {2024}, author = {Xie, S and Ma, J and Lu, Z}, title = {Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505218}, pmid = {39723138}, issn = {1664-302X}, abstract = {This study probes into the unique metabolic responses of Bacteroides thetaiotaomicron (B. thetaiotaomicron), a key player in the gut microbiota, when it metabolizes rhamnose rather than typical carbohydrates. Known for its predominant role in the Bacteroidetes phylum, B. thetaiotaomicron efficiently breaks down poly- and mono-saccharides into beneficial short-chain fatty acids (SCFAs), crucial for both host health and microbial ecology balance. Our research focused on how this bacterium's SCFA production differ when utilizing various monosaccharides, with an emphasis on the oxidative stress responses triggered by rhamnose consumption. Notably, rhamnose use results in unique metabolic byproducts, including substantial quantities of 1,2-propanediol, which differs significantly from those produced during glucose metabolism. Our research reveals that rhamnose consumption is associated with a reduction in reactive oxygen species (ROS), signifying improved resistance to oxidative stress compared to other sugars. This effect is attributed to specific gene expressions within the rhamnose metabolic pathway. Notably, overexpression of the rhamnose metabolism regulator RhaR in B. thetaiotaomicron enhances its survival in oxygen-rich conditions by reducing hydrogen peroxide production. This reduction is linked to decreased expression of pyruvate:ferredoxin oxidoreductase (PFOR). In contrast, experiments with a rhaR-deficient strain demonstrated that the absence of RhaR causes B. thetaiotaomicron cells growing on rhamnose to produce ROS at rates comparable to cells grown on glucose, therefore, losing their advantage in oxidative resistance. Concurrently, the expression of PFOR is no longer suppressed. These results indicate that when B. thetaiotaomicron is cultured in a rhamnose-based medium, RhaR can restrain the expression of PFOR. Although PFOR is not a primary contributor to intracellular ROS production, its sufficient inhibition does reduce ROS levels to certain extent, consequently improving the bacterium's resistance to oxidative stress. It highlights the metabolic flexibility and robustness of microbes in handling diverse metabolic challenges and oxidative stress in gut niches through the consumption of alternative carbohydrates.}, }
@article {pmid39721552, year = {2025}, author = {IJdema, F and Lievens, S and Smets, R and Poma, G and Van Der Borght, M and Lievens, B and De Smet, J}, title = {Modulating the fatty acid composition of black soldier fly larvae via substrate fermentation.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {1}, pages = {101383}, doi = {10.1016/j.animal.2024.101383}, pmid = {39721552}, issn = {1751-732X}, mesh = {Animals ; Larva/growth &amp; development/metabolism/chemistry ; Fermentation ; *Animal Feed/analysis ; *Simuliidae/growth &amp; development/metabolism ; *Mortierella/metabolism ; *Fatty Acids/metabolism ; Dietary Fiber/metabolism ; Fatty Acids, Omega-6/metabolism ; Fatty Acids, Omega-3/metabolism ; Aquaculture/methods ; }, abstract = {Black soldier fly larvae (BSFL, Hermetia illucens) contain high amounts of proteins and essential amino acids and are therefore an appropriate feed source. However, they lack essential fatty acids (FAs), specifically ω-3 and ω-6, making them a less desirable feed choice for aquaculture. The aim of this study was to increase the ω-3 and ω-6 FA concentrations in BSFL by manipulating the FA composition in their rearing substrate. Specifically, the potential of substrate fermentation using the ω-3 and ω-6 FA-producing fungus Mortierella alpina was assessed. Fermentation of two agricultural side streams (wheat bran (WB) and WB with distiller's dried grains with solubles (DDGS)) increased substrate total crude fat concentration by 2.1 - 4.6%, as well as the concentration of several essential FAs, including the ω-6 FAs arachidonic acid (from less than 0.2 mg/g fat to a maximum of 44.2 mg/g fat) and gamma-linolenic acid (from less than 1.2 mg/g fat to a maximum of 45.8 mg/g fat and the ω-3 FA eicosapentaenoic acid (EPA) (from less than 0.7 mg/g fat to a maximum of 49.9 mg/g fat). Rearing BSFL on feeds from such fermented substrates resulted in similar changes in larval FA composition, specifically a higher concentration of EPA (from less than 0.2 mg/g fat to a maximum of 26.6 mg/g fat in the larvae fed on fermented diets), however, larval growth was reduced. Feeds made from fermented substrates were prone to stickiness and dehydration, possibly limiting larval movement and feeding, thereby affecting larval growth. Furthermore, proximate analysis of the substrates revealed sugar depletion after fermentation, which could be detrimental for larval growth and illustrate important attention points going forward. This study shows that fermentation of agricultural side streams WB and a mixture of WB with DDGS with Mortierella alpina alters their FA profile, increasing their ω-3 and ω-6 FA concentrations and that of BSFL fed with those substrates. Therefore, these results suggest that BSFL with tailor-made FA profiles for a specific application could be successfully produced.}, }
@article {pmid39716780, year = {2025}, author = {Quevedo-Caraballo, S and de Vega, C and Lievens, B and Fukami, T and Álvarez-Pérez, S}, title = {Tiny but mighty? Overview of a decade of research on nectar bacteria.}, journal = {The New phytologist}, volume = {245}, number = {5}, pages = {1897-1910}, pmid = {39716780}, issn = {1469-8137}, support = {//Agentschap Innoveren en Ondernemen/ ; //Fonds Wetenschappelijk Onderzoek/ ; //KU Leuven/ ; PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; CNS2022-135237//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2022-136719NB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //Complutense University of Madrid, Spain/ ; DEB 1737758//Directorate for Biological Sciences/ ; //ESF Investing in your future/ ; }, mesh = {*Plant Nectar/chemistry/metabolism ; *Bacteria/metabolism/genetics ; Microbiota ; *Research ; Animals ; Flowers/microbiology ; }, abstract = {An emerging focus of research at the intersection of botany, zoology, and microbiology is the study of floral nectar as a microbial habitat, referred to as the nectar microbiome, which can alter plant-pollinator interactions. Studies on these microbial communities have primarily focused on yeasts, and it was only about a decade ago that bacteria began to be studied as widespread inhabitants of floral nectar. This review aims to give an overview of the current knowledge on nectar bacteria, with emphasis on evolutionary origin, dispersal mode, effects on nectar chemistry and plant-animal interactions, community assembly, agricultural applications, and their use as model systems in ecological research. We further outline gaps in our understanding of the ecological significance of these microorganisms, their response to environmental changes, and the potential cascading effects.}, }
@article {pmid39716385, year = {2025}, author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ}, title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39716385}, issn = {1751-7370}, mesh = {*Phytoplankton/growth &amp; development/genetics/metabolism ; *Carbon Dioxide/metabolism ; *Alteromonas/growth &amp; development/genetics/metabolism ; *Seawater/microbiology/chemistry ; *Biological Evolution ; Diatoms/growth &amp; development/genetics ; Coculture Techniques ; Prochlorococcus/growth &amp; development/genetics ; }, abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.}, }
@article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&amp;D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, }
@article {pmid39714209, year = {2025}, author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU}, title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116224}, pmid = {39714209}, issn = {2379-5077}, support = {2342607//National Science Foundation (NSF)/ ; 1643486//National Science Foundation (NSF)/ ; 1438092//National Science Foundation (NSF)/ ; 503678//Joint Genome Institute (JGI)/ ; }, mesh = {*Wetlands ; Rhizosphere ; Metagenome ; Soil Microbiology ; Ecosystem ; Genome, Bacterial ; }, abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.}, }
@article {pmid39714150, year = {2025}, author = {Beizman-Magen, Y and Orevi, T and Kashtan, N}, title = {Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0200424}, pmid = {39714150}, issn = {1098-5336}, support = {220020475//James S. McDonnell Foundation (JSMF)/ ; 12-02-0046//The minisitry of Agriculture and rural development, Israel/ ; }, mesh = {*Bacillus/physiology/metabolism/drug effects ; *Pseudomonas syringae/physiology/drug effects ; *Xanthomonas/physiology/drug effects ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Microbial Interactions ; *Water ; *Antibiosis ; }, abstract = {Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.}, }
@article {pmid39711055, year = {2025}, author = {Mant, D and Orevi, T and Kashtan, N}, title = {Impact of micro-habitat fragmentation on microbial population growth dynamics.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39711055}, issn = {1751-7370}, support = {//Interdisciplinary Data Science Research/ ; 220020475//James S. McDonnell Foundation/ ; 1322/23//Israel Science Foundation/ ; }, mesh = {*Ecosystem ; *Escherichia coli/growth &amp; development ; Population Dynamics ; }, abstract = {Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria Escherichia coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.}, }
@article {pmid39710833, year = {2024}, author = {Bullington, JA and Langenfeld, K and Phaneuf, JR and Boehm, AB and Francis, CA}, title = {Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70009}, doi = {10.1111/1462-2920.70009}, pmid = {39710833}, issn = {1462-2920}, support = {2024504//National Science Foundation, Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM)/ ; //Stanford McGee and Levorsen Research Grant/ ; //ARCO Stanford Graduate Fellowship/ ; }, mesh = {*Microbiota/genetics ; *Estuaries ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Bathing Beaches ; California ; *Seawater/microbiology ; Archaea/genetics/classification ; Phylogeny ; }, abstract = {Subterranean estuaries (STEs) are critical ecosystems at the interface of meteoric groundwater and subsurface seawater that are threatened by sea level rise. To characterize the influence of tides and waves on the STE microbial community, we collected porewater samples from a high-energy beach STE at Stinson Beach, California, USA, over the two-week neap-spring tidal transition during both a wet and dry season. The microbial community, analyzed by 16S rRNA gene (V4) amplicon sequencing, clustered according to consistent physicochemical features found within STEs. The porewater community harbored relatively abundant Proteobacteria, Verrucomicrobiota, and Bacteroidota, as well as members of the archaeal DPANN superphylum and bacterial Candidate Phyla Radiation (CPR). Tidal conditions were not associated with microbial community composition; however, a wave overtopping event significantly impacted the beach microbiome. As a baseline for environmental change, our results elucidate the unique dynamics of a STE microbiome with unprecedented temporal resolution, highlighting the transport of cellular material through beach porewater due to waves.}, }
@article {pmid39710772, year = {2025}, author = {Ali, A and Zhong, X and Wang, Q and Xu, H}, title = {Use of a broad β-diversity for bioassessment of salinity stress on community homogeneity in marine environments.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {3}, pages = {1167-1175}, pmid = {39710772}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//Youth Project of the Natural Science Foundation of Shandong Province, China/ ; }, mesh = {*Salinity ; China ; *Salt Stress ; *Biodiversity ; Ecosystem ; Seawater/chemistry ; }, abstract = {To determine the feasibility of β-diversity measures to evaluate the impact of salinity stress on community homogeneity in marine environments, a 1-month bioassay was conducted using the protozoan assemblage as the test community. The test samples were collected using the slide method in coastal waters of the Yellow Sea, northern China. Five treatments were designed according to a salinity gradient of 9, 19, 29, 39, and 49 PSU. The homogeneity of the test community showed significant variability in both composition and abundance patterns among five treatments. The multivariate dispersion measure on compositional data was linearly associated with the salinity stress compared to those on abundance alone or in combination with occurrence. The traditional β-diversity index represented a different behavior from that of the multivariate dispersion measures. These findings suggest that the composition-based multivariate dispersion may be a useful tool to evaluate the global salinity stress on community homogeneity in marine ecosystems.}, }
@article {pmid39710259, year = {2025}, author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL}, title = {International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology-More of the same, or something new and meaningful to food quality, food security, and animal health?.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7567-7575}, doi = {10.3168/jds.2024-25847}, pmid = {39710259}, issn = {1525-3198}, mesh = {Animals ; *Ruminants/physiology/microbiology ; Gastrointestinal Microbiome ; Humans ; *Food Security ; *Food Quality ; Food Supply ; }, abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as affected by the microbial communities that colonize and co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been pushed by the advent of high throughput DNA sequencing and, to a lesser extent, other omics-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant holobiont is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the holobiont approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinal microbiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. Although the holobiont approach might improve food quality, food security, and animal health, these benefits will most likely be achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale as well as its generation, in context with the forgotten knowledge of ruminant and human physiology.}, }
@article {pmid39709274, year = {2025}, author = {Kerkar, AU and Sutherland, KR and Thompson, AW}, title = {Non-viral predators of marine picocyanobacteria.}, journal = {Trends in microbiology}, volume = {33}, number = {5}, pages = {558-568}, doi = {10.1016/j.tim.2024.11.010}, pmid = {39709274}, issn = {1878-4380}, mesh = {*Prochlorococcus/physiology/growth &amp; development ; *Synechococcus/physiology/growth &amp; development ; Ecosystem ; *Seawater/microbiology ; Aquatic Organisms ; Food Chain ; }, abstract = {The Earth's most abundant photosynthetic cells, the picocyanobacteria - Prochlorococcus and Synechococcus - play a fundamental global role in aquatic ecosystems. The success of these picocyanobacteria is interpreted through a cross-scale systems framework that integrates bottom-up controls on growth (e.g., nutrients and light), diversity, and the selective pressures and response to predation. While viral predators are well studied and experimentally tractable, the diverse non-viral predators of picocyanobacteria are disconnected from this framework and experimentally challenging, leaving a major gap in understanding the picocyanobacteria. This review presents existing research on non-viral picocyanobacterial predators and promising research frontiers that will expand knowledge of the ecology and evolution of these crucial microorganisms.}, }
@article {pmid39708482, year = {2025}, author = {Zhao, H and Hu, X and Guan, S and Cai, J and Li, W and Zhang, D and Feng, Y and Zhu, W and Marzorati, M and Li, B and Zhang, X and Tian, J}, title = {Capilliposide A alleviates DSS-induced colitis by regulating the intestinal flora and its metabolites of origin.}, journal = {International immunopharmacology}, volume = {146}, number = {}, pages = {113858}, doi = {10.1016/j.intimp.2024.113858}, pmid = {39708482}, issn = {1878-1705}, mesh = {Animals ; Dextran Sulfate ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Saponins/therapeutic use/pharmacology ; Disease Models, Animal ; Colon/pathology/drug effects/microbiology ; *Anti-Inflammatory Agents/therapeutic use/pharmacology ; *Colitis/drug therapy/chemically induced ; Male ; *Triterpenes/therapeutic use/pharmacology ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Intestinal Mucosa/drug effects ; Humans ; }, abstract = {Ulcerative colitis is a chronic idiopathic inflammatory disease that impacts the mucous membrane of the colon. Lately, the incidence and prevalence of UC has been increasing globally. However, there are significant side effects of existing drugs for UC intervention. Accordingly, there is a pressing demand to explore novel bioactive substances for addressing UC. Natural product saponins have attracted great attention due to their obvious anti-colitis potential. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl., exhibits good anti-inflammatory activity. Nonetheless, the impact and mechanism of CPS-A on ulcerative colitis remains obscure. This study aimed to investigate the therapeutic effects of CPS-A on the dextran sulphate sodium induced colitis mouse model and explore its mechanism. The efficacy and safety of CPS-A were evaluated in a well-established dextran sodium sulfate (DSS)-induced colitis mice model. Disease progression was monitored via clinical symptoms, histopathological examination, quantification of inflammatory cytokines, and epithelial barrier function evaluation. Plasma samples and intestinal contents were collected for non-targeted metabolomics and 16sRNA sequencing, respectively, to jointly evaluate the mechanism of action. CPS-A alleviated colitis by improving weight, Disease activity index score, histopathology, goblet cell, colon length, and expression of inflammatory factors. Moreover, CPS-A effectively preserved the integrity of the intestinal barrier by enhancing the expression of tight junction proteins and mucin in the colonic tissue of mice. Furthermore, CPS-A exerted a regulatory effect on the composition of the gut microbiota, promoting bacterial richness and diversity. It not only suppressed the abundance of detrimental bacteria while enhancing the abundance of advantageous bacteria, but also modulated the metabolites derived from the intestinal flora. Importantly, correlation analysis shows that these indicators are highly correlated. This study revealed that CPS-A exhibits a favorable therapeutic efficacy against colitis, primarily attributed to its ability to modulate the gut microbiota their associated metabolites as the key mechanisms of action.}, }
@article {pmid39708146, year = {2024}, author = {Zhao, L and Zhang, S and Li, J and Zhang, C and Xiao, R and Bai, X and Xu, H and Zhang, F}, title = {Unveiling Diversity and Function: Venom-Associated Microbes in Two Spiders, Heteropoda venatoria and Chilobrachys guangxiensis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {156}, pmid = {39708146}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Spider Venoms ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Apoptosis ; Symbiosis ; Humans ; Cell Line, Tumor ; High-Throughput Nucleotide Sequencing ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {Spiders are natural predators of agricultural pests, primarily due to the potent venom in their venom glands. Spider venom is compositionally complex and holds research value. This study analyzes the diversity of symbiotic bacteria in spider venom glands and venom, as well as the biological activity of culturable symbiotic bacteria. Focusing on the venom glands and venom of Heteropoda venatoria and Chilobrachys guangxiensis, we identified a diverse array of microorganisms. High-throughput sequencing detected 2151 amplicon sequence variants (ASVs), spanning 31 phyla, 75 classes, and 617 genera. A total of 125 strains of cultivable bacteria were isolated. Using the Oxford cup method, crude extracts from 46 of these strains exhibited inhibitory effects against at least one indicator bacterium. MTT (Thiazolyl blue) assays revealed that the crude extracts from 43 strains had inhibitory effects on tumor cell line MGC-803 growth. Additionally, DAPI (4',6-diamidino-2'-phenylindole) staining and flow cytometry were employed to detect cell apoptosis. The anti-inflammatory activity of nine bacterial strains was assessed using a NO assay kit and enzyme-linked immunosorbent assay (ELISA). This study further investigated the biological activity of venom, exploring the relationship between the venom and the functional activity of venom-associated bacteria.}, }
@article {pmid39708144, year = {2024}, author = {Quevedo-Caraballo, S and Roldán, A and Álvarez-Pérez, S}, title = {Demethylation Inhibitor Fungicides Have a Significantly Detrimental Impact on Population Growth and Composition of Nectar Microbial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {160}, pmid = {39708144}, issn = {1432-184X}, support = {PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; RYC2018-023847-I, CNS2022-135237//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Fungicides, Industrial/pharmacology ; *Plant Nectar ; *Microbiota/drug effects ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Demethylation ; Fungi/drug effects/classification/isolation &amp; purification ; Metschnikowia/drug effects ; Flowers/microbiology/growth &amp; development ; }, abstract = {Demethylation inhibitor (DMI) fungicides are a mainstay of modern agriculture due to their widespread use for crop protection against plant-pathogenic fungi. However, DMI residues can disperse and persist in the environment, potentially affecting non-target fungi. Previous research has demonstrated that DMIs and other fungicides inhibit yeast growth in floral nectar microbial communities and decrease fungal richness and diversity of exposed flowers with no apparent effect on bacteria. Nevertheless, the effect of DMIs on the population growth of different species of nectar inhabitants and the dynamics of these microbial communities remains understudied. To address these issues, in this study we created synthetic microbial communities including yeasts (Metschnikowia reukaufii and Metschnikowia pulcherrima) and bacteria (Rosenbergiella epipactidis and Comamonas sp.) and propagated them in culture media containing different DMIs (imazalil, propiconazole, and prothioconazole) at different doses or no fungicide. Our results showed that DMIs have a significant impact on some of the most common microbial inhabitants of floral nectar by favoring the growth of bacteria over yeasts. Furthermore, habitat generalists such as M. pulcherrima and Comamonas sp. were more impacted by the presence of fungicides than the nectar specialists M. reukaufii and R. epipactidis, especially upon dispersal across habitat patches. Future research should determine if the patterns observed in the present study hold true for other species of nectar microbes and explore the interaction between growth limitation due to fungicide presence, dispersal limitation, and other mechanisms involved in community assembly in floral nectar.}, }
@article {pmid39708139, year = {2024}, author = {Zhao, Z and Liu, S and Jiang, S and Zhang, D and Sha, Z}, title = {Diversity and Potential Metabolic Characteristics of Culturable Copiotrophic Bacteria That Can Grow on Low-Nutrient Medium in Zhenbei Seamount in the South China Sea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {157}, pmid = {39708139}, issn = {1432-184X}, support = {LSKJ202203102//the Science and Technology Innovation Project of Laoshan Laboratory/ ; XDB42000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 42221005//the NSFC Innovative Group Grant/ ; 42376143//the National Natural Science Foundation of China/ ; }, mesh = {*Seawater/microbiology ; China ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/growth &amp; development ; Gammaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Nitrates/metabolism ; Culture Media/chemistry ; Nutrients/metabolism ; Alphaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Vibrio/metabolism/genetics/isolation &amp; purification/growth &amp; development/classification ; }, abstract = {Oligotrophs are predominant in nutrient-poor environments, but copiotrophic bacteria may tolerate conditions of low energy and can also survive and thrive in these nutrient-limited conditions. In the present study, we isolated 648 strains using a dilution plating method after enrichment for low-nutrient conditions. We collected 150 seawater samples at 21 stations in different parts of the water column at the Zhenbei Seamount in the South China Sea. The 648 isolated copiotrophic strains that could grow on low-nutrient medium were in 21 genera and 42 species. A total of 99.4% (644/648) of the bacteria were in the phylum Pseudomonadota, with 73.3% (472/644) in the class Gammaproteobacteria and 26.7% (172/644) in the class Alphaproteobacteria. Among the 42 representative isolates, Pseudoalteromonas arabiensis, Roseibium aggregatum, and Vibrio neocaledonicus were present in all layers of seawater and at almost all of the stations. Almost half of these species (20/42) contained genes that performed nitrate reduction, with confirmation by nitrate reduction testing. These isolates also contained genes that functioned in sulfur metabolism, including sulfate reduction, thiosulfate oxidation, thiosulfate disproportionation, and dimethylsulfoniopropionate degradation. GH23, CBM50, GT4, GT2, and GT51 were the main carbohydrate-active enzymes (CAZymes), and these five enzymes were present in all or almost all of the isolated strains. The most abundant classes of CAZymes were those associated with the degradation of chitin, starch, and cellulose. Collectively, our study of marine copiotrophic bacteria capable of growing on low-nutrient medium demonstrated the diversity of these species and their potential metabolic characteristics.}, }
@article {pmid39708121, year = {2024}, author = {Grisnik, M and Walker, DM}, title = {Bat Cutaneous Microbial Assemblage Functional Redundancy Across a Host-Mediated Disturbance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {161}, pmid = {39708121}, issn = {1432-184X}, support = {32801-00803//Tennessee Wildlife Resources Agency,United States/ ; }, mesh = {*Chiroptera/microbiology ; Animals ; *Seasons ; *Bacteria/genetics/classification/isolation &amp; purification ; *Skin/microbiology ; *Microbiota ; Ascomycota/genetics/physiology ; Ecosystem ; }, abstract = {Understanding the processes and factors that influence the structure of host-associated microbial assemblages has been a major area of research as these assemblages play a role in host defense against pathogens. Previous work has found that bacterial taxa within bat cutaneous microbial assemblages have antifungal capabilities against the emerging fungal pathogen, Pseudogymnoascus destructans. However, our understanding of natural fluctuations in these cutaneous microbial assemblages over time due to shifts in host habitat is lacking. The objective of this work was to understand how the taxonomic and functional bat cutaneous microbial assemblage responds to seasonal shifts in host habitat. We hypothesized that at the community level, there will be turnover in taxonomic structure but functional redundancy across seasons. On a finer scale, we hypothesized that there will be differences in the relative abundance of functional genes that code for select pathways across seasons. Results showed that, on a broad scale, the bat cutaneous microbial assemblage is seasonally taxonomically dynamic but functionally redundant. Additionally, although there was almost complete taxonomic turnover between winter and summer bat microbial assemblages, there was no difference in assemblage structure across winters. This functional redundancy was also observed at finer scales, with no differences in the abundance of genes within pathways of hypothesized importance across seasons or winters. Taken together, results suggest species sorting mechanisms correlated with shifts in host habitat use, drive taxonomic but not functional host-associated cutaneous microbial community assembly.}, }
@article {pmid39708106, year = {2024}, author = {Singh, S and Singh, AK and Pradhan, B and Tripathi, S and Kumar, KS and Chand, S and Rout, PR and Shahid, MK}, title = {Harnessing Trichoderma Mycoparasitism as a Tool in the Management of Soil Dwelling Plant Pathogens.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {158}, pmid = {39708106}, issn = {1432-184X}, mesh = {*Trichoderma/physiology ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Pest Control, Biological/methods ; Agriculture/methods ; Plants/microbiology ; Biological Control Agents ; Soil/chemistry ; }, abstract = {Maintaining and enhancing agricultural productivity for food security while preserving the ecology and environment from the harmful effects of toxicants is the main challenge in modern monoculture farming systems. Microbial biological agents can be a promising substitute for traditional synthetic pesticides to manage plant diseases. Trichoderma spp. are soil-dwelling ascomycete fungi and are common biocontrol agents against diverse phytopathogens. Trichoderma-based biocontrol techniques can regulate and control soil-borne plant diseases through mechanisms such as mycoparasitism, the production of antibiotics and hydrolytic enzymes, rhizo-sphere competence, the effective competition for available resources, induction of plant resistance and facilitation of plant growth. Numerous secondary metabolites produced by Trichoderma spp. are reported to prevent the development of soil-borne plant disease. Thus, Trichoderma spp. may have direct and indirect biological impacts on the targeted plant pathogens. Furthermore, this review discusses the convenient implications and challenges of applying Trichoderma-based strategies in agricultural settings. Overall, the assessment underscores the potential of Trichoderma as a sustainable and effective tool for mitigating soil-borne pathogens, highlighting avenues for future research and applications.}, }
@article {pmid39708073, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Correction to: Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {159}, doi = {10.1007/s00248-024-02478-w}, pmid = {39708073}, issn = {1432-184X}, }
@article {pmid39708062, year = {2024}, author = {Nonthijun, P and Tanunchai, B and Schroeter, SA and Wahdan, SFM and Alves, EG and Hilke, I and Buscot, F and Schulze, ED and Disayathanoowat, T and Purahong, W and Noll, M}, title = {Feels Like Home: A Biobased and Biodegradable Plastic Offers a Novel Habitat for Diverse Plant Pathogenic Fungi in Temperate Forest Ecosystems.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {155}, pmid = {39708062}, issn = {1432-184X}, mesh = {*Forests ; *Fungi/genetics/metabolism/classification ; *Biodegradable Plastics/metabolism ; *Trees/microbiology ; Soil Microbiology ; Plant Diseases/microbiology ; Biodegradation, Environmental ; Ecosystem ; Soil/chemistry ; Plant Leaves/microbiology ; }, abstract = {Poly(butylene succinate-co-adipate) (PBSA), a biodegradable plastic, is significantly colonized and degraded by soil microbes under natural field conditions, especially by fungal plant pathogens, raising concerns about potential economic losses. This study hypothesizes that the degradation of biodegradable plastics may increase the presence and abundance of plant pathogens by serving as an additional carbon source, ultimately posing a risk to forest ecosystems. We investigated (i) fungal plant pathogens during the exposure of PBSA in European broadleaved and coniferous forests (two forest types), with a specific focus on potential risk to tree health, and (ii) the response of such fungi to environmental factors, including tree species, soil pH, nutrient availability, moisture content, and the physicochemical properties of leaf litter layer. Next-generation sequencing (NGS) revealed that PBSA harbored a total of 318 fungal plant pathogenic amplicon sequence variants (ASVs) belonging to 108 genera. Among the identified genera (Alternaria, Nectria, Phoma, Lophodermium, and Phacidium), some species have been reported as causative agents of tree diseases. Plenodomus was present in high relative abundances on PBSA, which have not previously been associated with disease in broadleaved and coniferous forests. Furthermore, the highest number of fungal plant pathogens were detected at 200 days of PBSA exposure (112 and 99 fungal plant pathogenic ASV on PBSA degraded under Q. robur and F. sylvatic-dominated forest, respectively), which was double compared mature leaves and needles from the same forest sites. These findings suggest that PBSA attracts fungal plant pathogens in forests as an additional carbon source, potentially leading to increased disease outbreaks and disrupting the stability of forest ecosystems. The fungal plant pathogenic community compositions were mainly shaped by forest type, PBSA exposure time, site locations, leaf litter layer water content, and N:P ratio from leaf litter layer in both forest types. This study provides valuable insights into the potential risks posed by biodegradable plastic degradation in forests after 200 and 400 days of exposure, respectively. Further comprehensive evaluations of their effects on tree health and ecosystems, ideally on a long-term basis, are needed. These evaluations should include integrating microbial investigation, soil health monitoring, and ecosystem interaction assessments. Nevertheless, it should be noted that our interpretation of plant pathogens is solely based on high-throughput sequencing, bioinformatics, and annotation tools.}, }
@article {pmid39703713, year = {2024}, author = {Sheng, Y and Zeng, X and Zhao, L and Li, Y}, title = {Editorial: Microbial involvement in biogeochemical cycling and contaminant transformations at land-water ecotones.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1525521}, pmid = {39703713}, issn = {1664-302X}, }
@article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, }
@article {pmid39701529, year = {2025}, author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB}, title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7511-7529}, doi = {10.3168/jds.2024-25863}, pmid = {39701529}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology/metabolism/physiology ; *Dietary Fiber/metabolism ; *Ruminants/microbiology/physiology ; *Digestion/physiology ; Animal Feed ; Fermentation ; Diet/veterinary ; Bacteria/metabolism ; }, abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding to the array of enzymes needed for depolymerization and resulting fermentation of sugars. Carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi and emphasize the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic acid), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.}, }
@article {pmid39699229, year = {2025}, author = {Anuforo, PC and Würz, B and Wick, LY and Kallies, R}, title = {Draft genome sequences of Pseudomonas chengduensis strain BW1 and Sphingobium sp. strain MK2 isolated from oil sands process-affected water.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0067724}, pmid = {39699229}, issn = {2576-098X}, support = {57610608//Deutscher Akademischer Austauschdienst (DAAD)/ ; 57610608//MPR | Petroleum Technology Development Fund (PTDF)/ ; }, abstract = {Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively.}, }
@article {pmid39699221, year = {2025}, author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG}, title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0125924}, pmid = {39699221}, issn = {2379-5077}, support = {DNRF136//Danmarks Grundforskningsfond (DNRF)/ ; S004523N//Flanders Research FWO/ ; TopBOF//University Antwerp TopBOF program/ ; Microflora Danica//Poul Due Jensens Fond (Poul Due Jensen Foundation)/ ; HORIZON-MSCA-2023-PF-01: 101152850//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Geologic Sediments/microbiology ; Electron Transport/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.<br><br>IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.}, }
@article {pmid39698295, year = {2024}, author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C}, title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae050}, pmid = {39698295}, issn = {2730-6151}, abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.}, }
@article {pmid39697668, year = {2024}, author = {Roy, A and Ghosh, A and Bhadury, P}, title = {Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39697668}, issn = {2516-8290}, abstract = {Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.}, }
@article {pmid39695543, year = {2024}, author = {Qin, K and Qing, J and Wang, Q and Li, Y}, title = {Epidemiological shifts in chronic kidney disease: a 30-year global and regional assessment.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {3519}, pmid = {39695543}, issn = {1471-2458}, support = {82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; }, mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/mortality ; Male ; Incidence ; *Global Health/statistics &amp; numerical data ; Female ; Middle Aged ; Adult ; Prevalence ; Aged ; *Global Burden of Disease ; Risk Factors ; Disability-Adjusted Life Years ; Adolescent ; Young Adult ; Quality-Adjusted Life Years ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) presents a growing global health challenge, with significant variability in disease burden across different regions and countries. This study aimed to analyze the trends in incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for CKD from 1990 to 2019, utilizing data from the Global Burden of Disease Study.<br><br>METHODS: We conducted an in-depth study on the global and age-standardized incidence, prevalence, mortality, and DALYs of CKD, and assessed trends over a 30-year period. Additionally, we explored the associations between healthcare access and quality (HAQ), the Socio-Demographic Index (SDI), and CKD. Furthermore, we conducted a detailed analysis of six risk factors closely related to CKD, and based on these findings, provided strong evidence for enhancing the management of CKD.<br><br>RESULTS: In 2019, there were 18,986,903 cases of CKD, with an average annual percent change (AAPC) of 1.82 (95% CI&#x2009;=&#x2009;1.8 to 1.82) in incidence since 1990. The age-standardized incidence rate increased from 192.45 per 100,000 in 1990 to 233.65 per 100,000 in 2019. Prevalence also rose, with a total of 69,729,430 cases in 2019 and an AAPC of 1.19 (95% CI&#x2009;=&#x2009;1.19 to 1.2). Mortality and DALYs have increased correspondingly, with the mortality rate reaching 18.29 per 100,000 and total DALYs at 41,538,592 in 2019. The analysis showed that higher HAQ levels are associated with better outcomes in terms of lower mortality and DALY rates, whereas lower HAQ levels correlate with poorer outcomes. In addition, high fasting plasma glucose and high systolic blood pressure are the main contributors to CKD-related deaths, with their population attributable fraction&#xa0;(PAF) significantly decreasing as the SDI decreases.<br><br>CONCLUSION: The burden of CKD has significantly increased over the past three decades, influenced by demographic changes and variations in healthcare quality and access. Effective public health strategies and improvements in healthcare delivery are needed to address the disparities in CKD outcomes globally.}, }
@article {pmid39695352, year = {2025}, author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM}, title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2440120}, pmid = {39695352}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; }, abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.}, }
@article {pmid39694113, year = {2025}, author = {Van Peteghem, L and Matassa, S and Sakarika, M}, title = {Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131990}, doi = {10.1016/j.biortech.2024.131990}, pmid = {39694113}, issn = {1873-2976}, mesh = {*Bacterial Proteins/biosynthesis ; Biomass ; *Ethanol/isolation &amp; purification/metabolism ; Fermentation ; *Waste Products ; }, abstract = {Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.}, }
@article {pmid39693383, year = {2024}, author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL}, title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae247}, pmid = {39693383}, issn = {1751-7370}, abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.}, }
@article {pmid39693347, year = {2024}, author = {Sun, X and Buchanan, PJ and Zhang, IH and San Roman, M and Babbin, AR and Zakem, EJ}, title = {Ecological dynamics explain modular denitrification in the ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2417421121}, pmid = {39693347}, issn = {1091-6490}, support = {LS-FMME-00871981//Simons Foundation (SF)/ ; OCE-2138890 and OCE-2142998//NSF (NSF)/ ; N/A//MIT School of Science MathWorks Science Fellowship/ ; 2125142//NSF (NSF)/ ; }, mesh = {*Denitrification/physiology ; *Oceans and Seas ; *Ecosystem ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Oxygen/metabolism ; Bacteria/metabolism ; }, abstract = {Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3[-]→NO2[-]→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2[-] and N2O in a NO3[-]-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3[-]→NO2[-] module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3[-]→NO2[-] module. Results also capture observations that NO3[-] is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.}, }
@article {pmid39692747, year = {2025}, author = {Wallace, EJ and O'Dwyer, J and Dolan, EB and Burke, LP and Wylie, R and Bellavia, G and Straino, S and Cianfarani, F and Ciotti, G and Serini, S and Calviello, G and Roche, ET and Mitra, T and Duffy, GP}, title = {Actuation-Mediated Compression of a Mechanoresponsive Hydrogel by Soft Robotics to Control Release of Therapeutic Proteins.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {7}, pages = {e2401744}, pmid = {39692747}, issn = {2198-3844}, support = {713690//Horizon 2020/ ; 812865//Horizon 2020/ ; GOIPD/2020/157//Irish Research Council/ ; 13/RC/2073/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Rats ; *Vascular Endothelial Growth Factor A/administration &amp; dosage ; *Hydrogels/chemistry ; *Robotics/methods ; *Drug Delivery Systems/methods ; Diabetes Mellitus, Experimental/drug therapy ; Male ; Rats, Sprague-Dawley ; }, abstract = {Therapeutic proteins, the fastest growing class of pharmaceuticals, are subject to rapid proteolytic degradation in vivo, rendering them inactive. Sophisticated drug delivery systems that maintain protein stability, prolong therapeutic effects, and reduce administration frequency are urgently required. Herein, a mechanoresponsive hydrogel is developed contained within a soft robotic drug delivery (SRDD) device. In a step-change from previously reported systems, pneumatic actuation of this system releases the cationic therapeutic protein Vascular Endothelial Growth Factor (VEGF) in a bioactive form which is required for therapeutic angiogenesis, the growth of new blood vessels, in numerous clinical conditions. The ability of the SRDD device to release bioactive VEGF in a spatiotemporal manner from the hydrogel is tested in diabetic rats - a model in which angiogenesis is difficult to stimulate. Daily actuation of the SRDD device in the diabetic rat model significantly increased cluster of differentiation 31+ (CD31+) blood vessel number (p = 0.0335) and the diameter of alpha-smooth muscle actin+ (α-SMA+) blood vessels (p = 0.0025) compared to passive release of VEGF from non-actuated devices. The SRDD device combined with the mechanoresponsive hydrogel offers the potential to deliver an array of bioactive therapeutics in a spatiotemporal manner to mimic their natural release in vivo.}, }
@article {pmid39691821, year = {2024}, author = {Ghosh, A and Bhambra, SK and Chandrasekaran, R and Bhadury, P}, title = {Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {12}, pages = {}, pmid = {39691821}, issn = {2516-8290}, abstract = {A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.}, }
@article {pmid39689568, year = {2025}, author = {Sumerta, IN and Ruan, X and Howell, K}, title = {The forgotten wine: Understanding palm wine fermentation and composition.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111022}, doi = {10.1016/j.ijfoodmicro.2024.111022}, pmid = {39689568}, issn = {1879-3460}, mesh = {*Arecaceae/microbiology/chemistry ; Bacteria/metabolism/classification/isolation &amp; purification ; *Fermentation ; Microbiota ; *Wine/microbiology/analysis ; }, abstract = {Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. Here, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assessed palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this unique, yet overlooked, fermented beverage.}, }
@article {pmid39689238, year = {2024}, author = {Yang, Q and Defoirdt, T}, title = {Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39689238}, issn = {1751-7370}, support = {//Special Research Fund of Ghent University/ ; G016823N//Scientific Research Fund of Flanders/ ; }, mesh = {*Quorum Sensing/drug effects ; *Vibrio/drug effects/physiology/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Animals ; Vibrio Infections/microbiology ; Selection, Genetic ; }, abstract = {Quorum sensing (QS) inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether QS inhibition will impose selective pressure for the spread of resistance against QS inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using QS inhibitor-susceptible and -resistant mimics, we show that resistance to QS inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.}, }
@article {pmid39689178, year = {2024}, author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z}, title = {Metabolites limiting predator growth wane with prey biodiversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2410210121}, pmid = {39689178}, issn = {1091-6490}, support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; }, abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.}, }
@article {pmid39687379, year = {2024}, author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M}, title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111125}, pmid = {39687379}, issn = {2352-3409}, abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.}, }
@article {pmid39683937, year = {2024}, author = {Liu, S and Teng, L and Ping, J}, title = {Graphitic Carbon Nitride Confers Bacterial Tolerance to Antibiotics in Wastewater Relating to ATP Depletion.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {23}, pages = {}, pmid = {39683937}, issn = {1420-3049}, support = {62105175//National Natural Science Foundation of China/ ; ZR2021QF058//Natural Science Foundation of Shandong Province/ ; 2022PY036//The Education and Industry Integration Pilot Project of Qilu University of Technology/ ; 432413/01090//Start-up fund of Tianjin Renai College/ ; }, mesh = {*Graphite/chemistry ; *Wastewater/microbiology/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Adenosine Triphosphate/metabolism ; Nitrogen Compounds/chemistry ; Staphylococcus aureus/drug effects ; Ofloxacin/pharmacology ; Drug Resistance, Bacterial/drug effects ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Water Purification/methods ; }, abstract = {Graphitic carbon nitride (C3N4) is a kind of visible light-responsive photocatalyst that has been of great interest in wastewater treatment. However, its environmental impact and biological effect remains to be elucidated. This study investigated the effect of C3N4 nanosheets on bacterial abundance and antibiotic tolerance in wastewater. Interestingly, as compared to the wastewater containing the antibiotic ofloxacin alone, the wastewater containing both ofloxacin and C3N4 had much higher numbers of total living bacteria, but lower levels of the ofloxacin-resistant bacteria and the ofloxacin-resistant gene qnrS. The model bacterium Staphylococcus aureus was then used to explore the mechanism of C3N4-induced antibiotic tolerance. The nanosheets neither adsorbed the antibiotic nor promoted drug efflux, uncovering that drug adsorption and efflux were not involved in antibiotic tolerance. Further investigations revealed that the nanosheets, like arsenate and menadione, drastically reduced ATP levels and induced the production of reactive oxygen species for enhanced antibiotic tolerance. This study revealed an antibiotic-tolerating mechanism associated with C3N4-induced ATP depletion, and shed a light on the effect of photocatalysts on microbial ecology during their application in wastewater treatment.}, }
@article {pmid39682491, year = {2024}, author = {Suriyasathaporn, W and Kongkaew, A and Intanon, M and Srithanasuwan, A and Saipinta, D and Pangprasit, N and Thongtharb, A and Chuasakhonwilai, A and Chaisri, W}, title = {Non-aureus Staphylococci Cause the Spontaneous Cure or Persistent Infection of Major Bovine Mastitis Pathogens in the Murine Mammary Glands.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, pmid = {39682491}, issn = {2076-2615}, support = {FF66/017//The Fundamental Fund, Chiang Mai University/ ; }, abstract = {The microbial ecology in mastitis involves the interactions between bacteria and the mammary gland environment. Poor mastitis control, for which understanding these microbial relationships is crucial, increases the risk of mastitis and co-infections. The aim of this study was to determine the pathogenesis and bacterial ecology of murine mammary glands following intramammary infection (IMI) with S. aureus (AU), S. agalactiae (SA), and four isolates of selected non-aureus staphylococci (NAS), as well as co-infections of AU or SA with NAS. Selected NAS demonstrated resistance to growth inhibition after co-culture with AU and SA and were proven to be protective in vitro against AU and SA. Both single infections and co-infections of AU, SA, two selected isolates of S. hominis (NAS1 and NAS2), and two selected isolates of S. chromogens (NAS3 and NAS4) were injected into the murine mammary glands at 10[5] CFU/mL. After 72 h of inoculation, the results showed that AU, AU-NAS2, and AU-NAS3 expressed severe inflammation with clinical signs of mastitis. The persistence of AU was found for AU, NAS3, and AU-NAS3, whereas the persistence of SA was found for SA-NAS1, SA-NAS3, and SA-NAS, although single SA could not persist. Interestingly, NAS2 in both the single- and co-IMIs with AU or SA resulted in a spontaneous cure 72 h after the IMI. In conclusion, some NAS have beneficial results because they can eliminate S. aureus and S. agalactiae, but some NAS have negative effects because they can support persistent S. agalactiae infection. These results may be used to explain both the advantages and disadvantages of NAS on farms with poor mastitis control. In addition, the beneficial S. hominis may initiate natural live antibiotics and reduce antibiotic resistance problems.}, }
@article {pmid39681734, year = {2024}, author = {Rajendran, D and Vinayagam, S and Sekar, K and Bhowmick, IP and Sattu, K}, title = {Symbiotic Bacteria: Wolbachia, Midgut Microbiota in Mosquitoes and Their Importance for Vector Prevention Strategies.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {154}, pmid = {39681734}, issn = {1432-184X}, mesh = {Animals ; Culicidae/microbiology ; Gastrointestinal Microbiome ; *Mosquito Control/methods ; *Mosquito Vectors/microbiology ; Symbiosis ; *Wolbachia/physiology ; }, abstract = {Mosquito-borne illnesses pose a significant threat to eradication under existing vector management measures. Chemo-based vector control strategies (use of insecticides) raise a complication of resistance and environmental pollution. Biological control methods are an alternative approach to overcoming this complication arising from insecticides. The mosquito gut microbiome is essential to supporting the factors that involve metabolic regulation and metamorphic development (from juvenile to adult), as well as the induction of an immune response. The induced immune response includes the JAK-STAT, IMD, and Toll pathways due to the microbial interaction with the midgut cells (MG cells) that prevent disease transmission to humans. The aforementioned sequel to the review provides information about endosymbiont Wolbachia, which contaminates insect cells, including germline and somatic cytoplasm, and inhibits disease-causing pathogen development and transmission by competing for resources within the cell. Moreover, it reduces the host population via cytoplasmic incompatibility (CI), feminization, male killing, and parthenogenesis. Furthermore, the Cif factor in Wolbachia is responsible for CI induction that produces inviable cells with the translocating systems and the embryonic defect-causing protein factor, WalE1 (WD0830), which manipulates the host actin. This potential of Wolbachia can be used to design a paratransgenic system to control vectors in the field. An extracellular symbiotic bacterium such as Asaia, which is grown in the growth medium, is used to transfer lethal genes within itself. Besides, the genetically transferred symbiotic bacteria infect the wild mosquito population and are easily manifold. So, it might be suitable for vector control strategies in the future.}, }
@article {pmid39681034, year = {2025}, author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM}, title = {Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109202}, doi = {10.1016/j.envint.2024.109202}, pmid = {39681034}, issn = {1873-6750}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; Anti-Bacterial Agents ; Manure ; Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Agriculture ; }, abstract = {Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.}, }
@article {pmid39680930, year = {2024}, author = {Li, XY and Zhu, CW and Chen, S and Xiang, Q and Lu, C and Lin, XY and Chen, QL}, title = {Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {52}, pages = {23190-23200}, doi = {10.1021/acs.est.4c09625}, pmid = {39680930}, issn = {1520-5851}, mesh = {*Carbon Dioxide ; Seeds/microbiology ; *Endophytes ; Bacteria ; Fungi ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Microbiota ; Soil Microbiology ; }, abstract = {Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.}, }
@article {pmid39680691, year = {2025}, author = {Yang, JC and Lagishetty, V and Aja, E and Arias-Jayo, N and Chang, C and Hauer, M and Katzka, W and Zhou, Y and Sedighian, F and Koletic, C and Liang, F and Dong, TS and Situ, J and Troutman, R and Buri, H and Bhute, S and Simpson, CA and Braun, J and Jacob, N and Jacobs, JP}, title = {Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39680691}, issn = {1751-7370}, support = {CDA2 IK2CX001717//Crohn's and Colitis Foundation Career Development/ ; //Vatche and Tamar Manoukian Division of Digestive Diseases/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Fecal Microbiota Transplantation ; Germ-Free Life ; RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Colon/microbiology ; Specific Pathogen-Free Organisms ; Male ; }, abstract = {Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.}, }
@article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Mining ; Phylogeny ; Acids ; Stochastic Processes ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.<br><br>IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, }
@article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, }
@article {pmid39675658, year = {2025}, author = {Yan, R and Xu, X and Niu, Y and Ying, S and Cai, J and Chen, R and Gu, Y and Kan, H}, title = {Microbial diversity and environmental determinants at Shanghai Hongqiao railway station: A comprehensive microbial assessment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {366}, number = {}, pages = {125534}, doi = {10.1016/j.envpol.2024.125534}, pmid = {39675658}, issn = {1873-6424}, mesh = {China ; *Railroads ; *Environmental Monitoring ; *Air Microbiology ; *Microbiota ; Seasons ; RNA, Ribosomal, 16S/analysis ; *Air Pollution, Indoor/analysis ; Humans ; SARS-CoV-2 ; }, abstract = {The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.}, }
@article {pmid39673336, year = {2024}, author = {Liu, J and He, Y and Qiu, Z and Fahad, S and Zhao, S and Zhu 朱, M&#x58a8;}, title = {Erysiphe russellii Causing Powdery Mildew on Oxalis corniculata L. in Central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-24-2249-PDN}, pmid = {39673336}, issn = {0191-2917}, abstract = {Oxalis corniculata L. (Creeping woodsorrel) is a perennial plant of the genus Oxalis in Oxalidaceae family, which has the high ornamental and medicinal value. Extracts of creeping woodsorrel are used as antioxidants and cholinesterase inhibitors and for anti-inflammatory, antiseptic, analgesic, antirheumatic ache, and antimicrobial purposes (Leporatti et al. 2003). In June 2024, powdery mildew was found on the leaves of Creeping woodsorrel in Xinxiang City, Henan Province, China (113.925°E, 35.294°N). About 100 plants were examined and 80 % were infected with disease symptoms, i.e. curling and senescence. The white masses were on the both sides of plant leaves covering up to 90% of the leaves area. The slightly or straight curved conidiophores (n = 50) were 68 to 99× 6 to 12 μm in size and consisted of foot cells, shorter cells and singly conidia. The ellipsoidal to oval conidia (n =50), were 26 to 10 ×11 to 5 μm in size and had a length/width ratio of 1.6 to 2.2. These morphological characteristics were similar to the previously reported Creeping woodsorrel powdery mildew fungus, Erysiphe russellii (Thuong et al. 2017; Takamatsu et al. 2015). Following previously described methods (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022), the ITS (ribosomal transcribed spacer), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), RPB2 (RNA polymerase II), GS (glutamine synthetase) and CAM (calmodulin) gene regions of three isolates were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3'; ITS4 5'-TCCTCCGCTTATTGATATGC-3'), PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), CAM1/CAM4R (CAM1 5'-CTTTGCATCATGAGTTGGAC-3'; CAM4R 5'-GGCTCGAAAAATGAAAGATACCG-3'), Rpb2_4/Rpb2_6R (Rpb2_4 5'-GCAAGCTCAACTGCTGGTG-3'; Rpb2_6R 5'-TCCAGCGATGTGCTGTTGG-3'), GSPM2/GSPM3R (GSPM2 5'-CCAATCAGTTACTGTTTGTTCCC-3'; GSPM3R 5'-GGACTTCCTGATATTATGCC3'). Sanger sequencing results showed that each sequence of the three isolates were the same. Then sequences of one isolate were uploaded in GenBank (Accession No. PQ044579, PQ149219, PQ149220, PQ149221and PQ149222, respectively). The sequences were 100% identical to those of a previously reported E russellii on O. corniculata (Thuong et al. 2017; Takamatsu et al. 2015). The pathogen and the previously reported E russellii are clustered in the same branch in the phylogenetic tree (Thuong et al. 2017; Takamatsu et al. 2015). The pathogenicity was tested according to the method previously described (Zhu et al. 2021). By blowing conidia on infected leaves with pressurized air, the fungus was inoculated onto the leaves of three healthy plants (three-month-old), with three uninoculated plants (three-month-old) treated as controls. The infected plants and the control plants were placed in the culture room with the temperature 23 °C, humidity 50% and light/Dark 16/8 h, respectively. 10-12 days post inoculation, the leaves of the inoculated plants showed signs and symptoms of powdery mildew, while the control group was unaffected. The pathogen of the infected plant disease was re-examined by morphological characteristics and was similar to the original fungus. The pathogenicity tests were repeated three times and same results were obtained. Therefore, the pathogen was identified and confirmed as E russellii (isolate ER-ZM2024). Previously, E russellii was reported on Oxalis corniculata L. in Japan and Korea (Thuong et al. 2017; Takamatsu et al. 2015). To the best our knowledge, this is the first report of powdery mildew caused by E russellii on O. corniculata L. in central China. This identification of E russellii on O. corniculata L. provides a new perspective for the study of the disease. The results of this study provide the sequences of E russellii for further phylogenetic analysis.}, }
@article {pmid39670887, year = {2025}, author = {Vlasselaer, L and Moons, J and De Clercq, T and Lievens, B and De Coninck, B}, title = {Development of a Toolbox to Study Phytophthora cryptogea-Lettuce Interactions: Characterization and Detection of P. cryptogea in Hydroponic Lettuce.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS09242018RE}, doi = {10.1094/PDIS-09-24-2018-RE}, pmid = {39670887}, issn = {0191-2917}, abstract = {Climate change poses a major threat to crop production, resulting in the emergence of new pests and diseases. Phytophthora cryptogea has recently emerged as a major concern in hydroponic lettuce cultivation, causing substantial yield and economic losses. This oomycete pathogen thrives in elevated water temperatures induced by warmer weather conditions (e.g., heatwaves), facilitating rapid pathogen propagation. Although the disease is already present for several decades in chicory cultivation, where it originates from the field, its origin in lettuce cultivation remains unclear. To get a better understanding of its origin, we conducted a multilocus sequence analysis using five reference genes (ITS, β-tub, COI, EF1α, and HSP90) and 33 P. cryptogea isolates from various hosts, including chicory and lettuce. Results revealed a clear separation between lettuce and chicory isolates. Furthermore, we developed and implemented a robust disease bioassay and qPCR assay to investigate the interaction between P. cryptogea strains and lettuce. Our findings revealed that while lettuce isolates exhibited the highest virulence, some chicory isolates also caused disease in lettuce, suggesting a potential evolutionary link between P. cryptogea in lettuce and chicory. Our experiments also revealed that even a low concentration of zoospores (100 zoospores/liter) can elicit severe symptoms, underscoring the pathogen's high virulence. Therefore, effective disease management strategies are needed for controlling (the spread of) the disease. Together, this research provides several tools that can be used to enhance our understanding of the interaction between P. cryptogea and its host plants, including the development of proper disease management strategies.}, }
@article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Ostreidae/microbiology ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; Biomineralization ; Viruses/classification/genetics/isolation &amp; purification ; Calcification, Physiologic ; Metagenomics ; Biodiversity ; Phylogeny ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.<br><br>IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, }
@article {pmid39660837, year = {2025}, author = {Lewin, GR}, title = {mSphere of Influence: How the single cell contributes to the collective.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0043124}, pmid = {39660837}, issn = {2379-5042}, support = {DP2 AI184733/AI/NIAID NIH HHS/United States ; R00 DE031018/DE/NIDCR NIH HHS/United States ; }, mesh = {*Single-Cell Analysis ; Humans ; *Bacteria/genetics/classification ; *Microbiota/genetics ; RNA-Seq ; }, abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.}, }
@article {pmid39659497, year = {2024}, author = {Ritsch, M and Brait, N and Harvey, E and Marz, M and Lequime, S}, title = {Endogenous viral elements: insights into data availability and accessibility.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae099}, pmid = {39659497}, issn = {2057-1577}, abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.}, }
@article {pmid39657855, year = {2025}, author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G}, title = {Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143925}, doi = {10.1016/j.chemosphere.2024.143925}, pmid = {39657855}, issn = {1879-1298}, mesh = {Animals ; Oligochaeta/growth &amp; development ; *Composting ; Sewage/microbiology ; Biodegradation, Environmental ; Metagenomics ; Genomics ; *Soil Microbiology ; *Refuse Disposal/methods ; Bacteria/genetics ; Lignin ; }, abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.}, }
@article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; R01 GM097142/GM/NIGMS NIH HHS/United States ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; R01 GM123998/GM/NIGMS NIH HHS/United States ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39651958, year = {2024}, author = {Werlang, CA and Sahoo, JK and Cárcarmo-Oyarce, G and Stevens, C and Uzun, D and Putnik, R and Hasturk, O and Choi, J and Kaplan, DL and Ribbeck, K}, title = {Selective Biofilm Inhibition through Mucin-Inspired Engineering of Silk Glycopolymers.}, journal = {Journal of the American Chemical Society}, volume = {146}, number = {50}, pages = {34661-34668}, pmid = {39651958}, issn = {1520-5126}, support = {P41 EB027062/EB/NIBIB NIH HHS/United States ; }, mesh = {*Biofilms/drug effects ; *Mucins/chemistry/metabolism ; *Streptococcus mutans/drug effects ; *Silk/chemistry ; Humans ; Streptococcus sanguis/drug effects ; Streptococcus/drug effects/chemistry ; }, abstract = {Mucins are key components of innate immune defense and possess remarkable abilities to manage pathogenic microbes while supporting beneficial ones and maintaining microbial homeostasis at mucosal surfaces. Their unique properties have garnered significant interest in developing mucin-inspired materials as novel therapeutic strategies for selectively controlling pathogens without disrupting the overall microbial ecology. However, natural mucin production is challenging to scale, driving the need for simpler materials that reproduce mucin's bioactivity. In this work, we generated silk-based glycopolymers with different monosaccharides (GalNAc, GlcNAc, NeuNAc, GlcN, and GalN) and different grafting densities. Using the oral cavity as a model system, we treated in vitro cultures of pathogenic Streptococcus mutans and commensal Streptococcus sanguinis with our glycopolymers, finding that silk-tethered GalNAc uniquely prevented biofilm formation without affecting overall bacterial growth of either species. This relatively simple material reproduced mucin's virulence-neutralizing effects while maintaining biocompatibility. These mucin-inspired materials represent a valuable tool for preventing infection-related harm and offer a strategy for the domestication of pathogens in other environments.}, }
@article {pmid39651889, year = {2025}, author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG}, title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0171224}, pmid = {39651889}, issn = {2165-0497}, mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation &amp; purification ; Metagenome ; Prevalence ; Soil/chemistry ; }, abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.}, }
@article {pmid39644970, year = {2025}, author = {Tumeo, A and McDonagh, F and Kovarova, A and Ryan, K and Clarke, C and Miliotis, G}, title = {Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland.}, journal = {Journal of global antimicrobial resistance}, volume = {40}, number = {}, pages = {62-65}, doi = {10.1016/j.jgar.2024.11.018}, pmid = {39644970}, issn = {2213-7173}, mesh = {*Escherichia coli/genetics/isolation &amp; purification/drug effects/classification ; Humans ; Ireland ; *beta-Lactamases/genetics ; *Genome, Bacterial ; *Escherichia coli Infections/microbiology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Colistin/pharmacology ; Virulence Factors/genetics ; Multilocus Sequence Typing ; Plasmids ; }, abstract = {OBJECTIVES: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.<br><br>METHODS: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).<br><br>RESULTS: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs, 17 of which acquired. Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. Forty-seven chromosomal VFs were identified, involved in adhesion and iron acquisition amongst other properties. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. wgMLST analysis showed the closest relative being a strain from the UK, exhibiting differences in the sequences of 851 genes.<br><br>CONCLUSION: This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health concern posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39641603, year = {2025}, author = {Grimm, H and Lorenz, J and Straub, D and Joshi, P and Shuster, J and Zarfl, C and Muehe, EM and Kappler, A}, title = {Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0126224}, pmid = {39641603}, issn = {1098-5336}, support = {project ID 431072007//Deutsche Forschungsgemeinschaft (DFG)/ ; project ID 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Nitrous Oxide/metabolism ; Oxidation-Reduction ; *Nitrates/metabolism ; *Soil Microbiology ; *Ferrous Compounds/metabolism ; China ; *Iron/metabolism ; Soil/chemistry ; *Gallionellaceae/metabolism/isolation &amp; purification ; }, abstract = {Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3[-]-N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3[-]-N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.}, }
@article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, }
@article {pmid39637512, year = {2025}, author = {Wilkie, I and Orellana, LH}, title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126562}, doi = {10.1016/j.syapm.2024.126562}, pmid = {39637512}, issn = {1618-0984}, mesh = {Phylogeny ; *Polysaccharides/metabolism ; *Sulfates/metabolism ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Seasons ; North Sea ; *Seawater/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenome ; }, abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.}, }
@article {pmid39633812, year = {2024}, author = {Bauchinger, F and Seki, D and Berry, D}, title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1454634}, pmid = {39633812}, issn = {1664-302X}, abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.}, }
@article {pmid39633134, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {153}, pmid = {39633134}, issn = {1432-184X}, support = {20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; }, abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.}, }
@article {pmid39633061, year = {2024}, author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A}, title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {152}, pmid = {39633061}, issn = {1432-184X}, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; }, abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.}, }
@article {pmid39632307, year = {2025}, author = {Delmoitié, B and Sakarika, M and Rabaey, K and De Wever, H and Regueira, A}, title = {Tailoring non-axenic lactic acid fermentation from cheese whey permeate targeting a flexible lactic acid platform.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123529}, doi = {10.1016/j.jenvman.2024.123529}, pmid = {39632307}, issn = {1095-8630}, mesh = {*Cheese ; Fermentation ; *Whey/metabolism ; *Lactic Acid/metabolism ; Hydrogen-Ion Concentration ; Temperature ; }, abstract = {Lactic acid (LA) is an important biobased platform chemical, with potential applications in synthetising a wide range of chemical products or serving as feedstock for various bioprocesses. Industrial LA production via pure culture fermentation is characterized by high operational costs and utilizes food-grade sugars, thereby reducing the feasibility of LA applications. In this context, our research focussed on valorising the largest dairy side stream, cheese whey permeate, through the use of mixed microbial communities. We evaluated the effect of different operational parameters (temperature, pH and hydraulic retention time) in non-axenic fermentations on productivity, yield, concentration, optical purity, and community. Our findings revealed that operating at mildly thermophilic conditions (45 °C) resulted in highly selective LA production, and significantly augmented the LA yield, and productivity, compared to higher temperatures (50-55 °C). In addition, operating at circumneutral pH conditions (6.0-6.5) led to significantly increased the LA fermentation performance compared to the conventional acid pH conditions (≤5.5). This led to an unprecedented LA productivity of 27.4 g/L/h with a LA yield of 70.0% which is 2.5 times higher compared to previous reported maximum. Additionally, varying pH levels influenced the optical purity of LA: we achieved an optical L-LA purity of 98.3% at pH 6.0-6.5, and an optical D-LA purity of 91.3% at a pH of 5.5. A short hydraulic retention time of less than 12 h was crucial for selective LA production. This process also yielded a microbial biomass composed of 90.3-98.6% Lactobacillus delbrueckii, which could be potentially valorised as probiotic or protein ingredient in food or feed products. Our work shows that by careful selection of operational conditions, the overall performance can be significantly increased compared to the state-of-the-art. These results highlight the potential of non-sterile LA fermentation and show that careful selection of simple reactor operation parameters can maximize process performance. A preliminary assessment suggests that valorising EU cheese whey permeate could increase LA and poly-LA production by 40 and 125 times, respectively. This could also lead to the production of 4,000 kton protein-rich biomass, potentially reducing CO2 emissions linked to EU food and feed production by 4.87% or 2.77% respectively.}, }
@article {pmid39629059, year = {2024}, author = {Pecsi, EL and Forbes, S and Guillemette, F}, title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.}, journal = {Journal of geophysical research. Biogeosciences}, volume = {129}, number = {12}, pages = {e2024JG008355}, pmid = {39629059}, issn = {2169-8953}, abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.}, }
@article {pmid39628456, year = {2024}, author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P}, title = {Effects of land cover and protected areas on flying insect diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e14425}, doi = {10.1111/cobi.14425}, pmid = {39628456}, issn = {1523-1739}, support = {//Hessisches Landesamt f&#xfc;r Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; }, abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.}, }
@article {pmid39624182, year = {2024}, author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC}, title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.}, journal = {Journal of open source software}, volume = {9}, number = {101}, pages = {}, pmid = {39624182}, issn = {2475-9066}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.}, }
@article {pmid39621250, year = {2024}, author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X}, title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {12}, pages = {1113-1124}, pmid = {39621250}, issn = {1976-3794}, support = {201224106490150//Shantou Science and Technology Project/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; Bacteremia/microbiology ; Disease Susceptibility ; DNA, Bacterial/genetics ; }, abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.}, }
@article {pmid39619625, year = {2024}, author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R}, title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1512756}, doi = {10.3389/fbioe.2024.1512756}, pmid = {39619625}, issn = {2296-4185}, }
@article {pmid39612478, year = {2025}, author = {Zhao, Y and Ran, W and Xu, W and Song, Y}, title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0188924}, pmid = {39612478}, issn = {2165-0497}, support = {32260120//MOST | National Natural Science Foundation of China (NSFC)/ ; Qiankehejichu-ZK [2023] General 257//Guizhou Natural Science Foundation/ ; Qiankehepingtairencai-GCC [2023]032//Training Program for High-level Innovative Talents of Guizhou Province/ ; Qiankehepingtairencai-CXTD [2023]010//Science and Techonlogy Innovation Talent Team Building Project of Guizhou Province/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Camellia sinensis/microbiology ; *Plant Diseases/microbiology ; China ; Symbiosis ; Tea/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.}, }
@article {pmid39611982, year = {2024}, author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W}, title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {151}, pmid = {39611982}, issn = {1432-184X}, support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; }, abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.}, }
@article {pmid39611949, year = {2024}, author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP}, title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {150}, pmid = {39611949}, issn = {1432-184X}, support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; }, mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; }, abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.}, }
@article {pmid39611829, year = {2025}, author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K}, title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0137624}, pmid = {39611829}, issn = {2165-0497}, support = {Mars Program Office//NASA | Jet Propulsion Laboratory (JPL)/ ; IBSE//Indian Institute of Technology Madras (IITM)/ ; WSAI//Indian Institute of Technology Madras (IITM)/ ; }, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Spacecraft ; *Mars ; Genome, Bacterial ; Fatty Acids/metabolism/analysis ; DNA, Bacterial/genetics ; Genomics ; Base Composition ; Bacillales/genetics/classification/isolation &amp; purification/metabolism ; Soil Microbiology ; Peptides/metabolism ; Whole Genome Sequencing ; }, abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.<br><br>IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.}, }
@article {pmid39611809, year = {2025}, author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N}, title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0100924}, pmid = {39611809}, issn = {2379-5077}, mesh = {*Flow Cytometry/methods ; RNA, Ribosomal, 16S/genetics ; Coculture Techniques/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics ; }, abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.}, }
@article {pmid39609949, year = {2024}, author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL}, title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70052}, pmid = {39609949}, issn = {1758-2229}, support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; }, mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; }, abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.}, }
@article {pmid39609930, year = {2024}, author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE}, title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {98}, pmid = {39609930}, issn = {2524-6372}, abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.<br><br>RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.<br><br>CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.}, }
@article {pmid39608606, year = {2025}, author = {Lee, JY and Jo, YH and Kim, TH and Lee, SE and Hong, ES and Kang, TS}, title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.}, journal = {Journal of food protection}, volume = {88}, number = {1}, pages = {100422}, doi = {10.1016/j.jfp.2024.100422}, pmid = {39608606}, issn = {1944-9097}, mesh = {*Probiotics ; *Food Microbiology ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; }, abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated improved sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.}, }
@article {pmid39605469, year = {2024}, author = {Woodruff, GC and Moser, KA and Wang, J}, title = {The Bacteria of a Fig Microcommunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.22.624729}, pmid = {39605469}, issn = {2692-8205}, abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.<br><br>IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.}, }
@article {pmid39605409, year = {2024}, author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Read, TD and Goldberg, JB}, title = {Intraspecific Diversity of Staphylococcus aureus Populations Isolated from Cystic Fibrosis Respiratory Infections.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605409}, issn = {2692-8205}, support = {R21 AI148847/AI/NIAID NIH HHS/United States ; T32 AI138952/AI/NIAID NIH HHS/United States ; }, abstract = {Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile. Isolating a recognized virulent or difficult to treat pathogen is an important part of informing clinical treatment and correlative research; however, these reductive methods alone, do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population structure and dynamics over time. To begin to address this limitation, in this study, we compare findings on Staphylococcus aureus single colonies versus and pools of colonies taken from fresh sputum samples from three patients with cystic fibrosis to isolates collected from the same sputum samples and processed by the clinical microbiology laboratory. Phenotypic and genotypic analysis of isolated S. aureus populations revealed coexisting lineages in two of three sputum samples as well as population structures that were not reflected in the single colony isolates. Altogether, our observations presented here demonstrate that clinically relevant diversity can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.}, }
@article {pmid39604741, year = {2024}, author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW}, title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {149}, pmid = {39604741}, issn = {1432-184X}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; }, abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.}, }
@article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, }
@article {pmid39601575, year = {2025}, author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP}, title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0090424}, pmid = {39601575}, issn = {2165-0497}, support = {773830//EC | Horizon 2020 Framework Programme (H2020)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; 2017-HW-LS-1//Environmental Protection Agency (EPA)/ ; 2017-HW-LS-1//Health Service Executive (HSE)/ ; }, mesh = {Humans ; *beta-Lactamases/genetics ; Ireland ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Inpatients ; Enterobacteriaceae Infections/microbiology/epidemiology ; Whole Genome Sequencing ; Wastewater/microbiology ; Genomics ; Ecosystem ; Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Cities ; Spatio-Temporal Analysis ; }, abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.}, }
@article {pmid39601521, year = {2025}, author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS}, title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0063724}, pmid = {39601521}, issn = {2576-098X}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE031470/DE/NIDCR NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; T90 DE021984/DE/NIDCR NIH HHS/United States ; T90DE021984, R01DE031470, R01DE023810, R01DE031274//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.}, }
@article {pmid39597739, year = {2024}, author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H}, title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597739}, issn = {2076-2607}, support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; }, abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.}, }
@article {pmid39597685, year = {2024}, author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F}, title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597685}, issn = {2076-2607}, support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; }, abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.}, }
@article {pmid39597671, year = {2024}, author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E}, title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597671}, issn = {2076-2607}, support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; }, abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.}, }
@article {pmid39597543, year = {2024}, author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D}, title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597543}, issn = {2076-2607}, abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.}, }
@article {pmid39597512, year = {2024}, author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP}, title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597512}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.}, }
@article {pmid39596705, year = {2024}, author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF}, title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596705}, issn = {2079-6382}, support = {FAPESP//001/ ; }, abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.}, }
@article {pmid39592542, year = {2025}, author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN}, title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.}, journal = {Folia microbiologica}, volume = {70}, number = {2}, pages = {293-319}, pmid = {39592542}, issn = {1874-9356}, mesh = {*Microbiota ; Phosphorus/metabolism ; Agriculture ; Soil Microbiology ; *Biodiversity ; Potassium/metabolism ; Nitrogen/metabolism ; *Biotechnology ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; }, abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.}, }
@article {pmid39587684, year = {2025}, author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS}, title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {2}, pages = {180-189}, doi = {10.1093/jeb/voae143}, pmid = {39587684}, issn = {1420-9101}, support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; }, mesh = {Animals ; *Drosophila/microbiology/genetics/classification/physiology ; *Phylogeny ; *Diet ; *Microbiota ; Symbiosis ; Desert Climate ; *Bacteria/classification ; }, abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.}, }
@article {pmid39587399, year = {2024}, author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF}, title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {49}, pages = {21589-21603}, pmid = {39587399}, issn = {1520-5851}, mesh = {*Wetlands ; Tea ; Climate ; Ecosystem ; Carbon ; Temperature ; }, abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.}, }
@article {pmid39587087, year = {2024}, author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD}, title = {Microbial trait multifunctionality drives soil organic matter formation potential.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10209}, pmid = {39587087}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; }, abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.}, }
@article {pmid39586934, year = {2024}, author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y}, title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {148}, pmid = {39586934}, issn = {1432-184X}, support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; }, abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.}, }
@article {pmid39585925, year = {2024}, author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG}, title = {Reconstructing the last common ancestor of all eukaryotes.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002917}, pmid = {39585925}, issn = {1545-7885}, support = {R35 GM143039/GM/NIGMS NIH HHS/United States ; }, mesh = {*Eukaryota/genetics ; *Phylogeny ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genomics/methods ; Biological Evolution ; }, abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.}, }
@article {pmid39583547, year = {2024}, author = {Yang, X and Gänzle, M and Wang, R}, title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501925}, pmid = {39583547}, issn = {1664-302X}, }
@article {pmid39578630, year = {2024}, author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK}, title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28934}, pmid = {39578630}, issn = {2045-2322}, support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.}, }
@article {pmid39572704, year = {2024}, author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C}, title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1548}, pmid = {39572704}, issn = {2399-3642}, support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; }, abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.}, }
@article {pmid39572621, year = {2024}, author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM}, title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28890}, pmid = {39572621}, issn = {2045-2322}, support = {07939716/2020//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.}, }
@article {pmid39572453, year = {2024}, author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A}, title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {147}, pmid = {39572453}, issn = {1432-184X}, support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ram&#xf3;n y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; }, mesh = {*Biofilms/radiation effects/growth &amp; development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; }, abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.}, }
@article {pmid39571806, year = {2025}, author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V}, title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.}, journal = {The Science of the total environment}, volume = {963}, number = {}, pages = {177598}, doi = {10.1016/j.scitotenv.2024.177598}, pmid = {39571806}, issn = {1879-1026}, mesh = {*Methane/metabolism/analysis ; Animals ; *Animal Feed/analysis ; Ruminants ; Rumen/metabolism ; Oxygen ; Oxidation-Reduction ; Fatty Acids, Volatile ; }, abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.}, }
@article {pmid39571521, year = {2025}, author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R}, title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.}, journal = {Water research}, volume = {269}, number = {}, pages = {122784}, doi = {10.1016/j.watres.2024.122784}, pmid = {39571521}, issn = {1879-2448}, mesh = {*Cyanobacteria/physiology ; *Rivers/microbiology ; *Lakes/microbiology ; China ; Ecosystem ; Eukaryota ; }, abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.}, }
@article {pmid39570409, year = {2024}, author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X}, title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {145}, pmid = {39570409}, issn = {1432-184X}, support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.}, }
@article {pmid39570377, year = {2024}, author = {Jensen, IC and Schramm, A and Offenberg, J}, title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {146}, pmid = {39570377}, issn = {1432-184X}, support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i &#xd8;kologisk Jordbrug og F&#xf8;devaresystemer/ ; }, mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation &amp; purification ; Ascomycota/physiology/drug effects ; }, abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.}, }
@article {pmid39568064, year = {2024}, author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB}, title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39568064}, issn = {1574-6941}, support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; }, abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.}, }
@article {pmid39567391, year = {2024}, author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL}, title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {144}, pmid = {39567391}, issn = {1432-184X}, support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth &amp; development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; }, abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.}, }
@article {pmid39567372, year = {2024}, author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F}, title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {143}, pmid = {39567372}, issn = {1432-184X}, support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth &amp; development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth &amp; development ; }, abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.}, }
@article {pmid39565130, year = {2025}, author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X}, title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0093424}, pmid = {39565130}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics/metabolism/isolation &amp; purification ; *Iron/metabolism ; *Phylogeny ; *Alteromonas/virology/metabolism/genetics ; Host Specificity ; Viral Tail Proteins/metabolism/genetics ; Genome, Viral/genetics ; Protein Domains ; }, abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.}, }
@article {pmid39563404, year = {2024}, author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN}, title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17550}, doi = {10.1111/gcb.17550}, pmid = {39563404}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; }, mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth &amp; development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; }, abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.}, }
@article {pmid39561700, year = {2024}, author = {Partida-Martínez, LP}, title = {Laila P. Partida-Martínez.}, journal = {Current biology : CB}, volume = {34}, number = {22}, pages = {R1121-R1122}, doi = {10.1016/j.cub.2024.09.085}, pmid = {39561700}, issn = {1879-0445}, mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; }, abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).}, }
@article {pmid39561304, year = {2024}, author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H}, title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0302954}, pmid = {39561304}, issn = {1932-6203}, mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; }, abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.}, }
@article {pmid39560406, year = {2024}, author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J}, title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0053524}, pmid = {39560406}, issn = {2379-5077}, support = {92351301//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022FY101100//National Science and Technology Fundamental Resources Investigation Program of China/ ; }, mesh = {*Phylogeny ; *Geologic Sediments/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; DNA, Bacterial/genetics ; }, abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.}, }
@article {pmid39558480, year = {2024}, author = {Zechner, EL and Kienesberger, S}, title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2430423}, pmid = {39558480}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Bacteria/drug effects/genetics/metabolism ; Enterotoxins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Host Microbial Interactions ; Mutagens/metabolism/toxicity ; Polyketides/metabolism/toxicity ; }, abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.}, }
@article {pmid39557685, year = {2024}, author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA}, title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {142}, pmid = {39557685}, issn = {1432-184X}, support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; }, mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation &amp; purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation &amp; purification ; Basidiomycota/isolation &amp; purification/genetics/classification ; }, abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.}, }
@article {pmid39551884, year = {2024}, author = {Mamo, Z and Abera, S and Tafesse, M}, title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {12}, pages = {384}, pmid = {39551884}, issn = {1573-0972}, support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; }, mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.}, }
@article {pmid39551202, year = {2024}, author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C}, title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177523}, doi = {10.1016/j.scitotenv.2024.177523}, pmid = {39551202}, issn = {1879-1026}, mesh = {*Eukaryota ; France ; *Microbiota ; *Wetlands ; Animals ; Bacteria/classification ; Salinity ; Archaea ; Seasons ; Environmental Monitoring ; }, abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.}, }
@article {pmid39549623, year = {2025}, author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L}, title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122727}, doi = {10.1016/j.watres.2024.122727}, pmid = {39549623}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; }, abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.}, }
@article {pmid39549075, year = {2024}, author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C}, title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {519}, pmid = {39549075}, issn = {1432-0614}, support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; }, mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; }, abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.}, }
@article {pmid39546027, year = {2024}, author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M}, title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {141}, pmid = {39546027}, issn = {1432-184X}, mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; }, abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.}, }
@article {pmid39545996, year = {2024}, author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {140}, pmid = {39545996}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; }, abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.}, }
@article {pmid39545729, year = {2024}, author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC}, title = {Enriching the future of public health microbiology with hybridization bait capture.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0006822}, pmid = {39545729}, issn = {1098-6618}, support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; }, abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.}, }
@article {pmid39544963, year = {2024}, author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM}, title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae124}, pmid = {39544963}, issn = {2730-6151}, abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.}, }
@article {pmid39543974, year = {2024}, author = {Gonsiorczyk, T and Hupfer, M and Hilt, S and Gessner, MO}, title = {Rapid Eutrophication of a Clearwater Lake: Trends and Potential Causes Inferred From Phosphorus Mass Balance Analyses.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17575}, doi = {10.1111/gcb.17575}, pmid = {39543974}, issn = {1365-2486}, mesh = {*Eutrophication ; *Lakes/chemistry ; *Phosphorus/analysis ; *Geologic Sediments/analysis/chemistry ; *Seasons ; Environmental Monitoring/methods ; }, abstract = {Many clearwater lakes increasingly show symptoms of eutrophication, but the underlying causes are largely unknown. We combined long-term water chemistry data, multi-year sediment trap measurements, sediment analyses and simple mass balance models to elucidate potential causes of eutrophication of a deep temperate clearwater lake, where total phosphorus (TP) concentrations quadrupled within a decade, accompanied by expanding hypolimnetic anoxia. Discrepancies between modeled and empirically determined P inputs suggest that the observed sharp rise in TP was driven by internal processes. The magnitude of seasonal variation in TP greatly increased at the same time, both in surface and deep water, partly decoupled from deep water oxygen conditions. A positive correlation between annual P loss from the upper water column and hypolimnetic P accumulation could hint at a short-circuited P cycle involving lateral TP transport from shallow-water zones and deposition and release from sediments in deep water. This hypothesis is also supported by P budgets for the upper 20 m during stable summer stratification, suggesting that sediments in shallow lake areas acted as a P net source until 2018. These changes are potentially related to shifts in submerged macrophytes from wintergreen charophyte meadows (Nitellopsis obtusa) to annual free-floating hornwort (Ceratophyllum demersum) and to increased sulfide formation, promoting iron fixation in the sediments. Iron bound to sulfur is unavailable for binding P, resulting in a positive feedback between P release in shallow lake areas, primary productivity, macrophyte community structure and redox-dependent sediment biogeochemistry. Overall, our results suggest that relationships more complex than the commonly invoked increase in internal P release under increasingly anoxic conditions can drive rapid lake eutrophication. Since the proportion of littoral areas is typically large even in deep stratified lakes, littoral processes may contribute more frequently to the rapid lake eutrophication trends observed around the world than is currently recognized.}, }
@article {pmid39541983, year = {2024}, author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH}, title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.}, journal = {Cell systems}, volume = {15}, number = {11}, pages = {1002-1017.e4}, pmid = {39541983}, issn = {2405-4720}, support = {R35 GM143056/GM/NIGMS NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 GM130777/GM/NIGMS NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; }, abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39541852, year = {2025}, author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R}, title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122776}, doi = {10.1016/j.watres.2024.122776}, pmid = {39541852}, issn = {1879-2448}, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Wastewater ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Plasmids/genetics ; Bacteria/virology/genetics ; }, abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.}, }
@article {pmid39540979, year = {2024}, author = {Frew, A and Aguilar-Trigueros, CA}, title = {Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {139}, pmid = {39540979}, issn = {1432-184X}, support = {DE220100479//Australian Research Council/ ; }, mesh = {*Mycorrhizae/genetics/physiology ; *Phosphorus/metabolism ; *Plant Roots/microbiology/growth &amp; development ; *Phylogeny ; *Symbiosis ; *Sorghum/microbiology/growth &amp; development ; Soil Microbiology ; Mycobiome ; Biomass ; Plant Development ; }, abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.}, }
@article {pmid39537004, year = {2025}, author = {Bernetti, A and Barili, S and Sannino, C and Mugnai, G and Borruso, L and Pinchuk, I and Pezzolla, D and Turchetti, B and Gigliotti, G and Buzzini, P}, title = {Selective response of soil bacterial and fungal taxa to biodegradable polymers.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120344}, doi = {10.1016/j.envres.2024.120344}, pmid = {39537004}, issn = {1096-0953}, mesh = {*Fungi/metabolism/classification ; *Soil Microbiology ; *Bacteria/classification/metabolism/drug effects ; *Biodegradation, Environmental ; Polymers ; Soil/chemistry ; }, abstract = {Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.}, }
@article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, }
@article {pmid39524341, year = {2024}, author = {Dzialo, MC and Arumugam, S and Piampongsant, S and Cool, L and Vanderaa, C and Herrera-Malaver, B and Opsomer, T and Dehaen, W and Wenseleers, T and Roncoroni, M and Alawamleh, A and Wäckers, F and Lievens, B and Hansson, BS and Voordeckers, K and Sachse, S and Verstrepen, KJ}, title = {Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111141}, pmid = {39524341}, issn = {2589-0042}, abstract = {Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.}, }
@article {pmid39535358, year = {2024}, author = {Tidimalo, C and Maximiliano, O and Karen, J and Lebre, PH and Bernard, O and Michelle, G and Oagile, D and Cowan, DA}, title = {Microbial diversity in the arid and semi-arid soils of Botswana.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70044}, pmid = {39535358}, issn = {1758-2229}, support = {//PhD bursary for Tidimalo Coetzee from the University of Botswana/ ; //Oppenheimer Foundation/ ; 674-AA-2010-A1//United States Agency for International Development/ ; //University of Pretoria for postdoctoral support/ ; }, mesh = {*Soil Microbiology ; Botswana ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; *Biodiversity ; Microbiota/genetics ; Phylogeny ; Hydrogen-Ion Concentration ; DNA, Bacterial/genetics ; }, abstract = {To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.}, }
@article {pmid39532738, year = {2024}, author = {Fu, M and Liu, Y and Li, S and Yan, D and Liu, P and Liu, Y and Ji, M}, title = {The Spatial Dynamics of Diazotrophs in the Forefield of Three Tibetan Glaciers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {138}, pmid = {39532738}, issn = {1432-184X}, support = {42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; }, mesh = {*Ice Cover/microbiology ; Tibet ; *Soil Microbiology ; *Nitrogen Fixation ; Soil/chemistry ; Nitrogen/metabolism ; Ecosystem ; Bacteria/classification/metabolism/genetics/isolation &amp; purification/enzymology ; Nitrogen-Fixing Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.}, }
@article {pmid39528791, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {1}, pages = {1-2}, pmid = {39528791}, issn = {1740-1534}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528727, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3084-3085}, pmid = {39528727}, issn = {2058-5276}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528652, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {34}, pmid = {39528652}, issn = {2731-4243}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528617, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1466}, pmid = {39528617}, issn = {2399-3642}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528577, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {122}, pmid = {39528577}, issn = {2055-5008}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528441, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9637}, pmid = {39528441}, issn = {2041-1723}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528211, year = {2024}, author = {Jang, J and Park, J and Hwang, CY and Gim, Y and Park, KT and Yoon, YJ and Seo, M and Lee, BY}, title = {Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177462}, doi = {10.1016/j.scitotenv.2024.177462}, pmid = {39528211}, issn = {1879-1026}, mesh = {Pacific Ocean ; *Air Microbiology ; *Seawater/microbiology ; *Bacteria/classification ; Environmental Monitoring ; Atmosphere/chemistry ; Aerosols/analysis ; }, abstract = {This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.}, }
@article {pmid39527614, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39527614}, issn = {1751-7370}, }
@article {pmid39527081, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Adoukè Agbodjato, N and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39527081}, issn = {1574-6941}, abstract = {Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.}, }
@article {pmid39526991, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0141624}, pmid = {39526991}, issn = {2379-5077}, }
@article {pmid39526896, year = {2024}, author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L}, title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.}, journal = {Food &amp; function}, volume = {15}, number = {23}, pages = {11667-11685}, doi = {10.1039/d4fo02704c}, pmid = {39526896}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.}, }
@article {pmid39526802, year = {2024}, author = {Schiml, VC and Walter, JM and Hagen, LH and Varnai, A and Bergaust, LL and De Leon, AVP and Elsgaard, L and Bakken, LR and Arntzen, M&#xd8;}, title = {Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0174224}, pmid = {39526802}, issn = {1098-5336}, support = {295910//Norges Forskningsr&#xe5;d (Forskningsr&#xe5;det)/ ; NNF20OC0061313//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Bioreactors/microbiology ; *Lignin/metabolism ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Denitrification ; Agriculture ; RNA, Ribosomal, 16S/genetics ; Cellulose/metabolism ; Wood/metabolism/microbiology ; }, abstract = {UNLABELLED: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.<br><br>IMPORTANCE: Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.}, }
@article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, }
@article {pmid39520558, year = {2024}, author = {Boadella, J and Butturini, A and Doménech-Pascual, A and Freixinos, Z and Perujo, N and Urmeneta, J and Vidal, A and Romaní, AM}, title = {Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {137}, pmid = {39520558}, issn = {1432-184X}, support = {PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; 2020 FISDU 00465//Catalan Government Ministry of Business and Knowledge, Area of Universities and Research/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Biofilms/growth &amp; development ; *Salinity ; *Bacteria/classification/genetics/metabolism ; Biomass ; Droughts ; Water ; }, abstract = {Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.}, }
@article {pmid39516195, year = {2024}, author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J}, title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9682}, pmid = {39516195}, issn = {2041-1723}, mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; }, abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.}, }
@article {pmid39513042, year = {2024}, author = {Park, KJ and Gao, Y}, title = {Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials.}, journal = {Frontiers in neuroscience}, volume = {18}, number = {}, pages = {1481390}, pmid = {39513042}, issn = {1662-4548}, abstract = {This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.}, }
@article {pmid39511174, year = {2024}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9628}, pmid = {39511174}, issn = {2041-1723}, support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; }, abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.}, }
@article {pmid39509969, year = {2024}, author = {Aparicio, S and Ríos-Mejía, A and Gallardo-Mejías, JP and Robles, &#xc1; and Borrás, L}, title = {Microalgae-bacteria consortia dynamics in a long term operated membrane-coupled high-rate algal pond (MHRAP).}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123186}, doi = {10.1016/j.jenvman.2024.123186}, pmid = {39509969}, issn = {1095-8630}, mesh = {*Microalgae ; *Wastewater/microbiology ; *Bacteria/metabolism/classification ; Ponds/microbiology ; Waste Disposal, Fluid/methods ; Biomass ; }, abstract = {Traditional activated sludge-based technologies have significant drawbacks, including high energy requirements and greenhouse gas emissions. Microalgae-based processes offer a promising, low-cost, and environmentally friendly alternative. However, the knowledge of treatment systems based on microalgae-bacteria consortia is limited, and even more so is their microbial composition and its relationship with operational parameters. Thus, this study explores the dynamics of microalgae-bacteria consortia in a long-term operated membrane-coupled high-rate algal pond (MHRAP) for wastewater treatment. For this, a pilot-scale MHRAP plant, located in a wastewater treatment plant in Valencia (Spain), was monitored under various hydraulic retention times (HRT) and wastewater influents: i) effluent from a primary settler and ii) effluent form pre-treatment. The biomass retention time was kept constant at 6 days. The composition of the bacterial community was studied through 16S rDNA sequencing, while 18S rDNA sequencing was used to study the microalgae. The results indicate that shorter HRTs significantly increased bacterial diversity, but not eukarya. Principal Co-ordinates Analysis (PCoA) revealed that the HRT and the incoming wastewater quality control the type of the bacterial populations. However, this effect was not observed in eukaryotic organisms. The dominant microalgae genera identified were Desmodesmus and Coelastrella, with Coelastrella becoming more prevalent at shorter HRTs. For bacteria, Verrumicrobiota dominated (18-56%) at high HRT while Proteobacteria was dominant (28-44%) at HRTs below 6 days. The changes observed in the bacterial composition, including the ammonia oxidizing bacteria (AOB) community (mainly Nitrosomonas), suggest that photo-inhibition could be taking place. The nitrite oxidizing bacteria (NOB) community was dominated by Nitrospira and Candidatus Nitrotoga. Operational parameters such as light intensity, pH, and nitrite concentration were found to significantly influence the microbial community structure. Higher light intensity and alkaline pH favored the growth of Desmodesmus, while Coelastrella thrived under lower HRTs. Bacterial diversity plays a crucial role in the treatment process, while microalgae primarily support aerobic bacterial processes by providing oxygen. These findings contribute to a deeper understanding of the complex biological processes in microalgae-bacteria consortia and offer insights into improving wastewater treatment technologies.}, }
@article {pmid39508609, year = {2024}, author = {Xue, S-J and Liu, J and Zhao, F-Y and Zhang, X-T and Zhu, Z-Q and Zhang, J-Y}, title = {Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0157024}, pmid = {39508609}, issn = {1098-5336}, support = {1120015//the Advanced Talents Foundation of Qingdao Agricultural University/ ; tsqn201909133//the Young experts of Taishan Scholars in Shandong Province/ ; 1120011//the Initiative grant for high-level personnel recruitment in Qingdao Agricultural University/ ; CARS-47//the earmarked fund/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Seawater/microbiology ; *Yeasts/genetics/classification/isolation &amp; purification/metabolism ; *Bays/microbiology ; Biodiversity ; Biotechnology ; Spatio-Temporal Analysis ; Ecosystem ; Microbiota ; }, abstract = {Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with Candida emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.}, }
@article {pmid39505133, year = {2025}, author = {Hu, Y and Song, Y and Cai, J and Chao, J and Gong, Y and Jiang, X and Shao, K and Tang, X and Gao, G}, title = {Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120294}, doi = {10.1016/j.envres.2024.120294}, pmid = {39505133}, issn = {1096-0953}, mesh = {China ; *Biofilms/growth &amp; development ; *Rivers/microbiology ; *Plankton ; *Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.}, }
@article {pmid39503489, year = {2024}, author = {Teixeira, GM and Cordeiro Montanari, GC and Nicoletto, MLA and da Silva, DV and Noriler, SA and de Oliveira, JP and da Silva Rodrigues, MV and Sipoli Sanches, D and de Padua Pereira, U and Nunes da Rocha, U and Oliveira, AGd}, title = {Draft genome of Bacillus velezensis CMRP6330, a suitable biocontrol agent for disease management in crops.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0065724}, pmid = {39503489}, issn = {2576-098X}, support = {305899/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 465133/2014-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {As a biological alternative to managing diseases in crop production, we highlight the Bacillus velezensis strain LABIM41 (CMRP6330). Its genome, composed of 3,970,959 bp, possesses a rich metabolic machinery and a wide range of molecules with different biological activities and roles in its symbiotic relationship with its plant hosts.}, }
@article {pmid39502209, year = {2024}, author = {Kipkoech, R and Takase, M and Ahogle, AMA and Ocholla, G}, title = {Analysis of properties of biodiesel and its development and promotion in Ghana.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39078}, pmid = {39502209}, issn = {2405-8440}, abstract = {The increasing global population and the challenges associated with fossil fuel has led to a surge in energy demand, necessitating research on renewable and environmentally friendly energy sources. Biodiesel, is produced from biomass materials like vegetable oil and fats, is a promising alternative. Transesterification is a principal method used in biodiesel production, as it is simple, versatile, and efficient. Biodiesel offers several advantages, including emissions, lubricity, and safety, making it a sustainable fuel option and its properties conforms to the international standards. However, it has lower energy content, cold weather performance issues, and slightly reduced engine power compared to petroleum diesel. The choice of biodiesel feedstock depends on its properties, with jatropha oil and other feedstocks being potential in Ghana. Research on biodiesel in Ghana is still in early stages and the Ghanaian government's policy aims to replace 10 % of petroleum fuel with biofuel by 2020 and 20 % by 2030, but these goals have not been achieved due to barriers. Despite these challenges, the government and stakeholders in the biofuel industry are working to optimize the biodiesel sector for sustainability, efficiency, and scalability. Innovative cultivation techniques and low-cost oil extraction methods are required, necessitating interdisciplinary research collaborations. By capitalizing on these opportunities and implementing targeted interventions, Ghana can become a regional leader in sustainable biodiesel production.}, }
@article {pmid39501667, year = {2025}, author = {You, Z and Zhang, X and Huang, S and Chen, D and Zhu, Y and Li, G and Chen, X}, title = {The influence of skin microbial ecology on γδ T-cell immune pathways in allergic dermatitis models in mice.}, journal = {Journal of leukocyte biology}, volume = {117}, number = {5}, pages = {}, doi = {10.1093/jleuko/qiae244}, pmid = {39501667}, issn = {1938-3673}, mesh = {Animals ; *Dermatitis, Atopic/immunology/microbiology/pathology ; *Skin/microbiology/immunology/pathology ; *Microbiota/immunology ; Disease Models, Animal ; Mice ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; Cytokines/metabolism ; Immunoglobulin E/blood ; Female ; *Intraepithelial Lymphocytes/immunology ; }, abstract = {Atopic dermatitis is a complex disease influenced by alterations in the skin microbiome and immune dysregulation. Despite the recognized role of these factors, the specific pathways by which distinct microbial populations affect skin immunity remain insufficiently understood. On a molecular level, the pathogenesis of atopic dermatitis involves critical cytokines such as IL-4, IL-17, interferon-γ, and IL-10, which contribute to the imbalance in T helper cell responses. Importantly, gamma-delta (γδ) T cells, which produce these cytokines and infiltrate affected epithelial cells in atopic dermatitis, have been underexplored. This study seeks to alleviate atopic dermatitis symptoms in mice by adjusting both peripheral and local immune environments through the transplantation of skin microbiota. By employing 16S rRNA sequencing, we characterized the skin microbiome of the mouse model. Our results demonstrate that microbiota intervention significantly reduces skin thickening and serum IgE levels in DNCB-induced atopic dermatitis mice. Additionally, changes in skin microbiota modulated immune cell dynamics, restoring the T helper 1 / T helper 2 balance and leading to clinical improvement. These findings highlight the critical role of skin microbiota in shaping immune responses, positioning microbiota-based therapies as a potential treatment for atopic dermatitis.}, }
@article {pmid39501615, year = {2025}, author = {Prost-Boxoen, L and Bafort, Q and Van de Vloet, A and Almeida-Silva, F and Paing, YT and Casteleyn, G and D'hondt, S and De Clerck, O and Van de Peer, Y}, title = {Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.}, journal = {The New phytologist}, volume = {245}, number = {2}, pages = {869-884}, pmid = {39501615}, issn = {1469-8137}, support = {833522//H2020 European Research Council/ ; I001621N//European Marine Biological Resource Centre Belgium/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; G0C0116N//Fonds Wetenschappelijk Onderzoek/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1168420N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Genome, Plant ; *Transcriptome/genetics ; *Chlamydomonas reinhardtii/genetics ; *Cell Nucleus/metabolism/genetics ; *Cytoplasm/metabolism/genetics ; Triploidy ; Gene Expression Regulation, Plant ; Genetic Fitness ; }, abstract = {Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.}, }
@article {pmid39500284, year = {2024}, author = {Arrigan, D and Kothe, CI and Oliverio, A and Evans, JD and Wolfe, BE}, title = {Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes.}, journal = {Current biology : CB}, volume = {34}, number = {21}, pages = {R1094-R1108}, doi = {10.1016/j.cub.2024.09.047}, pmid = {39500284}, issn = {1879-0445}, mesh = {*Fermented Foods/microbiology ; *Fermentation ; *Microbiota ; *Food Microbiology/methods ; Humans ; }, abstract = {Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address.}, }
@article {pmid39499580, year = {2024}, author = {Zhang, X and Zhang, XX and Ma, L}, title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {48}, pages = {21251-21264}, doi = {10.1021/acs.est.4c08865}, pmid = {39499580}, issn = {1520-5851}, mesh = {*Oxidative Stress ; Anaerobiosis ; Free Radicals/metabolism ; *Reactive Oxygen Species/metabolism ; }, abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.}, }
@article {pmid39498487, year = {2024}, author = {Dooley, KD and Henry, LP and Bergelson, J}, title = {Impact of timing on the invasion of synthetic bacterial communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39498487}, issn = {1751-7370}, support = {//Hutchinson Fund at The University of Chicago/ ; //The Simons Foundation/ ; 951444//ERC Synergy/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Biodiversity ; Introduced Species ; Time Factors ; }, abstract = {Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24 h into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7 days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.}, }
@article {pmid39498135, year = {2024}, author = {Gu, Y and Meng, D and Liu, Z and Zhang, M and Yang, Z and Yin, H and Liang, Y and Xiao, N}, title = {Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479670}, pmid = {39498135}, issn = {1664-302X}, abstract = {A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.}, }
@article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, }
@article {pmid39496952, year = {2024}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {136}, pmid = {39496952}, issn = {1432-184X}, support = {JP22H02382//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/classification ; *Soil/chemistry ; *Soil Microbiology ; *Cryptomeria/microbiology ; *Plant Roots/microbiology ; Japan ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.}, }
@article {pmid39496518, year = {2024}, author = {Khaleque, HN and Fathollahzadeh, H and Kaksonen, AH and Valdés, J and Vergara, E and Holmes, DS and Watkin, ELJ}, title = {Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39496518}, issn = {1574-6941}, support = {//Curtin University/ ; //CSIRO/ ; }, mesh = {*Phosphates/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Genome, Bacterial ; Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; }, abstract = {In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.}, }
@article {pmid39494810, year = {2024}, author = {Malik, M and Das, S and Paul, P and Chakraborty, P and Roy, R and Maity, A and Das, A and Dasgupta, M and Trivedi, S and Tribedi, P}, title = {Cuminaldehyde in combination with tetracycline shows promising antibiofilm activity against drug-resistant Pseudomonas aeruginosa.}, journal = {Biofouling}, volume = {40}, number = {10}, pages = {862-881}, doi = {10.1080/08927014.2024.2422874}, pmid = {39494810}, issn = {1029-2454}, mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; *Tetracycline/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; *Cymenes/pharmacology ; Drug Synergism ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/drug effects ; Virulence Factors ; }, abstract = {Pseudomonas aeruginosa, an opportunistic pathogen often causes biofilm-linked infections. A combinatorial approach involving tetracycline (antibiotic) and cuminaldehyde (phytochemical) was explored to combat this infectious pathogen. The results showed that both tetracycline and cuminaldehyde individually demonstrated antibacterial effects. However, when the compounds were applied together, there was a significant increase in their antimicrobial potential. The determined fractional inhibitory concentration index of 0.43 indicated a synergistic interaction between the two compounds. Furthermore, a series of experiments demonstrated that the combined application of cuminaldehyde and tetracycline could lead to a significant enhancement of their antibiofilm potential. This enhanced antibiofilm potential was attributed to the accumulation of reactive oxygen species and increased cell membrane permeability. Besides, this combinatorial application reduced the secretion of various virulence factors from P. aeruginosa. Therefore, this combined approach holds promise for effectively treating P. aeruginosa biofilms.}, }
@article {pmid39493671, year = {2024}, author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M}, title = {NovoLign: metaproteomics by sequence alignment.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae121}, pmid = {39493671}, issn = {2730-6151}, abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.}, }
@article {pmid39491387, year = {2023}, author = {González-Alonso, V and Pradal, I and Wardhana, YR and Cnockaert, M and Wieme, AD and Vandamme, P and De Vuyst, L}, title = {Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale.}, journal = {International journal of food microbiology}, volume = {408}, number = {}, pages = {110445}, doi = {10.1016/j.ijfoodmicro.2023.110445}, pmid = {39491387}, issn = {1879-3460}, abstract = {Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.}, }
@article {pmid39482450, year = {2024}, author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ}, title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {135}, pmid = {39482450}, issn = {1432-184X}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; }, abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.}, }
@article {pmid39480531, year = {2024}, author = {Dobrzyński, J and Naziębło, A}, title = {Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {134}, pmid = {39480531}, issn = {1432-184X}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Paenibacillus/physiology/metabolism ; *Paenibacillus polymyxa/physiology ; Biological Control Agents ; Fusarium/physiology ; Colletotrichum/physiology/growth &amp; development ; Pest Control, Biological ; Rhizoctonia/physiology/growth &amp; development ; Botrytis/growth &amp; development/physiology ; Fungi/physiology ; }, abstract = {Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.}, }
@article {pmid39488271, year = {2024}, author = {Allen, J and Sire, M and Belouard, N and Gorzerino, C and Coutellec, MA and Mony, C and Pannard, A and Piscart, C}, title = {Could landscape ecology principles apply at the microscale? A metabarcoding approach on Trichoptera larvae-associated microbial diversity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177304}, doi = {10.1016/j.scitotenv.2024.177304}, pmid = {39488271}, issn = {1879-1026}, mesh = {Animals ; *Larva ; *Microbiota ; *Insecta ; *DNA Barcoding, Taxonomic ; *Bacteria/classification/genetics ; Fungi ; Biodiversity ; Ecology ; Diatoms ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Landscape heterogeneity is known as a major factor of community structure and composition. Whether this effect of the landscape extends at different scales and particularly at the relevant scale for microorganisms remained to be determined. We used the cases produced by aquatic larvae of Trichoptera, which assemble organic or mineral particles, as naturally replicated experimental systems representing structured substrates to determine the effect of landscape structuration on microbial communities. A metabarcoding approach was used to characterise fungal, bacterial and diatom communities on cases produced by six Trichoptera species and related unstructured organic and mineral substrates. The structuration of the particles constituting the cases was also determined as a measure of microscale landscape. Structured substrates harboured communities of diatoms, fungi and bacteria that differed from those found on unstructured substrates. Microbial communities also differed between organic and mineral substrates. We found a higher microbial diversity on structured substrates than on unstructured substrates. The heterogeneity of the microscale landscape also affected bacterial and fungal communities within cases. These results highlight the importance of microscale landscape structuration for microbial diversity and demonstrate that approaches of landscape ecology could be downscaled to the microscale.}, }
@article {pmid39488149, year = {2024}, author = {Németh, Z and Svigruha, R and Ács, A and Farkas, A and Tapolczai, K and Elekes, K and Fodor, I and Pirger, Z}, title = {Developmental, behavioral, and biochemical effects of chronic exposure to sublethal concentrations of organic UV-filter compounds on a freshwater model species.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {277}, number = {}, pages = {107134}, doi = {10.1016/j.aquatox.2024.107134}, pmid = {39488149}, issn = {1879-1514}, mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Sunscreening Agents/toxicity ; *Daphnia/drug effects ; Reproduction/drug effects ; Ultraviolet Rays ; Heart Rate/drug effects ; Fresh Water/chemistry ; Catalase/metabolism ; Swimming ; Behavior, Animal/drug effects/radiation effects ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Acrylates ; }, abstract = {The prevalence of organic/chemical UV-filter compounds in aquatic ecosystems represents a growing environmental issue. The long-term toxicity risks of many UV-filters at environmentally relevant concentrations to aquatic biota are still less studied, especially in the case of invertebrates. This study was designed to evaluate the chronic toxicity of avobenzone (AVO), octocrylene (OCTO), and octinoxate (OCTI), three UV-filters which frequently occur in the aquatic environment, to the water flea (Daphnia magna) at an environmentally relevant concentration of 200 ng l[-1] in a 21-day exposure. Potential alterations in the growth, reproduction, and heart rate were continuously monitored during the treatments. Filtration rate, swimming, and the state of the antioxidant- and metabolic functions were evaluated at the end of exposures. Avobenzone significantly increased the reproductive output, heart rate, and filtration rate, while evoked a significant decrease of swimming behavior, and inhibited the activity of catalase (CAT) and glutathione S-transferase (GST) enzymes. The body size, reproduction, heart rate, and superoxide dismutase (SOD) activity were significantly increased whereas the activity of GST and CAT was significantly reduced by OCTO. OCTI significantly increased reproduction, heart rate, CAT and SOD activity but significantly decreased the swimming behavior. Our results confirmed that chronic exposure to organic UV-filters even at environmentally relevant concentrations affect basic physiological traits and cellular defense pathways in D. magna. Highlighting, our observations revealed previously unknown physiological changes (e.g., altered heart rate, filtration rate, SOD activity) caused by the investigated UV-filter compounds. Future research is to be aimed at investigating the mixture effects of these compounds and at the understanding of the potential cellular and molecular mechanisms underlying the changes induced.}, }
@article {pmid39485000, year = {2024}, author = {Kortekaas Krohn, I and Callewaert, C and Belasri, H and De Pessemier, B and Diez Lopez, C and Mortz, CG and O'Mahony, L and Pérez-Gordo, M and Sokolowska, M and Unger, Z and Untersmayr, E and Homey, B and Gomez-Casado, C}, title = {The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report.}, journal = {Allergy}, volume = {79}, number = {12}, pages = {3269-3284}, pmid = {39485000}, issn = {1398-9995}, support = {//European Academy of Allergy and Clinical Immunology/ ; }, mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology ; *Homeostasis ; *Life Style ; Skin Diseases/etiology/immunology/microbiology ; Environment ; }, abstract = {Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.}, }
@article {pmid39482383, year = {2024}, author = {Gaborieau, B and Vaysset, H and Tesson, F and Charachon, I and Dib, N and Bernier, J and Dequidt, T and Georjon, H and Clermont, O and Hersen, P and Debarbieux, L and Ricard, JD and Denamur, E and Bernheim, A}, title = {Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2847-2861}, pmid = {39482383}, issn = {2058-5276}, support = {R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; }, mesh = {*Host Specificity ; *Bacteriophages/genetics/physiology/classification ; *Genomics/methods ; Algorithms ; Escherichia coli/virology/genetics ; Phage Therapy ; Escherichia/genetics/virology ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions ; ROC Curve ; Host Microbial Interactions ; }, abstract = {Predicting bacteriophage infection of specific bacterial strains promises advancements in phage therapy and microbial ecology. Whether the dynamics of well-established phage-host model systems generalize to the wide diversity of microbes is currently unknown. Here we show that we could accurately predict the outcomes of phage-bacteria interactions at the strain level in natural isolates from the genus Escherichia using only genomic data (area under the receiver operating characteristic curve (AUROC) of 86%). We experimentally established a dataset of interactions between 403 diverse Escherichia strains and 96 phages. Most interactions are explained by adsorption factors as opposed to antiphage systems which play a marginal role. We trained predictive algorithms and pinpoint poorly predicted interactions to direct future research efforts. Finally, we established a pipeline to recommend tailored phage cocktails, demonstrating efficiency on 100 pathogenic E. coli isolates. This work provides quantitative insights into phage-host specificity and supports the use of predictive algorithms in phage therapy.}, }
@article {pmid39481794, year = {2024}, author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q}, title = {Methodology comparison of environmental sediment fungal community analysis.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120260}, doi = {10.1016/j.envres.2024.120260}, pmid = {39481794}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation &amp; purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; }, abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.}, }
@article {pmid39476778, year = {2025}, author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX}, title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122678}, doi = {10.1016/j.watres.2024.122678}, pmid = {39476778}, issn = {1879-2448}, mesh = {*Viral Proteins/genetics/metabolism ; Phylogeny ; *Viruses/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Water Purification ; Genetic Variation ; *Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/metabolism ; Models, Molecular ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sewage/virology ; }, abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.}, }
@article {pmid39472801, year = {2024}, author = {Valiei, A and Dickson, AM and Aminian-Dehkordi, J and Mofrad, MRK}, title = {Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {441}, pmid = {39472801}, issn = {1471-2180}, mesh = {*Bacteria/metabolism/classification/growth &amp; development/genetics ; *Biofilms/growth &amp; development ; Humans ; *Gastrointestinal Microbiome ; Microbial Interactions ; Bacterial Physiological Phenomena ; Models, Biological ; Kinetics ; Symbiosis ; Ecosystem ; Nutrients/metabolism ; }, abstract = {Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.}, }
@article {pmid39470240, year = {2024}, author = {Dumann, G and Rohland, O and Abdel-Glil, MY and Allen, RJ and Bauer, M and Busch, A}, title = {Draft genomes of the bile duct microbiome strains Klebsiella pneumoniae and Enterococcus lactis isolated from bilioenteric drainages with biofilm-forming abilities.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0020224}, pmid = {39470240}, issn = {2576-098X}, support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {We describe the genetic properties of two strains isolated from the elusive bile duct microbiome from solid organ transplant patients. Bacterial strains Enterococcus lactis (MS-STENT-08-E-001) and Klebsiella pneumoniae (MS-STENT-01-M-001) were isolated from the biofilms of bile duct catheters.}, }
@article {pmid39468827, year = {2024}, author = {Flores, JN and Lubin, JB and Silverman, MA}, title = {The case for microbial intervention at weaning.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2414798}, pmid = {39468827}, issn = {1949-0984}, support = {R01 DK133453/DK/NIDDK NIH HHS/United States ; T32 GM008562/GM/NIGMS NIH HHS/United States ; }, mesh = {*Weaning ; *Gastrointestinal Microbiome ; Humans ; Animals ; *Probiotics/administration &amp; dosage ; Host Microbial Interactions ; Diet ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Intestines/microbiology/immunology ; }, abstract = {Weaning, the transition from a milk-based diet to solid food, coincides with the most significant shift in gut microbiome composition in the lifetime of most mammals. Notably, this period also marks a "window of opportunity" where key components of the immune system develop, and host-microbe interactions shape long-term immune homeostasis thereby influencing the risk of autoimmune and inflammatory diseases. This review provides a comprehensive analysis of the changes in nutrition, microbiota, and host physiology that occur during weaning. We explore how these weaning-associated processes differ across species, lifestyles, and regions of the intestine. Using prinicples of microbial ecology, we propose that the weaning transition is an optimal period for microbiome-targeted therapeutic interventions. Additionally, we suggest that replicating features of the weaning microbiome in adults could promote the successful engraftment of probiotics. Finally, we highlight key research areas that could deepen our understanding of the complex relationships between diet, commensal microbes, and the host, informing the development of more effective microbial therapies.}, }
@article {pmid39468208, year = {2024}, author = {Ilicic, D and Woodhouse, J and Karsten, U and Schimani, K and Zimmermann, J and Grossart, HP}, title = {Chytrid fungi infecting Arctic microphytobenthic communities under varying salinity conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25821}, pmid = {39468208}, issn = {2045-2322}, mesh = {Arctic Regions ; *Salinity ; *Chytridiomycota/genetics/isolation &amp; purification ; Diatoms/microbiology/genetics ; Mycobiome ; Ecosystem ; Biodiversity ; Food Chain ; }, abstract = {This study aimed to investigate the presence and diversity of fungal parasites in Arctic coastal microphytobenthic communities. These communities represent a key component in the functioning of Arctic trophic food webs. Fungal parasites, particularly Chytridiomycota (chytrids), play significant roles by controlling microalgal bloom events, impacting genetic diversity, modifying microbial interactions, and accelerating nutrient and energy transfer to higher trophic levels. In the context of rapid Arctic warming and increased glacier meltwater, which significantly affects these communities, we used high-throughput sequencing to explore fungal community composition. Our results show that chytrids dominate fungal communities in Arctic benthic habitats and that the overall fungal diversity is primarily influenced by the salinity gradient. Chytrid representation is positively correlated with the presence of potential benthic diatom (Surirella, Nitzschia, Navicula) and green algae (Ulvophyceae) hosts, while microscopic observations provide further evidence for the presence of active chytrid infections.}, }
@article {pmid39467902, year = {2024}, author = {Awais, M and Xiang, Y and Shah, N and Bilal, H and Yang, D and Hu, H and Li, T and Ji, X and Li, H}, title = {Unraveling the Role of Contaminants Reshaping the Microflora in Zea mays Seeds from Heavy Metal-Contaminated and Pristine Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {133}, pmid = {39467902}, issn = {1432-184X}, support = {KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; 42267059//National Natural Science Foundation of China/ ; SKLEG2023216//State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences/ ; }, mesh = {*Zea mays/microbiology ; *Metals, Heavy/analysis ; *Seeds/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; China ; *Soil Pollutants/analysis ; *Fungi/genetics/classification/isolation &amp; purification/drug effects ; *Microbiota/drug effects ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.}, }
@article {pmid39460615, year = {2024}, author = {Wen, J and Zhang, H and Chu, D and Chen, X and Feng, J and Wang, Y and Liu, G and Zhang, Y and Li, Y and Ning, K}, title = {Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {12817-12830}, pmid = {39460615}, issn = {1362-4962}, support = {32071465//National Natural Science Foundation of China/ ; 2023YFA1800900//National Key Research and Development Program of China/ ; }, mesh = {*Promoter Regions, Genetic ; *Deep Learning ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Phylogeny ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Metagenome/genetics ; Biofilms ; }, abstract = {Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.}, }
@article {pmid39454273, year = {2025}, author = {Xun, F and Feng, M and Zhao, C and Luo, W and Han, X and Ci, Z and Yin, Y and Wang, R and Wu, QL and Grossart, HP and Xing, P}, title = {Epilimnetic oligotrophication increases contribution of oxic methane production to atmospheric methane flux from stratified lakes.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122602}, doi = {10.1016/j.watres.2024.122602}, pmid = {39454273}, issn = {1879-2448}, mesh = {*Methane/metabolism ; *Lakes/microbiology ; Atmosphere ; Phosphorus/metabolism ; }, abstract = {Although considerable attention has been paid to the effects of eutrophication on aquatic methane (CH4) emissions to the atmosphere, the ecosystem-level effects of oligotrophication/re-oligotrophication on aquatic CH4 production and subsequent ecological responses remain to be elucidated. It has been hypothesized that dissolved inorganic phosphorus (DIP)-deficient conditions drive the ecosystem to utilize poorly bioavailable organic phosphorus for biomass formation, thereby generating CH4 as a by-product. To test this hypothesis, a mass balance approach was used to estimate in situ oxic methane production (OMP) in an oligotrophic, deep Lake Fuxian. The isotopic signature of dissolved [13]C-CH4, the potential substrates for OMP, and the phnJ/phnD genes associated with microbial demethylation of organic phosphorus compounds were analyzed. Our results indicate that CH4 accumulation was maximal in the surface mixed layer (SML, i.e., Epilimnion) during lake stratification, and ∼ 86 % of the total CH4 flux to the atmosphere was due to OMP. Decomposition of methylphosphonate (MPn) by Alphaproteobacteria (genera Sphingomonas and Mesorhizobium) contributed significantly to OMP. Furthermore, water temperature (Temp), chlorophyll a (Chla), and DIP were the most critical predictors of water OMP potential. Meta-analysis of currently available global data showed that OMP had a negative exponential distribution with DIP (OMP = 2.0 e[-0.71DIP], R[2] = 0.57, p < 0.05). DIP concentrations below a threshold of 3.40 ∼ 9.35 μg P L[-1] triggered OMP processes and increased the atmospheric CH4 emissions. Under future warming scenarios, stratification and catchment management induced oligotrophication or re-oligotrophication may systematically affect the biogeochemical cycling of phosphorus and the OMP contribution to CH4 emission in stratified lakes.}, }
@article {pmid39452361, year = {2024}, author = {Kiewra, D and Dyczko, D and Žákovská, A and Nejezchlebova, H}, title = {Prevalence of Borrelia and Rickettsia in Ixodes ricinus from Chosen Urban and Protected Areas in Poland and the Czech Republic.}, journal = {Insects}, volume = {15}, number = {10}, pages = {}, pmid = {39452361}, issn = {2075-4450}, abstract = {(1) Background: Ixodes ricinus is responsible for the spreading of medically important pathogens. Monitoring the level of tick infection in various areas is essential for determining the potential tick-born risk. This study aimed to detect Borrelia spp. and Rickettsia spp. in I. ricinus ticks collected in urban and protected areas both in Poland and the Czech Republic. (2) Methods: Ticks were collected by flagging in the years 2016-2017. Borrelia spp. was detected using nested PCR targeting the flaB gene and Rickettsia spp. using nested PCR targeting gltA. (3) Results: In total, DNA of Borrelia spp. was detected in 25.9% of samples. Ticks collected in Poland were more infected compared to the Czech Republic and ticks collected in protected areas were more infected with Borrelia spp. than ticks collected in urban areas. The RFLP analysis showed the occurrence of B. afzelii and B. garinii in both countries, and additionally B. valaisiana, B. burgdorferi s.s., and B. miyamotoi in Poland. Rickettsia spp. was detected in 17.4% of I. ricinus, with comparable infection level in both countries; however, regional differences were observed. (4) Conclusion: The regional differences in Borrelia spp. and Rickettsia spp. prevalence in I. ricinus indicate the complexity of factors influencing the level of infection and underline the need for adaptation public health surveillance strategies in each region.}, }
@article {pmid39450335, year = {2024}, author = {Hodžić, A and Veinović, G and Alić, A and Seki, D and Kunert, M and Nikolov, G and Sukara, R and Šupić, J and Tomanović, S and Berry, D}, title = {A metalloprotease secreted by an environmentally acquired gut bacterium hinders Borrelia afzelii colonization in Ixodes ricinus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1476266}, pmid = {39450335}, issn = {2235-2988}, mesh = {*Ixodes/microbiology ; Animals ; *Borrelia burgdorferi Group/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism ; Bacillus cereus/enzymology/metabolism/genetics ; Lyme Disease/microbiology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Although the importance of the microbiome in the context of tick biology and vector competence has recently come into a broader research focus, the field is still in its infancy and the complex ecological interactions between the tick residential bacteria and pathogens are obscure. Here, we show that an environmentally acquired gut bacterium has the potential to impair Borrelia afzelii colonization within the tick vector through a secreted metalloprotease. Oral introduction of either Bacillus cereus LTG-1 isolate or its purified enhancin (BcEnhancin) protein significantly reduces B. afzelii burden in the guts of Ixodes ricinus ticks. This effect is attributed to the ability of BcEnhancin to degrade a glycan-rich peritrophic matrix (PM), which is a gut protective barrier essential for Borrelia survival. Our study highlights the importance of the gut microbiome in determining tick vector competence and provides a deeper mechanistic insight into the complex network of interactions between Borrelia, the tick, and the tick microbiome.}, }
@article {pmid39450162, year = {2024}, author = {Nenciarini, S and Rivero, D and Ciccione, A and Amoriello, R and Cerasuolo, B and Pallecchi, M and Bartolucci, GL and Ballerini, C and Cavalieri, D}, title = {Impact of cooperative or competitive dynamics between the yeast Saccharomyces cerevisiae and lactobacilli on the immune response of the host.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1399842}, pmid = {39450162}, issn = {1664-3224}, mesh = {Humans ; *Saccharomyces cerevisiae/immunology ; *Gastrointestinal Microbiome/immunology ; *Lactobacillus/immunology ; Probiotics ; Animals ; Microbial Interactions/immunology ; Dysbiosis/immunology ; }, abstract = {Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between human- and fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies.}, }
@article {pmid39449043, year = {2024}, author = {Zhai, X and Gobbi, A and Kot, W and Krych, L and Nielsen, DS and Deng, L}, title = {A single-stranded based library preparation method for virome characterization.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {219}, pmid = {39449043}, issn = {2049-2618}, mesh = {*Virome/genetics ; *Genome, Viral/genetics ; *Gastrointestinal Microbiome/genetics ; *Gene Library ; Humans ; DNA, Viral/genetics ; DNA, Single-Stranded/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.<br><br>RESULTS: We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA&#x2009;+&#x2009;Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.<br><br>CONCLUSION: We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.}, }
@article {pmid39448159, year = {2025}, author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M}, title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104649}, doi = {10.1016/j.fm.2024.104649}, pmid = {39448159}, issn = {1095-9998}, mesh = {*Listeria monocytogenes/genetics/isolation &amp; purification/growth &amp; development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation &amp; purification/growth &amp; development/classification ; Food Contamination/analysis ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.}, }
@article {pmid39446706, year = {2024}, author = {Shinfuku, MS and Domeignoz-Horta, LA and Choudoir, MJ and Frey, SD and Mitchell, MF and Ranjan, R and DeAngelis, KM}, title = {Seasonal effects of long-term warming on ecosystem function and bacterial diversity.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0311364}, pmid = {39446706}, issn = {1932-6203}, mesh = {*Seasons ; *Soil Microbiology ; *Biodiversity ; *Bacteria/classification/genetics ; *Ecosystem ; *Climate Change ; Soil/chemistry ; Global Warming ; }, abstract = {Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.}, }
@article {pmid39445507, year = {2024}, author = {Liu, L and Zhang, X and Schorn, S and Doda, T and Kang, M and Bouffard, D and Kirillin, G and Milucka, J and Shi, X and Grossart, HP}, title = {Strong Subseasonal Variability of Oxic Methane Production Challenges Methane Budgeting in Freshwater Lakes.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {44}, pages = {19690-19701}, doi = {10.1021/acs.est.4c07413}, pmid = {39445507}, issn = {1520-5851}, mesh = {*Methane ; *Lakes ; Seasons ; Environmental Monitoring ; Fresh Water ; }, abstract = {Methane (CH4) accumulation in the well-oxygenated lake epilimnion enhances the diffusive atmospheric CH4 emission. Both lateral transport and in situ oxic methane production (OMP) have been suggested as potential sources. While the latter has been recently supported by increasing evidence, quantifying the exact contribution of OMP to atmospheric emissions remains challenging. Based on a large high-resolution field data set collected during 2019-2020 in the deep stratified Lake Stechlin and on three-dimensional hydrodynamic modeling, we improved existing CH4 budgets by resolving each component of the mass balance model at a seasonal scale and therefore better constrained the residual OMP. All terms in our model showed a large temporal variability at scales from intraday to seasonal, and the modeled OMP was most sensitive to the surface CH4 flux estimates. Future efforts are needed to reduce the uncertainties in estimating OMP rates using the mass balance approach by increasing the frequency of atmospheric CH4 flux measurements.}, }
@article {pmid39442306, year = {2024}, author = {Wen, X and Xiang, L and Harindintwali, JD and Wang, Y and He, C and Fu, Y and Wei, S and Hashsham, SA and Jiang, J and Jiang, X and Wang, F}, title = {Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136224}, doi = {10.1016/j.jhazmat.2024.136224}, pmid = {39442306}, issn = {1873-3336}, mesh = {*Atrazine/toxicity/metabolism ; *Glycine max/metabolism/drug effects/growth &amp; development/microbiology ; *Herbicides/toxicity/metabolism ; *Plant Leaves/metabolism/drug effects ; *Biodegradation, Environmental ; Soil Pollutants/toxicity/metabolism ; Chlorophyll/metabolism ; }, abstract = {Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.}, }
@article {pmid39440978, year = {2024}, author = {Soto Ocaña, J and Friedman, ES and Keenan, O and Bayard, NU and Ford, E and Tanes, C and Munneke, MJ and Beavers, WN and Skaar, EP and Bittinger, K and Zemel, BS and Wu, GD and Zackular, JP}, title = {Metal availability shapes early life microbial ecology and community succession.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0153424}, pmid = {39440978}, issn = {2150-7511}, support = {R01DK107565, P30DK050306//HHS | National Institutes of Health (NIH)/ ; R35GM138369//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01DK107565//HHS | National Institutes of Health (NIH)/ ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Metals/metabolism ; *Leukocyte L1 Antigen Complex/metabolism/analysis ; Bacteria/metabolism/classification/genetics ; Breast Feeding ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Infant, Newborn ; Microbiota ; Infant Formula ; }, abstract = {The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.}, }
@article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, }
@article {pmid39437908, year = {2024}, author = {Yang, X and Chen, N and Yu, H and Liu, X and Feng, Y and Xing, D and Tian, Y}, title = {Applying machine learning and genetic algorithms accelerated for optimizing ethanol production.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177027}, doi = {10.1016/j.scitotenv.2024.177027}, pmid = {39437908}, issn = {1879-1026}, mesh = {*Ethanol/metabolism ; *Machine Learning ; *Algorithms ; Zea mays ; Fermentation ; Neural Networks, Computer ; Biofuels ; }, abstract = {Corn straws can produce bioethanol via simultaneous saccharification and co-fermentation (SSCF). However, identifying optimal combinations of operating parameters from numerous possibilities through a cost-effective strategy to improve SSCF efficiency and yield remains challenging. The eXtreme Gradient Boost (XGB) and deep neural network (DNN) models were constructed to accurately predict ethanol yield from only five input variables, achieving >83 % accuracy. Subsequently, the XGB and the DNN models were merged with the genetic algorithm (GA) as the new optimization strategies. Experimental validation showed that the new strategy optimize the efficiency and yield of the SSCF ethanol production system quickly and accurately. Moreover, the potential optimization mechanism was investigated through the comprehensive interpretability analysis for XGB and the microbial ecology analysis. Enzyme Solution Volume (61.7 %) dominated, followed by time (12.9 %), substrate concentration (10.4 %), temperature (7.7 %), and inoculum volume (7.3 %). This efficient and accurate algorithm design strategy can significantly reduce the time required to optimize biochemical systems.}, }
@article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, }
@article {pmid39436933, year = {2024}, author = {Di Nezio, F and Ong, ILH and Riedel, R and Goshal, A and Dhar, J and Roman, S and Storelli, N and Sengupta, A}, title = {Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310265}, pmid = {39436933}, issn = {1932-6203}, mesh = {*Lakes/microbiology ; *Phenotype ; *Adaptation, Physiological ; Chromatiaceae/physiology ; Microscopy, Atomic Force ; }, abstract = {Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.}, }
@article {pmid39436423, year = {2024}, author = {Hirota, A and Kouduka, M and Fukuda, A and Miyakawa, K and Sakuma, K and Ozaki, Y and Ishii, E and Suzuki, Y}, title = {Biofilm Formation on Excavation Damaged Zone Fractures in Deep Neogene Sedimentary Rock.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {132}, pmid = {39436423}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Phylogeny ; Groundwater/microbiology ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Gammaproteobacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; }, abstract = {Deep underground galleries are used to access the deep biosphere in addition to mining and other engineering applications, such as geological disposal of radioactive waste. Fracture networks developed in the excavation damaged zone (EDZ) are concerned with accelerating mass transport, where microbial colonization might be possible due to the availability of space and nutrients. In this study, microbial biofilms at EDZ fractures were investigated by drilling from a 350-m-deep gallery and subsequent borehole logging at the Horonobe Underground Research Laboratory (URL). By using microscopic and spectroscopic techniques, the dense colonization of microbial cells was demonstrated at the surfaces of the EDZ fractures with high hydraulic conductivity. 16S rRNA gene sequence analysis revealed the dominance of gammaproteobacterial lineages, the cultivated members of which are aerobic methanotrophs. The near-complete genomes from Horonobe groundwater, affiliated with the methanotrophic lineages, were fully equipped with genes involved in aerobic methanotrophy. Although the mediation of aerobic methanotrophy remains to be demonstrated, microbial O2 production was supported by the presence of genes in the near-complete genomes, such as catalase and superoxide dismutase that produce O2 from reactive oxygen species and a nitric oxide reductase gene with the substitutions of amino acids in motifs. It is concluded that the EDZ fractures provide energetically favorable subsurface habitats for microorganisms.}, }
@article {pmid39435521, year = {2024}, author = {Muratore, TJ and Knorr, MA and Simpson, MJ and Stephens, RB and Phillips, RP and Frey, SD}, title = {Response of Root Respiration to Warming and Nitrogen Addition Depends on Tree Species.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17530}, doi = {10.1111/gcb.17530}, pmid = {39435521}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; 2106096//National Science Foundation/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; //Natural Sciences and Engineering Research Council (NSERC) of Canada/ ; }, mesh = {*Plant Roots/metabolism/growth &amp; development ; *Nitrogen/metabolism ; *Acer/physiology/metabolism/growth &amp; development ; *Quercus/physiology/metabolism ; Soil/chemistry ; Global Warming ; Biomass ; Carbon Dioxide/metabolism ; Trees/growth &amp; development/metabolism/physiology ; }, abstract = {Roots contribute a large fraction of CO2 efflux from soils, yet the extent to which global change factors affect root-derived fluxes is poorly understood. We investigated how red maple (Acer rubrum) and red oak (Quercus rubra) root biomass and respiration respond to long-term (15 years) soil warming, nitrogen addition, or their combination in a temperate forest. We found that ecosystem root respiration was decreased by 40% under both single-factor treatments (nitrogen addition or warming) but not under their combination (heated × nitrogen). This response was driven by the reduction of mass-specific root respiration under warming and a reduction in maple root biomass in both single-factor treatments. Mass-specific root respiration rates for both species acclimated to soil warming, resulting in a 43% reduction, but were not affected by N addition or the combined heated × N treatment. Notably, the addition of nitrogen to warmed soils alleviated thermal acclimation and returned mass-specific respiration rates to control levels. Oak roots contributed disproportionately to ecosystem root respiration despite the decrease in respiration rates as their biomass was maintained or enhanced under warming and nitrogen addition. In contrast, maple root respiration rates were consistently higher than oak, and this difference became critical in the heated × nitrogen treatment, where maple root biomass increased, contributing significantly more CO2 relative to single-factor treatments. Our findings highlight the importance of accounting for the root component of respiration when assessing soil carbon loss in response to global change and demonstrate that combining warming and N addition produces effects that cannot be predicted by studying these factors in isolation.}, }
@article {pmid39435438, year = {2024}, author = {Michalska-Smith, M and Schlatter, DC and Pombubpa, N and Castle, SC and Grandy, AS and Borer, ET and Seabloom, EW and Kinkel, LL}, title = {Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452534}, pmid = {39435438}, issn = {1664-302X}, abstract = {Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.}, }
@article {pmid39435044, year = {2024}, author = {Gruseck, R and Palatinszky, M and Wagner, M and Hofmann, T and Zumstein, M}, title = {Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis.}, journal = {MethodsX}, volume = {13}, number = {}, pages = {102972}, pmid = {39435044}, issn = {2215-0161}, abstract = {The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection. We adapted this analytical approach using benzoin as the derivatization agent to sensitively and selectively quantify guanidine in environmental samples, thereby facilitating future research on the biological and environmental roles of guanidine. This adapted method was applied to human urine, raw wastewater, and biological growth media as relevant matrices. Our liquid chromatography-tandem mass spectrometry analyses of the derivatized solutions identified a different major derivatization product than previously reported. This product was consistently observed across various substrates (guanidine, methylguanidine, and arginine) and derivatization agents (benzoin and anisoin). We observed a constant background signal, restricting our analyses to a lower limit of quantification of 50 nM. Despite this limitation, our method allowed for the quantification of guanidine concentrations significantly lower than those reported in previous derivatization-based studies.•Selective and sensitive detection of guanidine by LC-MS.•Method development and validation for robust detection of guanidine in environmental samples.•Reduction of sample preparation steps and reduced usage of toxic chemicals compared to previous methods.}, }
@article {pmid39432984, year = {2024}, author = {Sun, Y and Wang, N and Zhong, X and Xu, G}, title = {Can microplastics variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt A}, pages = {117148}, doi = {10.1016/j.marpolbul.2024.117148}, pmid = {39432984}, issn = {1879-3363}, mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Biodiversity ; Animals ; Aquatic Organisms ; }, abstract = {In recent years, microplastics have become a global environmental hot topic of concern. To explore the effects of different concentrations of microplastics on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems. Periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1], identification and enumeration were conducted on days 3, 5, 7, 10, 14 and 21. The results showed that the colonization dynamics were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. However, a notable decline in maximum species richness and abundance was observed in the high concentrations of microplastic, along with significant deviations in colonization patterns from the control group (0 mg l[-1]). Therefore, it is suggested that the colonization dynamics of periphytic protozoa can serve as a bioindicator for assessing microplastic concentrations in marine environments.}, }
@article {pmid39432094, year = {2024}, author = {Shafana Farveen, M and Narayanan, R}, title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.}, journal = {Archives of microbiology}, volume = {206}, number = {11}, pages = {441}, pmid = {39432094}, issn = {1432-072X}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; }, abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.}, }
@article {pmid39431865, year = {2024}, author = {Daly, SE and Feng, J and Daeschel, D and Kovac, J and Snyder, AB}, title = {The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0062024}, pmid = {39431865}, issn = {2379-5077}, support = {2022-67017-36289//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics/classification ; Food Microbiology ; Food Handling ; Dairying ; Dairy Products/microbiology ; }, abstract = {Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm[2]) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.}, }
@article {pmid39430784, year = {2024}, author = {Li, X and Wang, Q and Wu, F and Ye, Z and Li, Y}, title = {Association between advanced lung cancer inflammation index and chronic kidney disease: a cross-sectional study.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1430471}, pmid = {39430784}, issn = {2296-861X}, abstract = {BACKGROUND: Chronic kidney disease (CKD) is one of the common chronic diseases, and malnutrition and inflammation play a key role in the development of CKD. The advanced lung cancer inflammation index (ALI) is a novel index of nutrition and inflammation, and its association with CKD has not yet been clarified. The aim of this study was to explore the potential association between ALI and CKD.<br><br>METHODS: We conducted a cross-sectional survey using data extracted from the National Health and Nutrition Examination Survey (NHANES, 2003-2018). Weighted multivariate logistic regression was used to assess the association between ALI and CKD, and smoothed curve fitting and threshold effect analyses were used to describe the nonlinear association between ALI and CKD. Subgroup analyses were performed to further assess the influence of other covariates on the relationship between ALI and CKD.<br><br>RESULTS: A total of 39,469 adult participants were included in the study, of whom 7,204 (18.25%) were diagnosed with CKD. After adjusting for multiple confounders, we found a significant negative correlation between ALI and CKD (OR&#x2009;=&#x2009;0.93; 95%CI, 0.91-0.95; p&#x2009;<&#x2009;0.0001). The risk of CKD tended to decrease with increasing quartiles of ALI. Smoothed curve fitting showed an L-shaped negative correlation between ALI and CKD. Threshold analysis showed a saturation effect of ALI at the inflection point of 55.09. Subgroup analyses and interaction tests showed that this negative association was maintained across age, sex, race, BMI, diabetes, hypertension, cardiovascular disease, and cancer subgroups (P for interaction >0.05).<br><br>CONCLUSION: Our findings suggest a significant correlation between ALI and CKD in the US adult population. However, more large-scale prospective studies are still needed to further confirm our findings.}, }
@article {pmid39430052, year = {2025}, author = {Qin, K and Wang, Q and Qing, J and Li, Y and Gong, H and Zha, Z and Zhou, B and Li, Y}, title = {Analysis of mutations in Chinese patients with polycystic kidney disease by targeted exome sequencing.}, journal = {Genes &amp; diseases}, volume = {12}, number = {1}, pages = {101246}, pmid = {39430052}, issn = {2352-3042}, }
@article {pmid39425011, year = {2024}, author = {Sánchez, V and Baumann, A and Kromm, F and Yergaliyev, T and Brandt, A and Scholda, J and Kopp, F and Camarinha-Silva, A and Bergheim, I}, title = {Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD).}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {30}, number = {1}, pages = {181}, pmid = {39425011}, issn = {1528-3658}, mesh = {Animals ; *Choline/administration &amp; dosage/metabolism ; *Liver Diseases, Alcoholic/metabolism/etiology/prevention &amp; control/pathology/drug therapy ; *Dietary Supplements ; Mice ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects/pathology ; Administration, Oral ; Permeability ; Ethanol/adverse effects ; Disease Models, Animal ; }, abstract = {BACKGROUND: Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.<br><br>METHODS: Female C57BL/6&#xa0;J mice (n&#x2009;=&#x2009;8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol)&#x2009;&#xb1;&#x2009;2.7&#xa0;g choline/kg diet for 29&#xa0;days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.<br><br>RESULTS: ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.<br><br>CONCLUSION: Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.}, }
@article {pmid39423562, year = {2024}, author = {Dal Bello, M and Abreu, CI}, title = {Temperature structuring of microbial communities on a global scale.}, journal = {Current opinion in microbiology}, volume = {82}, number = {}, pages = {102558}, pmid = {39423562}, issn = {1879-0364}, support = {F32 GM145148/GM/NIGMS NIH HHS/United States ; }, mesh = {*Temperature ; *Microbiota ; *Bacteria/metabolism/genetics/classification/growth &amp; development ; Bacterial Physiological Phenomena ; Ecosystem ; }, abstract = {Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.}, }
@article {pmid39423289, year = {2024}, author = {Steensen, K and Séneca, J and Bartlau, N and Yu, XA and Hussain, FA and Polz, MF}, title = {Tailless and filamentous prophages are predominant in marine Vibrio.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39423289}, issn = {1751-7370}, support = {//Life Science Compute Cluster of the University of Vienna/ ; 572792//Simons Foundation/ ; //Austrian Science Fund/ ; }, mesh = {*Prophages/genetics/isolation &amp; purification ; *Vibrio/virology/genetics ; *Genome, Viral ; Phylogeny ; Genomics ; }, abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.}, }
@article {pmid39419992, year = {2024}, author = {Mei, S and Wang, M and Salles, JF and Hackl, T}, title = {Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1140}, pmid = {39419992}, issn = {2052-4463}, support = {[2020]596//China Scholarship Council (CSC)/ ; }, mesh = {*Rhizosphere ; *Pseudomonas/genetics ; *Soil Microbiology ; *Wetlands ; *Genome, Bacterial ; Artemisia/genetics/microbiology ; Biodiversity ; }, abstract = {Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas' role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.}, }
@article {pmid39419884, year = {2024}, author = {Mohammed, FA and Abu-Hussien, SH and Dougdoug, NKE and Koutb, N and Korayem, AS}, title = {Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {131}, pmid = {39419884}, issn = {1432-184X}, mesh = {*Solanum tuberosum/virology/microbiology ; *Streptomyces/isolation &amp; purification/physiology/genetics ; *Potyvirus/physiology ; *Plant Diseases/virology/microbiology ; *Disease Resistance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.}, }
@article {pmid39419230, year = {2024}, author = {Siebert, C and Ionescu, D and Mallast, U and Merchel, S and Merkel, B and Möller, P and Pavetich, S and Pohl, T and Rödiger, T and Yechieli, Y}, title = {A new type of submarine chimneys built of halite.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176752}, doi = {10.1016/j.scitotenv.2024.176752}, pmid = {39419230}, issn = {1879-1026}, abstract = {In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.}, }
@article {pmid39419211, year = {2024}, author = {Santos-Silva, L and Roque, WF and de Moura, JM and Mello, IS and de Carvalho, LAL and Pinheiro, DG and Bouzan, RS and Brescovit, AD and de Andrade, RLT and da Silva, GF and Battirola, LD and Soares, MA}, title = {Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176915}, doi = {10.1016/j.scitotenv.2024.176915}, pmid = {39419211}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; Animals ; *Bacteria/drug effects/classification ; *Microbiota/drug effects ; Arthropods/drug effects ; Soil Microbiology ; Cadmium/toxicity ; Brazil ; Mercury/toxicity/metabolism ; Soil/chemistry ; Environmental Monitoring ; Rainforest ; }, abstract = {Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg[-1]), mercury (35 mg.kg[-1]) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.}, }
@article {pmid39419002, year = {2024}, author = {Meroz, N and Livny, T and Toledano, G and Sorokin, Y and Tovi, N and Friedman, J}, title = {Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species.}, journal = {Cell systems}, volume = {15}, number = {10}, pages = {930-940.e5}, doi = {10.1016/j.cels.2024.09.007}, pmid = {39419002}, issn = {2405-4720}, mesh = {*Biological Evolution ; Microbial Interactions/physiology ; Adaptation, Physiological ; Mutation ; Bacteria/genetics/metabolism ; Evolution, Molecular ; }, abstract = {Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39418776, year = {2024}, author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M}, title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.}, journal = {Multiple sclerosis and related disorders}, volume = {92}, number = {}, pages = {105936}, doi = {10.1016/j.msard.2024.105936}, pmid = {39418776}, issn = {2211-0356}, mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.<br><br>METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.<br><br>RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the &#x3b1;-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.<br><br>CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.}, }
@article {pmid39418385, year = {2024}, author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M}, title = {Mechanism of bacterial predation via ixotrophy.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6719}, pages = {eadp0614}, doi = {10.1126/science.adp0614}, pmid = {39418385}, issn = {1095-9203}, mesh = {*Bacterial Adhesion ; *Bacteroidetes/physiology/ultrastructure ; Cryoelectron Microscopy ; Single-Cell Analysis ; *Type VI Secretion Systems/metabolism/ultrastructure ; *Vibrio/physiology/ultrastructure ; *Flagella/ultrastructure ; }, abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.}, }
@article {pmid39417884, year = {2024}, author = {Mircea, C and Rusu, I and Levei, EA and Cristea, A and Gridan, IM and Zety, AV and Banciu, HL}, title = {The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {130}, pmid = {39417884}, issn = {1432-184X}, support = {PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0634//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; }, mesh = {*Lakes/microbiology ; Romania ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; *Salinity ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Geologic Sediments/microbiology ; Soil Microbiology ; DNA, Fungal/genetics ; Phylogeny ; }, abstract = {Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.}, }
@article {pmid39415203, year = {2024}, author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH}, title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {198}, pmid = {39415203}, issn = {2049-2618}, support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; }, mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; }, abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.<br><br>RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.<br><br>CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.}, }
@article {pmid39414684, year = {2024}, author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC}, title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {129}, pmid = {39414684}, issn = {1432-184X}, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; }, abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.}, }
@article {pmid39411441, year = {2024}, author = {Pardo-Esté, C and Cortés, J and Castro-Severyn, J and Pérez, V and Henriquez-Aedo, K and Cuadros, F and Yañez, C and Cuadros-Orellana, S and Dorador, C and Molina, V and Eissler, Y and Paquis, P and Jeffrey, WH and Pozo, P and Pérez, PA and Hengst, MB}, title = {Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1477458}, pmid = {39411441}, issn = {1664-302X}, abstract = {Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.}, }
@article {pmid39411429, year = {2024}, author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R}, title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479158}, pmid = {39411429}, issn = {1664-302X}, abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&amp;ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.<br><br>METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.<br><br>RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.}, }
@article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, }
@article {pmid39406893, year = {2025}, author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C}, title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {3}, pages = {162-177}, pmid = {39406893}, issn = {1740-1534}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Akkermansia/physiology/genetics/classification ; Probiotics/therapeutic use ; *Host Microbial Interactions ; *Verrucomicrobia/physiology/genetics/classification ; Animals ; Intestinal Mucosa/microbiology ; Phylogeny ; Mucins/metabolism ; }, abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.}, }
@article {pmid39406702, year = {2024}, author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N}, title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8783}, pmid = {39406702}, issn = {2041-1723}, support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; }, mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; }, abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.}, }
@article {pmid39404095, year = {2024}, author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Gut microbiota carbon and sulfur metabolisms support Salmonella infections.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404095}, issn = {1751-7370}, support = {T32GM132057//NIH Predoctoral Training/ ; DE-SC0021350//DOE/ ; R01AI143288//NIH NIAID/ ; R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Sulfur/metabolism ; *Carbon/metabolism ; *Salmonella typhimurium/genetics ; Feces/microbiology ; Mice, Inbred C57BL ; Salmonella Infections/microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Female ; }, abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.}, }
@article {pmid39404077, year = {2024}, author = {Ellington, AJ and Walters, K and Christner, BC and Fox, S and Bonfantine, K and Walker, C and Lampman, P and Vuono, DC and Strickland, M and Lambert, K and Kobziar, LN}, title = {Dispersal of microbes from grassland fire smoke to soils.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404077}, issn = {1751-7370}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; 2039531//National Science Foundation/ ; P20GM103408//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, mesh = {*Soil Microbiology ; *Smoke ; *Grassland ; *Soil/chemistry ; Bacteria/classification/isolation &amp; purification/radiation effects ; Microbiota ; Wildfires ; Fires ; Biomass ; Poaceae/microbiology ; Carbon/analysis/metabolism ; }, abstract = {Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.}, }
@article {pmid39402079, year = {2024}, author = {Ashraf, H and Dikarlo, P and Masia, A and Zarbo, IR and Solla, P and Ijaz, UZ and Sechi, LA}, title = {Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24027}, pmid = {39402079}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification ; *Paratuberculosis/microbiology ; *Multiple Sclerosis/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Middle Aged ; }, abstract = {The microbial ecology of Mycobacterium avium subspecies paratuberculosis infections (MAP) within the context of Multiple Sclerosis (MS) is largely an unexplored topic in the literature. Thus, we have characterized the compositional and predicted functional differences of the gut microbiome between MS patients with MAP (MAP+) and without (MAP-) infection. This was done in the context of exposome differences (through self-reported filled questionnaires), principally in anthropometric and sociodemographic patterns to gain an understanding of the gut microbiome dynamics. 16S rRNA microbiome profiling of faecal samples (n = 69) was performed for four groups, which differed by disease and MAP infection: healthy cohort (HC) MAP-; HC MAP+ ; MS MAP-; and MS MAP+ . Using a dynamic strategy, with MAP infection and time of sampling as occupancy models, we have recovered the core microbiome for both HC and MS individuals. Additional application of neutral modeling suggests key genera that are under selection pressure by the hosts. These include members of the phyla Actinobacteriota, Bacteroidota, and Firmicutes. As several subjects provided multiple samples, a Quasi Conditional Association Test that incorporates paired-nature of samples found major differences in Archaea. To consolidate treatment groups, confounders, microbiome, and the disease outcome parameters, a mediation analysis is performed for MS cohort. This highlighted certain genera i.e., Sutterella, Akkermansia, Bacteriodes, Gastranaerophilales, Alistipes, Balutia, Faecalibacterium, Lachnospiraceae, Anaerostipes, Ruminococcaceae, Eggerthellaceae and Clostridia-UCG-014 having mediatory effect using disease duration as an outcome and MAP infection as a treatment group. Our analyses indicate that the gut microbiome may be an important target for dietary and lifestyle intervention in MS patients with and without MAP infection.}, }
@article {pmid39401449, year = {2024}, author = {Ahmerkamp, S and Pacherres, CO and Mosshammer, M and Godefroid, M and Wind-Hansen, M and Kuypers, M and Behrendt, L and Koren, K and Kühl, M}, title = {Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling.}, journal = {ACS sensors}, volume = {9}, number = {10}, pages = {5531-5540}, pmid = {39401449}, issn = {2379-3694}, mesh = {*Luminescent Measurements/methods ; Luminescence ; Oxygen/chemistry ; }, abstract = {Optode-based chemical imaging is a rapidly evolving field that has substantially enhanced our understanding of the role of microenvironments and chemical gradients in biogeochemistry, microbial ecology, and biomedical sciences. Progress in sensor chemistry has resulted in a broadened spectrum of analytes, alongside enhancements in sensor performance (e.g., sensitivity, brightness, and photostability). However, existing imaging techniques are often costly, challenging to implement, and limited in their recording speed. Here we use the "frame-straddling" technique, originally developed for particle image velocimetry for imaging the O2-dependent, integrated luminescence decay of optical O2 sensor materials. The method synchronizes short excitation pulses and camera exposures to capture two frames at varying brightness, where the first excitation pulse occurs at the end of the exposure of the first frame and the second excitation pulse at the beginning of the second frame. Here the first frame truncates the luminescence decay, whereas the second frame fully captures it. The difference between the frames quantifies the integral of the luminescence decay curve, which is proportional to the luminescence lifetime, at time scales below one millisecond. Short excitation pulses avoid depopulation of the ground state of luminophores, resulting in a linear Stern-Volmer response with increasing concentrations of the quencher (O2), which can be predicted through a simple model. This methodology is compatible with a wide range of camera systems, making it a versatile tool for various optode based chemical imaging applications. We showcase the utility of frame straddling in measuring O2 dynamics around algae and by observing O2 scavenging sodium dithionite particles sinking through oxygenated water.}, }
@article {pmid39399973, year = {2024}, author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC}, title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39399973}, issn = {2047-217X}, support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; }, mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.}, }
@article {pmid39398475, year = {2024}, author = {Kumar, G and Bhadury, P}, title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110961}, pmid = {39398475}, issn = {2352-3409}, abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.}, }
@article {pmid39397203, year = {2024}, author = {Liu, K and Yan, Q and Guo, X and Wang, W and Zhang, Z and Ji, M and Wang, F and Liu, Y}, title = {Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {128}, pmid = {39397203}, issn = {1432-184X}, support = {ANSO-CR-KP-2021-04//the Key Collaborative Research Program of the Alliance of International Science Organizations/ ; 42330410//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; }, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Microbiota ; Ecosystem ; Tibet ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.}, }
@article {pmid39388223, year = {2024}, author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM}, title = {Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39388223}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; *Gills/microbiology ; *Sulfur/metabolism ; *In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.}, }
@article {pmid39387587, year = {2024}, author = {Akob, DM and Oates, AE and Girguis, PR and Badgley, BD and Cooper, VS and Poretsky, RS and Tierney, BT and Litchman, E and Whitaker, RJ and Whiteson, KL and Metcalf, CJE and , }, title = {Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.}, journal = {mSphere}, volume = {9}, number = {11}, pages = {e0030724}, pmid = {39387587}, issn = {2379-5042}, mesh = {*Biodiversity ; *Ecology ; *Microbiology ; *Societies, Scientific ; United States ; Biological Evolution ; Humans ; Microbiota ; }, abstract = {The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.}, }
@article {pmid39387577, year = {2024}, author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E}, title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0084024}, pmid = {39387577}, issn = {2379-5077}, support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; }, abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.<br><br>IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.}, }
@article {pmid39387551, year = {2024}, author = {Halbrook, S and Wilber, W and Barrow, ME and Farrer, EC}, title = {Bacterial community response to novel and repeated disturbances.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e70022}, pmid = {39387551}, issn = {1758-2229}, support = {LEQSF(2017-20)-RD-A-14//Louisiana Board of Regents/ ; //Tulane University/ ; DEB-2141922//National Science Foundation/ ; }, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Salinity ; Microbiota ; Ecosystem ; Biodiversity ; }, abstract = {Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.}, }
@article {pmid39392836, year = {2024}, author = {Daisley, BA and Allen-Vercoe, E}, title = {Microbes as medicine.}, journal = {Annals of the New York Academy of Sciences}, volume = {1541}, number = {1}, pages = {63-82}, pmid = {39392836}, issn = {1749-6632}, support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; *Microbiota/drug effects/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Precision Medicine/methods ; Animals ; }, abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.}, }
@article {pmid39392487, year = {2024}, author = {Legeay, J and Basiru, S and Ziami, A and Errafii, K and Hijri, M}, title = {Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {127}, pmid = {39392487}, issn = {1432-184X}, support = {Project AS-85//OPC Africa and OCP Innovation/ ; }, mesh = {Morocco ; *Fusarium/physiology/isolation &amp; purification/classification ; *Droughts ; *Alternaria/physiology/classification ; *Plant Roots/microbiology ; *Rain ; Soil Microbiology ; Mycobiome ; Rhizosphere ; }, abstract = {The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.}, }
@article {pmid39390291, year = {2025}, author = {Delzenne, NM and Bindels, LB and Neyrinck, AM and Walter, J}, title = {The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {4}, pages = {225-238}, pmid = {39390291}, issn = {1740-1534}, mesh = {*Dietary Fiber/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology ; *Neoplasms/microbiology/prevention &amp; control ; *Cardiovascular Diseases/microbiology/prevention &amp; control ; *Metabolic Diseases/microbiology ; Animals ; Bacteria/classification/metabolism/genetics ; }, abstract = {Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.}, }
@article {pmid39389280, year = {2024}, author = {Lima, M and Muddana, C and Xiao, Z and Bandyopadhyay, A and Wangikar, PP and Pakrasi, HB and Tang, YJ}, title = {The new chassis in the flask: Advances in Vibrio natriegens biotechnology research.}, journal = {Biotechnology advances}, volume = {77}, number = {}, pages = {108464}, doi = {10.1016/j.biotechadv.2024.108464}, pmid = {39389280}, issn = {1873-1899}, mesh = {*Vibrio/genetics ; *Biotechnology/methods ; *Metabolic Engineering/methods ; *Synthetic Biology/methods ; Systems Biology/trends ; }, abstract = {Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.}, }
@article {pmid39386005, year = {2024}, author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM}, title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.}, journal = {PNAS nexus}, volume = {3}, number = {10}, pages = {pgae411}, pmid = {39386005}, issn = {2752-6542}, abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.}, }
@article {pmid39383960, year = {2024}, author = {Goswami, V and Deepika, S and Sharma, P and Kothamasi, D}, title = {Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176750}, doi = {10.1016/j.scitotenv.2024.176750}, pmid = {39383960}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Fertilizers ; *Mycorrhizae/physiology ; *Soil Microbiology ; *Symbiosis ; Steel ; Hordeum/microbiology ; Recycling ; Soil/chemistry ; }, abstract = {Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha[-1]. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.}, }
@article {pmid39382725, year = {2024}, author = {Wang, L and Liu, Z and Bres, C and Jin, G and Fanin, N}, title = {Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {126}, pmid = {39382725}, issn = {1432-184X}, support = {2572021AW30//Fundamental Research Funds for the Central Universities/ ; 2022YFD2201100//National Key R &amp; D Program of China/ ; 2572022DS13//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Trees/microbiology/growth &amp; development ; Fungi/classification/genetics/physiology/isolation &amp; purification ; Pinus/microbiology/growth &amp; development ; Abies/microbiology ; Picea/microbiology/growth &amp; development ; Biodiversity ; Tracheophyta/microbiology ; }, abstract = {Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.}, }
@article {pmid39382674, year = {2024}, author = {Murray, MLH and Dopheide, A and Leonard, J and Padamsee, M and Schwendenmann, L}, title = {Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {125}, pmid = {39382674}, issn = {1432-184X}, mesh = {*Plant Leaves/microbiology ; *Phytophthora/isolation &amp; purification/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Combretaceae/microbiology ; }, abstract = {Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.}, }
@article {pmid39382297, year = {2024}, author = {Eigemann, F and Hoffmann, J and Schampera, C and Liu, S and Bolaños, LM and Heemeyer, M and Carlson, CA and Giovannoni, S and Hellweger, FL}, title = {Emergent ecology in a microscale model of the surface ocean.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0237224}, pmid = {39382297}, issn = {2150-7511}, support = {BIOS-SCOPE//Simons Foundation (SF)/ ; //North-German Supercomputing Alliance/ ; }, mesh = {*Phytoplankton/metabolism/physiology ; *Oceans and Seas ; *Ecosystem ; *Seawater/microbiology/chemistry ; Bacteria/metabolism/genetics ; Models, Biological ; Chemotaxis ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Cyanobacteria/metabolism/physiology/growth &amp; development ; Ecology ; }, abstract = {Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.}, }
@article {pmid39381885, year = {2024}, author = {Witzgall, K and Hesse, BD and Pacay-Barrientos, NL and Jansa, J and Seguel, O and Oses, R and Buegger, F and Guigue, J and Rojas, C and Rousk, K and Grams, TEE and Pietrasiak, N and Mueller, CW}, title = {Soil carbon and nitrogen cycling at the atmosphere-soil interface: Quantifying the responses of biocrust-soil interactions to global change.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17519}, doi = {10.1111/gcb.17519}, pmid = {39381885}, issn = {1365-2486}, support = {MU3021/6-2//Deutsche Forschungsgemeinschaft/ ; EAR-2012475//National Science Foundation (NSF)/ ; }, mesh = {*Soil/chemistry ; *Climate Change ; *Nitrogen Cycle ; *Soil Microbiology ; *Carbon Cycle ; *Droughts ; *Atmosphere/chemistry ; Carbon/metabolism/analysis ; Carbon Dioxide/metabolism/analysis ; Nitrogen/metabolism/analysis ; Ecosystem ; }, abstract = {In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro- and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust-soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses ([13]CO2 and [15]N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral-associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems.}, }
@article {pmid39380680, year = {2024}, author = {Karavaeva, V and Sousa, FL}, title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1433224}, pmid = {39380680}, issn = {1664-302X}, abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.}, }
@article {pmid39379763, year = {2024}, author = {Peng, Z and Xu, Z and Tong, H and Xing, Y and Luo, Z and Wu, Y and Yu, Z}, title = {Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {122}, pmid = {39379763}, issn = {1432-184X}, support = {2023YFC2604800-03//National Key Research and Development Program of China/ ; }, mesh = {China ; *Hypericum/microbiology/classification ; *Phylogeny ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Basidiomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Spores, Fungal ; }, abstract = {Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.}, }
@article {pmid39379709, year = {2024}, author = {Larrouy, JL and Ridgway, HJ and Dhami, MK and Jones, EE}, title = {Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {124}, pmid = {39379709}, issn = {1432-184X}, support = {C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Plastids/genetics ; *DNA, Mitochondrial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Lamiales/microbiology/genetics ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Sequence Analysis, DNA ; }, abstract = {Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.}, }
@article {pmid39379544, year = {2024}, author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B}, title = {Lake Bacterial Communities in North Patagonian Andes: The Effect of the Nothofagus pumilio Treeline.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {123}, pmid = {39379544}, issn = {1432-184X}, support = {PICT 2015-2138//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2017-1940//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2018-1563//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Cyanobacteria/genetics/classification ; Microbiota ; Nitrogen/analysis ; Carbon/analysis/metabolism ; Phosphorus/analysis ; Biodiversity ; Altitude ; Trees/microbiology ; Argentina ; }, abstract = {One of the most noticeable environmental discontinuities in mountains is the transition that exists in vegetation below and above the treeline. In the North Patagonian Andean lakes (between 900 and 1950 m a.s.l.), we analyzed the bacterial community composition of lakes in relation to surrounding vegetation (erected trees, krummholz belt, and bare rocks), dissolved organic carbon (DOC), and total dissolved nutrients (nitrogen, TDN and phosphorus, TDP). We observed a decrease in DOC, TDP, and TDN concentrations with altitude, reflecting shifts in the source inputs entering the lakes by runoff. Cluster analysis based on bacterial community composition showed a segregation of the lakes below treeline, from those located above. This first cluster was characterized by the cyanobacteria Cyanobium PCC-6307, while in the krummholz belt and bare rocks, bacterial communities were dominated by Actinobacteria hgcl-clade and Proteobacteria (Sandarakinorhabdus and Rhodovarius), with the presence of pigments such as actinorhodopsin, carotenoids, and bacteriochlorophyll a. The net relatedness index (NRI), which considers the community phylogenetic dispersion, showed that lakes located on bare rocks were structured by environmental filtering, while communities of lakes below treeline were structured by species interactions such as competition. Beta-diversity was higher among lakes below than among lakes located above the treeline. The contribution of species turnover was more important than nestedness. Our study brings light on how bacterial communities may respond to changes in the surrounding vegetation, highlighting the importance of evaluating different aspects of community structure to understand metacommunity organization.}, }
@article {pmid39378744, year = {2025}, author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B}, title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122570}, doi = {10.1016/j.watres.2024.122570}, pmid = {39378744}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Ecosystem ; Water Pollutants, Chemical/toxicity ; }, abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.}, }
@article {pmid39377576, year = {2024}, author = {Woldetsadik, YA and Lazinski, DW and Camilli, A}, title = {A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0245724}, pmid = {39377576}, issn = {2150-7511}, support = {AI055058//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; GM139772//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R37 AI055058/AI/NIAID NIH HHS/United States ; R01 AI055058/AI/NIAID NIH HHS/United States ; R21 AI147658/AI/NIAID NIH HHS/United States ; T32 GM139772/GM/NIGMS NIH HHS/United States ; AI147658//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*NAD/metabolism ; *Bacteriophages/genetics/physiology ; *Vibrio cholerae/virology/genetics ; Virulence ; Bacterial Proteins/genetics/metabolism ; Genomic Islands ; Virus Replication ; }, abstract = {Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems in bacteria that are still being discovered, as well as numerous ways of interference or circumvention on the part of phages. Here, we identify a unique molecular battle between the classical biotype of Vibrio cholerae and virulent phages ICP1, ICP2, and ICP3. We show that classical biotype strains resist almost all isolates of these phages due to a 25-kb genomic island harboring several putative anti-phage systems. We observed that one of these systems, Nezha, encoding SIR2-like and helicase proteins, inhibited the replication of all three phages. Bacterial SIR2-like enzymes degrade the essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD[+]), thereby preventing replication of the invading phage. In support of this mechanism, we identified one phage isolate, ICP1_2001, which circumvents Nezha by encoding two putative NAD[+] regeneration enzymes. By restoring the NAD[+] pool, we hypothesize that this system antagonizes Nezha without directly interacting with its proteins and should be able to antagonize other anti-phage systems that deplete NAD[+].IMPORTANCEBacteria and phages are in a perpetual molecular arms race, with bacteria evolving an extensive arsenal of anti-phage systems and phages evolving mechanisms to overcome these systems. This study identifies a previously uncharacterized facet of the arms race between Vibrio cholerae and its phages. We identify an NAD[+]-depleting anti-phage defensive system called Nezha, potent against three virulent phages. Remarkably, one phage encodes proteins that regenerate NAD[+] to counter the effects of Nezha. Without Nezha, the NAD[+] regeneration genes are detrimental to the phage. Our study provides new insight into the co-evolutionary dynamics between bacteria and phages and informs the microbial ecology and phage therapy fields.}, }
@article {pmid39376571, year = {2024}, author = {Qian, C and Hui, J and Peng, Z and Sun, X and Zhang, J}, title = {Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1435334}, pmid = {39376571}, issn = {1664-3224}, mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/genetics/mortality ; *Gastric Mucosa/microbiology/immunology/metabolism ; Female ; *Tumor Microenvironment/immunology ; Male ; Middle Aged ; *Gastrointestinal Microbiome/immunology/genetics ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/immunology/genetics ; Adult ; }, abstract = {Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs [high] group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.}, }
@article {pmid39375832, year = {2024}, author = {Obiol, A and Del Campo, J and de Vargas, C and Mahé, F and Massana, R}, title = {How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39375832}, issn = {1574-6941}, support = {PID2019-108457RB-I00//Spanish Ministry of Science and Innovation/ ; EUR2022-134047//GENEXLAB/ ; PID2022-137508NB-I00//EPIC/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; }, mesh = {*Phylogeny ; *Seawater/microbiology ; *Stramenopiles/genetics/classification ; Aquatic Organisms/genetics ; Biodiversity ; Ecosystem ; Sequence Analysis, DNA ; Genes, rRNA ; }, abstract = {Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyse the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4, and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analysed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.}, }
@article {pmid39366327, year = {2024}, author = {Xu, J and Li, X and Xi, C and Weir, MH}, title = {Development of a machine learning model to support low cost real-time Legionella monitoring in premise plumbing systems.}, journal = {Water research}, volume = {267}, number = {}, pages = {122510}, doi = {10.1016/j.watres.2024.122510}, pmid = {39366327}, issn = {1879-2448}, mesh = {*Machine Learning ; *Water Microbiology ; *Legionella pneumophila ; Legionella ; Water Quality ; Environmental Monitoring/methods ; Water Supply ; Amoeba ; }, abstract = {Legionella pneumophila (L. pneumophila) is a pathogenic bacterium primarily known for causing Legionnaires' Disease which is known for high mortality rates, particularly in the elderly. With caseloads continuing to increase, further research is needed to improve our understanding of optimized sampling schema and safe limits of L. pneumophila, in part to target improved treatment options and realistic population-level risk modeling. Particularly in healthcare and other high-risk locations these become crucial and time sensitive needs. Therefore, we conceptualized this research as a means of incorporating easily measured physiochemical water quality parameters and generalization of the unique ecology of building water systems to build a computational model that can allow for more rapid and accurate decision making. This research uses the specific machine learning (ML) method called statistical learning theory to incorporate concentration of host cells, such as native amoeba, and physiochemical water quality parameters to estimate the probability of observing ranges of Legionella gene copy concentrations. Using data from previously published research on Legionella prevalence in a large building, our ML method trains the model on the relative impacts of physiochemical parameters on likely amoeba host cell occurrences. The model is expanded to estimate host cell concentrations using correlations and regressions operated through LASSO algorithms. After categorization variables from these results are then used to inform a logistic regression to provide an estimate of the probability of Legionella gene copy concentration ranges. In summary, conventional results generated by logistic regression and multiple linear regression quantified the associations among ecological conditions in the water and ability to predict a likely range of Legionella concentration in a management focused way. Further, two ML methods, PCA and LASSO, demonstrated feasibility in accurate real-time monitoring of Legionella through physiochemical indicators as evidenced with good accuracy of predictions based for validation results. Furthermore results demonstrate the vital need to account for the impact of water quality on building on host cells, and via their quantified water microbial ecology, not just Legionella concentrations.}, }
@article {pmid39365014, year = {2024}, author = {Arnold, ND and Paper, M and Fuchs, T and Ahmad, N and Jung, P and Lakatos, M and Rodewald, K and Rieger, B and Qoura, F and Kandawa-Schulz, M and Mehlmer, N and Brück, TB}, title = {High-quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures.}, journal = {MicrobiologyOpen}, volume = {13}, number = {5}, pages = {e70000}, pmid = {39365014}, issn = {2045-8827}, support = {031B0838B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031A305A//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; //Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; }, mesh = {Namibia ; *Cyanobacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Phylogeny ; *Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Hot Temperature ; Sequence Analysis, DNA ; Proteome/analysis ; DNA, Bacterial/genetics ; }, abstract = {Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies.}, }
@article {pmid39364584, year = {2025}, author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F}, title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14023}, pmid = {39364584}, issn = {1755-0998}, support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Germany ; *Biodiversity ; *Insecta/classification/genetics/physiology ; }, abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.}, }
@article {pmid39361898, year = {2024}, author = {Ramoneda, J and Hoffert, M and Stallard-Olivera, E and Casamayor, EO and Fierer, N}, title = {Leveraging genomic information to predict environmental preferences of bacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39361898}, issn = {1751-7370}, support = {OPP 2133684//US National Science Foundation/ ; AEROSMIC PID2021-127701NB-I00//European Regional Development Fund/ ; //Spanish Agency of Research/ ; PID2023-151209NA-I00//Spanish Agency of Research/ ; 2022-BP-00050//Generalitat de Catalunya/ ; P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Bacteria/genetics/classification ; Genome, Bacterial ; Genomics ; Environment ; Bacterial Physiological Phenomena ; }, abstract = {Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.}, }
@article {pmid39360821, year = {2024}, author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y}, title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0216924}, pmid = {39360821}, issn = {2150-7511}, support = {2019R1A6A1A10072987//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1008303//National Research Foundation of Korea (NRF)/ ; 2022R1A4A503144711//National Research Foundation of Korea (NRF)/ ; ZK74//Austrian Science Fund (FWF)/ ; 2023RIS-009//Regional Innovation Strategy (RIS)/ ; }, mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Archaea/genetics/metabolism/classification ; *Nitrification ; *Phylogeny ; Genome, Archaeal ; Adaptation, Physiological ; Genomics ; }, abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.}, }
@article {pmid39360459, year = {2024}, author = {Li, X and Leizeaga, A and Rousk, J and Zhou, S and Hugelius, G and Manzoni, S}, title = {Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17522}, doi = {10.1111/gcb.17522}, pmid = {39360459}, issn = {1365-2486}, support = {101001608//H2020 European Research Council/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; //Schmidt Sciences, LLC/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Fungi/physiology/metabolism ; *Climate Change ; Bacteria/metabolism/growth &amp; development ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.}, }
@article {pmid39360321, year = {2024}, author = {MacGregor, H and Fukai, I and Ash, K and Arkin, AP and Hazen, TC}, title = {Potential applications of microbial genomics in nuclear non-proliferation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1410820}, pmid = {39360321}, issn = {1664-302X}, abstract = {As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.}, }
@article {pmid39359935, year = {2024}, author = {Li, Y and Li, Z and Zheng, S and Xu, X}, title = {Probiotics in the management of radiation-induced oral mucositis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1477143}, pmid = {39359935}, issn = {2235-2988}, mesh = {*Probiotics/therapeutic use ; Humans ; *Stomatitis/etiology/microbiology/therapy/prevention &amp; control ; *Radiation Injuries/therapy ; *Dysbiosis ; Microbiota ; Head and Neck Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Mouth/microbiology ; Quality of Life ; }, abstract = {Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.}, }
@article {pmid39358950, year = {2024}, author = {Zhang, J and Qin, L and Chang, Y and He, Y and Zhao, W and Zhao, Y and Ding, Y and Gao, J and Zhao, X}, title = {One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a.}, journal = {ACS synthetic biology}, volume = {13}, number = {10}, pages = {3400-3412}, doi = {10.1021/acssynbio.4c00481}, pmid = {39358950}, issn = {2161-5063}, mesh = {*Stenotrophomonas maltophilia/genetics ; *CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism/genetics ; DNA, Bacterial/genetics ; CRISPR-Associated Proteins/genetics ; Endodeoxyribonucleases/genetics ; Bacterial Proteins ; }, abstract = {Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL[-1] of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.}, }
@article {pmid39358586, year = {2025}, author = {de Lorenzo, V and Baquero, F and Aguilar, A}, title = {Carlos Asensio and the dawn of molecular microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {5}, pages = {897-908}, pmid = {39358586}, issn = {1618-1905}, support = {CL6-2021-UE 101060625//Horizon 2020 Framework Programme/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; }, mesh = {History, 20th Century ; Spain ; Humans ; Gastrointestinal Microbiome ; *Microbiology/history ; }, abstract = {At near 50 years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.}, }
@article {pmid39358432, year = {2024}, author = {Zhi, W and Li, A and Wang, Q and Yuan, X and Qing, J and Zhang, C and Wang, Y and Li, Y}, title = {Safety and efficacy assessment of fecal microbiota transplantation as an adjunctive treatment for IgA nephropathy: an exploratory clinical trial.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22935}, pmid = {39358432}, issn = {2045-2322}, support = {82170716//National Science Foundation of China/ ; }, mesh = {Humans ; *Glomerulonephritis, IGA/therapy ; Male ; Female ; Adult ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Gastrointestinal Microbiome ; Middle Aged ; Treatment Outcome ; Cytokines/blood/metabolism ; }, abstract = {To assess the safety and efficacy of fecal microbiota transplantation (FMT) as an adjunctive therapeutic intervention for IgA nephropathy (IgAN). Fifteen patients with IgA nephropathy were recruited based on inclusion and exclusion criteria and underwent FMT using enteric microbial capsules. Clinical indicators, intestinal microbiota and metabolomic profiles, as well as changes in serum immune cells and cytokines, were monitored before and after FMT. No severe adverse reactions were observed in the subjects. After FMT, there was a reduction in the 24-h urinary protein quantification in subjects. The relative abundances of Phocaeicola_vulgatus, Bacteroides_uniformis, Prevotella_copri, Phocaeicola_dorei, Bacteroides_ovatus, Bacteroides_xylanisolvens, Parabacteroides _distasonis, Bifidobacterium_pseudocatenulatum, Bacteroides_sp._HF-162, and Bifidobacterium_longum changed after FMT. In terms of intestinal metabolites, the levels of acylcarnitine18:0 (ACar.18:0), cotinine, N-arachidonoyl-L-serine, phosphatidylcholine (PC. (18:3e/22:6)), serotonin, and fumagillin showed significant changes. Flow cytometry analysis showed the absolute count of plasma B cells decreased in subjects, and this change correlated with alterations in the intestinal microbiota and metabolites. This study preliminarily evaluates the safety and efficacy of FMT in patients with IgAN. No significant adverse reactions were observed, and the administration of FMT alongside ACEI/ARB therapy was effective in reducing urinary protein levels in patients with IgAN, a process that may be associated with B-cell immunity.}, }
@article {pmid39357457, year = {2024}, author = {Olavarria, K and Sousa, DZ}, title = {Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide.}, journal = {Current opinion in biotechnology}, volume = {90}, number = {}, pages = {103212}, doi = {10.1016/j.copbio.2024.103212}, pmid = {39357457}, issn = {1879-0429}, mesh = {*Carbon Monoxide/metabolism ; *Hydroxybutyrates/metabolism ; *Thermodynamics ; *Polyesters/metabolism/chemistry ; *Biotechnology/methods ; Metabolic Engineering/methods ; Polyhydroxybutyrates ; }, abstract = {Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.}, }
@article {pmid39357161, year = {2024}, author = {Wan, W and Grossart, HP and Zhang, W and Xiong, X and Yuan, W and Liu, W and Yang, Y}, title = {Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.}, journal = {Water research}, volume = {267}, number = {}, pages = {122516}, doi = {10.1016/j.watres.2024.122516}, pmid = {39357161}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Bacteria ; *Eutrophication ; Nitrogen ; Phosphorus ; Ecosystem ; Phylogeny ; }, abstract = {Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.}, }
@article {pmid39353102, year = {2024}, author = {He, J and Castilla-Alcantara, JC and Ortega-Calvo, JJ and Harms, H and Wick, LY}, title = {DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {41}, pages = {18234-18243}, pmid = {39353102}, issn = {1520-5851}, mesh = {*Biodegradation, Environmental ; Filtration ; Electricity ; Water Pollutants, Chemical/metabolism ; Naphthalenes/metabolism ; }, abstract = {Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm[-1]) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10[-5] mol·L[-1]) and Darcy velocities typical for biofiltration (U¯ = 0.2-1.2 × 10[-4] m·s[-1]). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on U¯, suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.}, }
@article {pmid39354222, year = {2024}, author = {Suzuki, Y and Webb, SJ and Kouduka, M and Kobayashi, H and Castillo, J and Kallmeyer, J and Moganedi, K and Allwright, AJ and Klemd, R and Roelofse, F and Mapiloko, M and Hill, SJ and Ashwal, LD and Trumbull, RB}, title = {Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {116}, pmid = {39354222}, issn = {1432-184X}, support = {AB0502//Astrobiology Center Program of National Institutes of Natural Sciences (NINS)/ ; }, mesh = {South Africa ; *Bacteria/isolation &amp; purification/classification ; Geologic Sediments/microbiology ; Minerals/analysis/metabolism ; Clay/chemistry ; Soil Microbiology ; }, abstract = {Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.}, }
@article {pmid39354152, year = {2024}, author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and ,  and ,  and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM}, title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2892-2908}, pmid = {39354152}, issn = {2058-5276}, support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; }, mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; }, abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.}, }
@article {pmid39350412, year = {2024}, author = {Khan, A and Abass, S and Nizami, SAI and Shariq, M and Zahiruddin, S and Parveen, B and Parveen, R}, title = {The Gut Health Revolution: Herbs and Dietary Phytochemicals in Balancing Gut Microbiota for Optimal Human Health.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010313921240923125946}, pmid = {39350412}, issn = {1873-4316}, abstract = {The gut microbiota is a varied population of microorganisms that live in the human gastrointestinal system. Emerging research emphasizes the importance of this microbial ecology in general health and its influence on a variety of disorders. The review explores the synergy between herbal treatment and traditional medicine, emphasizing their cultural significance and therapeutic benefits. It delves into the intricate relationship between herbal remedies, traditional healing practices, and their sustained usage over centuries. The review highlights the pivotal role of the gut microbiota in herbal medicine, elucidating how treatments influence the gastrointestinal microorganisms, impacting overall health. Dietary phytochemicals are underscored for their significance in herbal medicine and nutritional well-being, along with the interdependence of plant extracts and botanicals. The investigation explores the molecular connections between phytoconstituents and gut microbiota, aiming to deepen the understanding of herbal medicine's tailored approach to specific health challenges. The summary concludes by emphasizing herbal treatments' unique ability to regulate gut flora, contributing to overall gastrointestinal wellbeing. In closing, the review provides a concise overview, serving as a valuable resource for integrative medicine research, with recommendations for future exploration of herbal medicine's potential in healthcare.}, }
@article {pmid39349736, year = {2024}, author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM}, title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22742}, pmid = {39349736}, issn = {2045-2322}, mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth &amp; development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; }, abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.}, }
@article {pmid39349195, year = {2024}, author = {Cheng, X and Zhao, R and Bodelier, PLE and Song, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Differential response of subterranean microbiome to exogenous organic matter input in a cave ecosystem.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176584}, doi = {10.1016/j.scitotenv.2024.176584}, pmid = {39349195}, issn = {1879-1026}, mesh = {*Microbiota ; *Caves/microbiology ; Soil Microbiology ; Bacteria/metabolism ; Fungi ; Ecosystem ; Climate Change ; }, abstract = {As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.}, }
@article {pmid39349071, year = {2024}, author = {Toporowska, M and Żebracki, K and Mazur, A and Mazur-Marzec, H and Šulčius, S and Alzbutas, G and Lukashevich, V and Dziga, D and Mieczan, T}, title = {Biodegradation of microcystins by microbiota of duckweed Spirodelapolyrhiza.}, journal = {Chemosphere}, volume = {366}, number = {}, pages = {143436}, doi = {10.1016/j.chemosphere.2024.143436}, pmid = {39349071}, issn = {1879-1298}, mesh = {*Microcystins/metabolism ; *Biodegradation, Environmental ; *Microbiota ; *Araceae/metabolism ; Tandem Mass Spectrometry ; Cyanobacteria/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; }, abstract = {Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 953), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.}, }
@article {pmid39348267, year = {2024}, author = {Clegg, T and Pawar, S}, title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39348267}, issn = {2050-084X}, support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; }, mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; }, abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.}, }
@article {pmid39346682, year = {2024}, author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK}, title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.}, journal = {Access microbiology}, volume = {6}, number = {9}, pages = {}, pmid = {39346682}, issn = {2516-8290}, abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.}, }
@article {pmid39346007, year = {2024}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae111}, pmid = {39346007}, issn = {2730-6151}, abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.}, }
@article {pmid39340684, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A}, title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {120}, pmid = {39340684}, issn = {1432-184X}, mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention &amp; control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; }, abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.}, }
@article {pmid39340560, year = {2024}, author = {Charalampous, G and Kormas, KA and Antoniou, E and Kalogerakis, N and Gontikaki, E}, title = {Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {381}, pmid = {39340560}, issn = {1432-0991}, support = {1874//Hellenic Foundation for Research and Innovation/ ; 1510//Hellenic Foundation for Research and Innovation/ ; }, mesh = {Mediterranean Sea ; *Bacteria/classification/genetics/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Microbiota ; *RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Phylogeny ; Ecosystem ; }, abstract = {Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.}, }
@article {pmid39340556, year = {2024}, author = {Fernandez de Landa, G and Alberoni, D and Braglia, C and Baffoni, L and Fernandez de Landa, M and Revainera, PD and Quintana, S and Zumpano, F and Maggi, MD and Di Gioia, D}, title = {The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {121}, pmid = {39340556}, issn = {1432-184X}, support = {777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Nosema/physiology/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; South America ; }, abstract = {South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.}, }
@article {pmid39340548, year = {2024}, author = {Radouane, N and Errafii, K and Mouhib, S and Mhand, KA and Legeay, J and Hijri, M}, title = {Potential Plant-To-Plant Transmission: Shared Endophytic Bacterial Community Between Ziziphus lotus and Its Parasite Cuscuta epithymum.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {119}, pmid = {39340548}, issn = {1432-184X}, support = {Projects AS-77 and AS-85//OCP Group/ ; }, mesh = {*Cuscuta/physiology/microbiology/genetics ; *Ziziphus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Endophytes/genetics/physiology/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; Host-Parasite Interactions ; DNA, Bacterial/genetics ; }, abstract = {Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.}, }
@article {pmid39338505, year = {2024}, author = {Shah, H and Trivedi, M and Gurjar, T and Sahoo, DK and Jergens, AE and Yadav, VK and Patel, A and Pandya, P}, title = {Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338505}, issn = {2076-2607}, abstract = {The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.}, }
@article {pmid39338496, year = {2024}, author = {Denux, M and Armenteros, M and Weber, L and Miller, CA and Sántha, K and Apprill, A}, title = {Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338496}, issn = {2076-2607}, abstract = {Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.}, }
@article {pmid39338466, year = {2024}, author = {Lauzon, J and Caron, D and Lazar, CS}, title = {The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338466}, issn = {2076-2607}, support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; }, abstract = {The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.}, }
@article {pmid39338465, year = {2024}, author = {Cruz, LG and Shen, FT and Chen, CP and Chen, WC}, title = {Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338465}, issn = {2076-2607}, support = {MOST 110-2313-B-005-015-//National Science and Technology Council/ ; }, abstract = {Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.}, }
@article {pmid39338425, year = {2024}, author = {Lyu, G and Hu, J and Ma, J}, title = {Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338425}, issn = {2076-2607}, support = {41571304//National Natural Science Foundation of China/ ; }, abstract = {Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3[-]-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.}, }
@article {pmid39338386, year = {2024}, author = {Galinytė, D and Bernatoniene, J and Žilius, M and Rysevaitė-Kyguolienė, K and Savickas, A and Karosienė, J and Briedis, V and Pauža, DH and Savickienė, N}, title = {In Vitro Study of Cyano-Phycocyanin Release from Hydrogels and Ex Vivo Study of Skin Penetration.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {9}, pages = {}, pmid = {39338386}, issn = {1424-8247}, abstract = {BACKGROUND: This study explored the most suitable materials for incorporating cyano-phycocyanin (C-PC) into hydrogels, focusing on maintaining the C-PC's long-term structural integrity and stabilityNext, the release of C-PC from the hydrogels and its skin penetration were investigated.<br><br>METHODS: A series of 1% (w/w) C-PC hydrogels was prepared using various gelling agents and preservatives. Spectrophotometric measurements compared the amount of C-PC in the hydrogels to the initially added amount. After selecting the most suitable gelling agent and preservative, two C-PC hydrogels, with and without propylene glycol (PG) (Sigma-Aldrich, St. Louis, MO, USA), were produced for further testing. In vitro release studies utilized modified Franz-type diffusion cells, while ex vivo skin-permeation studies employed Bronaugh-type cells and human skin. Confocal laser scanning microscopy analyzed C-PC accumulation in the skin.<br><br>RESULTS: The findings demonstrated that sodium alginate (Sigma-Aldrich, St. Louis, MO, USA), hydroxyethyl cellulose (HEC) (Sigma-Aldrich, St. Louis, MO, USA), and Soligel[TM] (Givaudan, Vernier, Switzerland) are effective biopolymers for formulating hydrogels while maintaining C-PC stability. After 6 h, C-PC release from the hydrogel containing PG was approximately 10% or 728.07 (&#xb1;19.35) &#x3bc;g/cm[2], significantly higher than the nearly 7% or 531.44 (&#xb1;26.81) &#x3bc;g/cm[2] release from the hydrogel without PG (p < 0.05). The ex vivo qualitative skin-permeation study indicated that PG enhances C-PC penetration into the outermost skin layer.<br><br>CONCLUSION: PG's ability to enhance the release of C-PC from the hydrogel, coupled with its capacity to modify the skin barrier ex vivo, facilitates the penetration of C-PC into the stratum corneum.}, }
@article {pmid39335049, year = {2024}, author = {Afonso, L and Grzegorczyk, KG and Salomão, JM and Basso, KR and Alves, LC and Silva, MCD and Chryssafidis, AL and Gionco-Cano, B and Yamada-Ogatta, SF and Andrade, G}, title = {Fluopsin C Promotes Biofilm Removal of XDR Acinetobacter baumannii and Presents an Additive Effect with Polymyxin B on Planktonic Cells.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39335049}, issn = {2079-6382}, support = {439754/2018-6//National Council for Scientific and Technological Development/ ; 406016/2022-4//National Council for Scientific and Technological Development/ ; }, abstract = {Acinetobacter baumannii emerged as one of the most important pathogens for the development of new antimicrobials due to the worldwide detection of isolates resistant to all commercial antibiotics, especially in nosocomial infections. Biofilm formation enhances A. baumannii survival by impairing antimicrobial action, being an important target for new antimicrobials. Fluopsin C (FlpC) is an organocupric secondary metabolite with broad-spectrum antimicrobial activity. This study aimed to evaluate the antibiofilm activity of FlpC in established biofilms of extensively drug-resistant A. baumannii (XDRAb) and the effects of its combination with polymyxin B (PolB) on planktonic cells. XDRAb susceptibility profiles were determined by Vitek 2 Compact, disk diffusion, and broth microdilution. FlpC and PolB interaction was assessed using the microdilution checkerboard method and time-kill kinetics. Biofilms of XDRAb characterization and removal by FlpC exposure were assessed by biomass staining with crystal violet. Confocal Laser Scanning Microscopy was used to determine the temporal removal of the biofilms using DAPI, and cell viability using live/dead staining. The minimum inhibitory concentration (MIC) of FlpC on XDRAb was 3.5 µg mL[-1]. Combining FlpC + PolB culminated in an additive effect, increasing bacterial susceptibility to both antibiotics. FlpC-treated 24 h biofilms reached a major biomass removal of 92.40 ± 3.38% (isolate 230) using 7.0 µg mL[-1] FlpC. Biomass removal occurred significantly over time through the dispersion of the extracellular matrix and decreasing cell number and viability. This is the first report of FlpC's activity on XDRAb and the compound showed a promissory response on planktonic and sessile cells, making it a candidate for the development of a new antimicrobial product.}, }
@article {pmid39332295, year = {2024}, author = {Tapia, N and Gallardo-Bustos, C and Rojas, C and Vargas, IT}, title = {Long-term evaluation of soil-based bioelectrochemical green roof systems for greywater treatment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122643}, doi = {10.1016/j.jenvman.2024.122643}, pmid = {39332295}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Bioelectric Energy Sources ; Water Purification/methods ; Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; }, abstract = {Water scarcity has generated the need to identify new sources. Due to its low organic contaminant load, greywater reuse has emerged as a potential alternative. Moreover, the search for decentralized treatment systems in urban areas has prompted research on using green roofs for greywater treatment. However, the performance of organic matter removal is limited by the type of substrate and height of the growing media. Bioelectrochemical systems (BESs) improve treatment performance by providing an additional electron acceptor (the electrode). In this study, nine reactors under three different conditions, i.e., open circuit (OC), microbial fuel cell (MFC), and microbial electrolysis cell (MEC), were built to evaluate the treatment of synthetic greywater in a substrate-growing medium composed of perlite and coconut fiber and operated in batch-cycle mode for 397 days. The results suggested that using BESs enables greywater treatment and the removal of pollutants to levels that allow their reuse for irrigation. Furthermore, electrical conductivity was reduced from 732.4 ± 41.2 μS/cm[2] in OC to 637.32 ± 22.73 μS/cm[2] and 543.15 ± 19.69 μS/cm[2] in MEC and MFC, respectively. The soluble chemical oxygen demand in the latter treatments reached 76% removal, compared to levels above the OC, which only reached approximately 67%. Microbial community analysis revealed differences, mainly in the cathodes, showing a higher development of Flavobacterium, Azospirillum, and Zoogloea in MFCs, which could explain the higher levels of organic matter removal in the other conditions, suggesting that the BES could produce an enrichment of beneficial bacterial groups for treatment. Therefore, implementing BESs in green roofs enables sustainable long-term greywater treatment.}, }
@article {pmid39331293, year = {2024}, author = {Bianchelli, J and Sagua, MI and Quiroga, MP and Nuozzi, G and Fernández, J and Schiaffino, MR}, title = {Temporal dynamics of Legionella (Proteobacteria, Legionellaceae) in two Pampean shallow lakes from Argentina.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {49}, pages = {59058-59070}, pmid = {39331293}, issn = {1614-7499}, support = {PICT 0891-2017//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICTO 00006-2019//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; SIB 2053-2022//Universidad Nacional del Noroeste de la Provincia de Buenos Aires/ ; }, mesh = {Argentina ; *Lakes/microbiology ; *Legionella/genetics ; Water Microbiology ; Real-Time Polymerase Chain Reaction ; }, abstract = {Aquatic systems have traditionally played a key role in the development of human life, providing multiple ecosystem services to society and being a reservoir for a wide biodiversity of organisms. Among them, bacteria belonging to Legionella stand out, mainly because they are of great interest both in the field of microbial ecology and public health, since some of them turn out to be pathogenic for humans. The aim of this work was to study the monthly temporal dynamics of Legionella spp. and its relationship with the environmental variables measured in two Pampean shallow lakes (Gómez and Carpincho, Buenos Aires Province, Argentina). The analysis was carried out using a quantitative approach by real-time polymerase chain reaction (qPCR) and a non-quantitative approach using bacterial diversity data obtained by next-generation sequencing (NGS), using the Illumina MiSeq platform. Our results showed that the overall Legionella abundance was very high in the studied Pampean shallow lakes. Notably, fluctuations in dissolved organic carbon and temperature influenced the dynamics shifts in Legionella abundances. Correlation analyses between Legionella reads from NGS and copy numbers obtained through qPCR revealed positive relationships, unveiling distinctions attributable to the diverse sequence processing algorithms employed in the analysis of NGS data.}, }
@article {pmid39330355, year = {2024}, author = {Abbà, S and Valentini, B and Stefanini, I}, title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {39330355}, issn = {2309-608X}, support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; }, abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.}, }
@article {pmid39328926, year = {2024}, author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {44}, number = {}, pages = {e00857}, pmid = {39328926}, issn = {2215-017X}, abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.}, }
@article {pmid39327479, year = {2024}, author = {Tavaddod, S and Dawson, A and Allen, RJ}, title = {Bacterial aggregation triggered by low-level antibiotic-mediated lysis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {90}, pmid = {39327479}, issn = {2055-5008}, support = {682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/R012415/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/drug effects/genetics ; *Bacteriolysis/drug effects ; Biofilms/drug effects/growth &amp; development ; Microbial Sensitivity Tests ; }, abstract = {Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates may have different ecological implications since they do not show increased biofilm-forming potential or increased antibiotic resistance. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the possible consequences of widespread low-dose antibiotic exposure in the environment and in the body.}, }
@article {pmid39327101, year = {2024}, author = {Goldman, AD and Fournier, GP}, title = {The very early evolution of biological complexity.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {11}, pages = {912-913}, doi = {10.1016/j.tig.2024.09.001}, pmid = {39327101}, issn = {0168-9525}, mesh = {*Biological Evolution ; Phylogeny ; Evolution, Molecular ; }, abstract = {All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.}, }
@article {pmid39326062, year = {2024}, author = {Sun, X and Favier, A and Folmar, J and Pyenson, NC and Sanchez, A and Rebolleda-Gómez, M}, title = {Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.}, journal = {The American naturalist}, volume = {204}, number = {4}, pages = {381-399}, doi = {10.1086/731997}, pmid = {39326062}, issn = {1537-5323}, mesh = {*Temperature ; *Microbiota ; Bacteria/metabolism ; Fermentation ; Carbon/metabolism ; Ecosystem ; }, abstract = {AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.}, }
@article {pmid39321934, year = {2024}, author = {Liu, YC and Ramiro-Garcia, J and O'Connor, S and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V}, title = {Microbial community response to temperature reduction during anaerobic treatment of long chain fatty acids-containing wastewater.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131529}, doi = {10.1016/j.biortech.2024.131529}, pmid = {39321934}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; Anaerobiosis ; *Fatty Acids/metabolism ; *Bioreactors ; *Temperature ; Bacteria/metabolism ; Water Purification/methods ; Biomass ; Microbiota/physiology ; }, abstract = {Acclimating mesophilic biomass to low temperatures have been used to start-up psychrophilic anaerobic reactors, but limited microbial information is available during the acclimation. To investigate microbial responses to temperature reductions, duplicate lab-scale anaerobic digestion (AD) reactors were operated for 166 days, with the temperature being reduced from 37°C to 15°C, using synthetic long chain fatty acid (LCFA)-containing wastewater as the feedstock. The acclimated biomass at 15°C exhibited efficient removal of organic matter (total COD>75%, soluble COD>88%, and LCFA>99%). Temperature reductions lead to significant reductions in microbiome diversity. Fermentative bacteria were highly dynamic and functional redundant during temperature reductions. Smithella was the dominant syntrophic bacteria involved in LCFA degradation coupled with Methanothrix and Methanocorpusculum at 15°C. Membrane modifications and compatible cellular solutes production were triggered by temperature reductions as microbial response to cold stress. This study provided molecular insights in microbial acclimation to low temperatures for psychrophilic AD.}, }
@article {pmid39319483, year = {2024}, author = {Rasmussen, KL and Thieringer, PH and Nevadomski, S and Martinez, AM and Dawson, KS and Corsetti, FA and Zheng, XY and Lv, Y and Chen, X and Celestian, AJ and Berelson, WM and Rollins, NE and Spear, JR}, title = {Living to Lithified: Construction and Preservation of Silicified Biomarkers.}, journal = {Geobiology}, volume = {22}, number = {5}, pages = {1-30}, doi = {10.1111/gbi.12620}, pmid = {39319483}, issn = {1472-4669}, support = {/NASA/NASA/United States ; //Geological Society of America/ ; }, mesh = {*Biomarkers/analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism ; Hot Springs/microbiology/chemistry ; }, abstract = {Whole microorganisms are rarely preserved in the fossil record but actively silicifying environments like hot springs provide an opportunity for microbial preservation, making silicifying environments critical for the study of microbial life through time on Earth and possibly other planetary bodies. Yet, the changes that biosignatures may undergo through lithification and burial remain unconstrained. At Steep Cone Geyser in Yellowstone National Park, we collected microbial material from (1) the living system across the active outflows, (2) the silicified areas adjacent to flows, and (3) lithified and buried material to assess the preservation of biosignatures and their changes across the lithification transect. Five biofabrics, built predominantly by Cyanobacteria Geitlerinema, Pseudanabaenaceae, and Leptolyngbya with some filamentous anoxygenic phototrophs contributions, were identified and tracked from the living system through the process of silicification/lithification. In the living systems, δ[30]Si values decrease from +0.13‰ in surficial waters to -2‰ in biomat samples, indicating a kinetic isotope effect potentially induced by increased association with actively growing biofabrics. The fatty acids C16:1 and iso-C14:0 and the hydrocarbon C17:0 were disentangled from confounding signals and determined to be reliable lipid biosignatures for living biofabric builders and tenant microorganisms. Builder and tenant microbial biosignatures were linked to specific Cyanobacteria, anoxygenic phototrophs, and heterotrophs, which are prominent members of the living communities. Upon lithification and burial, silicon isotopes of silicified biomass began to re-equilibrate, increasing from δ[30]Si -2‰ in living biomats to -0.55‰ in lithified samples. Active endolithic microbial communities were identified in lithified samples and were dominated by Cyanobacteria, heterotrophic bacteria, and fungi. Results indicate that distinct microbial communities build and inhabit silicified biofabrics through time and that microbial biosignatures shift over the course of lithification. These findings improve our understanding of how microbial communities silicify, the biomarkers they retain, and transitionary impacts that may occur through lithification and burial.}, }
@article {pmid39317790, year = {2024}, author = {Knorr, MA and Contosta, AR and Morrison, EW and Muratore, TJ and Anthony, MA and Stoica, I and Geyer, KM and Simpson, MJ and Frey, SD}, title = {Unexpected sustained soil carbon flux in response to simultaneous warming and nitrogen enrichment compared with single factors alone.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {12}, pages = {2277-2285}, pmid = {39317790}, issn = {2397-334X}, mesh = {*Soil/chemistry ; *Nitrogen/analysis/metabolism ; *Carbon Cycle ; *Carbon/analysis/metabolism ; Global Warming ; Forests ; Climate Change ; }, abstract = {Recent observations document that long-term soil warming in a temperate deciduous forest leads to significant soil carbon loss, whereas chronic soil nitrogen enrichment leads to significant soil carbon gain. Most global change experiments like these are single factor, investigating the impacts of one stressor in isolation of others. Because warming and ecosystem nitrogen enrichment are happening concurrently in many parts of the world, we designed a field experiment to test how these two factors, alone and in combination, impact soil carbon cycling. Here, we show that long-term continuous soil warming or nitrogen enrichment when applied alone followed the predicted response, with warming resulting in significant soil carbon loss and nitrogen fertilization tending towards soil carbon gain. The combination treatment showed an unanticipated response, whereby soil respiratory carbon loss was significantly higher than either single factor alone, but without a concomitant decline in soil carbon storage. Observations suggest that when soils are exposed to both factors simultaneously, plant carbon inputs to the soil are enhanced, counterbalancing soil carbon loss and helping maintain soil carbon stocks near control levels. This has implications for both atmospheric CO2 emissions and soil fertility and shows that coupling two important global change drivers results in a distinctive response that was not predicted by the behaviour of the single factors in isolation.}, }
@article {pmid39311575, year = {2024}, author = {Han, C-J and Huang, J-P and Chiang, M-R and Jean, OSM and Nand, N and Etebari, K and Shelomi, M}, title = {The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0098724}, pmid = {39311575}, issn = {1098-5336}, support = {MOST-109-2311-B-002-016-MY3//National Science and Technology Council (NSTC)/ ; 111L7822,112L7814,113L7801//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Cocos/microbiology ; Genetic Variation ; }, abstract = {The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.}, }
@article {pmid39311333, year = {2025}, author = {Deo, R and Lakra, U and Ojha, M and Nigam, VK and Sharma, SR}, title = {Exopolysaccharides in microbial interactions: signalling, quorum sensing, and community dynamics.}, journal = {Natural product research}, volume = {39}, number = {11}, pages = {3224-3239}, doi = {10.1080/14786419.2024.2405867}, pmid = {39311333}, issn = {1478-6427}, mesh = {*Quorum Sensing/physiology ; *Microbial Interactions ; *Polysaccharides, Bacterial/metabolism ; Ecosystem ; Signal Transduction ; }, abstract = {Microbial interactions within diverse ecosystems are intricately governed by the dynamic interplay of exopolysaccharides (EPSs) produced by microorganisms. This review delves into the multifaceted roles of EPS in microbial signalling, quorum sensing (QS), and community dynamics, highlighting their significance in orchestrating cooperative behaviours and shaping community structures. EPSs serve as pivotal signalling molecules, influencing chemical communication and promoting intricate interactions among microorganisms. The integration of EPS into QS mechanisms adds an additional layer of complexity, allowing microorganisms to assess population density and synchronise communal responses. Furthermore, EPSs actively contribute to community dynamics by influencing spatial organisation, adhesion, and resistance to environmental stressors. By providing comprehensive knowledge of EPS dynamics, this review offers valuable insights into microbial ecology, serving as a foundational resource for future research. It will benefit the research community by advancing our understanding of microbial ecosystems, with broad applications in biotechnology, environmental science, and beyond.}, }
@article {pmid39297874, year = {2024}, author = {Castledine, M and Pennycook, J and Newbury, A and Lear, L and Erdos, Z and Lewis, R and Kay, S and Sanders, D and Sünderhauf, D and Buckling, A and Hesse, E and Padfield, D}, title = {Characterizing a stable five-species microbial community for use in experimental evolution and ecology.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {9}, pages = {}, pmid = {39297874}, issn = {1465-2080}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Ecology ; Biological Evolution ; Microbial Interactions ; }, abstract = {Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.}, }
@article {pmid39303870, year = {2024}, author = {McDonagh, F and Tumeo, A and Murray, EK and Hallahan, B and Miliotis, G}, title = {Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva.}, journal = {Journal of global antimicrobial resistance}, volume = {39}, number = {}, pages = {149-152}, doi = {10.1016/j.jgar.2024.08.011}, pmid = {39303870}, issn = {2213-7173}, mesh = {Humans ; *Escherichia coli/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Phylogeny ; *Escherichia coli Infections/microbiology ; *Saliva/microbiology ; Virulence/genetics ; Genotype ; beta-Lactamases/genetics ; Whole Genome Sequencing ; Schizophrenia/genetics/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.<br><br>METHODS: E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n = 55).<br><br>RESULTS: E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.<br><br>CONCLUSION: This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.}, }
@article {pmid39301056, year = {2024}, author = {Smith, L and Fullerton, H and Moyer, CL}, title = {Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama'ehuakanaloa Seamount.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18099}, pmid = {39301056}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; DNA Primers/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama'ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama'ehuakanaloa Seamount.}, }
@article {pmid39303138, year = {2024}, author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R}, title = {Global freshwater distribution of Telonemia protists.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39303138}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; }, abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.}, }
@article {pmid39302483, year = {2024}, author = {Nelson, K and Schloter, M}, title = {Special Collection on Pollution, Bioremediation, and the Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {118}, pmid = {39302483}, issn = {1432-184X}, mesh = {*Biodegradation, Environmental ; *Environmental Pollution ; }, }
@article {pmid39299325, year = {2024}, author = {Ren, W and Ren, G and Kuramae, EE and Bodelier, PLE and Chen, S and Teng, Y and Luo, Y}, title = {Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176295}, doi = {10.1016/j.scitotenv.2024.176295}, pmid = {39299325}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Graphite ; *Metals, Heavy/analysis/metabolism ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Soil/chemistry ; Bacteria/metabolism ; Cadmium/metabolism/analysis ; }, abstract = {Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg[-1] significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %-40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg[-1] after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.}, }
@article {pmid39298326, year = {2024}, author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T}, title = {Establishing human microbial observatory programs in low- and middle-income countries.}, journal = {Annals of the New York Academy of Sciences}, volume = {1540}, number = {1}, pages = {13-20}, doi = {10.1111/nyas.15224}, pmid = {39298326}, issn = {1749-6632}, support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; }, abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.}, }
@article {pmid39296299, year = {2024}, author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F}, title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452101}, pmid = {39296299}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.<br><br>METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.<br><br>RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.<br><br>DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.}, }
@article {pmid39296290, year = {2024}, author = {Wang, Z and Gao, Z and Yu, Y and Li, H and Luo, W and Ji, Z and Ding, H}, title = {New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463144}, pmid = {39296290}, issn = {1664-302X}, abstract = {The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.}, }
@article {pmid39294302, year = {2024}, author = {Sousa, LGV and Novak, J and França, A and Muzny, CA and Cerca, N}, title = {Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {117}, pmid = {39294302}, issn = {1432-184X}, support = {R01AI146065-01A1//National Institute of Allergy and Infectious Diseases/ ; UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.04912.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1377/CT0032//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; R01 AI146065/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms/growth &amp; development ; *Gardnerella vaginalis/genetics ; *Transcriptome ; *Prevotella/genetics/physiology ; Female ; Humans ; Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; }, abstract = {Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other's transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.}, }
@article {pmid39290267, year = {2024}, author = {Zhang, K and Zhang, Q and Qiu, H and Ma, Y and Hou, N and Zhang, J and Kan, C and Han, F and Sun, X and Shi, J}, title = {The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e37609}, pmid = {39290267}, issn = {2405-8440}, abstract = {Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.}, }
@article {pmid39288091, year = {2024}, author = {Liu, X and Salles, JF}, title = {Drivers and consequences of microbial community coalescence.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39288091}, issn = {1751-7370}, support = {//China Scholarship Council and the European Research Council/ ; }, mesh = {*Microbiota ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.}, }
@article {pmid39287748, year = {2024}, author = {Kujawska, M and Neuhaus, K and Huptas, C and Jiménez, E and Arboleya, S and Schaubeck, M and Hall, LJ}, title = {Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39287748}, issn = {1867-1314}, abstract = {Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.}, }
@article {pmid39287688, year = {2024}, author = {Demin, K and Prazdnova, E and Kulikov, M and Mazanko, M and Gorovtsov, A}, title = {Alternative agar substitutes for culturing unculturable microorganisms.}, journal = {Archives of microbiology}, volume = {206}, number = {10}, pages = {405}, pmid = {39287688}, issn = {1432-072X}, support = {SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; }, mesh = {*Agar/chemistry ; *Culture Media/chemistry ; *Polysaccharides, Bacterial/metabolism ; *Bacteria/growth &amp; development/metabolism/drug effects ; Gels/chemistry ; }, abstract = {Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the "familiarity of conditions" hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.}, }
@article {pmid39287374, year = {2024}, author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0058524}, pmid = {39287374}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics &amp; numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics &amp; numerical data ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Young Adult ; }, abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.<br><br>IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.}, }
@article {pmid39283121, year = {2024}, author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR}, title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0211324}, pmid = {39283121}, issn = {2165-0497}, support = {E-26/210.012/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Spores, Bacterial/genetics/growth &amp; development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; }, abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.}, }
@article {pmid39282566, year = {2024}, author = {Abdelshafy Mohamad, OA and Liu, YH and Huang, Y and Kuchkarova, N and Dong, L and Jiao, JY and Fang, BZ and Ma, JB and Hatab, S and Li, WJ}, title = {Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439798}, pmid = {39282566}, issn = {1664-302X}, abstract = {In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties. The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture.}, }
@article {pmid39282232, year = {2024}, author = {Taylor, T and Daksa, J and Shimels, MZ and Etalo, DW and Thiombiano, B and Walmsey, A and Chen, AJ and Bouwmeester, HJ and Raaijmakers, JM and Brady, SM and Kawa, D}, title = {Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum.}, journal = {Bio-protocol}, volume = {14}, number = {17}, pages = {e5058}, pmid = {39282232}, issn = {2331-8325}, abstract = {The root parasitic weed Striga hermonthica has a devastating effect on sorghum and other cereal crops in Sub-Saharan Africa. Available Striga management strategies are rarely sufficient or not widely accessible or affordable. Identification of soil- or plant-associated microorganisms that interfere in the Striga infection cycle holds potential for development of complementary biological control measures. Such inoculants should be preferably based on microbes native to the regions of their application. We developed a method to assess microbiome-based soil suppressiveness to Striga with a minimal amount of field-collected soil. We previously used this method to identify the mechanisms of microbe-mediated suppression of Striga infection and to test individual microbial strains. Here, we present protocols to assess the functional potential of the soil microbiome and individual bacterial taxa that adversely affect Striga parasitism in sorghum via three major known suppression mechanisms. These methods can be further extended to other Striga hosts and other root parasitic weeds. Key features • This protocol provides a detailed description of the methods used in Kawa et al. [1]. • This protocol is optimized to assess soil suppressiveness to Striga infection by using natural field-collected soil and the same soil sterilized by gamma-radiation. • This protocol is optimized to test bacterial (and not fungal) isolates. • This protocol can be easily extended to other host-parasite-microbiome systems.}, }
@article {pmid39277779, year = {2024}, author = {Boltz, JP and Rittmann, BE}, title = {Microbial ecology of nitrate-, selenate-, selenite-, and sulfate-reducing bacteria in a H2-driven bioprocess.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39277779}, issn = {1574-6941}, mesh = {*Nitrates/metabolism ; *Sulfates/metabolism ; *Bioreactors/microbiology ; *Selenic Acid/metabolism ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development/classification ; *Selenious Acid/metabolism ; *Oxidation-Reduction ; Wastewater/microbiology ; Selenium Compounds/metabolism ; Biofilms/growth &amp; development ; Autotrophic Processes ; }, abstract = {A hydrogen (H2)-based membrane biofilm reactor (H2-MBfR) can reduce electron acceptors nitrate (NO3-), selenate (SeO42-), selenite (HSeO3-), and sulfate (SO42-), which are in wastewaters from coal mining and combustion. This work presents a model to describe a H2-driven microbial community comprised of hydrogenotrophic and heterotrophic bacteria that respire NO3-, SeO42-, HSeO3-, and SO42-. The model provides mechanistic insights into the interactions between autotrophic and heterotrophic bacteria in a microbial community that is founded on H2-based autotrophy. Simulations were carried out for a range of relevant solids retention times (SRT; 0.1-20 days) and with adequate H2-delivery capacity to reduce all electron acceptors. Bacterial activity began at an ∼0.6-day SRT, when hydrogenotrophic denitrifiers began to accumulate. Selenate-reducing and selenite-reducing hydrogenotrophs became established next, at SRTs of ∼1.2 and 2 days, respectively. Full NO3-, SeO42-, and HSeO3- reductions were complete by an SRT of ∼5 days. SO42- reduction began at an SRT of ∼10 days and was complete by ∼15 days. The desired goal of reducing NO3-, SeO42-, and HSeO3-, but not SO42-, was achievable within an SRT window of 5-10 days. Autotrophic hydrogenotrophs dominated the active biomass, but nonactive solids were a major portion of the solids, especially for an SRT ≥ 5 days.}, }
@article {pmid39267336, year = {2024}, author = {Du, X and Guo, Y and Zhao, X and Zhang, L and Fan, R and Li, Y}, title = {METTL3-mediated TIM1 promotes macrophage M1 polarization and inflammation through IGF2BP2-dependent manner.}, journal = {Journal of biochemical and molecular toxicology}, volume = {38}, number = {10}, pages = {e23845}, doi = {10.1002/jbt.23845}, pmid = {39267336}, issn = {1099-0461}, support = {20210302124578//This study was supported by the Shanxi Province Basic Research Program Project/ ; }, mesh = {Humans ; *Macrophages/metabolism ; *Inflammation/metabolism/pathology/genetics ; *Hepatitis A Virus Cellular Receptor 1/metabolism/genetics ; *Methyltransferases/metabolism/genetics ; *RNA-Binding Proteins/metabolism/genetics ; THP-1 Cells ; Lipopolysaccharides/pharmacology ; }, abstract = {Macrophage polarization and inflammation may play an important role in the development of sepsis. T-cell immunoglobulin mucin 1 (TIM1) has been demonstrated to promote macrophage inflammatory responses. However, whether TIM1 regulates macrophage polarization and inflammation to affect sepsis development remains unclear. Human monocytic leukemia cell line was induced into macrophages, followed by stimulated with LPS and IL-4 to induce M1 polarization and M2 polarization. The expression levels of TIM1, methyltransferase 3 (METTL3), and insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) were examined by qRT-PCR and western blot. IL-6, IL-1β, and TNF-α levels were tested by ELISA. CD86[+]cell rate was analyzed by flow cytometry. The m[6]A methylation level of TIM1 was assessed by MeRIP assay. The interaction of between TIM1 and METTL3 or IGF2BP2 was assessed by dual-luciferase reporter assay and RIP assay. TIM1 knockdown repressed LPS-induced macrophage M1 polarization and inflammation. In terms of mechanism, METTL3 promoted TIM1 expression through m[6]A modification, and this modification could be recognized by IGF2BP2. Besides, knockdown of METTL3/IGF2BP2 suppressed LPS-induced macrophage M1 polarization and inflammation, while this effect could be eliminated by TIM1 overexpression. METTL3/IGF2BP2/TIM1 axis promoted macrophage M1 polarization and inflammation, which might provide potential target for sepsis treatment.}, }
@article {pmid39273112, year = {2024}, author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T}, title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273112}, issn = {1422-0067}, mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; }, abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.}, }
@article {pmid39272492, year = {2024}, author = {Nerini, M and Russo, A and Decorosi, F and Meriggi, N and Viti, C and Cavalieri, D and Marvasi, M}, title = {A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39272492}, issn = {2304-8158}, support = {2/SSL/16/TO-1/ICR/21/TO//Regione Toscana with the project PO FEAMP 2014-2020 - Misura 1.39 SSL FLAG Costa degli Etrusch/ ; }, abstract = {BACKGROUND: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity.<br><br>METHODS: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h.<br><br>RESULTS: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as &#x3b1;-cyclodextrin, D-cellobiose, glycogen, &#x3b1;-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.}, }
@article {pmid39268533, year = {2024}, author = {Wilson, T and Siddiqi, M and Xi, Y and LaPointe, G}, title = {Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1404795}, pmid = {39268533}, issn = {1664-302X}, abstract = {Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.}, }
@article {pmid39266780, year = {2024}, author = {Cao, X and Li, M and Wu, X and Fan, S and Lin, L and Xu, L and Zhang, X and Zhou, F}, title = {Gut fungal diversity across different life stages of the onion fly Delia antiqua.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {115}, pmid = {39266780}, issn = {1432-184X}, mesh = {Animals ; *Diptera/microbiology/growth &amp; development ; *Fungi/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; Male ; Female ; Pupa/microbiology/growth &amp; development ; Biodiversity ; Life Cycle Stages ; Mycobiome ; }, abstract = {A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.}, }
@article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, }
@article {pmid39264809, year = {2024}, author = {Boverhoff, D and Kool, J and Pijnacker, R and Ducarmon, QR and Zeller, G and Shetty, S and Sie, S and Mulder, AC and van der Klis, F and Franz, E and Mughini-Gras, L and van Baarle, D and Fuentes, S}, title = {Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114729}, doi = {10.1016/j.celrep.2024.114729}, pmid = {39264809}, issn = {2211-1247}, mesh = {Netherlands ; Humans ; *Feces/microbiology ; Adult ; Aged ; Middle Aged ; Adolescent ; Child, Preschool ; Aged, 80 and over ; Child ; Infant ; Male ; Female ; Young Adult ; Infant, Newborn ; Longevity ; Gastrointestinal Microbiome/genetics ; Microbiota ; }, abstract = {Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.}, }
@article {pmid39264366, year = {2024}, author = {Yüksel, E and Voragen, AGJ and Kort, R}, title = {The pectin metabolizing capacity of the human gut microbiota.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/10408398.2024.2400235}, pmid = {39264366}, issn = {1549-7852}, abstract = {The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.}, }
@article {pmid39264291, year = {2024}, author = {Jones, BS and DeWitt, ME and Wenner, JJ and Sanders, JW}, title = {Lyme Disease Under-Ascertainment During the COVID-19 Pandemic in the United States: Retrospective Study.}, journal = {JMIR public health and surveillance}, volume = {10}, number = {}, pages = {e56571}, pmid = {39264291}, issn = {2369-2960}, mesh = {Humans ; *Lyme Disease/epidemiology ; *COVID-19/epidemiology ; United States/epidemiology ; North Carolina/epidemiology ; Retrospective Studies ; Pandemics ; Bayes Theorem ; }, abstract = {BACKGROUND: The COVID-19 pandemic resulted in a massive disruption in access to care and thus passive, hospital- and clinic-based surveillance programs. In 2020, the reported cases of Lyme disease were the lowest both across the United States and North Carolina in recent years. During this period, human contact patterns began to shift with higher rates of greenspace utilization and outdoor activities, putting more people into contact with potential vectors and associated vector-borne diseases. Lyme disease reporting relies on passive surveillance systems, which were likely disrupted by changes in health care-seeking behavior during the pandemic.<br><br>OBJECTIVE: This study aimed to quantify the likely under-ascertainment of cases of Lyme disease during the COVID-19 pandemic in the United States and North Carolina.<br><br>METHODS: We fitted publicly available, reported Lyme disease cases for both the United States and North Carolina prior to the year 2020 to predict the number of anticipated Lyme disease cases in the absence of the pandemic using a Bayesian modeling approach. We then compared the ratio of reported cases divided by the predicted cases to quantify the number of likely under-ascertained cases. We then fitted geospatial models to further quantify the spatial distribution of the likely under-ascertained cases and characterize spatial dynamics at local scales.<br><br>RESULTS: Reported cases of Lyme Disease were lower in 2020 in both the United States and North Carolina than prior years. Our findings suggest that roughly 14,200 cases may have gone undetected given historical trends prior to the pandemic. Furthermore, we estimate that only 40% to 80% of Lyme diseases cases were detected in North Carolina between August 2020 and February 2021, the peak months of the COVID-19 pandemic in both the United States and North Carolina, with prior ascertainment rates returning to normal levels after this period. Our models suggest both strong temporal effects with higher numbers of cases reported in the summer months as well as strong geographic effects.<br><br>CONCLUSIONS: Ascertainment rates of Lyme disease were highly variable during the pandemic period both at national and subnational scales. Our findings suggest that there may have been a substantial number of unreported Lyme disease cases despite an apparent increase in greenspace utilization. The use of counterfactual modeling using spatial and historical trends can provide insight into the likely numbers of missed cases. Variable ascertainment of cases has implications for passive surveillance programs, especially in the trending of disease morbidity and outbreak detection, suggesting that other methods may be appropriate for outbreak detection during disturbances to these passive surveillance systems.}, }
@article {pmid39260494, year = {2024}, author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S}, title = {Metagenomic approaches and opportunities in arid soil research.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176173}, doi = {10.1016/j.scitotenv.2024.176173}, pmid = {39260494}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; }, abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.}, }
@article {pmid39259499, year = {2024}, author = {Schwab, ST and Bühler, LY and Schleheck, D and Nelson, TF and Mecking, S}, title = {Correlation of Enzymatic Depolymerization Rates with the Structure of Polyethylene-Like Long-Chain Aliphatic Polyesters.}, journal = {ACS macro letters}, volume = {13}, number = {10}, pages = {1245-1250}, pmid = {39259499}, issn = {2161-1653}, abstract = {Long-chain aliphatic polyesters are emerging sustainable materials that exhibit polyethylene-like properties while being amenable to chemical recycling and biodegradation. However, varying polyester chemical structures results in markedly different degradation rates, which cannot be predicted from commonly correlated bulk polyester properties, such as polymer melting temperature. To elucidate these structure-degradability relationships, long-chain polyesters varying in their monomer composition and crystallinity were subjected to enzymatic hydrolysis, the rates of which were quantified via detection of formed monomers. Copolymers with poorly water-soluble, long-chain diol monomers (e.g., 1,18-octadecanediol) demonstrated strongly reduced depolymerization rates compared to copolymers with shorter chain length diol monomers. This was illustrated by, e.g., the 20× faster hydrolysis of PE-4,18, consisting of 1,4-butanediol and 1,18-octadecanedicarboxylic acid monomers, relative to PE-18,4. The insoluble long-chain diol monomer released upon hydrolysis was proposed to remain attached to the bulk polymer surface, decreasing the accessibility of the remaining ester bonds to enzymes for further hydrolysis. Tuning of polyester crystallinity via the introduction of branched monomers led to variable hydrolysis rates, which increased by an order of magnitude when crystallinity decreased from 72% to 45%. The results reported enables the informed design of polyester structures with balanced material properties and amenability to depolymerization.}, }
@article {pmid39259393, year = {2024}, author = {Berlow, M and Mesa, M and Creek, M and Duarte, JG and Carpenter, E and Phinizy, B and Andonian, K and Dlugosch, KM}, title = {Plant G × Microbial E: Plant Genotype Interaction with Soil Bacterial Community Shapes Rhizosphere Composition During Invasion.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {113}, pmid = {39259393}, issn = {1432-184X}, support = {1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 2023-67012-40306//USDA/ ; 2023-67013-40169//USDA/ ; 2023-67013-40169//USDA/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Introduced Species ; *Genotype ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Centaurea/microbiology/genetics ; Plant Roots/microbiology ; California ; Soil/chemistry ; }, abstract = {It is increasingly recognized that different genetic variants of hosts can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for their microbial associations to change during invasion as a result. We asked whether host genotype (G), microbial environment (E), or their interaction (G × E) affected the composition and diversity of host-associated microbiomes in Centaurea solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes and phenotypes and to have altered microbial interactions, in its severe invasion of CA, USA. We conducted an experiment in which native and invading plant genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that native and invading plant genotypes accumulated different microbial associations at the family level in each soil community, often counter to differences in family abundance between soil communities. Root associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range field soil and accumulated on invading genotypes. We also found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Thus variation in microbial associations of invaders was driven by the interaction of plant G and microbial E, and rhizosphere microbial communities appear to change in composition in response to host evolution during invasion.}, }
@article {pmid39259373, year = {2024}, author = {Zhang, K and Tan, X and Zhang, Q}, title = {Nutritional Quality of Basal Resource in Stream Food Webs Increased with Light Reduction-Implications for Riparian Revegetation.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {114}, pmid = {39259373}, issn = {1432-184X}, support = {Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; }, mesh = {*Rivers/microbiology/chemistry ; *Food Chain ; *Fatty Acids, Unsaturated/analysis/metabolism ; *Light ; Cyanobacteria/metabolism/growth &amp; development ; Chlorophyta/metabolism/growth &amp; development ; Diatoms/metabolism/growth &amp; development ; Nutritive Value ; }, abstract = {Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.}, }
@article {pmid39258201, year = {2024}, author = {Iliopoulou, S and Kourteli, M and Damialis, A and Kapsanaki-Gotsi, E and Pyrri, I}, title = {Air mycobiome in the National Library of Greece following relocation to novel premises.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36362}, pmid = {39258201}, issn = {2405-8440}, abstract = {The aim of this work was to study the diversity and spatiotemporal fluctuations of airborne fungi in the National Library of Greece after its relocation from the Vallianeio historic building in the center of Athens to entirely new premises at the Stavros Niarchos Foundation Cultural Center, and also to compare the fungal aerosol in between the two sites. The air mycobiota were studied by a volumetric culture-based method, during the year 2019 in order to assess their diversity and abundance and to compare with those previously reported in the historic building. Twenty-eight genera of filamentous fungi were recovered indoors and 17 outdoors, in addition to yeasts registered as a group. The number of fungal genera recovered was almost similar in both premises, whereas seventeen genera indoors were identical, dominated by Penicillium, Cladosporium and Aspergillus. The mean daily fungal concentration was found to be 66 CFU m[-3] indoors and 927 CFU m[-3] outdoors in the new location vs 293 and 428 CFU m[-] [3] indoors and 707 and 648 CFU m[-] [3] outdoors in the previous one. The mean daily concentration indoors was consistently and significantly lower (P < 0.05) in the new building than in the historic one, although it was higher outdoors. The indoor/outdoor ratio for the total fungi was 0.07 in the new vs 0.41 and 0.66 in the previous one and reveals a superior indoor air quality in the new site. Air temperature and occupancy had a statistically significant impact on the concentration of indoor fungi. The remarkably reduced concentration of the mycobiota in the new premises indicated a considerable decline in fungal burden, mainly due to technological excellency of the facility and continuous preventive measures to ensure an enhanced indoor air quality in the National Library of Greece. This case study provides a paradigm about upgrading of indoor air after re-establishment of a facility in another setting.}, }
@article {pmid39256405, year = {2024}, author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y}, title = {Author Correction: Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21131}, doi = {10.1038/s41598-024-71652-4}, pmid = {39256405}, issn = {2045-2322}, }
@article {pmid39256399, year = {2024}, author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ}, title = {Author Correction: Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7910}, doi = {10.1038/s41467-024-52322-5}, pmid = {39256399}, issn = {2041-1723}, }
@article {pmid39255667, year = {2024}, author = {Mei, Z and Wang, F and Fu, Y and Liu, Y and Hashsham, SA and Wang, Y and Harindintwali, JD and Dou, Q and Virta, M and Jiang, X and Deng, Y and Zhang, T and Tiedje, JM}, title = {Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135721}, pmid = {39255667}, issn = {1873-3336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Sulfadiazine/pharmacology ; *Biofilms/drug effects ; *Trimethoprim/pharmacology ; *Soil Pollutants/toxicity ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Manure/microbiology ; Arthrobacter/genetics/drug effects/metabolism ; Charcoal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.}, }
@article {pmid39254334, year = {2024}, author = {Lyng, M and Þórisdóttir, B and Sveinsdóttir, SH and Hansen, ML and Jelsbak, L and Maróti, G and Kovács, &#xc1;T}, title = {Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0021224}, pmid = {39254334}, issn = {2379-5077}, support = {DNRF137//Danmarks Grundforskningsfond (DNRF)/ ; NNF19SA0059360//Novo Nordisk Fonden (NNF)/ ; NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; PhD fellowship//Technical University of Denmark/ ; }, mesh = {*Pseudomonas/physiology ; *Bacillus subtilis/physiology ; *Soil Microbiology ; *Microbial Interactions/physiology ; Rhizosphere ; }, abstract = {UNLABELLED: Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.<br><br>IMPORTANCE: There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.}, }
@article {pmid39252061, year = {2024}, author = {Trego, A and O'Sullivan, S and O'Flaherty, V and Collins, G and Ijaz, UZ}, title = {Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {68}, pmid = {39252061}, issn = {2524-6372}, support = {3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 17/CDA/4658/SFI_/Science Foundation Ireland/Ireland ; NE/L011956/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs).<br><br>RESULTS: Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter.<br><br>CONCLUSIONS: We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.}, }
@article {pmid39250422, year = {2024}, author = {Vijay, S and Bao, NLH and Vinh, DN and Nhat, LTH and Thu, DDA and Quang, NL and Trieu, LPT and Nhung, HN and Ha, VTN and Thai, PVK and Ha, DTM and Lan, NH and Caws, M and Thwaites, GE and Javid, B and Thuong, NT}, title = {Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39250422}, issn = {2050-084X}, support = {10.35802/207487/WT_/Wellcome Trust/United Kingdom ; R21 AI169005/AI/NIAID NIH HHS/United States ; R21AI169005//National Institute of Allergy and Infectious Diseases/ ; 10.35802/106680/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 10.35802/206724/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Rifampin/pharmacology ; *Mycobacterium tuberculosis/drug effects/genetics ; *Isoniazid/pharmacology ; Longitudinal Studies ; *Microbial Sensitivity Tests ; Humans ; *Antitubercular Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Tuberculosis/microbiology/drug therapy ; }, abstract = {Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.}, }
@article {pmid39249553, year = {2024}, author = {Morimura, H and Ishigami, K and Sato, T and Sone, T and Kikuchi, Y}, title = {Geographical, Seasonal, and Growth-Related Dynamics of Gut Microbiota in a Grapevine Pest, Apolygus spinolae (Heteroptera: Miridae).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {112}, pmid = {39249553}, issn = {1432-184X}, support = {22KJ0057//Japan Society for the Promotion of Science/ ; 21K20579//Japan Society for the Promotion of Science/ ; S-3-7//Northern Advancement Center for Science and Technology/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Vitis/microbiology ; *Heteroptera/microbiology/growth &amp; development ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Symbiosis ; Japan ; Nymph/microbiology/growth &amp; development ; }, abstract = {A number of insects are associated with gut symbiotic microorganisms, wherein symbiotic partners play pivotal metabolic roles for each other such as nutrient supplementation, diet degradation, and pesticide detoxification. Despite the ecological and evolutionary importance of gut microbial communities in insects, their diversity and dynamics remain unclear in many species. The green plant bug Apolygus spinolae, a notorious grapevine pest in Japan, damages grape shoots and severely reduces grape berry yield and quality. The plant bug possesses a simple tubular gut housing ~ 10[4] bacteria. Here, we investigated geographic, seasonal, and growth-related dynamics of gut microbiota by high-throughput sequencing in 82 individuals (11 nymphs and 71 adults) from five locations in Hokkaido, Japan. In plant bugs, gut microbiota changed dynamically depending on region, season, and developmental stage. Among the gut bacteria, Serratia was consistently and abundantly detected and was significantly affected by seasonal changes. In addition, Caballeronia, known as a specific symbiont in some stinkbug species, was abundantly detected, especially in insects collected in late summer despite A. spinolae complete lack of midgut crypts known as symbiotic organ harboring Caballeronia in other stinkbug species. Considering their prevalence among host bug populations, it is possible these gut microorganisms play a pivotal role in the adaptation of the green plant bug to grapevine fields, although further confirmation through rearing experiments is needed.}, }
@article {pmid39248572, year = {2024}, author = {Sivaloganathan, DM and Wan, X and Leon, G and Brynildsen, MP}, title = {Loss of Gre factors leads to phenotypic heterogeneity and cheating in Escherichia coli populations under nitric oxide stress.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0222924}, pmid = {39248572}, issn = {2150-7511}, support = {CBET-1453325//National Science Foundation (NSF)/ ; PGSD3 - 516782 - 2018//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Focused Research Team award on Precision Antibiotics//Princeton University (PU)/ ; }, mesh = {*Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Peroxide/pharmacology/metabolism/toxicity ; *Nitric Oxide/metabolism ; Phenotype ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptional Elongation Factors/metabolism/genetics ; }, abstract = {Nitric oxide (·NO) is one of the toxic metabolites that bacteria can be exposed to within phagosomes. Gre factors, which are also known as transcript cleavage factors or transcription elongation factors, relieve back-tracked transcription elongation complexes by cleaving nascent RNAs, which allows transcription to resume after stalling. Here we discovered that loss of both Gre factors in Escherichia coli, GreA and GreB, significantly compromised ·NO detoxification due to ·NO-induced phenotypic heterogeneity in ΔgreAΔgreB populations, which did not occur in wild-type cultures. Under normal culturing conditions, both wild-type and ΔgreAΔgreB synthesized transcripts uniformly, whereas treatment with ·NO led to bimodal transcript levels in ΔgreAΔgreB that were unimodal in wild-type. Interestingly, exposure to another toxic metabolite of phagosomes, hydrogen peroxide (H2O2), produced analogous results. Furthermore, we showed that loss of Gre factors led to cheating under ·NO stress where transcriptionally deficient cells benefited from the detoxification activities of the transcriptionally proficient subpopulation. Collectively, these results show that loss of Gre factor activities produces phenotypic heterogeneity under ·NO and H2O2 stress that can yield cheating between subpopulations.IMPORTANCEToxic metabolite stress occurs in a broad range of contexts that are important to human health, microbial ecology, and biotechnology, whereas Gre factors are highly conserved throughout the bacterial kingdom. Here we discovered that loss of Gre factors in E. coli leads to phenotypic heterogeneity under ·NO and H2O2 stress, which we further show with ·NO results in cheating between subpopulations. Collectively, these data suggest that Gre factors play a role in coping with toxic metabolite stress, and that loss of Gre factors can produce cheating between neighbors.}, }
@article {pmid39248476, year = {2024}, author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Niestrawska, A and Mucha, J}, title = {The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0080724}, pmid = {39248476}, issn = {2165-0497}, mesh = {*Pinus sylvestris/microbiology ; *Endophytes/classification/isolation &amp; purification/genetics/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics/physiology ; *Plant Roots/microbiology ; *Microbiota ; Seasons ; Phylogeny ; Biodiversity ; }, abstract = {UNLABELLED: Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.<br><br>IMPORTANCE: This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.}, }
@article {pmid39248406, year = {2024}, author = {Yuan, X and Qing, J and Zhi, W and Wu, F and Yan, Y and Li, Y}, title = {Gut and respiratory microbiota landscapes in IgA nephropathy: a cross-sectional study.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2399749}, pmid = {39248406}, issn = {1525-6049}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Machine Learning ; Case-Control Studies ; Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Young Adult ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is intimately linked to mucosal immune responses, with nasopharyngeal and intestinal lymphoid tissues being crucial for its abnormal mucosal immunity. The specific pathogenic bacteria in these sites associated with IgAN, however, remain elusive. Our study employs 16S rRNA sequencing and machine learning (ML) approaches to identify specific pathogenic bacteria in these locations and to investigate common pathogens that may exacerbate IgAN.<br><br>METHODS: In this cross-sectional analysis, we collected pharyngeal swabs and stool specimens from IgAN patients and healthy controls. We applied 16SrRNA sequencing to identify differential microbial populations. ML algorithms were then used to classify IgAN based on these microbial differences. Spearman correlation analysis was employed to link key bacteria with clinical parameters.<br><br>RESULTS: We observed a reduced microbial diversity in IgAN patients compared to healthy controls. In the gut microbiota of IgAN patients, increases in Bacteroides, Escherichia-Shigella, and Parabacteroides, and decreases in Parasutterella, Dialister, Faecalibacterium, and Subdoligranulum were notable. In the respiratory microbiota, increases in Neisseria, Streptococcus, Fusobacterium, Porphyromonas, and Ralstonia, and decreases in Prevotella, Leptotrichia, and Veillonella were observed. Post-immunosuppressive therapy, Oxalobacter and Butyricoccus levels were significantly reduced in the gut, while Neisseria and Actinobacillus levels decreased in the respiratory tract. Veillonella and Fusobacterium appeared to influence IgAN through dual immune loci, with Fusobacterium abundance correlating with IgAN severity.<br><br>CONCLUSIONS: This study revealing that changes in flora structure could provide important pathological insights for identifying therapeutic targets, and ML could facilitate noninvasive diagnostic methods for IgAN.}, }
@article {pmid39247694, year = {2024}, author = {Nasher, F and Wren, BW}, title = {Unravelling mechanisms of bacterial recognition by Acanthamoeba: insights into microbial ecology and immune responses.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1405133}, pmid = {39247694}, issn = {1664-302X}, abstract = {Acanthamoeba, are ubiquitous eukaryotic microorganisms, that play a pivotal role in recognizing and engulfing various microbes during predation, offering insights into microbial dynamics and immune responses. An intriguing observation lies in the apparent preference of Acanthamoeba for Gram-negative over Gram-positive bacteria, suggesting potential differences in the recognition and response mechanisms to bacterial prey. Here, we comprehensively review pattern recognition receptors (PRRs) and microbe associated molecular patterns (MAMPs) that influence Acanthamoeba interactions with bacteria. We analyze the molecular mechanisms underlying these interactions, and the key finding of this review is that Acanthamoeba exhibits an affinity for bacterial cell surface appendages that are decorated with carbohydrates. Notably, this parallels warm-blooded immune cells, underscoring a conserved evolutionary strategy in microbial recognition. This review aims to serve as a foundation for exploring PRRs and MAMPs. These insights enhance our understanding of ecological and evolutionary dynamics in microbial interactions and shed light on fundamental principles governing immune responses. Leveraging Acanthamoeba as a model organism, provides a bridge between ecological interactions and immunology, offering valuable perspectives for future research.}, }
@article {pmid39247294, year = {2024}, author = {Grimm, H and Drabesch, S and Nicol, A and Straub, D and Joshi, P and Zarfl, C and Planer-Friedrich, B and Muehe, EM and Kappler, A}, title = {Arsenic immobilization and greenhouse gas emission depend on quantity and frequency of nitrogen fertilization in paddy soil.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e35706}, pmid = {39247294}, issn = {2405-8440}, abstract = {Nitrogen (N) fertilization in paddy soils decreases arsenic mobility and methane emissions. However, it is unknown how quantity and frequency of N fertilization affects the interlinked redox reactions of iron(II)-driven denitrification, iron mineral (trans-)formation with subsequent arsenic (im-)mobilization, methane and nitrous oxide emissions, and how this links to microbiome composition. Thus, we incubated paddy soil from Vercelli, Italy, over 129 days and applied nitrate fertilizer at different concentrations (control: 0, low: ∼35, medium: ∼100, high: ∼200 mg N kg[-1] soil[-1]) once at the beginning and after 49 days. In the high N treatment, nitrate reduction was coupled to oxidation of dissolved and solid-phase iron(II), while naturally occurring arsenic was retained on iron minerals due to suppression of reductive iron(III) mineral dissolution. In the low N treatment, 40 μg L[-1] of arsenic was mobilized into solution after nitrate depletion, with 69 % being immobilized after a second nitrate application. In the non-fertilized control, concentrations of dissolved arsenic were as high as 76 μg L[-1], driven by mobilization of 36 % of the initial mineral-bound arsenic. Generally, N fertilization led to 1.5-fold higher total GHG emissions (sum of CO2, CH4 and N2O as CO2 equivalents), 158-fold higher N2O, and 7.5-fold lower CH4 emissions compared to non-fertilization. On day 37, Gallionellaceae, Comamonadaceae and Rhodospirillales were more abundant in the high N treatment compared to the non-fertilized control, indicating their potential role as key players in nitrate reduction coupled to iron(II) oxidation. The findings underscore the dual effect of N fertilization, immobilizing arsenic in the short-term (low/medium N) or long-term (high N), while simultaneously increasing N2O and lowering CH4 emissions. This highlights the significance of both the quantity and frequency of N fertilizer application in paddy soils.}, }
@article {pmid39244747, year = {2024}, author = {Bayer, B and Liu, S and Louie, K and Northen, TR and Wagner, M and Daims, H and Carlson, CA and Santoro, AE}, title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39244747}, issn = {1751-7370}, support = {J 4426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Seawater/microbiology ; *Nitrification ; Oceans and Seas ; Nitrites/metabolism ; Heterotrophic Processes ; Microbial Interactions ; Metabolome ; Coculture Techniques ; Ammonia/metabolism ; }, abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.}, }
@article {pmid39244369, year = {2024}, author = {Baptista, RC and Ferrocino, I and Pavani, M and Guerreiro, TM and Câmara, AA and Lang, &#xc9; and Dos Santos, JLP and Catharino, RR and Alves Filho, EG and Rodrigues, S and de Brito, ES and Caturla, MYR and Sant'Ana, AS and Cocolin, L}, title = {Microbiota diversity of three Brazilian native fishes during ice and frozen storage.}, journal = {Food microbiology}, volume = {124}, number = {}, pages = {104617}, doi = {10.1016/j.fm.2024.104617}, pmid = {39244369}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Storage ; *Fishes/microbiology ; Brazil ; *Seafood/microbiology/analysis ; *RNA, Ribosomal, 16S/genetics ; *Freezing ; Ice ; Food Microbiology ; Biodiversity ; Female ; }, abstract = {This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. [1]H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.}, }
@article {pmid39243903, year = {2024}, author = {Macedo Silva, JR and Petra de Oliveira Barros, V and Terceiro, PS and Nunes de Oliveira, &#xcd; and Francisco da Silva Moura, O and Duarte de Freitas, J and Crispim, AC and Maciel Melo, VM and Thompson, FL and Maraschin, M and Landell, MF}, title = {Brazilian mangrove sediments as a source of biosurfactant-producing yeast Pichia pseudolambica for bioremediation.}, journal = {Chemosphere}, volume = {365}, number = {}, pages = {143285}, doi = {10.1016/j.chemosphere.2024.143285}, pmid = {39243903}, issn = {1879-1298}, mesh = {*Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; Brazil ; *Pichia/metabolism ; *Geologic Sediments/microbiology/chemistry ; Surface Tension ; Wetlands ; Hydrocarbons/metabolism ; }, abstract = {This work highlights the biosurfactant production potential of yeasts from mangroves in northeastern Brazil. The biosurfactants were evaluated by their emulsifying capacity (EI24), with 6 isolates showing values between 50% and 62%. Surfactant properties from crude extract were measured using drop collapse, oil displacement, Parafilm® M, surface tension and critical micellar concentration tests. The effects of temperature, salinity, pH, and the ability to emulsify different hydrocarbons were analyzed, showing a promising potential of the yeast species investigated to tolerance to high temperatures and acidic pH, in addition to emulsifying different sources of hydrocarbons with environmental impact. It is important to note that the Pichia pseudolambica isolates showed a remarkable ability to reduce the surface tension of water, from 70.82 mN/m to 36.47 mN/m. In addition, the critical micellar concentration (CMC) values ranged from 7 to 16 mg/mL, highlighting the promising surfactant activity of these isolates for future applications. It was identified that the biosurfactant adhered to the yeast cell wall, and FTIR and 1H NMR spectroscopy analysis was carried out on the yeast biomass and its post-sonication supernatant. The results indicate the presence of characteristic functional groups and peaks found in biosurfactants of a glycolipid nature. Taking together the results reveals the promising potential of biosurfactant biosynthesis of P. pseudolambica yeast, a trait not reported in the literature so far for this species. P. pseudolambica presents a relevant metabolic potential for alternative substrate use and resilience to adverse conditions that could enable it to produce biosurfactants for the biotechnological remediation of areas contaminated by oil derivatives. The metabolic properties herein investigated, together with their presence in Brazilian mangroves, make P. pseudolambica an emerging candidate for developing industrial processes and sustainable strategies for the recovery of ecosystems impacted by oil spills, being positioned as a sustainable alternative to conventional surfactants.}, }
@article {pmid39243542, year = {2024}, author = {Song, Y and Zhang, Z and Liu, Y and Peng, F and Feng, Y}, title = {Enhancement of anaerobic treatment of antibiotic pharmaceutical wastewater through the development of iron-based and carbon-based materials: A critical review.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135514}, doi = {10.1016/j.jhazmat.2024.135514}, pmid = {39243542}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; Carbon/chemistry ; Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; Water Purification/methods ; }, abstract = {The extensive use of antibiotics has created an urgent need to address antibiotic wastewater treatment, posing significant challenges for environmental protection and public health. Recent advances in the efficacy and mechanisms of conductive materials (CMs) for enhancing the anaerobic biological treatment of antibiotic pharmaceutical wastewater are reviewed. For the first time, the focus is on the various application forms of iron-based and carbon-based CMs in strengthening the anaerobic methanogenic system. This includes the use of single CMs such as zero-valent iron (ZVI), magnetite, biochar (BC), activated carbon (AC), and graphene (GP), as well as iron-based and carbon-based composite CMs with diverse structures. These structures include mixed, surface-loaded, and core-shell combinations, reflecting the development of CMs. Iron-based and carbon-based CMs promote the rapid removal of antibiotics through adsorption and enhanced biodegradation. They also mitigate the inhibitory effects of toxic pollutants on microbial activity and reduce the expression of antibiotic resistance genes (ARGs). Additionally, as effective electron carriers, these CMs enrich microorganisms with direct interspecies electron transfer (DIET) functions, accelerate interspecies electron transfer, and facilitate the conversion of organic matter into methane. Finally, this review proposes the use of advanced molecular detection technologies to clarify microbial ecology and metabolic mechanisms, along with microscopic characterization techniques for the modification of CMs. These methods can provide more direct evidence to analyze the mechanisms underlying the cooperative anaerobic treatment of refractory organic wastewater by CMs and microorganisms.}, }
@article {pmid39239791, year = {2024}, author = {Fouad, AM and Abo-Al-Ela, HG and Negm, EA and Abdelhaseib, M and Alian, A and Abdelsater, N and Said, REM and Anwar, FAS and Assar, DH and Mohamed, SA}, title = {Impact of Polyonchobothrium magnum on health and gut microbial ecology of African catfish (Clarias gariepinus): Insights from morphological, molecular, and microbiological analyses.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14013}, doi = {10.1111/jfd.14013}, pmid = {39239791}, issn = {1365-2761}, abstract = {Parasites pose significant challenges to aquaculture and fisheries industries. Our study focuses on the Polyonchobothrium magnum and African catfish to address a potential health issue in aquaculture, explore host-parasite interactions that can help develop effective management practices to ensure fish health and industry sustainability. P. magnum was isolated from the stomach of African catfish (Clarias gariepinus) as the primary site of infection, with a prevalence of 10%. Most affected fish were heavily infected (8 out of 10). Infection was confirmed by sequencing the PCR-targeted region of the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, along with light and scanning electron microscopes. The parasite had an elongated scolex with deep bothria, a prominent apical disc wider than the scolex itself, and a four-lobed appearance. The scolex contained a central rostellum divided into two semicircles, bearing 26-30 hooks, with an average of 28. The apical disc had large hooks arranged in four quadrants, with 6-8 hooks each, averaging 7 per quadrant. No neck was observed. Phylogenetic analysis of our sequence showed a 100% match with isolates from Guangzhou, China. In infected fish, the anterior kidney showed increased expression levels of nuclear factor kappa B and lysozyme, but decreased levels of in major histocompatibility complex antigen II. Plasma analysis revealed a significant drop in superoxide dismutase, a rise in interleukin-1 beta, and lower IgM levels compared to non-infected controls. Non-infected fish displayed greater gut microbiota diversity, with dominant families including Moraxellaceae, Enterobacteriaceae, Fusobacteriaceae, and Caulobacteraceae, and prevalent genera such as Acinetobacter, Cetobacterium, and Brevundimonas. In contrast, infected fish exhibited very low diversity, with significantly higher proportions of Enterobacteriaceae (45.99%) and Aeromonadaceae (41.79%) compared to non-infected fish, which had 13.76% and 3.64% respectively. Cetobacterium somerae was prevalent in non-infected fish, while infected fish harboured Aeromonas fluvialis, Plesiomonas shigelloides, and Gallaecimonas xiamenensis. Overall, P. magnum disrupted the immune status and gut microbiota of the host, thereby impacting its health.}, }
@article {pmid39236824, year = {2024}, author = {Guo, Q and Xiao, Y and Zhu, Y and Korpelainen, H and Li, C}, title = {Selenium availability in tea: Unraveling the role of microbiota assembly and functions.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175995}, doi = {10.1016/j.scitotenv.2024.175995}, pmid = {39236824}, issn = {1879-1026}, mesh = {*Selenium/metabolism/analysis ; *Microbiota ; *Camellia sinensis/metabolism ; *Soil Microbiology ; Tea ; Soil/chemistry ; Soil Pollutants/metabolism/analysis ; Bacteria/metabolism ; }, abstract = {Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4[+] and NO3[-] contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.}, }
@article {pmid39236233, year = {2024}, author = {Richards, L and Cremin, K and Coates, M and Vigor, F and Schäfer, P and Soyer, OS}, title = {Ammonia leakage can underpin nitrogen-sharing among soil microorganisms.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39236233}, issn = {1751-7370}, support = {//Gordon and Betty Moore Foundation/ ; //Midlands Integrative Biosciences Training Partnership/ ; P3141153//Baden-W&#xfc;rttemberg Stiftung/ ; }, mesh = {*Ammonia/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Nitrates/metabolism ; *Bacillus subtilis/metabolism/growth &amp; development/genetics ; Soil/chemistry ; Microbial Interactions ; Hydrogen-Ion Concentration ; Ammonium Compounds/metabolism ; }, abstract = {Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.}, }
@article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, }
@article {pmid39235736, year = {2025}, author = {Islam, DT and Mobasser, S and Kotaru, S and Telli, AE and Telli, N and Cupples, AM and Hashsham, SA}, title = {Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {47-64}, pmid = {39235736}, issn = {1940-6029}, mesh = {*Graphite/chemistry ; *Electrodes ; *Electrochemical Techniques/methods/instrumentation ; *Biosensing Techniques/methods/instrumentation ; Nucleic Acids/analysis ; Humans ; DNA/analysis ; }, abstract = {Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). There are numerous modifications to the electrode surfaces as well (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). These approaches offer distinct advantages, primarily due to their demonstrated superior limit of detection without amplification. Using the SPEs and potentiostats, we can detect cells, proteins, DNA, and RNA concentrations in the nanomolar (nM) to attomolar (aM) range. The focus of this chapter is to describe the basic approach adopted for the use of SPEs for nucleic acid measurement.}, }
@article {pmid39235733, year = {2025}, author = {Williams, MR and Telli, AE and Telli, N and Islam, DT and Hashsham, SA}, title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {3-17}, pmid = {39235733}, issn = {1940-6029}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Food Microbiology/methods ; Animals ; *Milk/microbiology ; *Salmonella/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; Foodborne Diseases/microbiology ; Escherichia coli/genetics/isolation &amp; purification ; Molecular Diagnostic Techniques/methods ; Swine ; }, abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.}, }
@article {pmid39234658, year = {2024}, author = {King, WL and Hayward, RJ and Goebel, M and Fleishman, SM and Bauerle, TL and Bell, TH}, title = {Getting to the root of root-microbe interactions.}, journal = {Science progress}, volume = {107}, number = {3}, pages = {368504241278783}, pmid = {39234658}, issn = {2047-7163}, mesh = {Ecosystem ; Microbiota/physiology ; *Plant Roots/microbiology/metabolism ; Plants/microbiology/metabolism ; *Soil Microbiology ; }, abstract = {Microbial relationships with roots influence many ecosystem functions and nutrient fluxes, including their sometimes-profound effects on plant health and productivity. Fine roots were often classified with a diameter less than 2 mm, but fine roots under that size perform distinct functional roles in the environment. Importantly, two broad functional categories of fine roots are absorptive and transportive, with absorptive fine roots acting as metabolic hotspots for root activity. In two of our recent studies, we have shown that several microbial community characteristics differ between absorptive and transportive fine roots, including composition, abundance, and function, as well as the root metabolome. This highlights a growing recognition within microbial ecology that we must consider fine-scale environmental variability, such as root physiology and morphology, when interpreting microbial patterns. In this commentary, we summarize the findings of our latest article, further speculate on some of these patterns, and suggest future studies for examining decomposition and applying cutting-edge single-cell sequencing techniques.}, }
@article {pmid39234547, year = {2024}, author = {Marshall, IPG}, title = {Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1407868}, pmid = {39234547}, issn = {1664-302X}, abstract = {Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.}, }
@article {pmid39233440, year = {2024}, author = {Hosseiniyan Khatibi, SM and Dimaano, NG and Veliz, E and Sundaresan, V and Ali, J}, title = {Exploring and exploiting the rice phytobiome to tackle climate change challenges.}, journal = {Plant communications}, volume = {5}, number = {12}, pages = {101078}, pmid = {39233440}, issn = {2590-3462}, mesh = {*Climate Change ; *Oryza/microbiology/growth &amp; development ; *Microbiota ; Crops, Agricultural/growth &amp; development/genetics ; Agriculture/methods ; }, abstract = {The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.}, }
@article {pmid39233079, year = {2024}, author = {Zhang, G and Guo, Z and Ke, Y and Li, H and Xiao, X and Lin, D and Lin, L and Wang, Y and Liu, J and Lu, H and Hong, H and Yan, C}, title = {Comparative analysis of size-fractional eukaryotic microbes in subtropical riverine systems inferred from 18S rRNA gene V4 and V9 regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175972}, doi = {10.1016/j.scitotenv.2024.175972}, pmid = {39233079}, issn = {1879-1026}, mesh = {*RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; *Eukaryota/genetics ; Microbiota/genetics ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Eukaryotic microbes play key ecological roles in riverine ecosystems. Amplicon sequencing has greatly facilitated the identification and characterization of eukaryotic microbial communities. Currently, 18S rRNA gene V4 and V9 hypervariable regions are widely used for sequencing eukaryotic microbes. Identifying optimal regions for the profiling of size-fractional eukaryotic microbial communities is critical for microbial ecological studies. In this study, we spanned three rivers with typical natural-human influenced transition gradients to evaluate the performance of the 18S rRNA gene V4 and V9 hypervariable regions for sequencing size-fractional eukaryotic microbes (>180 μm, 20-180 μm, 5-20 μm, 3-5 μm, 0.8-3 μm). Our comparative analysis revealed that amplicon results depend on the specific species and microbial size. The V9 region was most effective for detecting a broad taxonomic range of species. The V4 region was superior to the V9 region for the identification of microbes in the minor 3 μm and at the family and genus levels, especially for specific microbial groups, such as Labyrinthulomycetes. However, the V9 region was more effective for studies of diverse eukaryotic groups, including Archamoebae, Heterolobosea, and Microsporidia, and various algae, such as Haptophyta, Florideophycidae, and Bangiales. Our results highlight the importance of accounting for potential misclassifications when employing both V4 and V9 regions for the identification of microbial sequences. The use of optimal regions for amplification could enhance the utility of amplicon sequencing in environmental studies. The insights gained from this work will aid future studies that employ amplicon-based identification approaches for the characterization of eukaryotic microbial communities and contribute to our understanding of microbial ecology within aquatic systems.}, }
@article {pmid39231820, year = {2024}, author = {Song, X and Li, J and Xiong, Z and Sha, H and Wang, G and Liu, Q and Zeng, T}, title = {Effects of Detoxifying Substances on Uranium Removal by Bacteria Isolated from Mine Soils: Performance, Mechanisms, and Bacterial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {111}, pmid = {39231820}, issn = {1432-184X}, support = {52170164//National Natural Science Foundation of China/ ; 2022RC1184//Science and Technology Innovation Program of Hunan Province of China/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/isolation &amp; purification/classification ; *Mining ; *Biodegradation, Environmental ; Acyl-Butyrolactones/metabolism ; Glutathione/metabolism ; Soil Pollutants, Radioactive/metabolism ; }, abstract = {In this study, we investigated the effect of detoxifying substances on U(VI) removal by bacteria isolated from mine soil. The results demonstrated that the highest U(VI) removal efficiency (85.6%) was achieved at pH 6.0 and a temperature of 35 °C, with an initial U(VI) concentration of 10 mg/L. For detoxifying substances, signaling molecules acyl homoserine lactone (AHLs, 0.1 µmol/L), anthraquinone-2, 6-disulfonic acid (AQDS, 1 mmol/L), reduced glutathione (GSH, 0.1 mmol/L), selenium (Se, 1 mg/L), montmorillonite (MT, 1 g/L), and ethylenediaminetetraacetic acid (EDTA, 0.1 mmol/L) substantially enhanced the bacterial U(VI) removal by 34.9%, 37.4%, 54.5%, 35.1%, 32.8%, and 47.8% after 12 h, respectively. This was due to the alleviation of U(VI) toxicity in bacteria through detoxifying substances, as evidenced by lower malondialdehyde (MDA) content and higher superoxide dismutase (SOD) and catalase (CAT) activities for bacteria exposed to U(VI) and detoxifying substances, compared to those exposed to U(VI) alone. FTIR results showed that hydroxyl, carboxyl, phosphorus, and amide groups participated in the U(VI) removal. After exposure to U(VI), the relative abundances of Chryseobacterium and Stenotrophomonas increased by 48.5% and 12.5%, respectively, suggesting their tolerance ability to U(VI). Gene function prediction further demonstrated that the detoxifying substances AHLs alleviate U(VI) toxicity by influencing bacterial metabolism. This study suggests the potential application of detoxifying substances in the U(VI)-containing wastewater treatment through bioremediation.}, }
@article {pmid39230264, year = {2024}, author = {Rodriguez-Gonzalez, RA and Balacheff, Q and Debarbieux, L and Marchi, J and Weitz, JS}, title = {Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0017124}, pmid = {39230264}, issn = {2379-5077}, support = {R01 AI146592/AI/NIAID NIH HHS/United States ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; }, mesh = {*Pseudomonas aeruginosa/virology ; *Phage Therapy/methods ; *Pseudomonas Infections/therapy/immunology ; Animals ; Mice ; Bacteriophages/physiology ; Lung/microbiology/immunology/virology ; Models, Biological ; Mice, Inbred C57BL ; Humans ; Drug Resistance, Multiple, Bacterial ; }, abstract = {UNLABELLED: Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions in vivo. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for Pseudomonas aeruginosa infections. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, including host innate immune responses and the emergence of phage-resistant bacterial mutants. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a P. aeruginosa infection due to the combined effects of phage and neutrophils, given the sufficient innate immune activity and efficient phage-induced lysis. The metapopulation model simulations also predict that MDR bacteria are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of in vivo experiments further supports the use of phage therapy for treating acute lung infections caused by P. aeruginosa, while highlighting potential limits to therapy in a spatially structured environment given impaired innate immune responses and/or inefficient phage-induced lysis.<br><br>IMPORTANCE: Phage therapy is increasingly employed as a compassionate treatment for severe infections caused by multidrug-resistant (MDR) bacteria. However, the mixed outcomes observed in larger clinical studies highlight a gap in understanding when phage therapy succeeds or fails. Previous research from our team, using in vivo experiments and single-compartment mathematical models, demonstrated the synergistic clearance of acute P. aeruginosa pneumonia by phage and neutrophils despite the emergence of phage-resistant bacteria. In fact, the lung environment is highly structured, prompting the question of whether immunophage synergy explains the curative treatment of P. aeruginosa when incorporating realistic physical connectivity. To address this, we developed a metapopulation network model mimicking the lung branching structure to assess phage therapy efficacy for MDR P. aeruginosa pneumonia. The model predicts the synergistic elimination of P. aeruginosa by phage and neutrophils but emphasizes potential challenges in spatially structured environments, suggesting that higher innate immune levels may be required for successful bacterial clearance. Model simulations reveal a spatial pattern in pathogen clearance where P. aeruginosa are cleared faster at distal nodes of the bronchial tree than in primary nodes. Interestingly, image analysis of infected mice reveals a concordant and statistically significant pattern: infection intensity clears in the bottom before the top of the lungs. The combined use of modeling and image analysis supports the application of phage therapy for acute P. aeruginosa pneumonia while emphasizing potential challenges to curative success in spatially structured in vivo environments, including impaired innate immune responses and reduced phage efficacy.}, }
@article {pmid39229495, year = {2024}, author = {Li, L and Chen, S and Xue, X and Chen, J and Tian, J and Huo, L and Zhang, T and Zeng, X and Su, S}, title = {Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae106}, pmid = {39229495}, issn = {2730-6151}, abstract = {Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.}, }
@article {pmid39226184, year = {2024}, author = {Zhai, Z and Yang, Y and Chen, S and Wu, Z}, title = {Long-Term Exposure to Polystyrene Microspheres and High-Fat Diet-Induced Obesity in Mice: Evaluating a Role for Microbiota Dysbiosis.}, journal = {Environmental health perspectives}, volume = {132}, number = {9}, pages = {97002}, pmid = {39226184}, issn = {1552-9924}, mesh = {Animals ; *Dysbiosis/microbiology ; Mice ; *Obesity/microbiology ; *Diet, High-Fat ; *Mice, Inbred C57BL ; *Microspheres ; *Polystyrenes/toxicity ; *Gastrointestinal Microbiome/drug effects ; Male ; Microplastics/toxicity ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Microplastics (MPs) have become a global environmental problem, emerging as contaminants with potentially alarming consequences. However, long-term exposure to polystyrene microspheres (PS-MS) and its effects on diet-induced obesity are not yet fully understood.<br><br>OBJECTIVES: We aimed to investigate the effect of PS-MS exposure on high-fat diet (HFD)-induced obesity and underlying mechanisms.<br><br>METHODS: In the present study, C57BL/6J mice were fed a normal diet (ND) or a HFD in the absence or presence of PS-MS via oral administration for 8 wk. Antibiotic depletion of the microbiota and fecal microbiota transplantation (FMT) were performed to assess the influence of PS-MS on intestinal microbial ecology. We performed 16S rRNA sequencing to dissect microbial discrepancies and investigated the dysbiosis-associated intestinal integrity and inflammation in serum.<br><br>RESULTS: Compared with HFD mice, mice fed the HFD with PS-MS exhibited higher body weight, liver weight, metabolic dysfunction-associated steatotic liver disease (MASLD) activity scores, and mass of white adipose tissue, as well as higher blood glucose and serum lipid concentrations. Furthermore, 16S rRNA sequencing of the fecal microbiota revealed that mice fed the HFD with PS-MS had greater &#x3b1;-diversity and greater relative abundances of Lachnospiraceae, Oscillospiraceae, Bacteroidaceae, Akkermansiaceae, Marinifilaceae, Deferribacteres, and Desulfovibrio, but lower relative abundances of Atopobiaceae, Bifidobacterium, and Parabacteroides. Mice fed the HFD with PS-MS exhibited lower expression of MUC2 mucin and higher levels of lipopolysaccharide and inflammatory cytokines [tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), interleukin-6 (IL-6), IL-1&#x3b2;, and IL-17A] in serum. Correlation analyses revealed that differences in the microbial flora of mice exposed to PS-MS were associated with obesity. Interestingly, microbiota-depleted mice did not show the same PS-MS-associated differences in Muc2 and Tjp1 expression in the distal colon, expression of inflammatory cytokines in serum, or obesity outcomes between HFD and HFD + PS-MS. Importantly, transplantation of feces from HFD + PS-MS mice to microbiota-depleted HFD-fed mice resulted in a lower expression of mucus proteins, higher expression of inflammatory cytokines, and obesity outcomes, similar to the findings in HFD + PS-MS mice.<br><br>CONCLUSIONS: Our findings provide a new gut microbiota-driven mechanism for PS-MS-induced obesity in HFD-fed mice, suggesting the need to reevaluate the adverse health effects of MPs commonly found in daily life, particularly in susceptible populations. https://doi.org/10.1289/EHP13913.}, }
@article {pmid39224076, year = {2024}, author = {McMillan, AS and Theriot, CM}, title = {Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393766}, pmid = {39224076}, issn = {1949-0984}, support = {R35 GM149222/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bile Acids and Salts/metabolism ; Humans ; *Fecal Microbiota Transplantation ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Animals ; }, abstract = {Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.}, }
@article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid39221110, year = {2024}, author = {Mohr, AE and Jasbi, P and van Woerden, I and Chi, J and Gu, H and Bruening, M and Whisner, CM}, title = {Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {1-23}, pmid = {39221110}, issn = {2993-3935}, support = {DP5 OD017910/OD/NIH HHS/United States ; T32 DK137525/DK/NIDDK NIH HHS/United States ; }, abstract = {The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.}, }
@article {pmid39218095, year = {2024}, author = {Anedda, E and Alexa, EA and Farrell, ML and Croffie, M and Madigan, G and Morris, D and Burgess, CM}, title = {Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175905}, doi = {10.1016/j.scitotenv.2024.175905}, pmid = {39218095}, issn = {1879-1026}, mesh = {*Zinc/analysis ; *Enterobacteriaceae/drug effects ; *Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Dairying ; Drug Resistance, Bacterial/genetics ; Ireland ; Animals ; Milk/microbiology ; Cattle ; Soil Pollutants/analysis ; }, abstract = {Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.}, }
@article {pmid39216241, year = {2024}, author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A}, title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135675}, doi = {10.1016/j.jhazmat.2024.135675}, pmid = {39216241}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; }, abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.}, }
@article {pmid39215820, year = {2024}, author = {Thompson, C and Silva, R and Gibran, FZ and Bacha, L and de Freitas, MAM and Thompson, M and Landuci, F and Tschoeke, D and Zhang, XH and Wang, X and Zhao, W and Gatts, PV and de Almeida, MG and de Rezende, CE and Thompson, F}, title = {The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {110}, pmid = {39215820}, issn = {1432-184X}, mesh = {Animals ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Herbivory ; Species Specificity ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Perciformes/microbiology ; Diet/veterinary ; }, abstract = {Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ[13]C and δ[15]N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.}, }
@article {pmid39215735, year = {2024}, author = {Paulo, LM and Liu, YC and Castilla-Archilla, J and Ramiro-Garcia, J and Hughes, D and Mahony, T and Holohan, BC and Wilmes, P and O'Flaherty, V}, title = {Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {90}, number = {4}, pages = {1239-1249}, pmid = {39215735}, issn = {0273-1223}, support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; TC/2014/0016//Enterprise Ireland/ ; }, mesh = {*Bioreactors ; Anaerobiosis ; *Wastewater ; *Waste Disposal, Fluid/methods ; Temperature ; Biological Oxygen Demand Analysis ; Bacteria/metabolism/classification ; Biofuels ; Industrial Waste ; }, abstract = {The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.}, }
@article {pmid39212186, year = {2024}, author = {Junker Mentzel, CM and Hui, Y and Hammerich, TMS and Klug-Dambmann, M and Liu, Y and Zachariassen, LF and Hansen, LH and Aslampaloglou, A and Kiersgaard, M and Nielsen, DS and Hansen, AK and Krych, L}, title = {Low-gainer diet-induced obese microbiota transplanted mice exhibit increased fighting.}, journal = {Clinical and translational science}, volume = {17}, number = {9}, pages = {e13906}, pmid = {39212186}, issn = {1752-8062}, support = {//LIFEPHARM/ ; //Novo Nordisk A/S/ ; //Center for Applied Laboratory Animal Research/ ; }, mesh = {Animals ; Male ; *Obesity/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Weight Gain ; Mice ; Disease Models, Animal ; Leptin/blood/metabolism ; Feces/microbiology ; }, abstract = {Weight gain variation is a great challenge in diet-induced obesity studies since low-gainer animals are of limited experimental value. The inbred C57BL/6 (B6) mice are frequently used models due to their genetic homogeneity and susceptibility to diet-induced obesity (DIO). The aim of this study is to investigate if the gut microbiota (GM) influences the fraction of low weight gainers in DIO studies. A total of 100 male B6 mice (donor population) were fed a high-fat diet for 14 weeks and divided into the study groups high gainer (HG) and low gainer (LG) based on their weight gain. Subsequently, fecal matter transplantation (FMT) was done on germ-free B6 mice with GM from HG and LG donors (FMT population). LG (13.35 ± 2.5 g) and HG (25.52 ± 2.0 g) animals were identified by the weight gain from week 1 to week 12. Interestingly, the start weight of the LG (20.36 ± 1.4 g) and HG (21.59 ± 0.7 g) groups differed significantly. Transplanting LG or HG fecal matter to germ-free mice resulted in significant differences in weight gain between HG and LG, as well as differences in serum leptin levels and epididymal fat pad weight. A clear LG-specific GM composition could not be distinguished by 16S rRNA gene amplicon sequencing. Surprisingly, significantly more fighting was recorded in LG groups of both donor populations and when transplanted to germ-free mice. The HG and LG phenotypes could be transferred to germ-free mice. The increased fighting in the LG group in both studies suggests not only that the tendency to fight can be transferred by FMT in these mice, but also that fighting should be prevented in DIO studies to minimize the number of LG animals.}, }
@article {pmid39214074, year = {2024}, author = {Letourneau, J and Carrion, VM and Zeng, J and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA}, title = {Interplay between particle size and microbial ecology in the gut microbiome.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39214074}, issn = {1751-7370}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; 2016-IDG-1013//North Carolina Biotechnology Center/ ; N00014-18-1-2616//Office of Naval Research/ ; 1R01DK116187/NH/NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Feces/microbiology ; Mice ; *Particle Size ; Adult ; Male ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Young Adult ; Mice, Inbred C57BL ; Mastication ; Middle Aged ; }, abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Contrary to our initial hypothesis, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that human and mouse gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion. This finding has important implications for our understanding of energy extraction and subsequent uptake in gastrointestinal tract. FPS may therefore be viewed as an informative functional readout, providing new insights into the metabolic state of the gut microbiome.}, }
@article {pmid39211880, year = {2024}, author = {Schluter, J and Matheis, F and Ebina, W and Jogia, W and Sullivan, AP and Gordon, K and Fanega de la Cruz, E and Victory-Hays, ME and Heinly, MJ and Diefenbach, CS and Peled, JU and Foster, KR and Levitt, A and McLaughlin, E}, title = {A randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health associated taxa.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.25.24311015}, pmid = {39211880}, abstract = {Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. No interventions are currently available that effectively target the microbial ecosystem in the gut to prevent this negative collateral damage of antibiotics. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic therapy for gastrointestinal (GI)-unrelated infections. Postbiotics comprise complex mixtures of metabolites produced by bacteria during fermentation and other processes, which can mediate microbial ecology. Bacterial ecosystem alpha diversity, quantified by the inverse Simpson index, during the end of the antibiotic course was significantly higher (+40%) across the 16 postbiotic-treated patients compared with the 16 patients who received a placebo, and the postbiotic was well-tolerated. Secondary analyses of 157 stool samples collected longitudinally revealed that the increased diversity was driven by enrichment in health-associated microbial genera: obligate anaerobe Firmicutes, in particular taxa belonging to the Lachnospiraceae family, were higher in treated patients; conversely, Escherichia/Shigella abundances, which comprise pathobionts and antimicrobial-resistant strains, were reduced in postbiotic-treated patients at the end of their antibiotic course and up to 10 days later. Taken together, these results indicate that postbiotic co-administration during antibiotic therapy could support a health-associated gut microbiome community and may reduce antibiotic-induced microbiome injury.}, }
@article {pmid39204682, year = {2024}, author = {Andreata, MFL and Afonso, L and Niekawa, ETG and Salomão, JM and Basso, KR and Silva, MCD and Alves, LC and Alarcon, SF and Parra, MEA and Grzegorczyk, KG and Chryssafidis, AL and Andrade, G}, title = {Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39204682}, issn = {2223-7747}, abstract = {The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.}, }
@article {pmid39203927, year = {2024}, author = {Govaert, M and Rotsaert, C and Vannieuwenhuyse, C and Duysburgh, C and Medlin, S and Marzorati, M and Jarrett, H}, title = {Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.}, journal = {Nutrients}, volume = {16}, number = {16}, pages = {}, pmid = {39203927}, issn = {2072-6643}, support = {Not applicable//Heights/ ; }, mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Colon/microbiology ; *Upper Gastrointestinal Tract/microbiology ; Microbial Viability ; Bacteria/growth &amp; development ; Fatty Acids, Volatile/metabolism ; }, abstract = {Many health-promoting effects have been attributed to the intake of probiotic cells. However, it is important that probiotic cells arrive at the site of their activity in a viable state in order to exert their beneficial effects. Careful selection of the appropriate probiotic formulation is therefore required as mainly the type of probiotic species/strain and the administration strategy may affect survival of the probiotic cells during the upper gastrointestinal (GIT) passage. Therefore, the current study implemented Simulator of the Human Microbial Ecosystem (SHIME[®]) technology to investigate the efficacy of different commercially available probiotic formulations on the survival and culturability of probiotic bacteria during upper GIT passage. Moreover, Colon-on-a-Plate (CoaP™) technology was applied to assess the effect of the surviving probiotic bacteria on the gut microbial community (activity and composition) of three human donors. Significantly greater survival and culturability rates were reported for the delayed-release capsule formulation (>50%) as compared to the powder, liquid, and standard capsule formulations (<1%) (p < 0.05), indicating that the delayed-release capsule was most efficacious in delivering live bacteria cells. Indeed, administration of the delayed-release capsule probiotic digest resulted in enhanced production of SCFAs and shifted gut microbial community composition towards beneficial bacterial species. These results thus indicate that careful selection of the appropriate probiotic formulation and administration strategy is crucial to deliver probiotic cells in a viable state at the site of their activity (distal ileum and colon).}, }
@article {pmid39203578, year = {2024}, author = {Yan, Y and Shi, Z and Wang, C and Jin, Z and Yin, J and Zhu, G}, title = {Viral Diversity and Ecological Impact of DNA Viruses in Dominant Tick Species in China.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203578}, issn = {2076-2607}, support = {RCYJ2012//Basic Scientific Research Funds of Hangzhou Medical College/ ; }, abstract = {Ticks are blood-feeding ectoparasites that also transmit various pathogens, posing severe risks to human and animal health. DNA viruses play a crucial role in the microbial ecology of ticks, but their distribution and ecological significance remain largely undetermined. Here, we assembled an extensive catalog encompassing 4320 viral operational taxonomic units (vOTUs) from six main dominant tick species in China, of which 94.8% have not been found in any other environment. To bridge the knowledge gap in tick DNA virus research and provide a crucial resource platform, we developed the Tick DNA Virus Database. This database includes the vOTUs that are known to cause diseases. Most of the predicted vOTUs are associated with dominant bacterial and archaeal phyla. We identified 105 virus-encoded putative auxiliary metabolic genes (AMGs) that are involved in host metabolism and environmental adaptation, potentially influencing ticks through both top-down and bottom-up mechanisms. The identification of microbial communities and antibiotic resistance in wild tick species suggests that wild ticks are reservoirs of antibiotic resistance and potential spreaders of antibiotic resistance. These findings reveal the potential role of tick viruses in ecosystems, highlighting the importance of monitoring tick microbiomes to address global public health challenges.}, }
@article {pmid39203418, year = {2024}, author = {Barazetti, AR and Dealis, ML and Basso, KR and Silva, MCD and Alves, LDC and Parra, MEA and Simionato, AS and Cely, MVT and Macedo, AL and Silva, DB and Andrade, G}, title = {Evaluation of Resistance Induction Promoted by Bioactive Compounds of Pseudomonas aeruginosa LV Strain against Asian Soybean Rust.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203418}, issn = {2076-2607}, abstract = {Pseudomonas are known as higher producers of secondary metabolites with antimicrobial properties and plant growth promoters, including resistance induction. These mechanisms should be an alternative to pesticide use in crop production. Phakopsora pachyrhizi causes Asian soybean rust, representing a high loss of yield around the world. The objective of this paper was to evaluate the application of secondary metabolites produced by Pseudomonas aeruginosa LV strain from the semi-purified fraction F4A in soybean plants to induce plant resistance against P. pachyrhizi in field conditions. The experimental design was performed in randomized blocks with three replicates using two F4A doses (1 and 10 μg mL[-1]) combined or not with fungicides (Unizeb Gold[®] or Sphere Max[®]). The control treatment, with Uni + Sph, saponins, flavonoids, and sphingolipids, showed higher intensities in the plants. In contrast, plants treated with the F4A fraction mainly exhibited fatty acid derivatives and some non-identified compounds with nitrogen. Plants treated with Sphere Max[®], with or without F4A10, showed higher intensities of glycosylated flavonoids, such as kaempferol, luteolin, narigenin, and apigenin. Plants treated with F4A showed higher intensities of genistein and fatty acid derivatives. These increases in flavonoid compound biosynthesis and antioxidant properties probably contribute to the protection against reactive oxygen species (ROS).}, }
@article {pmid39203403, year = {2024}, author = {Al-Tarshi, M and Dobretsov, S and Al-Belushi, M}, title = {Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203403}, issn = {2076-2607}, support = {RC/GRG-AGR/FISH/22/01//Ministry of Higher Education, Research and Innovation/ ; RC/GRG-AGR/FISH/22/01//Sultan Qaboos University/ ; }, abstract = {Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.}, }
@article {pmid39200461, year = {2024}, author = {Han, D and Yang, Y and Guo, Z and Dai, S and Jiang, M and Zhu, Y and Wang, Y and Yu, Z and Wang, K and Rong, C and Yu, Y}, title = {A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39200461}, issn = {2304-8158}, support = {32200012//National Natural Science Foundation of China/ ; 22KJB180016//Basic Science Research Program for Higher Education Institutions in Jiangsu Province (Natural Science)/ ; }, abstract = {In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.}, }
@article {pmid39198281, year = {2024}, author = {He, Z and Smets, BF and Dechesne, A}, title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {109}, pmid = {39198281}, issn = {1432-184X}, support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.}, }
@article {pmid39197278, year = {2024}, author = {Peng, C and Wang, Y and Sha, X and Li, M and Wang, X and Wang, J and Wang, Y and Liu, C and Wang, L}, title = {Adverse effect of TWPs on soil fungi and the contribution of benzothiazole rubber additives.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135574}, doi = {10.1016/j.jhazmat.2024.135574}, pmid = {39197278}, issn = {1873-3336}, mesh = {*Benzothiazoles ; *Soil Microbiology ; *Fungi/drug effects ; *Rubber ; *Soil Pollutants/toxicity/analysis ; Biomass ; }, abstract = {Tire wear particles (TWPs) pollution is widely present in soil, especially in areas severely affected by traffic. Herein, regular variation of fungal biomass with TWPs was found in soils with different distances from the highway. In addition, the concentrations of benzothiazole compounds (BTHs), an important class of rubber vulcanization accelerators, were found to be positively correlated to the TWPs abundance. Sixty days' soil microcosm experiments were conducted to further confirm the adverse effect of TWPs and BTHs on soil fungi. TWPs spiking at 1000 mg/kg, a detectable level in the roadside, resulted in significant reduction of biomass and significant changes of soil fungal community structure, with Eurotium and Polyporales being the sensitive species. BTH+ 2-hydroxybenzothiazole (OHBT) (the dominant BTHs in soil) spiking at 200 ng/kg, the dose equivalent to 1000 mg/kg TWPs pollution, also caused a similar magnitude of soil fungal biomass reduction. Adonis demonstrated no significant difference of fungal community structure between TWPs and BTH+OHBT spiked soil, suggesting the adverse effect of TWPs on soil fungi may be explained by the act of BTHs. Pure culture using the representative soil fungi Eurotium and Polyporales also confirmed that BTHs were the main contributors to the adverse effect of TWPs on soil fungi.}, }
@article {pmid39196435, year = {2024}, author = {Tenore, A and Russo, F and Jacob, J and Grattepanche, JD and Buttaro, B and Klapper, I}, title = {A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {10}, pages = {123}, pmid = {39196435}, issn = {1522-9602}, support = {1951532//National Science Foundation/ ; 2325170//National Science Foundation/ ; }, mesh = {*Biofilms/growth &amp; development ; *Models, Biological ; *Mathematical Concepts ; *Phototrophic Processes/physiology ; *Cyanobacteria/physiology/metabolism ; *Computer Simulation ; Biomass ; Heterotrophic Processes/physiology ; Microbial Interactions/physiology ; Bacterial Physiological Phenomena ; }, abstract = {Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.}, }
@article {pmid39196422, year = {2024}, author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A}, title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {108}, pmid = {39196422}, issn = {1432-184X}, mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation &amp; purification/physiology ; *Seeds/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation &amp; purification ; Genotype ; Biodiversity ; }, abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.}, }
@article {pmid39295780, year = {2022}, author = {Mesnage, R and Calatayud, M and Duysburgh, C and Marzorati, M and Antoniou, MN}, title = {Alterations in infant gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME technology.}, journal = {Gut microbiome (Cambridge, England)}, volume = {3}, number = {}, pages = {e6}, pmid = {39295780}, issn = {2632-2897}, abstract = {Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. We describe the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology. SHIME microbiota culture was undertaken in the presence of a concentration of 100-mg/L glyphosate and the same glyphosate equivalent concentration of Roundup. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large-scale disturbances, including an increased abundance of long-chain polyunsaturated fatty acids. Changes in bacterial composition measured by qPCR and 16S rRNA suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota.}, }
@article {pmid39193431, year = {2024}, author = {Ding, J and Cui, X and Wang, X and Zhai, F and Wang, L and Zhu, L}, title = {Multi-omics analysis of gut microbiota and metabolites reveals contrasting profiles in domestic pigs and wild boars across urban environments.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450306}, pmid = {39193431}, issn = {1664-302X}, abstract = {The gut microbiota plays a crucial role in host health and metabolism. This study explores the differences in gut microbiota and metabolites between domestic pigs (DP) and wild boars (WB) in urban environments. We analyzed gut microbial composition, metabolic profiles, virome composition, antibiotic resistance genes (ARGs), and human pathogenic bacteria (HPB) in both DP and WB. Our results revealed that DP exhibited a higher Firmicutes/Bacteroidetes ratio and were enriched in bacterial genera associated with domestication and modern feeding practices. Metabolomic analysis showed distinct profiles, with WB significantly enriched in the Pantothenate and CoA biosynthesis pathway, highlighting dietary and environmental influences on host metabolism. Additionally, DP had a distinct gut virome composition, particularly enriched in lytic phages of the Chaseviridae family. ARG analysis indicated a higher abundance of tetracycline resistance genes in DP, likely due to antibiotic use in pig farms. Furthermore, variations in HPB composition underscored potential health risks associated with contact with pig feces. These findings provide valuable insights into the microbial ecology of domestic pigs and wild boars, emphasizing the importance of these comparisons in identifying zoonotic pathogen transmission pathways and managing antibiotic resistance. Continued research in this area is essential for developing effective strategies to mitigate public health risks and promote sustainable livestock management practices.}, }
@article {pmid39191402, year = {2024}, author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM}, title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0032324}, pmid = {39191402}, issn = {2150-7511}, support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; }, mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.}, }
@article {pmid39190978, year = {2024}, author = {Xu, M and Wang, F and Stedtfeld, RD and Fu, Y and Xiang, L and Sheng, H and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Transfer of antibiotic resistance genes from soil to rice in paddy field.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108956}, doi = {10.1016/j.envint.2024.108956}, pmid = {39190978}, issn = {1873-6750}, mesh = {*Oryza/genetics ; *Soil Microbiology ; *Fertilizers ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Animals ; Agriculture ; Swine ; Composting ; Genes, Bacterial ; }, abstract = {The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.}, }
@article {pmid39189736, year = {2024}, author = {Wang, L and Ducoste, JJ and de Los Reyes, FL}, title = {Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0029824}, pmid = {39189736}, issn = {1098-5336}, support = {15-05-U//North Carolina Water Resources Research Institute/ ; CBET 1805666//National Science Foundation (NSF)/ ; }, mesh = {*Microbiota/physiology ; *Bioreactors/microbiology ; Anaerobiosis ; *Methane/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.}, }
@article {pmid39188310, year = {2024}, author = {Berrios, L and Venturini, AM and Ansell, TB and Tok, E and Johnson, W and Willing, CE and Peay, KG}, title = {Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae104}, pmid = {39188310}, issn = {2730-6151}, abstract = {Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.}, }
@article {pmid39187952, year = {2024}, author = {Stryker, J and White, E and Díaz-Almeyda, E and Sidoti, B and Oberle, B}, title = {Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria.}, journal = {American journal of botany}, volume = {111}, number = {12}, pages = {e16396}, doi = {10.1002/ajb2.16396}, pmid = {39187952}, issn = {1537-2197}, mesh = {*Nitrogen/metabolism ; *Plant Leaves/microbiology/metabolism ; *Bacteria/metabolism/classification ; Tillandsia/metabolism/physiology ; Microbiota ; Bromeliaceae/metabolism/microbiology/physiology ; }, abstract = {PREMISE: Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity.<br><br>METHODS: We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata.<br><br>RESULTS: Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19&#x2009;cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank.<br><br>CONCLUSIONS: Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.}, }
@article {pmid39182301, year = {2024}, author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C}, title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135567}, doi = {10.1016/j.jhazmat.2024.135567}, pmid = {39182301}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; }, abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.}, }
@article {pmid39180136, year = {2024}, author = {Khadem, S and Berry, D and Al-Khlifeh, E}, title = {Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {358}, pmid = {39180136}, issn = {1756-3305}, mesh = {Jordan ; Animals ; Mice ; Rats ; *Eukaryota/classification/genetics/growth &amp; development ; *Climate ; *Gastrointestinal Microbiome/genetics ; *Rodentia/parasitology ; *Animals, Wild/parasitology ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 18S ; Feces/parasitology ; }, abstract = {BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).<br><br>METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.<br><br>RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p&#x2009;=&#x2009;0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.<br><br>CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.}, }
@article {pmid39178936, year = {2024}, author = {Anedda, E and Ekhlas, D and Alexa, E and Farrell, ML and Gaffney, MT and Madigan, G and Morris, D and Burgess, CM}, title = {Characterization of antimicrobial resistant Enterobacterales isolated from spinach and soil following zinc amendment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124774}, doi = {10.1016/j.envpol.2024.124774}, pmid = {39178936}, issn = {1873-6424}, mesh = {*Spinacia oleracea/microbiology ; *Soil Microbiology ; *Zinc/pharmacology ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Soil Pollutants ; Soil/chemistry ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistant bacteria can occur in the primary food production environment. The emergence and dissemination of antimicrobial resistance (AMR) in the environment can be influenced by several factors, including the presence of heavy metals. The aim of this study was to examine the presence and characteristics of antimicrobial resistant Enterobacterales in soils and spinach grown in soils with and without zinc amendment. A total of 160 samples (92 soil and 68 spinach) were collected from two locations, in which some plots had been amended with zinc. Samples were cultured on selective agars for detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL), carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales. Samples were also cultured for enumeration of total Enterobacterales. Isolates were identified by MALDI-TOF. Antimicrobial susceptibility testing was carried out in accordance with EUCAST and CLSI criteria. The whole genome sequence (WGS) of selected isolates was determined. Inductively coupled plasma atomic emission spectrometry was also performed on soil samples in order to measure the concentration of zinc. In total 20 antimicrobial resistant Enterobacterales were isolated from the soil (n = 8) and spinach samples (n = 12). In both sample types, Serratia fonticola (n = 16) was the dominant species, followed by Escherichia coli (n = 1), Citrobacter freundii (n = 1) and Morganella morganii (n = 1) detected in spinach samples, and Enterobacter cloacae (n = 1) detected in a soil sample. The WGS identified genes conferring resistance to different antimicrobials in agreement with the phenotypic results; 14 S. fonticola isolates were confirmed as ESBL producers and harboured the blaFONA gene. Genes that encoded for zinc resistance and multidrug efflux pumps, transporters that can target both antimicrobials and heavy metals, were also identified. Overall, the findings of this study suggest the presence of zinc did not influence the AMR Enterobacterales in soil or spinach samples.}, }
@article {pmid39178591, year = {2024}, author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG}, title = {Unveiling the overlooked small-sized microbiome in river ecosystems.}, journal = {Water research}, volume = {265}, number = {}, pages = {122302}, doi = {10.1016/j.watres.2024.122302}, pmid = {39178591}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; }, abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.}, }
@article {pmid39175749, year = {2024}, author = {Peña-Salinas, ME and Speth, DR and Utter, DR and Spelz, RM and Lim, S and Zierenberg, R and Caress, DW and Núñez, PG and Vázquez, R and Orphan, VJ}, title = {Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17724}, pmid = {39175749}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Seawater/microbiology/chemistry ; California ; Bacteria/genetics/classification ; }, abstract = {Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.}, }
@article {pmid39175056, year = {2024}, author = {Sbardellati, DL and Vannette, RL}, title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {155}, pmid = {39175056}, issn = {2049-2618}, support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; }, mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; }, abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.}, }
@article {pmid39174521, year = {2024}, author = {Foulquier, A and Datry, T and Corti, R and von Schiller, D and Tockner, K and Stubbington, R and Gessner, MO and Boyer, F and Ohlmann, M and Thuiller, W and Rioux, D and Miquel, C and Albariño, R and Allen, DC and Altermatt, F and Arce, MI and Arnon, S and Banas, D and Banegas-Medina, A and Beller, E and Blanchette, ML and Blessing, J and Boëchat, IG and Boersma, K and Bogan, M and Bonada, N and Bond, N and Brintrup, K and Bruder, A and Burrows, R and Cancellario, T and Canhoto, C and Carlson, S and Cid, N and Cornut, J and Danger, M and de Freitas Terra, B and De Girolamo, AM and Del Campo, R and Díaz Villanueva, V and Dyer, F and Elosegi, A and Febria, C and Figueroa Jara, R and Four, B and Gafny, S and Gómez, R and Gómez-Gener, L and Guareschi, S and Gücker, B and Hwan, J and Jones, JI and Kubheka, PS and Laini, A and Langhans, SD and Launay, B and Le Goff, G and Leigh, C and Little, C and Lorenz, S and Marshall, J and Martin Sanz, EJ and McIntosh, A and Mendoza-Lera, C and Meyer, EI and Miliša, M and Mlambo, MC and Morais, M and Moya, N and Negus, P and Niyogi, D and Pagán, I and Papatheodoulou, A and Pappagallo, G and Pardo, I and Pařil, P and Pauls, SU and Polášek, M and Rodríguez-Lozano, P and Rolls, RJ and Sánchez-Montoya, MM and Savić, A and Shumilova, O and Sridhar, KR and Steward, A and Taleb, A and Uzan, A and Valladares, Y and Vander Vorste, R and Waltham, NJ and Zak, DH and Zoppini, A}, title = {Unravelling large-scale patterns and drivers of biodiversity in dry rivers.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7233}, pmid = {39174521}, issn = {2041-1723}, support = {869226 (DRYvER)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; }, mesh = {*Biodiversity ; *Rivers/microbiology ; Animals ; Fungi/classification/genetics ; Geologic Sediments/microbiology ; Bacteria/classification/genetics ; Invertebrates/classification ; DNA Barcoding, Taxonomic ; Plants/classification ; Archaea/classification/genetics ; }, abstract = {More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.}, }
@article {pmid39172818, year = {2024}, author = {Frazier, AN and Belk, AD and Beck, MR and Koziel, JA}, title = {Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308914}, pmid = {39172818}, issn = {1932-6203}, mesh = {*Methane/metabolism ; *Ruminants/microbiology ; Animals ; *Microbiota ; *Systematic Reviews as Topic ; *RNA, Ribosomal, 16S/genetics ; *Meta-Analysis as Topic ; }, abstract = {Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).}, }
@article {pmid39171106, year = {2024}, author = {Pi, X and Du, Z and Teng, W and Fu, H and Hu, L and Li, J and Ding, J and Yang, X and Zhang, Y}, title = {Characteristics of stachyose-induced effects on gut microbiota and microbial metabolites in vitro associated with obesity in children.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1411374}, pmid = {39171106}, issn = {2296-861X}, abstract = {Childhood obesity presents a serious health concern associated with gut microbiota alterations. Dietary interventions targeting the gut microbiota have emerged as promising strategies for managing obesity in children. This study aimed to elucidate the impact of stachyose (STS) supplementation on the gut microbiota composition and metabolic processes in obese children. Fecal samples were collected from 40 obese children (20 boys and 20 girls) aged between 6 and 15 and in vitro fermentation was conducted with or without the addition of STS, respectively, followed by 16S rRNA amplicon sequencing and analysis of short-chain fatty acids (SCFAs) and gases. Notably, our results revealed that STS supplementation led to significant alterations in gut microbiota composition, including an increase in the abundance of beneficial bacteria such as Bifidobacterium and Faecalibacterium, and a decrease in harmful bacteria including Escherichia-Shigella, Parabacteroides, Eggerthella, and Flavonifractor. Moreover, STS supplementation resulted in changes in SCFAs production, with significant increases in acetate levels and reductions in propionate and propionate, while simultaneously reducing the generation of gases such as H2S, H2, and NH3. The Area Under the Curve (AUC)-Random Forest algorithm and PICRUSt 2 were employed to identify valuable biomarkers and predict associations between the gut microbiota, metabolites, and metabolic pathways. The results not only contribute to the elucidation of STS's modulatory effects on gut microbiota but also underscore its potential in shaping metabolic activities within the gastrointestinal environment. Furthermore, our study underscores the significance of personalized nutrition interventions, particularly utilizing STS supplementation, in the management of childhood obesity through targeted modulation of gut microbial ecology and metabolic function.}, }
@article {pmid39168311, year = {2024}, author = {MacGibeny, MA and Adjei, S and Pyle, H and Bunick, CG and Ghannoum, M and Grada, A and Harris-Tryon, T and Tyring, SK and Kong, HH}, title = {The Human Skin Microbiome in Health: CME Part 1.}, journal = {Journal of the American Academy of Dermatology}, volume = {}, number = {}, pages = {}, pmid = {39168311}, issn = {1097-6787}, support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Human skin is home to a myriad of microorganisms, including bacteria, viruses, fungi, and mites, many of which are considered commensal microbes that aid in maintaining the overall homeostasis or steady-state condition of the skin and contribute to skin health. Our understanding of the complexities of the skin's interaction with its microorganisms is evolving. This knowledge is based primarily on in vitro and animal studies, and more work is needed to understand how this knowledge relates to humans. Here, we introduce the concept of the skin microbiome and discuss skin microbial ecology, some intrinsic factors with potential influence on the human skin microbiome, and possible microbiome-host interactions. The second article of this two-part CME series describes how microbiome alterations may be associated with skin disease, how medications can affect the microbiome, and what microbiome-based therapies are under investigation.}, }
@article {pmid39165397, year = {2024}, author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L}, title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae046}, pmid = {39165397}, issn = {2730-6151}, abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.}, }
@article {pmid39165109, year = {2024}, author = {Gloder, G and Bourne, ME and Cuny, MAC and Verreth, C and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B}, title = {Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39165109}, issn = {1574-6941}, support = {G.0961.19//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Larva/microbiology ; *Microbiota ; *Butterflies/microbiology/parasitology ; *Host-Parasite Interactions ; Wolbachia/genetics ; Species Specificity ; Nosema/pathogenicity ; Wasps/microbiology ; Bacteria/classification/genetics/growth &amp; development ; }, abstract = {There is increasing evidence that host-parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitized by Cotesia glomerata or Cotesia rubecula with nonparasitized caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitized and nonparasitized caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitized by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitized caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.}, }
@article {pmid39163484, year = {2024}, author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39163484}, issn = {1751-7370}, support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; }, abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.}, }
@article {pmid39162854, year = {2024}, author = {Joshi, S and Pham, K and Moe, L and McNees, R}, title = {Exploring the Microbial Diversity and Composition of Three Cigar Product Categories.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {107}, pmid = {39162854}, issn = {1432-184X}, mesh = {*Tobacco Products ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; Phylogeny ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; }, abstract = {Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types.}, }
@article {pmid39162497, year = {2024}, author = {Chatzigiannidou, I and Heyse, J and Props, R and Rubbens, P and Mermans, F and Teughels, W and Van de Wiele, T and Boon, N}, title = {Real-time flow cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0095524}, pmid = {39162497}, issn = {2165-0497}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G020119//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {*Flow Cytometry/methods ; *Anti-Infective Agents, Local/pharmacology ; *Chlorhexidine/pharmacology ; Humans ; *Bacteria/drug effects ; *Triclosan/pharmacology ; Cetylpyridinium/pharmacology ; Microbial Sensitivity Tests/methods ; Mouth/microbiology ; Periodontitis/microbiology ; }, abstract = {UNLABELLED: Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years. This stresses the urgency for surveillance against tolerant organisms, as well as the discovery of novel antimicrobials. Traditionally, susceptibility to antimicrobials is assessed by broth micro-dilution or disk diffusion assays, both of which are time-consuming, labor-intensive, and provide limited information on the mode of action of the antimicrobials. The abovementioned limitations highlight the need for the development of new methods to monitor and further understand antimicrobial susceptibility. In this study, we used real-time flow cytometry, combined with membrane permeability staining, as a quick and sensitive technology to study the quantitative and qualitative responses of two oral pathobionts to different concentrations of chlorhexidine (CHX), cetylpyridinium chloride (CPC), or triclosan. Apart from the real-time monitoring of cell damage, we further applied a phenotypic fingerprinting method to differentiate between the bacterial subpopulations that arose due to treatment. We quantified the pathobiont damage rate of different antiseptics at different concentrations within 15 minutes of exposure and identified the conditions under which the bacteria were most susceptible. Moreover, we detected species-specific and treatment-specific phenotypic subpopulations. This proves that real-time flow cytometry can provide information on the susceptibility of different microorganisms in a short time frame while differentiating between antiseptics and thus could be a valuable tool in the discovery of novel antimicrobial compound, while at the same time deciphering their mode of action.<br><br>IMPORTANCE: With increasing evidence that microorganisms are becoming more tolerant to standard antimicrobials, faster and more accessible antimicrobial susceptibility testing methods are needed. However, traditional susceptibility assays are laborious and time-consuming. To overcome the abovementioned limitations, we introduce a novel approach to define antimicrobial susceptibility in a much shorter time frame with the use of real-time flow cytometry. Furthermore, phenotypic fingerprinting analysis can be applied on the data to study the way antiseptics affect the bacterial cell morphology over time and, thus, gain information on the mode of action of a certain compound.}, }
@article {pmid39162262, year = {2024}, author = {Liu, M and Li, Q and Xu, W and Wang, L and Wu, F and Tan, L and Li, L and Zhang, G}, title = {Characterization of water microbiota and their relationship with resident oysters during an oyster mortality event.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0288123}, pmid = {39162262}, issn = {2165-0497}, support = {2022YFD2400304//National Key R&amp;D Program of China/ ; 2022LZGC015//Key Research and Development Program of Shandong/ ; ZFJH202309//Key Research and Development Program of Shandong/ ; CARS-49//Earmarked Fund for CARS/ ; }, mesh = {Animals ; *Microbiota/physiology ; *Ostreidae/microbiology ; *Water Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Cyanobacteria/genetics/physiology/growth &amp; development ; Temperature ; }, abstract = {Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mortality threats are largely unknown. This study examines the shifts in water microbiota during an oyster mortality event using amplicon sequencing and compared with those of resident oysters to disentangle the balance of the deterministic and stochastic factors involved. Water temperature and dissolved oxygen significantly shape the microbial community with a distinct monthly pattern, and Cyanobacteria blooms might exacerbate oyster mortality. The comparative analysis of microbial communities in oysters and water revealed that ≤ 21% of the genera were shared between oysters and water, implying that water microbiota cannot easily transfer into oysters. Furthermore, these shared genera had different functions, with oysters more involved in promoting host digestion and nutrient acquisition and water bacteria enriched more in functions promoting their own growth and survival. These findings illustrate that oysters may possess specific selection or barrier mechanisms that permit a small percentage of transients, controlled by stochastic factors and having a minimal effect on oyster mortality, to enter, whereas the majority of oyster microbiota are residents governed by deterministic factors. Consequently, oysters exhibit some plasticity in their symbiotic microbiota, enabling them to maintain microbial homeostasis and adapt to complex microbial surroundings. This may be a shared mechanism among marine invertebrates for survival in complex marine environments.IMPORTANCEPacific oysters are widely cultured and play vital ecological roles. However, the summer mortality hinders sustainable oyster farming. Untangling causative mechanisms of oyster mortality is a complex task due to the intricate "interactome" involving environmental factors, hosts, and pathogens. Interactions between hosts and microorganisms offer an ideal avenue for investigating the truth. We systematically investigated the microbial community in water and resident oysters during a summer mortality event and proposed that the assembly of oyster microbiota is primarily governed by deterministic processes independent of mortality. Pathogens mainly originate from resident members of the oyster microbiota, with a limited influence from the microbial community in the water. Additionally, environmental degraders, such as Cyanobacteria blooms, cannot be overlooked as a contributing factor of oyster mortality. This study evaluated the weight of deterministic and stochastic factors in microbial assembly during an oyster mortality event and greatly broadened our understanding of the "interactome" through the interaction between oysters and water in microbiota.}, }
@article {pmid39161630, year = {2024}, author = {Blázquez, M and Pérez-Vargas, I and Garrido-Benavent, I and Villar-dePablo, M and Turégano, Y and Frías-López, C and Sánchez-Gracia, A and de Los Ríos, A and Gasulla, F and Pérez-Ortega, S}, title = {Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group.}, journal = {Persoonia}, volume = {52}, number = {}, pages = {44-93}, pmid = {39161630}, issn = {0031-5850}, abstract = {Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .}, }
@article {pmid39160591, year = {2024}, author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS}, title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {60}, pmid = {39160591}, issn = {2524-6372}, support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; }, abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.<br><br>RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.<br><br>CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.}, }
@article {pmid39159439, year = {2024}, author = {Dos Santos, A and Schultz, J and Almeida Trapp, M and Modolon, F and Romanenko, A and Kumar Jaiswal, A and Gomes, L and Rodrigues-Filho, E and Rosado, AS}, title = {Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus.}, journal = {Astrobiology}, volume = {24}, number = {8}, pages = {824-838}, doi = {10.1089/ast.2024.0017}, pmid = {39159439}, issn = {1557-8070}, mesh = {Saudi Arabia ; *Exobiology/methods ; *Extraterrestrial Environment ; Genome, Bacterial/genetics ; Mars ; Bacteria/genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.}, }
@article {pmid39158314, year = {2024}, author = {Guéneau, V and Jiménez, G and Castex, M and Briandet, R}, title = {Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0066324}, pmid = {39158314}, issn = {1098-5336}, support = {2020/0548//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; }, mesh = {*Genome, Bacterial ; *Phenotype ; *Bacillus/genetics/isolation &amp; purification ; *Biofilms ; *Chickens/microbiology ; Animals ; *Farms ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Biosynthetic Pathways/genetics ; Multigene Family ; Phylogeny ; Livestock/microbiology ; DNA, Bacterial/genetics ; Deoxyribonuclease I/metabolism ; }, abstract = {The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.}, }
@article {pmid39157765, year = {2024}, author = {de Santana, CO and Spealman, P and Oliveira, E and Gresham, D and de Jesus, T and Chinalia, F}, title = {Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17900}, pmid = {39157765}, issn = {2167-8359}, mesh = {Brazil ; *Rivers/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Forests ; Estuaries ; Biodiversity ; Archaea/genetics/classification/isolation &amp; purification ; Microbiota ; }, abstract = {The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.}, }
@article {pmid39155010, year = {2024}, author = {Wong, LC and Rodenburg, U and Leite, RR and Korthals, GW and Pover, J and Koerten, H and Kuramae, EE and Bodelier, PLE}, title = {Exploring microbial diversity and interactions for asbestos modifying properties.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175577}, doi = {10.1016/j.scitotenv.2024.175577}, pmid = {39155010}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/classification ; Fungi/metabolism ; Asbestos ; Soil Microbiology ; Iron/metabolism ; Asbestos, Serpentine ; }, abstract = {Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19-HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12-RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12-RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27-TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.}, }
@article {pmid39150265, year = {2024}, author = {Longhi, G and Lugli, GA and Tarracchini, C and Fontana, F and Bianchi, MG and Carli, E and Bussolati, O and van Sinderen, D and Turroni, F and Ventura, M}, title = {From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0124424}, pmid = {39150265}, issn = {1098-5336}, support = {PE00000003//National Recovery and Resilience Plan (NRRP)/ ; SFI/12/RC/2273a//Irish Government's National Development Plan/ ; SFI/12/RC/2273b//Irish Government's National Development Plan/ ; }, mesh = {*Cheese/microbiology ; *Bifidobacterium/genetics/metabolism/growth &amp; development ; Humans ; *Milk/microbiology ; *Gastrointestinal Microbiome ; Animals ; Italy ; }, abstract = {The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.}, }
@article {pmid39150230, year = {2024}, author = {Li, J and Yang, X and Zhang, X and Zhang, L}, title = {Effects and mechanisms of microbial ecology and diversity on phytoremediation of cadmium-contaminated soil under the influence of biodegradable organic acids.}, journal = {International journal of phytoremediation}, volume = {26}, number = {14}, pages = {2392-2403}, doi = {10.1080/15226514.2024.2391025}, pmid = {39150230}, issn = {1549-7879}, mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Cadmium/metabolism ; *Bacillus megaterium/metabolism ; *Soil Microbiology ; *Lolium/metabolism ; Rhizosphere ; Citric Acid/metabolism ; Bacteria/metabolism ; }, abstract = {In recent years, heavy metal pollution has become a global environmental problem and poses a great threat to the health of people and ecosystems. Therefore, strategies for the effective remediation of Cd from contaminated soil are urgently needed. In this study, ryegrass was utilized as a remediation plant, and its remediation potential was enhanced through the application of Citric Acid (CA) in conjunction with Bacillus megaterium (B. megaterium). The P3 treatment (CA + Bacillus megaterium) exhibited a significantly higher efficiency in promoting cadmium extraction by ryegrass, resulting in a 1.79-fold increase in shoot cadmium accumulation compared to the control group (CK) with no Bacillus megaterium or CA. Moreover, the P3 treatment led to an increased abundance of Actinobacteriota, Acidobacteriota, and Patescibacteria in the rhizosphere. The concentration of amino derivatives (such as betaine, sulfolithocholylglycine, N-alpha-acetyl-lysine, glycocholic acid, arginyl-threonine) showed significant upregulation following the P3 treatment. In summary, this study proposes a viable approach for phytoremediation of soil contaminated with cadmium by harnessing the mobilizing abilities of soil bacteria.}, }
@article {pmid39148674, year = {2024}, author = {Dyczko, D and Błażej, P and Kiewra, D}, title = {The influence of forest habitat type on Ixodes ricinus infections with Rickettsia spp. in south-western Poland.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {6}, number = {}, pages = {100200}, pmid = {39148674}, issn = {2667-114X}, abstract = {This study investigates the prevalence of Rickettsia spp. in Ixodes ricinus tick populations in different forest habitat types (broadleaf forest, mixed broadleaf and coniferous forest, and coniferous forest) in south-western Poland. During the survey periods from April to June 2018 and 2019 a total of 494 I. ricinus ticks, including 374 nymphs, 60 females and 60 males, were tested for Rickettsia infections by nested PCR targeting the gltA gene. The overall infection rate was 42.3%; however, we observed statistically significant year-to-year variation. Infection rates varied between tick developmental stages and were significantly influenced by forest habitat type. As assessed by a generalized linear mixed model (GLMM), the highest infection rates were observed in mixed broadleaf and coniferous forests, while coniferous forests had a significant negative effect on infection prevalence. DNA sequencing of selected samples confirmed the predominance of Rickettsia helvetica (91.2%) and less frequent Rickettsia monacensis (8.8%). This study suggests that the forest habitat types can influence Rickettsia spp. infection in tick populations; however, a comprehensive understanding of all factors influencing the level of infection requires future study.}, }
@article {pmid39143010, year = {2024}, author = {Ozbayram, EG and Kleinsteuber, S and Sträuber, H and Schroeder, BG and da Rocha, UN and Corrêa, FB and Harms, H and Nikolausz, M}, title = {Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e13324}, pmid = {39143010}, issn = {1758-2229}, mesh = {Animals ; *Larva/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.}, }
@article {pmid39142044, year = {2024}, author = {Battulga, B and Nakayama, M and Matsuoka, S and Kondo, T and Atarashi-Andoh, M and Koarashi, J}, title = {Dynamics and functions of microbial communities in the plastisphere in temperate coastal environments.}, journal = {Water research}, volume = {264}, number = {}, pages = {122207}, doi = {10.1016/j.watres.2024.122207}, pmid = {39142044}, issn = {1879-2448}, mesh = {*Biofilms ; *Bacteria/genetics/classification ; Fungi/genetics ; Microbiota ; Microplastics ; Japan ; Geologic Sediments/microbiology ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem.}, }
@article {pmid39141295, year = {2024}, author = {Turbant, F and Blache, A and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Use of Synchrotron Radiation Circular Dichroism to Analyze the Interaction and Insertion of Proteins into Bacterial Outer Membrane Vesicles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2843}, number = {}, pages = {73-94}, pmid = {39141295}, issn = {1940-6029}, mesh = {*Circular Dichroism/methods ; *Synchrotrons ; *Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Outer Membrane/metabolism/chemistry ; Protein Structure, Secondary ; Lipid Bilayers/metabolism/chemistry ; }, abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used for the analysis of proteins. Particularly, it allows the determination of protein secondary structure content in various media, including the membrane environment. In this chapter, we present how CD applications can be used to analyze the interaction of proteins with bacterial outer membrane vesicles (OMVs). Most CD studies characterizing the structure of proteins inserted into membranes rely on artificial lipid bilayers, mimicking natural membranes. Nevertheless, these artificial models lack the important features of the true membrane, especially for the outer membrane of Gram-negative bacteria. These features include lipid diversity, glycosylation, and asymmetry. Here, we show how to analyze the interactions of proteins, either integral or peripheral, with OMVs in solution and with supported membranes of OMVs, using conventional CD and orientated circular dichroism (OCD). We explain how to decipher the spectroscopic signals to obtain information on the molecular structure of the protein upon its interaction with an OMV and through its potential insertion into an OMV membrane.}, }
@article {pmid39141097, year = {2024}, author = {Papazachariou, V and Fernández-Juárez, V and Parfrey, LW and Riemann, L}, title = {Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {106}, pmid = {39141097}, issn = {1432-184X}, mesh = {*Nitrogen Fixation ; *Plant Leaves/microbiology ; *Seawater/microbiology/chemistry ; *Microbiota ; *Zosteraceae/microbiology/metabolism ; Nitrogen/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Denmark ; Cyanobacteria/metabolism/genetics/classification/isolation &amp; purification ; }, abstract = {Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g[-1] dw h[-1]) and 15 (light, 194.6 nmol N g[-1] dw h[-1]). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.}, }
@article {pmid39140100, year = {2024}, author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ}, title = {Fungal Planet description sheets: 1614-1696.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {183-440}, pmid = {39140100}, issn = {2589-3831}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.}, }
@article {pmid39136489, year = {2024}, author = {Brar, G and Floden, M and McFrederick, Q and Rajamohan, A and Yocum, G and Bowsher, J}, title = {Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0207623}, pmid = {39136489}, issn = {1098-5336}, support = {RII Track-2 FEC18268341826834//National Science Foundation (NSF)/ ; IOS-1557940//National Science Foundation (NSF)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Animals ; Bees/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; *Pollen/microbiology ; Female ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Lactobacillaceae/genetics/growth &amp; development/physiology/isolation &amp; purification ; }, abstract = {Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remains less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on nonhost-specific environmental bacteria may not impact fitness of M. rotundata.IMPORTANCEThis study investigates the impact of environmentally acquired gut microbes of solitary bee fitness with insights into the microbial ecology of bee and their health. While the symbiotic microbiome is well-studied in social bees, the role of environmental acquired microbiota in solitary bees remains unclear. Assessing this relationship in a solitary pollinator, the leaf-cutting bee, Megachile rotundata, we discovered that this bee species does not depend on the diverse environmental bacteria found in pollen for either its larval growth or survival. Surprisingly, high concentrations of the most abundant pollen bacteria, Apilactobacillus micheneri did not consistently benefit bee fitness, but caused larval mortality. Our findings also suggest an interaction between Apilactobacillus and the Sodalis and perhaps their role in bee nutrition. Hence, this study provides significant insights that contribute to understanding the fitness, conservation, and pollination ecology of other solitary bee species in the future.}, }
@article {pmid39133233, year = {2024}, author = {Kwiatkowska, K and Ormaniec, P}, title = {Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {105}, pmid = {39133233}, issn = {1432-184X}, mesh = {*Microplastics/analysis ; *Wastewater/microbiology/chemistry ; *Biofilms ; *Microbiota ; *Sewage/microbiology/chemistry ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Bacteria/classification/metabolism ; Plastics/chemistry ; }, abstract = {Despite some effectiveness of wastewater treatment processes, microplastics accumulate in sewage sludge and their further use may contribute to the release of plastic microplastics into the environment. There is an urgent need to reduce the amount of microplastics in sewage sludge. Plastic particles serve as solid substrates for various microorganisms, promoting the formation of microbial biofilms with different metabolic activities. The biofilm environment associated with microplastics will determine the efficiency of treatment processes, especially biological methods, and the mechanisms of organic compound conversion. A significant source of microplastics is the land application of sewage sludge from wastewater treatment plants. The detrimental impact of microplastics affects soil enzymatic activity, soil microorganisms, flora, fauna, and plant production. This review article summarizes the development of research related to microplastics and discusses the issue of microplastic introduction from sewage sludge. Given that microplastics can contain complex composite polymers and form a plastisphere, further research is needed to understand their potential environmental impact, pathogenicity, and the characteristics of biofilms in wastewater treatment systems. The article also discusses the physicochemical properties of microplastics in wastewater treatment plants and their role in biofilm formation. Then, the article explained the impact of these properties on the possibility of the formation of biofilms on their surface due to the peculiar structure of microorganisms and also characterized what factors enable the formation of specific plastisphere in wastewater treatment plants. It highlights the urgent need to understand the basic information about microplastics to assess environmental toxicity more rationally, enabling better pollution control and the development of regulatory standards to manage microplastics entering the environment.}, }
@article {pmid39132685, year = {2025}, author = {Ye, D and Liu, Y and Li, J and Zhou, J and Cao, J and Wu, Y and Wang, X and Fang, Y and Ye, X and Zou, J and Ma, Q}, title = {Competitive dynamics and balance between Streptococcus mutans and commensal streptococci in oral microecology.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {3}, pages = {532-543}, doi = {10.1080/1040841X.2024.2389386}, pmid = {39132685}, issn = {1549-7828}, mesh = {*Mouth/microbiology ; Humans ; Biofilms/growth &amp; development ; *Dental Caries/microbiology ; *Streptococcus mutans/physiology/growth &amp; development ; *Streptococcus/physiology/growth &amp; development ; Microbiota ; }, abstract = {Dental caries, as a biofilm-related disease, is closely linked to dysbiosis in microbial ecology within dental biofilms. Beyond its impact on oral health, bacteria within the oral cavity pose systemic health risks by potentially entering the bloodstream, thereby increasing susceptibility to bacterial endocarditis, among other related diseases. Streptococcus mutans, a principal cariogenic bacterium, possesses virulence factors crucial to the pathogenesis of dental caries. Its ability to adhere to tooth surfaces, produce glucans for biofilm formation, and metabolize sugars into lactic acid contributes to enamel demineralization and the initiation of carious lesions. Its aciduricity and ability to produce bacteriocins enable a competitive advantage, allowing it to thrive in acidic environments and dominate in changing oral microenvironments. In contrast, commensal streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, act as primary colonizers and compete with S. mutans for adherence sites and nutrients during biofilm formation. This competition involves the production of alkali, peroxides, and antibacterial substances, thereby inhibiting S. mutans growth and maintaining microbial balance. This dynamic interaction influences the balance of oral microbiota, with disruptions leading to shifts in microbial composition that are marked by rapid increases in S. mutans abundance, contributing to the onset of dental caries. Thus, understanding the dynamic interactions between commensal and pathogenic bacteria in oral microecology is important for developing effective strategies to promote oral health and prevent dental caries. This review highlights the roles and competitive interactions of commensal bacteria and S. mutans in oral microecology, emphasizing the importance of maintaining oral microbial balance for health, and discusses the pathological implications of perturbations in this balance.}, }
@article {pmid39128495, year = {2025}, author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C}, title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.}, journal = {The Journal of investigative dermatology}, volume = {145}, number = {3}, pages = {605-617.e14}, doi = {10.1016/j.jid.2024.07.020}, pmid = {39128495}, issn = {1523-1747}, mesh = {Humans ; *Psoriasis/microbiology/pathology ; *Metagenome ; Male ; Female ; *Scalp/microbiology/pathology ; Adult ; Middle Aged ; *Microbiota/genetics ; Metagenomics ; Staphylococcus aureus/isolation &amp; purification/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.}, }
@article {pmid39126446, year = {2025}, author = {Izumi, H}, title = {Abundances of ectomycorrhizal exploration types show the type-dependent temporal dynamics over the seasons-a controlled growth container experiment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {4}, pages = {633-641}, pmid = {39126446}, issn = {1618-1905}, mesh = {*Mycorrhizae/classification/growth &amp; development/physiology/isolation &amp; purification ; Seasons ; *Quercus/microbiology/growth &amp; development ; Soil Microbiology ; Symbiosis ; Forests ; Trees/microbiology ; }, abstract = {Ectomycorrhizas are ubiquitous symbiotic associations between host trees and soil fungi. While the seasonal changes of the taxonomic community structure of ectomycorrhizal fungi have been studied extensively, the temporal dynamics of ectomycorrhizal exploration types which have been proposed for elucidating the functional roles of ectomycorrhizas have not been fully examined. The purpose of the study is to test the hypothesis of whether the abundance of the exploration types in the hosts with different phenology shows different temporal patterns over the seasons. Two host species, deciduous Quercus acutissima and evergreen Q. glauca, were planted in growth containers with natural forest soils and were grown in single or combined species treatment, under similar environmental conditions and in shared soil spore banks of the ectomycorrhizal fungi. The ectomycorrhizal exploration types that occurred on these two host species in two different treatments were observed for two growing seasons. The observed exploration types, namely contact, short-distance, and long-distance type as well as the overall abundance of the ectomycorrhizas showed distinct temporal patterns although no specific response to the host seasonal phenology was found. The abundances of the contact type showed no relation to the seasons whereas those of the short- and the long-distance type increased with time. The formation of the long-distance type was strongly influenced by the host species treatments while that of the other two types was not so. Therefore, the different exploration types demonstrate distinct temporal patterns depending on the types but no specific seasonal responses.}, }
@article {pmid39123264, year = {2024}, author = {Rothrock, MJ and Zwirzitz, B and Al Hakeem, WG and Oladeinde, A and Guard, JY and Li, X}, title = {16S amplicon-based microbiome biomapping of a commercial broiler hatchery.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {46}, pmid = {39123264}, issn = {2524-4671}, abstract = {Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.}, }
@article {pmid39122657, year = {2024}, author = {Brenzinger, K and Glatter, T and Hakobyan, A and Meima-Franke, M and Zweers, H and Liesack, W and Bodelier, PLE}, title = {Exploring modes of microbial interactions with implications for methane cycling.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {9}, pages = {}, pmid = {39122657}, issn = {1574-6941}, support = {5535/1-1//DFG/ ; 870.15.073/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Methane/metabolism ; *Microbial Interactions ; *Volatile Organic Compounds/metabolism ; *Carbon Dioxide/metabolism ; Methylomonas/metabolism/genetics ; Proteomics ; Proteome ; Heterotrophic Processes ; Oxygenases/metabolism/genetics ; }, abstract = {Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.}, }
@article {pmid39122033, year = {2024}, author = {de Menezes, AB and Gashchak, S and Wood, MD and Beresford, NA}, title = {Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175381}, doi = {10.1016/j.scitotenv.2024.175381}, pmid = {39122033}, issn = {1879-1026}, mesh = {*Wildfires ; *Chernobyl Nuclear Accident ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants, Radioactive/analysis ; Radiation Monitoring ; Soil/chemistry ; Bacteria/classification ; Ukraine ; Forests ; }, abstract = {There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.}, }
@article {pmid39119822, year = {2024}, author = {West, NJ and Landa, M and Obernosterer, I}, title = {Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.}, journal = {MicrobiologyOpen}, volume = {13}, number = {4}, pages = {e1428}, pmid = {39119822}, issn = {2045-8827}, support = {LEFE-CYBER//Centre National de la Recherche Scientifique/ ; //Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; 10-BLAN-0614//Agence Nationale de la Recherche/ ; }, mesh = {*Diatoms/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Haptophyta/classification/growth &amp; development ; Phytoplankton/classification/growth &amp; development ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Seasons ; }, abstract = {Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.}, }
@article {pmid39118147, year = {2024}, author = {Xiong, Y and Mueller, RS and Feng, S and Guo, X and Pan, C}, title = {Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {148}, pmid = {39118147}, issn = {2049-2618}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R01AT011618/NH/NIH HHS/United States ; }, mesh = {*Proteomics/methods ; *Isotope Labeling ; *Algorithms ; Escherichia coli/metabolism ; Carbon Isotopes/metabolism ; Tandem Mass Spectrometry/methods ; Proteome ; }, abstract = {BACKGROUND: Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.<br><br>RESULTS: In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% [13]C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with&#x2009;&#x2265;&#x2009;5 atom% [13]C labeling. The computational speed on Sipros 4 was&#x2009;>&#x2009;20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two [13]C-SIP experiments on a real-world soil community. The labeled proteins were used to trace [13]C from [13]C-methanol and [13]C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.<br><br>CONCLUSION: Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.}, }
@article {pmid39113789, year = {2024}, author = {Strik, DPBTB and Ganigue, R}, title = {Editorial: Microbial chain elongation-carbon recovering biorefineries for the circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1448975}, pmid = {39113789}, issn = {2296-4185}, }
@article {pmid39113100, year = {2024}, author = {Nieto, EE and Jurburg, SD and Steinbach, N and Festa, S and Morelli, IS and Coppotelli, BM and Chatzinotas, A}, title = {DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {146}, pmid = {39113100}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *RNA, Ribosomal, 18S/genetics ; *Bacteria/metabolism/classification/genetics ; Biomass ; Carbon Isotopes/metabolism ; Food Chain ; Polycyclic Aromatic Hydrocarbons/metabolism ; Isotope Labeling ; }, abstract = {BACKGROUND: Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a [13]C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.<br><br>RESULTS: Inoculation effectively increased PAH removal in the&#xa0;short-term, but not in&#xa0;the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of [13]C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.<br><br>CONCLUSION: Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.}, }
@article {pmid39110233, year = {2024}, author = {Wei, L and Wang, Y and Li, N and Zhao, N and Xu, S}, title = {Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {104}, pmid = {39110233}, issn = {1432-184X}, support = {2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; 2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; }, mesh = {*Soil Microbiology ; Tibet ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Grassland ; Animals ; Carbon Sequestration ; Herbivory ; Bacteria/metabolism/classification ; }, abstract = {The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.}, }
@article {pmid39109653, year = {2024}, author = {Corich, L and Losasso, C and Meneghel, A and Blarasin, FI and Basaglia, G and Corich, MA}, title = {The first case of urosepsis caused by Corynebacterium aurimucosum in an immunocompetent patient.}, journal = {Future microbiology}, volume = {19}, number = {11}, pages = {963-970}, pmid = {39109653}, issn = {1746-0921}, mesh = {Humans ; *Corynebacterium/isolation &amp; purification/genetics/pathogenicity/classification ; Aged ; Female ; *Corynebacterium Infections/microbiology/diagnosis/drug therapy ; *Sepsis/microbiology/drug therapy ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Non-diphtheroid Corynebacterium sepsis is rare and has affected only immunocompromised or particularly predisposed patients so far. We present the first case of urosepsis caused by Corynebacterium aurimucosum in a 67-year-old woman, without any known immunodeficiencies and in absence of any immunosuppressive therapy, admitted to the hospital for fever and acute dyspnea. This work suggests a new approach in evaluating the isolation of Corynebacteria, especially if isolated from blood. In particular, it highlights the potential infectious role of C. aurimucosum (often considered a contaminant and only rarely identified as an etiological agent of infections) and its clinical consequences, detailing also interesting aspects about its microbiological diagnosis and relative therapy and clarifying contrasting data of literature.}, }
@article {pmid39109421, year = {2024}, author = {Alfahl, Z and Biggins, S and Higgins, O and Chueiri, A and Smith, TJ and Morris, D and O'Dwyer, J and Hynds, PD and Burke, LP and O'Connor, L}, title = {A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing Escherichia coli in water.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {8}, pages = {}, pmid = {39109421}, issn = {1465-2080}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; *Water Microbiology ; Molecular Diagnostic Techniques/methods/instrumentation ; Sensitivity and Specificity ; Rivers/microbiology ; Shiga Toxin 1/genetics ; Groundwater/microbiology ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (stx1 and/or stx2), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (n=28) were collected from groundwater wells (n=13), rivers (n=12), a turlough (n=2) and an agricultural drain (n=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting stx1, stx2 and E. coli phoA genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting stx1 and stx2 genes were used to confirm the results. The limit of detection for stx1, stx2 and phoA LAMP assays were 2, 2 and 6 copies, respectively. Overall, stx1, stx2 and phoA genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for stx1 and stx2 correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.}, }
@article {pmid39109205, year = {2024}, author = {Zhu, L and Chen, L and Lin, B and Xu, Y and Dong, W and Lv, Y and Tang, J and Zhang, G and Zhang, L and Yang, S and Yang, Q and Chen, S}, title = {Deciphering the microbial succession and color formation mechanism of "green-covering and red-heart" Guanyin Tuqu.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1412503}, pmid = {39109205}, issn = {1664-302X}, abstract = {"Green-covering and red-heart" Guanyin Tuqu (GRTQ), as a type of special fermentation starter, is characterized by the "green-covering" formed on the surface of Guanyin Tuqu (SQ) and the "red-heart" in the center of Guanyin Tuqu (CQ). However, the mechanisms that promote temporal succession in the GRTQ microbial ecology and the formation of "green-covering and red-heart" characteristics remain unclear. Herein, we correlated the temporal profiles of microbial community succession with the main environmental variables (temperature, moisture, and acidity) and spatial position (center and surface) in GRTQ throughout fermentation. According to the results of high-throughput sequencing and culture-dependent methods, the microbial communities in the CQ and SQ demonstrated functional complementarity. For instance, the bacterial richness index of the CQ was greater than that of SQ, and the fungal richness index of the SQ was greater than that of CQ at the later stage of fermentation. Furthermore, Saccharomycopsis, Saccharomyces, Aspergillus, Monascus, Lactobacillus, Bacillus, Rhodanobacter, and Chitinophaga were identified as the dominant microorganisms in the center, while the surface was represented by Saccharomycopsis, Aspergillus, Monascus, Lactobacillus, Acetobacter, and Weissella. By revealing the physiological characteristics of core microorganisms at different spatial positions of GRTQ, such as Aspergillus clavatus and Monascus purpureus, as well as their interactions with environmental factors, we elucidated the color formation mechanism behind the phenomenon of "green" outside and "red" inside. This study provides fundamental information support for optimizing the production process of GRTQ.}, }
@article {pmid39107417, year = {2024}, author = {Cordovez, V and Carrión, VJ and Rivas Torres, G and Ortiz, DA and Cabrera, W and Balian, H and Vivanco, AK and Pérez-Jaramillo, JE and Chaves, J and Pazmiño, DA and van 't Hof, P and Raaijmakers, JM}, title = {Darwin's expedition revisited to reveal the evolution of plant-microbe interactions on Galápagos.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1903-1905}, pmid = {39107417}, issn = {2058-5276}, support = {GSC fund 17150//Universidad San Francisco de Quito (USFQ)/ ; }, mesh = {*Plants/microbiology ; Ecuador ; *Biological Evolution ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; }, }
@article {pmid39106714, year = {2024}, author = {Qing, J and Li, C and Zhi, H and Zhang, L and Wu, J and Li, Y}, title = {Exploring macrophage heterogeneity in IgA nephropathy: Mechanisms of renal impairment and current therapeutic targets.}, journal = {International immunopharmacology}, volume = {140}, number = {}, pages = {112748}, doi = {10.1016/j.intimp.2024.112748}, pmid = {39106714}, issn = {1878-1705}, mesh = {*Glomerulonephritis, IGA/metabolism/immunology ; Humans ; *Macrophages/immunology/metabolism ; Kidney/pathology/metabolism/immunology ; Male ; Female ; Glomerular Filtration Rate ; Adult ; Single-Cell Analysis ; }, abstract = {The lack of understanding of the mechanism of renal injury in IgA nephropathy (IgAN) hinders the development of personalized treatment plans and targeted therapies. Improved insight into the cause of renal dysfunction in IgAN is necessary to enhance the effectiveness of strategies for slowing the progression of the disease. This study examined single cell RNA sequencing (scRNA seq) and bulk-RNA seq data and found that the gene expression of renal intrinsic cells (RIC) was significantly changed in patients with renal impairment, with a primary focus on energy metabolism. We discovered a clear metabolic reprogramming of RIC during renal function impairment (RF) using the 'scMetabolism' package, which manifested as a weakening of oxidative phosphorylation, alterations in fatty acid metabolism, and changes in glycolysis. Cellular communication analysis revealed that communication between macrophages (Ma) and RIC became more active and impacted cell function through the ligand-receptor-transcription factor (L-R-TF) axis in patients with RF. Our studies showed a notable upsurge in the expression of gene CLU and the infiltration of CLU[+] Ma in patients with RF. CLU is a multifunctional protein, extensively involved in processes such as cell apoptosis and immune responses. Data obtained from the Nephroseq V5 database and multiplex immunohistochemistry (mIHC) were used to validate the findings, which were found to be robustly correlated with estimated glomerular filtration rate (eGFR) of the IgAN patients, as demonstrated by linear regression (LR). This study provides new insights into the cellular and molecular changes that occur in IgAN during renal impairment, revealing that elevated expression of CLU and CLU[+] Ma percolation are common features in patients with RF. These findings offer potential targets and strategies for personalized management and targeted therapy of IgAN.}, }
@article {pmid39106212, year = {2024}, author = {Pottie, I and Vázquez Fernández, R and Van de Wiele, T and Briers, Y}, title = {Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2387144}, pmid = {39106212}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteriophages/physiology ; Animals ; *Endopeptidases/metabolism ; Bacteria/genetics/metabolism/virology/classification ; Probiotics ; Anti-Bacterial Agents/pharmacology ; Bacterial Infections/microbiology/drug therapy/therapy ; Viral Proteins/metabolism/genetics ; Peptidoglycan/metabolism ; }, abstract = {The importance of the microbiota in the intestinal tract for human health has been increasingly recognized. In this perspective, microbiome modulation, a targeted alteration of the microbial composition, has gained interest. Phage lysins, peptidoglycan-degrading enzymes encoded by bacteriophages, are a promising new class of antibiotics currently under clinical development for treating bacterial infections. Due to their high specificity, lysins are considered microbiome-friendly. This review explores the opportunities and challenges of using lysins as microbiome modulators. First, the high specificity of endolysins, which can be further modulated using protein engineering or targeted delivery methods, is discussed. Next, obstacles and possible solutions to assess the microbiome-friendliness of lysins are considered. Finally, lysin delivery to the intestinal tract is discussed, including possible delivery methods such as particle-based and probiotic vehicles. Mapping the hurdles to developing lysins as microbiome modulators and identifying possible ways to overcome these hurdles can help in their development. In this way, the application of these innovative antimicrobial agents can be expanded, thereby taking full advantage of their characteristics.}, }
@article {pmid39105581, year = {2024}, author = {Zhu, Y-X and Yang, T-Y and Deng, J-H and Yin, Y and Song, Z-R and Du, Y-Z}, title = {Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet.}, journal = {mSphere}, volume = {9}, number = {8}, pages = {e0038624}, pmid = {39105581}, issn = {2379-5042}, support = {BK20231330//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {Animals ; *Insecta/microbiology ; *Fungi/classification/genetics ; *Microbiota ; *Sympatry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stochastic Processes ; *Diet ; Mycobiome ; Citrus/microbiology ; }, abstract = {UNLABELLED: Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects.<br><br>IMPORTANCE: Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.}, }
@article {pmid39103310, year = {2024}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Plastisphere Microbiomes Respiring Persistent Organohalide Pollutants.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {33}, pages = {14740-14752}, doi = {10.1021/acs.est.4c02251}, pmid = {39103310}, issn = {1520-5851}, mesh = {*Microbiota ; Plastics ; Persistent Organic Pollutants/metabolism ; Bacteria/metabolism ; Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; }, abstract = {Plastics are invading nearly all ecosystems on earth, acting as emerging repositories for toxic organic pollutants and thereby imposing substantial threats to ecological integrity. The colonization of plastics by microorganisms, forming the plastisphere, has garnered attention due to its potential influence on biogeochemical cycles. However, the capability of plastisphere microorganisms to attenuate organohalide pollutants remains to be evaluated. This study revealed that the plastisphere, collected from coastal ecosystems, harbors unique microbiomes, while the natural accumulation of organohalide pollutants on plastics may favor the proliferation of organohalide-respiring bacteria (OHRB). Laboratory tests further elucidated the high potential of plastisphere microbiota to reductively dehalogenate a variety of organohalide pollutants. Notably, over 70% tested plastisphere completely debrominated tetrabromobisphenol A (TBBPA) and polybrominated diphenyl ethers (PBDEs) to nonhalogenated products, whereas polychlorinated biphenyls (PCBs) were converted to lower congeners under anaerobic conditions. Dehalococcoides, Dehalogenimonas, and novel Dehalococcoidia populations might contribute to the observed dehalogenation based on their growth during incubation and positive correlations with the quantity of halogens removed. Intriguingly, large fractions of these OHRB populations were identified in a lack of the currently known TBBPA/PBDEs/PCBs reductive dehalogenase (RDase) genes, suggesting the presence of novel RDase genes. Microbial community analyses identified organohalides as a crucial factor in determining the composition, diversity, interaction, and assembly of microbes derived from the plastisphere. Collectively, this study underscores the overlooked roles of the plastisphere in the natural attenuation of persistent organohalide pollutants and sheds light on the unignorable impacts of organohalide compounds on the microbial ecology of the plastisphere.}, }
@article {pmid39101559, year = {2024}, author = {Brar, NK and Dhariwal, A and Shekhar, S and Junges, R and Hakansson, AP and Petersen, FC}, title = {HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1406190}, pmid = {39101559}, issn = {1664-302X}, abstract = {Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.}, }
@article {pmid39101364, year = {2024}, author = {Elias Masiques, N and Vossen, E and De Vrieze, J and De Smet, S and Van Hecke, T}, title = {The formation of sulfur metabolites during in vitro gastrointestinal digestion of fish, white meat and red meat is affected by the addition of fructo-oligosaccharides.}, journal = {Food &amp; function}, volume = {15}, number = {17}, pages = {8729-8739}, doi = {10.1039/d4fo00928b}, pmid = {39101364}, issn = {2042-650X}, mesh = {Animals ; *Fermentation ; *Oligosaccharides/metabolism ; *Red Meat/analysis ; Cattle ; *Digestion ; Swine ; *Chickens ; Fishes/metabolism ; Gastrointestinal Tract/metabolism ; Sulfur/metabolism ; Meat/analysis ; Humans ; Fatty Acids, Volatile/metabolism ; Ammonia/metabolism ; }, abstract = {The formation of sulfur metabolites during large intestinal fermentation of red meat may affect intestinal health. In this study, four muscle sources with varying heme-Fe content (beef, pork, chicken and salmon), with or without fructo-oligosaccharides (FOS), were exposed to an in vitro gastrointestinal digestion and fermentation model, after which the formation of sulfur metabolites, protein fermentation metabolites, and short (SCFA) and branched (BCFA) chain fatty acids was assessed. When FOS were present during muscle fermentation, levels of SCFA (+54%) and H2S (+36%) increased, whereas levels of CS2 (-37%), ammonia (-60%) and indole (-30%) decreased, and the formation of dimethyl sulfides and phenol was suppressed. Red meat fermentation was not accompanied by higher H2S formation, but beef ferments tended to contain 33 to 49% higher CS2 levels compared to the ferments of other muscle sources. In conclusion, there is a greater effect on sulfur fermentation by the addition of FOS to the meats, than the intrinsic heme-Fe content of meat.}, }
@article {pmid39098418, year = {2024}, author = {Zhang, M and Duan, T and Luo, Y and Zhang, H and Li, W and Wang, X and Han, J}, title = {Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175225}, doi = {10.1016/j.scitotenv.2024.175225}, pmid = {39098418}, issn = {1879-1026}, mesh = {*Phenanthrenes/metabolism ; *Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Soil/chemistry ; Biological Availability ; Microbiota/drug effects ; Polysorbates ; Glycolipids ; }, abstract = {The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1-204.3 and 38.4-76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.}, }
@article {pmid39095861, year = {2024}, author = {Anthony, WE and Allison, SD and Broderick, CM and Chavez Rodriguez, L and Clum, A and Cross, H and Eloe-Fadrosh, E and Evans, S and Fairbanks, D and Gallery, R and Gontijo, JB and Jones, J and McDermott, J and Pett-Ridge, J and Record, S and Rodrigues, JLM and Rodriguez-Reillo, W and Shek, KL and Takacs-Vesbach, T and Blanchard, JL}, title = {From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {56}, pmid = {39095861}, issn = {2524-6372}, support = {DE-AC05-76RL01830//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 89233218CNA000001//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, abstract = {Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.}, }
@article {pmid39095500, year = {2024}, author = {}, title = {Bringing microbial ecology into focus.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1901-1902}, pmid = {39095500}, issn = {2058-5276}, mesh = {*Ecology ; Microbiota ; Humans ; Bacteria/genetics/classification/metabolism ; }, }
@article {pmid39095499, year = {2024}, author = {Carreira, C and Lønborg, C and Acharya, B and Aryal, L and Buivydaite, Z and Borim Corrêa, F and Chen, T and Lorenzen Elberg, C and Emerson, JB and Hillary, L and Khadka, RB and Langlois, V and Mason-Jones, K and Netherway, T and Sutela, S and Trubl, G and Wa Kang'eri, A and Wang, R and White, RA and Winding, A and Zhao, T and Sapkota, R}, title = {Integrating viruses into soil food web biogeochemistry.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1918-1928}, pmid = {39095499}, issn = {2058-5276}, support = {NNF21OC0072586//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 36223//Villum Fonden (Villum Foundation)/ ; 1127-00033B//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {*Soil Microbiology ; *Food Chain ; *Viruses/genetics/classification/isolation &amp; purification ; *Soil/chemistry ; *Microbiota ; Animals ; Plants/virology/microbiology ; Ecosystem ; Bacteria/virology/metabolism/genetics ; }, abstract = {The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.}, }
@article {pmid39094415, year = {2024}, author = {Song, Y and Cao, X and Li, SA and Li, Z and Grossart, HP and Ma, H}, title = {Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism.}, journal = {Journal of environmental management}, volume = {367}, number = {}, pages = {122011}, doi = {10.1016/j.jenvman.2024.122011}, pmid = {39094415}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Carbon/metabolism ; Humans ; Benzopyrans ; Bacteria/metabolism ; }, abstract = {Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.}, }
@article {pmid39088119, year = {2024}, author = {Ferreira, P and Benabderrahim, MA and Hamza, H and Marchesini, A and Rejili, M and Castro, J and Tavares, RM and Costa, D and Sebastiani, F and Lino-Neto, T}, title = {Exploring the Influence of Date Palm Cultivars on Soil Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {103}, pmid = {39088119}, issn = {1432-184X}, support = {2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Soil Microbiology ; *Phoeniceae/microbiology/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; Genotype ; Plant Roots/microbiology ; Soil/chemistry ; }, abstract = {Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.}, }
@article {pmid39087852, year = {2024}, author = {Wu, T and Bafort, Q and Mortier, F and Almeida-Silva, F and Natran, A and Van de Peer, Y}, title = {The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza.}, journal = {American journal of botany}, volume = {111}, number = {8}, pages = {e16383}, pmid = {39087852}, issn = {1537-2197}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Araceae/genetics/metabolism ; *Genome, Plant ; *Metabolomics ; *Gene Duplication ; Metabolome ; Polyploidy ; Biomass ; }, abstract = {PREMISE: In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.<br><br>METHODS: We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.<br><br>RESULTS: Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.<br><br>CONCLUSIONS: The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.}, }
@article {pmid39085652, year = {2024}, author = {Brinch, C and Otani, S and Munk, P and van den Beld, M and Franz, E and Aarestrup, FM}, title = {Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {102}, pmid = {39085652}, issn = {1432-184X}, support = {NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; }, mesh = {Denmark ; *Sewage/microbiology ; *Vibrio cholerae/genetics/isolation &amp; purification/classification ; Genome, Bacterial ; Wastewater/microbiology ; Cholera/microbiology/epidemiology ; }, abstract = {We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years. We, however, have recovered a near-complete genome out of 115 metagenomic sewage samples taken over the past 8 years, despite the extremely low relative abundance of one V. cholerae read out of 500,000 sequenced reads. Due to the very low relative abundance, routine screening of the individual samples did not reveal V. cholerae. The recovered genome lacks the gene responsible for cholerae toxin production, but although this strain may not pose an immediate public health risk, our finding illustrates the importance, challenges, and effectiveness of wastewater-based pathogen surveillance.}, }
@article {pmid39085298, year = {2024}, author = {Vidal-Verdú, &#xc0; and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M}, title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {65}, pmid = {39085298}, issn = {2055-5008}, support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.}, }
@article {pmid39083238, year = {2024}, author = {Romano, I and Ventorino, V and Schettino, M and Magaraci, G and Pepe, O}, title = {Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {101}, pmid = {39083238}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Biodegradation, Environmental ; *Temperature ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Fungi/genetics/metabolism/classification ; *Polyethylene ; *Microbiota ; *Soil/chemistry ; Biodegradable Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.}, }
@article {pmid39081364, year = {2024}, author = {Schmitz, DA and Wechsler, T and Mignot, I and Kümmerli, R}, title = {Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae045}, pmid = {39081364}, issn = {2730-6151}, abstract = {How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.}, }
@article {pmid39081075, year = {2024}, author = {Bontemps, Z and Paranjape, K and Guy, L}, title = {Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {4}, pages = {}, pmid = {39081075}, issn = {1574-6976}, support = {F23-0260//Helge Ax:son Johnsons Foundation/ ; //NSERC/ ; }, mesh = {*Symbiosis ; *Host Microbial Interactions/physiology ; *Biological Evolution ; Gammaproteobacteria/genetics/physiology/classification ; Animals ; Bacteria/genetics/classification ; Ecosystem ; }, abstract = {Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.}, }
@article {pmid39080099, year = {2024}, author = {Tiusanen, M and Becker-Scarpitta, A and Wirta, H}, title = {Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {100}, pmid = {39080099}, issn = {1432-184X}, support = {201801360//Koneen S&#xe4;&#xe4;ti&#xf6;/ ; }, mesh = {Bees/microbiology ; Animals ; *Flowers/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Honey/microbiology/analysis ; *Microbiota ; Finland ; Pollination ; DNA Barcoding, Taxonomic ; Seasons ; }, abstract = {Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.}, }
@article {pmid39079336, year = {2024}, author = {Zhang, Y and Li, X and Ren, A and Yao, M and Chen, C and Zhang, H and van der Meer, W and Liu, G}, title = {Impacts of water treatments on bacterial communities of biofilm and loose deposits in drinking water distribution systems.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108893}, doi = {10.1016/j.envint.2024.108893}, pmid = {39079336}, issn = {1873-6750}, mesh = {*Biofilms/growth &amp; development/drug effects ; *Drinking Water/microbiology ; *Water Purification/methods ; *Water Supply ; *Bacteria ; Water Microbiology ; }, abstract = {Treated drinking water is delivered to customers through drinking water distribution systems (DWDSs). Although studies have focused on exploring the microbial ecology of DWDSs, knowledge about the effects of different water treatments on the bacterial community of biofilm and loose deposits in DWDS is limited. This study assessed the effects of additional treatments on the bacterial communities developed in 10 months' old pilot DWDSs. The results showed a similar bacterial community in the pipe-wall biofilm, which was dominated by Novosphingobium spp. (20-82 %) and Sphingomonas spp. (11-53 %), regardless of the treatment applied. The bacterial communities that were retained in the distribution systems (including pipe-wall biofilm and loose deposits) were similar to the particle-associated bacteria (PAB) in the corresponding supply water. The additional treatments showed clear effects of the removal and/or introduction of particles. The genera Aeromonas spp., Clostridium spp., Legionella spp., and Pseudomonas spp., which contain opportunistic pathogenic species, were only detected among the PAB in ion exchange system. Our study demonstrated that the biofilm community is consistent across treatments, and the contribution from bacteria in loose deposits is important but can be controlled by removing particles. These findings offer more insight into the origin and development of microbial ecology in DWDSs and suggest paths for further research on the possibility of managing the microbial ecology in distribution systems.}, }
@article {pmid39079302, year = {2024}, author = {Zhou, W and Huang, D and Chen, S and Wang, G and Li, R and Xu, W and Lei, Y and Xiao, R and Yin, L and Chen, H and Li, F}, title = {Microplastic dilemma: Assessing the unexpected trade-offs between biodegradable and non-biodegradable forms on plant health, cadmium uptake, and sediment microbial ecology.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135240}, doi = {10.1016/j.jhazmat.2024.135240}, pmid = {39079302}, issn = {1873-3336}, mesh = {*Cadmium/metabolism/toxicity ; *Microplastics/toxicity/metabolism ; *Soil Microbiology ; *Geologic Sediments/microbiology/chemistry ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Plant Roots/metabolism/microbiology ; Biodegradable Plastics/metabolism ; Plants/metabolism ; Plant Development/drug effects ; }, abstract = {Despite extensive substitution of biodegradable plastics (BPs) for conventional plastics (CPs), research on their environmental ecological consequences as microplastics (MPs) is scarce. This study aimed to fill this gap by investigating the impacts of six prototypical MPs (categorized into BMPs and CMPs) on plant growth, cadmium (Cd) translocation, and bacterial communities in contaminated sediments. Results showed both BMPs and CMPs hindered plant development; yet interestingly, BMPs provoked more pronounced physiological and biochemical changes alongside increased oxidative stress due to reactive oxygen species accumulation. Notably, most MP types promoted the absorption of Cd by plant roots potentially via a "dilution effect". BMPs also induced larger shifts in soil microbial metabolic functions compared to CMPs. Ramlibacter was identified as a key biomarker distinguishing BMPs from CMPs, with link to multiple N metabolic pathways and N assimilation. This study offers novel insights into intricate biochemical mechanisms and environmental chemistry behaviors underpinning MP-Cd interactions within the plant-microbe-sediment system, emphasizing BMPs' higher potential ecological risks based on their significant effects on plant health and microbial ecology. This work contributes to enhancing the comprehensive understanding of their ecological implications and potential threats to environmental security.}, }
@article {pmid39077993, year = {2024}, author = {Jirsová, D and Wideman, JG}, title = {Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39077993}, issn = {1751-7370}, support = {2119963//National Science Foundation/ ; GBMF9201//Gordon and Betty Moore Foundation/ ; CZ.02.01.01/00/22_010/0008117//VEDA FELLOWSHIPS within the Operational program Jan Amos Komensky/ ; }, mesh = {Biological Evolution ; *Heterotrophic Processes ; Phylogeny ; Plastids/genetics ; *Stramenopiles/classification/genetics ; }, abstract = {Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.}, }
@article {pmid39074063, year = {2024}, author = {Nyathi, M and Dhlamini, Z and Ncube, T}, title = {Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome.}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {343-348}, pmid = {39074063}, issn = {2544-4646}, mesh = {*Cellulase/genetics/metabolism ; *Metagenome ; *Rainforest ; Soil Microbiology ; Cloning, Molecular ; Hydrogen-Ion Concentration ; Escherichia coli/genetics ; Temperature ; Metagenomics ; Bacteria/genetics/classification/enzymology/isolation &amp; purification ; }, abstract = {The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.}, }
@article {pmid39073401, year = {2024}, author = {Williams, SE and Varliero, G and Lurgi, M and Stach, JEM and Race, PR and Curnow, P}, title = {Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {7}, pages = {}, pmid = {39073401}, issn = {1465-2080}, mesh = {*Porifera/microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; Animals ; Atlantic Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.}, }
@article {pmid39073317, year = {2024}, author = {Bahri, S and Bouazizi, S and Nahdi, A and Mlika, M and Hamdi, M and Jameleddine, S}, title = {Insights on the Tunisian Prickly Pear Molasses as a Potential Antifibrotic and Antioxidant Candidate against Lung Fibrosis.}, journal = {Chemistry &amp; biodiversity}, volume = {21}, number = {11}, pages = {e202401030}, doi = {10.1002/cbdv.202401030}, pmid = {39073317}, issn = {1612-1880}, support = {//Tunisian Ministry of Higher Education/ ; //Scientific Research/ ; }, mesh = {Animals ; *Antioxidants/pharmacology/chemistry ; *Rats, Wistar ; Rats ; *Pulmonary Fibrosis/drug therapy/chemically induced/metabolism/pathology ; *Molasses ; Male ; Bleomycin ; Oxidative Stress/drug effects ; Pyrus/chemistry ; Tunisia ; Antifibrotic Agents/pharmacology/chemistry ; Disease Models, Animal ; Lung/drug effects/pathology/metabolism ; }, abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial disease leading to pulmonary damage and respiratory failure. We aimed to investigate the effect of prickly pear molasses (PPM) on an experimental model of pulmonary fibrosis induced by bleomycin (BLM) in Wistar rat. Animals were divided into 5 groups: the control group (G1), the BLM group (G2) and three groups (G3, G4, G5) receiving a single intra-tracheal injection of BLM (4 mg/kg) and PPM (at 2, 4.5 and10 %) that was introduced into the diet one week before BLM injection and continued for 3 weeks. Our phytochemical results revealed significant polyphenol and flavonoid content. LCMS analysis revealed the presence of Sinapinic acid, t-ferulic acid, t-cinnamic acid, Caffeic acid, gallic acid and vallinic acid among others. Our histological study revealed significant decrease in collagen deposition in the groups of rats treated with 4.5 % and 10 % molasses compared to BLM group. Oxidative stress in pulmonary tissues was investigated using catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA) assays. Treatment with PPM normalized the disturbance in the level of these oxidative markers in G3,G4, G5 compared to G2. In conclusion, PPM exhibit antifibrotic and antioxidant activities in BLM model of lung fibrosis.}, }
@article {pmid39073180, year = {2024}, author = {Bielčik, M and Schlägel, UE and Schäfer, M and Aguilar-Trigueros, CA and Lakovic, M and Sosa-Hernández, MA and Hammer, EC and Jeltsch, F and Rillig, MC}, title = {Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {99}, number = {6}, pages = {2211-2233}, doi = {10.1111/brv.13119}, pmid = {39073180}, issn = {1469-185X}, support = {GRK 2118//Deutsche Forschungsgemeinschaft/ ; SCHL 2259/1-1.//Deutsche Forschungsgemeinschaft/ ; 100619639//Fachagentur Nachwachsende Rohstoffe/ ; }, mesh = {*Fungi/physiology ; *Ecosystem ; Models, Biological ; }, abstract = {Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.}, }
@article {pmid39071402, year = {2024}, author = {Dieppa-Colón, E and Martin, C and Anantharaman, K}, title = {Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071402}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39066818, year = {2024}, author = {Castellano-Hinojosa, A and Tortosa, G and Fernández-Zambrano, A and Correa-Galeote, D and Bedmar, EJ and Medina-Sánchez, JM}, title = {Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {99}, pmid = {39066818}, issn = {1432-184X}, support = {A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Lakes/microbiology/chemistry ; *Dust/analysis ; Spain ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Africa, Northern ; }, abstract = {Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.}, }
@article {pmid39065051, year = {2024}, author = {Du, W and Li, J and Zhang, G and Yu, K and Liu, S}, title = {Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065051}, issn = {2076-2607}, support = {52100171//National Natural Science Foundation of China/ ; BYESS2023103//Young Elite Scientist Sponsorship Program by Beijing Association for Science and Technology/ ; }, abstract = {Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4[+]-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.}, }
@article {pmid39065031, year = {2024}, author = {Sapp, PA and Townsend, JR and Kirby, TO and Govaert, M and Duysburgh, C and Verstrepen, L and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®], a Novel Synbiotic, Maintains Gut Barrier Function following Inflammatory Challenge in a Caco-2/THP1-Blue™ Co-Culture Model.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065031}, issn = {2076-2607}, support = {n/a//Athletic Greens International (Carson City, NV 89701)/ ; }, abstract = {Nutritional interventions to reduce gastrointestinal (GI) permeability are of significant interest to physically active adults and those experiencing chronic health conditions. This in vitro study was designed to assess the impact of AG1, a novel synbiotic, on GI permeability following an inflammatory challenge. Interventions [AG1 (vitamins/minerals, pre-/probiotics, and phytonutrients) and control (control medium)] were fed separately into a human GI tract model (stomach, small intestine, and colon). In the colonic phase, the GI contents were combined with fecal inocula from three healthy human donors. GI permeability was evaluated with transepithelial electrical resistance (TEER) in a Caco-2 (apical)/THP1-Blue™ (basolateral) co-culture model. The apical side received sodium butyrate (positive control) or Caco-2 complete medium (negative control) during baseline testing. In the 24 h experiment, the apical side received colonic simulation isolates from the GI model, and the basolateral side was treated with Caco-2 complete medium, then 6 h treatment with lipopolysaccharide. TEER was assessed at 0 h and 24 h, and inflammatory markers were measured at 30 h in triplicate. Paired samples t-tests were used to evaluate endpoint mean difference (MD) for AG1 vs. control. TEER was higher for AG1 (mean ± SD: 99.89 ± 1.32%) vs. control (mean ± SD: 92.87 ± 1.22%) following activated THP1-induced damage [MD: 7.0% (p < 0.05)]. AG1 maintained TEER similar to the level of the negative control [-0.1% (p = 0.02)]. No differences in inflammatory markers were observed. These in vitro data suggest that acute supplementation with AG1 might stimulate protective effects on GI permeability. These changes may be driven by SCFA production due to the pre-/probiotic properties of AG1, but more research is needed.}, }
@article {pmid39062734, year = {2024}, author = {Zhang, H and Li, S and Zhou, S and Guo, W and Chen, P and Li, Y and Wu, W}, title = {Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062734}, issn = {2073-4425}, support = {2023KCXTD017//Guangdong Province University Innovative Team Project: Innovation and Development Application of Ornamental Plant Germplasm with Lingnan Characteristics/ ; }, mesh = {*Volatile Organic Compounds/metabolism ; *Microbiota ; *Introduced Species ; Brassicaceae/microbiology/genetics ; China ; }, abstract = {Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.}, }
@article {pmid39061809, year = {2024}, author = {Hriňová, K and Dlapová, J and Kubala, B and Kormanová, &#x13d; and Levarski, Z and Struhárňanská, E and Turňa, J and Stuchlík, S}, title = {Production of Reverse Transcriptase and DNA Polymerase in Bacterial Expression Systems.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {39061809}, issn = {2306-5354}, support = {APVV-17-0333//Slovak Research and Development Agency/ ; APVV-21-0215//Slovak Research and Development Agency/ ; APVV-21-0227//Slovak Research and Development Agency/ ; APVV-22-0161//Slovak Research and Development Agency/ ; }, abstract = {DNA amplification and reverse transcription enzymes have proven to be invaluable in fast and reliable diagnostics and research applications because of their processivity, specificity, and robustness. Our study focused on the production of mutant Taq DNA polymerase and mutant M-MLV reverse transcriptase in the expression hosts Vibrio natriegens and Escherichia coli under various expression conditions. We also examined nonspecific extracellular production in V. natriegens. Intracellularly, M-MLV was produced in V. natriegens at the level of 11% of the total cell proteins (TCPs) compared with 16% of TCPs in E. coli. We obtained a soluble protein that accounted for 11% of the enzyme produced in V. natriegens and 22% of the enzyme produced in E. coli. Taq pol was produced intracellularly in V. natriegens at the level of 30% of TCPs compared with 26% of TCPs in E. coli. However, Taq pol was almost non-soluble in E. coli, whereas in V. natriegens, we obtained a soluble protein that accounted for 23% of the produced enzyme. We detected substantial extracellular production of Taq pol. Thus, V. natriegens is a suitable alternative host with the potential for production of recombinant proteins.}, }
@article {pmid39060935, year = {2024}, author = {Baptista, MS and Lee, CK and Monteiro, MR and Torgo, L and Cary, SC and Magalhães, C}, title = {Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {52}, pmid = {39060935}, issn = {2524-6372}, abstract = {BACKGROUND: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.<br><br>RESULTS: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.<br><br>CONCLUSIONS: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.}, }
@article {pmid39059201, year = {2024}, author = {Bai, X and Samari-Kermani, M and Schijven, J and Raoof, A and Dinkla, IJT and Muyzer, G}, title = {Enhancing slow sand filtration for safe drinking water production: interdisciplinary insights into Schmutzdecke characteristics and filtration performance in mini-scale filters.}, journal = {Water research}, volume = {262}, number = {}, pages = {122059}, doi = {10.1016/j.watres.2024.122059}, pmid = {39059201}, issn = {1879-2448}, mesh = {*Filtration ; *Drinking Water/microbiology ; *Water Purification/methods ; *Sand ; *Escherichia coli ; Silicon Dioxide/chemistry ; Biofilms ; }, abstract = {The demand for safe drinking water is constantly challenged by increasing biohazards. One widely used solution is implementing indoor-operated slow sand filtration (SSF) as one of the final barriers in water production. SSF has gained popularity due to its low energy consumption and efficient removal of biohazards, especially microorganisms, without using chemicals. SSF involves both physical-chemical and biological removal, particularly in the "Schmutzdecke", which is a biofilm-like layer on the sand bed surface. To achieve the optimal performance of SSF, a systematic understanding of the influence of SSF operating parameters on the Schmutzdecke development and filter filtration performance is required. Our study focused on three operational parameters, i.e., sand material, sand size, and the addition of an inoculum (suspension of matured Schmutzdecke), on the mini-scale filters. The effects of these parameters on the Schmutzdecke development and SSF removal performance were studied by biochemical analyses and 16S amplicon sequencing, together with spiking experiments with Escherichia coli (E. coli) in the mini-scale filters. Our results indicate that the mini-scale filters successfully developed Schmutzdeckes and generated bacterial breakthrough curves efficiently. The sand size and material were found to have an impact on Schmutzdecke's development. The addition of inoculum to new filters did not induce significant changes in the microbial community composition of the Schmutzdecke, but we observed positive effects of faster Schmutzdecke development and better removal performance in some inoculated filters. Our study highlights the value of mini-scale filters for SSF studies, which provide insights into Schmutzdecke microbial ecology and bacterial removal with significantly reduced requirements of materials and effort as compared to larger-scale filters. We found that operational parameters have a greater impact on the Schmutzdecke biochemical characteristics and removal performances than on the microbial community composition. This suggests that Schmutzdecke characteristics may provide more reliable predictors of SSF removal performance, which could help to improve safe drinking water production.}, }
@article {pmid39055957, year = {2024}, author = {Zhang, Y and Gan, G and Li, Y and Li, W and Jiang, Y and Wang, P and Hu, J and Wang, N and Quan, X and Liu, J and Raza, W and Xu, Y and Hohmann, P and Jousset, A and Wang, Y and Shen, Q and Jiang, G and Wei, Z}, title = {Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110319}, pmid = {39055957}, issn = {2589-0042}, abstract = {The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.}, }
@article {pmid39052866, year = {2024}, author = {}, title = {Correction to: Alpine soil microbial ecology in a changing world.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, doi = {10.1093/femsec/fiae085}, pmid = {39052866}, issn = {1574-6941}, }
@article {pmid39052865, year = {2024}, author = {Vuilleumier, S and Barthelmebs, L and Corcoll, N and Hery, M and G Karpouzas, D and Wick, LY}, title = {Editorial: thematic issue on microbial ecotoxicology.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39052865}, issn = {1574-6941}, mesh = {*Ecotoxicology ; }, }
@article {pmid39051617, year = {2024}, author = {Pluym, T and Waegenaar, F and De Gusseme, B and Boon, N}, title = {Microbial drinking water monitoring now and in the future.}, journal = {Microbial biotechnology}, volume = {17}, number = {7}, pages = {e14532}, pmid = {39051617}, issn = {1751-7915}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; Water Microbiology ; Environmental Monitoring/methods ; }, abstract = {Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.}, }
@article {pmid39047455, year = {2024}, author = {Blair, MF and Vaidya, R and Salazar-Benites, G and Bott, CB and Pruden, A}, title = {Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train.}, journal = {Water research}, volume = {262}, number = {}, pages = {122091}, doi = {10.1016/j.watres.2024.122091}, pmid = {39047455}, issn = {1879-2448}, mesh = {*Ozone ; *Water Purification/methods ; *Filtration ; Microbiota ; Charcoal/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.}, }
@article {pmid39046569, year = {2024}, author = {Chen, X and Zhang, W and Geng, M and Shen, J and Wang, J}, title = {Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {97}, pmid = {39046569}, issn = {1432-184X}, support = {42230507//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology/chemistry ; China ; *Carbon/metabolism ; *Phosphorus/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; Nutrients/metabolism/analysis ; }, abstract = {Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.}, }
@article {pmid39046558, year = {2024}, author = {Xie, G and Sun, C and Gong, Y and Luo, W and Tang, X}, title = {Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {96}, pmid = {39046558}, issn = {1432-184X}, support = {WGKQ2022032//West Anhui University/ ; 41971062//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/classification ; *Eutrophication ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Seasons ; Ecosystem ; China ; }, abstract = {In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.}, }
@article {pmid39046491, year = {2024}, author = {Soto-Cortés, E and Marroquín-Rodríguez, M and Basanta, MD and Maldonado-López, Y and Parra-Olea, G and Rebollar, EA}, title = {Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {98}, pmid = {39046491}, issn = {1432-184X}, support = {CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; IN205521//PAPIIT/UNAM/ ; }, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Mexico ; *Fungi/classification/isolation &amp; purification/genetics ; Ambystoma mexicanum/microbiology ; Host Specificity ; Environment ; Biodiversity ; }, abstract = {Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.}, }
@article {pmid39043275, year = {2024}, author = {Fernández-Blanco, C and Pereira, A and Veiga, MC and Kennes, C and Ganigué, R}, title = {Comprehensive comparative study on n-caproate production by Clostridium kluyveri: batch vs. continuous operation modes.}, journal = {Bioresource technology}, volume = {408}, number = {}, pages = {131138}, doi = {10.1016/j.biortech.2024.131138}, pmid = {39043275}, issn = {1873-2976}, mesh = {*Ethanol/metabolism ; *Clostridium kluyveri/metabolism ; *Caproates/metabolism ; Batch Cell Culture Techniques ; Bioreactors ; Fermentation ; Acetates/metabolism ; Oxidation-Reduction ; }, abstract = {Recently, there has been notable interest in researching and industrially producing medium-chain carboxylic acids (MCCAs) like n-caproate and n-caprylate via chain elongation process. This study presents a comprehensive assessment of the behavior and MCCA production profiles of Clostridium kluyveri in batch and continuous modes, at different ethanol:acetate molar ratios (1.5:1, 3.5:1 and 5.5:1). The highest n-caproate concentration, 12.9 ± 0.67 g/L (92.9 ± 1.39 % MCCA selectivity), was achieved in batch mode at a 3.5:1 ratio. Interestingly, higher ratios favored batch mode selectivity over continuous mode when this was equal or higher to 3.5:1. Steady state operation yielded the highest n-caproate (9.5 ± 0.13 g/L) and n-caprylate (0.35 ± 0.020 g/L) concentrations at the 3.5:1 ratio. Increased ethanol:acetate ratios led to a higher excessive ethanol oxidation (EEO) in both operational modes, potentially limiting n-caproate production and selectivity, especially at the 5.5:1 ratio. Overall, this study reports the efficient MCCA production of both batch and continuous modes by C. kluyveri.}, }
@article {pmid39043163, year = {2024}, author = {DeWitt, ME and Sanders, JW}, title = {Tropical Diseases in the United States: Beyond Poverty - Advancing an Ecological Framework in Tropical Medicine.}, journal = {The American journal of tropical medicine and hygiene}, volume = {111}, number = {3}, pages = {449-451}, pmid = {39043163}, issn = {1476-1645}, mesh = {*Tropical Medicine ; Humans ; *Poverty ; United States/epidemiology ; }, }
@article {pmid39039555, year = {2024}, author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T}, title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {134}, pmid = {39039555}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; }, abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.<br><br>RESULTS: We uncovered distinct distribution&#xa0;patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as&#xa0;potentially host abundance- or phage/host ratio-driven phage population changes.<br><br>CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.}, }
@article {pmid39039015, year = {2024}, author = {Vanharanta, M and Santoro, M and Villena-Alemany, C and Piiparinen, J and Piwosz, K and Grossart, HP and Labrenz, M and Spilling, K}, title = {Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39039015}, issn = {1574-6941}, support = {731065//European Commission/ ; 2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; GR1540/37-1//DFG/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phosphates/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; *Phosphorus/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; Finland ; Oceans and Seas ; Eutrophication ; Heterotrophic Processes ; }, abstract = {The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.}, }
@article {pmid39030648, year = {2024}, author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE}, title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {50}, pmid = {39030648}, issn = {2524-6372}, support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.}, }
@article {pmid39030520, year = {2024}, author = {Joo, M and Nam, S}, title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {268}, pmid = {39030520}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation &amp; purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.<br><br>METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.<br><br>RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.<br><br>CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.}, }
@article {pmid39030408, year = {2024}, author = {Gilbert, JA and Hartmann, EM}, title = {The indoors microbiome and human health.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {12}, pages = {742-755}, pmid = {39030408}, issn = {1740-1534}, mesh = {Humans ; *Microbiota ; Air Microbiology ; Air Pollution, Indoor ; Built Environment ; }, abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.}, }
@article {pmid39029405, year = {2024}, author = {Kozaeva, E and Eida, AA and Gunady, EF and Dangl, JL and Conway, JM and Brophy, JA}, title = {Roots of synthetic ecology: microbes that foster plant resilience in the changing climate.}, journal = {Current opinion in biotechnology}, volume = {88}, number = {}, pages = {103172}, doi = {10.1016/j.copbio.2024.103172}, pmid = {39029405}, issn = {1879-0429}, mesh = {*Microbiota/physiology ; *Climate Change ; *Plants/microbiology ; Plant Development ; Ecosystem ; Synthetic Biology ; Ecology ; Plant Roots/microbiology ; }, abstract = {Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.}, }
@article {pmid39025292, year = {2024}, author = {Guo, X and Zhao, W and Yin, D and Mei, Z and Wang, F and Tiedje, J and Ling, S and Hu, S and Xu, T}, title = {Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124566}, doi = {10.1016/j.envpol.2024.124566}, pmid = {39025292}, issn = {1873-6424}, mesh = {*Zebrafish/genetics ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Sulfonamides/pharmacology ; *Aspirin/pharmacology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Sulfamethoxazole/pharmacology ; Water Pollutants, Chemical ; Bacteria/genetics/drug effects ; }, abstract = {Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.}, }
@article {pmid39021442, year = {2024}, author = {Bowers, RM and Gonzalez-Pena, V and Wardhani, K and Goudeau, D and Blow, MJ and Udwary, D and Klein, D and Vill, AC and Brito, IL and Woyke, T and Malmstrom, RR and Gawad, C}, title = {scMicrobe PTA: near complete genomes from single bacterial cells.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae085}, pmid = {39021442}, issn = {2730-6151}, support = {DP2 CA239145/CA/NCI NIH HHS/United States ; }, abstract = {Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.}, }
@article {pmid39021414, year = {2024}, author = {Marin, C and Migura-García, L and Rodríguez, JC and Ventero, MP and Pérez-Gracia, MT and Vega, S and Tort-Miró, C and Marco-Fuertes, A and Lorenzo-Rebenaque, L and Montoro-Dasi, L}, title = {Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1401561}, pmid = {39021414}, issn = {2297-1769}, abstract = {INTRODUCTION: Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.<br><br>METHODS: For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.<br><br>RESULTS AND DISCUSSION: This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.}, }
@article {pmid39019971, year = {2024}, author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N}, title = {Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16555}, pmid = {39019971}, issn = {2045-2322}, mesh = {*Charcoal/chemistry ; *Fertilizers ; *Crops, Agricultural/growth &amp; development ; *Minerals/chemistry ; Nitrogen/chemistry ; Brassica/growth &amp; development ; Soil/chemistry ; Nutrients ; Agriculture/methods ; Magnesium/chemistry ; }, abstract = {Mechanized biochar field application remains challenging due to biochar's poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it's unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha[-1] with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26-35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.}, }
@article {pmid39018765, year = {2024}, author = {Bittleston, LS}, title = {Connecting microbial community assembly and function.}, journal = {Current opinion in microbiology}, volume = {80}, number = {}, pages = {102512}, doi = {10.1016/j.mib.2024.102512}, pmid = {39018765}, issn = {1879-0364}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; Biodiversity ; Humans ; }, abstract = {Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.}, }
@article {pmid39017940, year = {2024}, author = {Kim, YS and Yun, HS and Lee, JH and Lee, KL and Choi, JS and Won, DH and Kim, YJ and Kim, HS and Yoon, HS}, title = {Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {95}, pmid = {39017940}, issn = {1432-184X}, support = {2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2021R1I1A205551711//National Research Foundation of Korea/ ; }, mesh = {*Diatoms/classification/growth &amp; development ; *DNA Barcoding, Taxonomic ; *Microscopy/methods ; *Estuaries ; Republic of Korea ; Biodiversity ; Phylogeny ; Ecosystem ; }, abstract = {The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.}, }
@article {pmid39012154, year = {2024}, author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS}, title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0062724}, pmid = {39012154}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; }, abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.<br><br>IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.}, }
@article {pmid39012115, year = {2024}, author = {Luyt, NA and de Witt, RN and Divol, B and Patterton, HG and Setati, ME and Taillandier, P and Bauer, FF}, title = {Physical cell-cell contact elicits specific transcriptomic responses in wine yeast species.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0057223}, pmid = {39012115}, issn = {2165-0497}, support = {UID85055//National Research Foundation (NRF)/ ; UID83471//National Research Foundation (NRF)/ ; }, mesh = {*Wine/microbiology ; *Saccharomyces cerevisiae/genetics/metabolism ; *Transcriptome ; *Fermentation ; *Gene Expression Regulation, Fungal ; Saccharomycetales/genetics/metabolism ; Gene Expression Profiling ; Vitis/microbiology/genetics ; Cell Wall/metabolism/genetics ; Fungal Proteins/genetics/metabolism ; Microbial Interactions ; }, abstract = {Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions. These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.}, }
@article {pmid39011025, year = {2024}, author = {Alam, M and Pandit, B and Moin, A and Iqbal, UN}, title = {Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture.}, journal = {Indian journal of microbiology}, volume = {64}, number = {2}, pages = {343-366}, pmid = {39011025}, issn = {0046-8991}, abstract = {Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.}, }
@article {pmid39010847, year = {2024}, author = {Qing, J and Zhang, L and Li, C and Li, Y}, title = {Mendelian randomization analysis revealed that albuminuria is the key factor affecting socioeconomic status in CKD patients.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2367705}, pmid = {39010847}, issn = {1525-6049}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Albuminuria ; *Renal Insufficiency, Chronic/complications ; *Social Class ; *Glomerular Filtration Rate ; }, abstract = {Previous studies indicate a strong correlation between the incidence of chronic kidney disease (CKD) and lower economic status. However, these studies often struggle to delineate a clear cause-effect relationship, leaving healthcare providers uncertain about how to manage kidney disease in a way that improves patients' financial outcomes. Our study aimed to explore and establish a causal relationship between CKD and socioeconomic status, identifying critical influencing factors. We utilized summary meta-analysis data from the CKDGen Consortium and UK Biobank. Genetic variants identified from these sources served as instrumental variables (IVs) to estimate the association between CKD and socioeconomic status. The presence or absence of CKD, estimated glomerular filtration rate (eGFR), and albuminuria were used as exposures, while income and regional deprivation were analyzed as outcomes. We employed the R packages 'TwoSampleMR' and 'Mendelianrandomization' to conduct both univariable and multivariable Mendelian randomization (MR) analyses, assessing for potential pleiotropy and heterogeneity. Our univariable MR analysis revealed a significant causal relationship between high levels of albuminuria and lower income (OR = 0.84, 95% CI: 0.73-0.96, p = 0.013), with no significant pleiotropy detected. In the multivariable MR analysis, both CKD (OR = 0.867, 95% CI: 0.786-0.957, p = 0.0045) and eGFR (OR = 0.065, 95% CI: 0.010-0.437, p = 0.0049) exhibited significant effects on income. This study underscores that higher albuminuria levels in CKD patients are associated with decreased income and emphasizes the importance of effective management and treatment of albuminuria in CKD patients to mitigate both social and personal economic burdens.}, }
@article {pmid39008123, year = {2024}, author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B}, title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {93}, pmid = {39008123}, issn = {1432-184X}, support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; }, abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.}, }
@article {pmid39008061, year = {2024}, author = {Helmy, KG and Abu-Hussien, SH}, title = {Root Rot Management in Common Bean (Phaseolus vulgaris L.) Through Integrated Biocontrol Strategies using Metabolites from Trichoderma harzianum, Serratia marcescens, and Vermicompost Tea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {94}, pmid = {39008061}, issn = {1432-184X}, mesh = {*Phaseolus/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Serratia marcescens/physiology/metabolism ; *Rhizoctonia/physiology ; *Plant Roots/microbiology ; Biological Control Agents/pharmacology ; Pest Control, Biological ; Antibiosis ; Hypocreales/physiology/metabolism ; Egypt ; Composting ; Soil Microbiology ; }, abstract = {Common bean (Phaseolus vulgaris L.) is an essential food staple and source of income for small-holder farmers across Africa. However, yields are greatly threatened by fungal diseases like root rot induced by Rhizoctonia solani. This study aimed to evaluate an integrated approach utilizing vermicompost tea (VCT) and antagonistic microbes for effective and sustainable management of R. solani root rot in common beans. Fourteen fungal strains were first isolated from infected common bean plants collected across three Egyptian governorates, with R. solani being the most virulent isolate with 50% dominance. Subsequently, the antagonistic potential of vermicompost tea (VCT), Serratia sp., and Trichoderma sp. was assessed against this destructive pathogen. Combinations of 10% VCT and the biocontrol agent isolates displayed potent inhibition of R. solani growth in vitro, prompting in planta testing. Under greenhouse conditions, integrated applications of 5 or 10% VCT with Serratia marcescens, Trichoderma harzianum, or effective microorganisms (EM1) afforded up to 95% protection against pre- and post-emergence damping-off induced by R. solani in common bean cv. Giza 6. Similarly, under field conditions, combining VCT with EM1 (VCT + EM1) or Trichoderma harzianum (VCT + Trichoderma harzianum) substantially suppressed disease severity by 65.6% and 64.34%, respectively, relative to untreated plants. These treatments also elicited defense enzyme activity and distinctly improved growth parameters including 136.68% and 132.49% increases in pod weight per plant over control plants. GC-MS profiling of Trichoderma harzianum, Serratia marcescens, and vermicompost tea (VCT) extracts revealed unique compounds dominated by cyclic pregnane, fatty acid methyl esters, linoleic acid derivatives, and free fatty acids like oleic, palmitic, and stearic acids with confirmed biocontrol and plant growth-promoting activities. The results verify VCT-mediated delivery of synergistic microbial consortia as a sustainable platform for integrated management of debilitating soil-borne diseases, enhancing productivity and incomes for smallholder bean farmers through regeneration of soil health. Further large-scale validation can pave the adoption of this climate-resilient approach for securing food and nutrition security.}, }
@article {pmid39007602, year = {2024}, author = {Jensen, N and Maldonado-Gomez, M and Krishnakumar, N and Weng, C-Y and Castillo, J and Razi, D and Kalanetra, K and German, JB and Lebrilla, CB and Mills, DA and Taft, DH}, title = {Dietary fiber monosaccharide content alters gut microbiome composition and fermentation.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0096424}, pmid = {39007602}, issn = {1098-5336}, support = {R01DK124193//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; F32HD093185//HHS | National Institutes of Health (NIH)/ ; //Mars (Mars Incorporated)/ ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 DK124193/DK/NIDDK NIH HHS/United States ; //Gut Microbiome Yogurt and Probiotics Fellowship/ ; //Bill and Melinda Gates Foundation (GF)/ ; }, mesh = {*Fermentation ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; *Monosaccharides/metabolism/analysis ; Animals ; *Bacteria/classification/metabolism/genetics ; Feces/microbiology/chemistry ; Fatty Acids, Volatile/metabolism ; }, abstract = {UNLABELLED: Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production.<br><br>IMPORTANCE: The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.}, }
@article {pmid39003240, year = {2024}, author = {Vass, M and Székely, AJ and Carlsson-Graner, U and Wikner, J and Andersson, A}, title = {Microeukaryote community coalescence strengthens community stability and elevates diversity.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39003240}, issn = {1574-6941}, support = {2018-05973//Swedish Research Council/ ; }, mesh = {*Biodiversity ; *Diatoms/growth &amp; development ; *Fungi/genetics/classification/growth &amp; development ; Rivers/microbiology ; Seawater/microbiology ; Ciliophora/growth &amp; development/genetics ; Cercozoa/genetics/growth &amp; development ; Microbiota ; Eukaryota/growth &amp; development ; }, abstract = {Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.}, }
@article {pmid39003046, year = {2025}, author = {Lamprea Pineda, PA and Demeestere, K and Alvarado-Alvarado, AA and Devlieghere, F and Boon, N and Van Langenhove, H and Walgraeve, C}, title = {Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development.}, journal = {Journal of environmental sciences (China)}, volume = {147}, number = {}, pages = {268-281}, doi = {10.1016/j.jes.2023.10.020}, pmid = {39003046}, issn = {1001-0742}, mesh = {*Rhodococcus/metabolism ; *Bioreactors/microbiology ; *Biodegradation, Environmental ; *Hydrocarbons/metabolism ; Carbon/metabolism ; Air Pollutants/metabolism/analysis ; Mass Spectrometry ; Toluene/metabolism ; Xylenes/metabolism ; Butanes/metabolism ; Benzene Derivatives ; Pentanes ; }, abstract = {The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.}, }
@article {pmid39002491, year = {2024}, author = {Meroz, N and Livny, T and Friedman, J}, title = {Quantifying microbial interactions: concepts, caveats, and applications.}, journal = {Current opinion in microbiology}, volume = {80}, number = {}, pages = {102511}, doi = {10.1016/j.mib.2024.102511}, pmid = {39002491}, issn = {1879-0364}, mesh = {*Microbial Interactions ; Ecosystem ; Microbiota ; Bacteria/metabolism/genetics ; }, abstract = {Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.}, }
@article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39001714}, issn = {1751-7370}, support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; }, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.}, }
@article {pmid38995161, year = {2024}, author = {Seixas, MH and Munroe, JS and Eggleston, EM}, title = {Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA.}, journal = {MicrobiologyOpen}, volume = {13}, number = {4}, pages = {e1426}, pmid = {38995161}, issn = {2045-8827}, support = {//Middlebury College/ ; }, mesh = {Utah ; *Bacteria/classification/genetics/isolation &amp; purification ; *Caves/microbiology ; *Ice ; Soil Microbiology ; Biodiversity ; Microscopy, Electron, Scanning ; Seasons ; Water Microbiology ; }, abstract = {The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.}, }
@article {pmid38995046, year = {2024}, author = {Gibson, C and Jauffur, S and Guo, B and Frigon, D}, title = {Activated sludge microbial community assembly: the role of influent microbial community immigration.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0059824}, pmid = {38995046}, issn = {1098-5336}, support = {RGPIN-2016-06498, STPGP-521349-18//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; McGill Engineering Doctoral Award//Faculty of Engineering, McGill University (Faculty of Engineering, McGill)/ ; }, mesh = {*Sewage/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Wastewater/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.}, }
@article {pmid38993674, year = {2024}, author = {Huang, C and Liu, D and Yang, S and Huang, Y and Wei, X and Zhang, P and Lin, J and Xu, B and Liu, Y and Guo, D and Li, Y and Li, J and Zhang, H}, title = {Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110202}, pmid = {38993674}, issn = {2589-0042}, abstract = {Time-restricted eating (TRE) is a promising obesity management strategy, but weight-loss efficacy varies among participants, and the underlying mechanism is unclear. The study aimed to investigate the role of gut microbiota in weight-loss response during long-term TRE intervention. We analyzed data from 51 obese adults in a 12-month TRE program, categorizing them into distinct weight loss groups (DG) and moderate weight loss groups (MG) based on their TRE responses. Shotgun metagenomic sequencing analysis revealed a significant increase in species closely associated with weight loss effectiveness and metabolic parameter changes in the DG group. Pathways related to fatty acid biosynthesis, glycogen biosynthesis, and nucleotide metabolism were reduced in the DG group and enhanced in the MG group. Next, we identified nine specific species at baseline that contributed better responses to TRE intervention and significant weight loss. Collectively, gut microbiota contributes to responsiveness heterogeneity in TRE and can predict weight-loss effectiveness.}, }
@article {pmid38992757, year = {2024}, author = {Zeng, X and Liu, Y and Wang, Q and Ma, H and Li, X and Wang, Q and Yang, Q}, title = {Tanning wastewater restructured nitrogen-transforming bacteria communities and promoted N2O emissions in receiving river riparian sediments.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119580}, doi = {10.1016/j.envres.2024.119580}, pmid = {38992757}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Wastewater/microbiology/chemistry/analysis ; *Geologic Sediments/microbiology/chemistry ; *Nitrogen/analysis ; *Tanning ; Water Pollutants, Chemical/analysis ; Bacteria ; Denitrification ; Nitrous Oxide/analysis ; }, abstract = {Physicochemical and toxicological characterization of leather tanning wastewater has been widely documented. However, few reports have examined the response of denitrification N2 and N2O emissions in riparian sediments of tannery wastewater-receiving rivers. In this study, [15]N-nitrate labeling was used to reveal the effects of tanning wastewater on denitrification N2 and N2O emission in a wastewater-receiving river (the old Mang River, OMR). OMR riparian sediments were highly polluted with total organic carbon (93.39 mg/kg), total nitrogen (5.00 g/kg) and heavy metals; specifically, Cr, Zn, Cd, and Pb were found at concentrations 47.3, 5.8, 1.6, 4.3, and 2.8 times that in a nearby parallel river without tanning wastewater input (the new Mang River, NMR), respectively. The denitrification N2 emission rates (0.0015 nmol N · g[-1] h[-1]) of OMR riparian sediments were significantly reduced by 2.5 times compared with those from the NMR (p < 0.05), but the N2O emission rates (0.31 nmol N · g[-1] h[-1]) were significantly increased (4.1 times, p < 0.05). Although the dominant nitrogen-transforming bacteria phylum was Proteobacteria in the riparian sediments of both rivers, 11 nitrogen-transforming bacteria genera in the OMR were found to be significantly enriched; five of these were related to pollutant degradation based on linear discriminant analysis (LDA >3). The average activity of the electron transport system in the OMR was 6.3 times lower than that of the NMR (p < 0.05). Among pollution factors, heavy metal complex pollution was the dominant factor driving variations in N2O emissions, microbial community structure, and electron transport system activity. These results provide a new understanding and reference for the treatment of tanning wastewater-receiving rivers.}, }
@article {pmid38987492, year = {2024}, author = {Ng, MS and Soon, N and Afiq-Rosli, L and Kunning, I and Mana, RR and Chang, Y and Wainwright, BJ}, title = {Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {92}, pmid = {38987492}, issn = {1432-184X}, mesh = {*Anthozoa/microbiology ; Animals ; *Biodiversity ; *Dinoflagellida/genetics/classification/physiology ; *Symbiosis ; *Coral Reefs ; Papua New Guinea ; Phylogeny ; High-Throughput Nucleotide Sequencing ; }, abstract = {Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.}, }
@article {pmid38987022, year = {2024}, author = {Litchman, E and Villéger, S and Zinger, L and Auguet, JC and Thuiller, W and Munoz, F and Kraft, NJB and Philippot, L and Violle, C}, title = {Refocusing the microbial rare biosphere concept through a functional lens.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {10}, pages = {923-936}, doi = {10.1016/j.tree.2024.06.005}, pmid = {38987022}, issn = {1872-8383}, mesh = {*Microbiota ; Ecosystem ; Biodiversity ; }, abstract = {The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.}, }
@article {pmid38985714, year = {2024}, author = {Ugwuanyi, IR and Steele, A and Glamoclija, M}, title = {Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology.}, journal = {Astrobiology}, volume = {24}, number = {7}, pages = {734-753}, doi = {10.1089/ast.2023.0130}, pmid = {38985714}, issn = {1557-8070}, mesh = {Arctic Regions ; *Exobiology ; *Hot Springs/microbiology/chemistry ; Mars ; Silicon Dioxide/chemistry ; Svalbard ; Carbonates/chemistry/analysis ; Microbiota ; Temperature ; Biofilms ; }, abstract = {Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.}, }
@article {pmid38983631, year = {2024}, author = {Hawes, I and García-Maldonado, JQ and Falcón, LI}, title = {Editorial: Exploring microbial mat communities in extreme environments.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1440619}, doi = {10.3389/fmicb.2024.1440619}, pmid = {38983631}, issn = {1664-302X}, }
@article {pmid38982970, year = {2024}, author = {Jiang, J and Xiang, X and Zhou, Q and Zhou, L and Bi, X and Khanal, SK and Wang, Z and Chen, G and Guo, G}, title = {Optimization of a Novel Engineered Ecosystem Integrating Carbon, Nitrogen, Phosphorus, and Sulfur Biotransformation for Saline Wastewater Treatment Using an Interpretable Machine Learning Approach.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {29}, pages = {12989-12999}, doi = {10.1021/acs.est.4c03160}, pmid = {38982970}, issn = {1520-5851}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Machine Learning ; *Wastewater/chemistry ; *Carbon/metabolism ; Biotransformation ; Ecosystem ; Waste Disposal, Fluid/methods ; Denitrification ; }, abstract = {The denitrifying sulfur (S) conversion-associated enhanced biological phosphorus removal (DS-EBPR) process for treating saline wastewater is characterized by its unique microbial ecology that integrates carbon (C), nitrogen (N), phosphorus (P), and S biotransformation. However, operational instability arises due to the numerous parameters and intricates bacterial interactions. This study introduces a two-stage interpretable machine learning approach to predict S conversion-driven P removal efficiency and optimize DS-EBPR process. Stage one utilized the XGBoost regression model, achieving an R[2] value of 0.948 for predicting sulfate reduction (SR) intensity from anaerobic parameters with feature engineering. Stage two involved the CatBoost classification and regression model integrating anoxic parameters with the predicted SR values for predicting P removal, reaching an accuracy of 94% and an R[2] value of 0.93, respectively. This study identified key environmental factors, including SR intensity (20-45 mg S/L), influent P concentration (<9.0 mg P/L), mixed liquor volatile suspended solids (MLVSS)/mixed liquor suspended solids (MLSS) ratio (0.55-0.72), influent C/S ratio (0.5-1.0), anoxic reaction time (5-6 h), and MLSS concentration (>6.50 g/L). A user-friendly graphic interface was developed to facilitate easier optimization and control. This approach streamlines the determination of optimal conditions for enhancing P removal in the DS-EBPR process.}, }
@article {pmid38982962, year = {2024}, author = {Sbibih, Y and Saddari, A and Alla, I and Abdesselami, O and Ben Moussa, C and Ezrari, S and Benaissa, E and Ben Lahlou, Y and Elouennass, M and Maleb, A}, title = {Microbial ecology of protective isolation room: Air and Surfaces.}, journal = {La Tunisie medicale}, volume = {102}, number = {7}, pages = {394-398}, pmid = {38982962}, issn = {2724-7031}, mesh = {Humans ; *Air Microbiology ; *Cross Infection/prevention &amp; control/epidemiology/microbiology ; Prospective Studies ; Patients' Rooms/organization &amp; administration/statistics &amp; numerical data ; Patient Isolation/methods ; Hospitals, University ; Immunocompromised Host ; Tunisia/epidemiology ; }, abstract = {INTRODUCTION: Healthcare-associated infections pose a significant public health burden, leading to morbidity, mortality, prolonged hospital stays, and substantial social and economic costs. Immunocompromised patients are at a heightened risk of nosocomial infections.<br><br>AIM: This prospective study conducted at Mohammed VI University Hospital of Oujda aimed to assess the microbial ecology of surfaces and air in an immunosuppressed patient room compared to a double hospitalization room.<br><br>METHODS: Microbiological air purity tests were conducted employing both the sedimentation method and the collision method with the assistance of Microflow Alpha. The sedimentation method used Mueller Hinton with 5% human blood, facilitating the free fall of contaminated dust particles. The collection program employed was set for 10 minutes per 1 m3. For surface sampling, swabs were taken from a 25 cm2 surface. The swabs were immediately forwarded to the Microbiology Laboratory. We carried out both macroscopic and microscopic identification of colonies, followed by definitive biochemical identification using the BD phoenixTM system. Antibiotic susceptibility was assessed through agar diffusion on Muller Hinton medium coupled with the determination of the minimum inhibitory concentration.<br><br>RESULTS: The results revealed a decreased bacterial count within the protective isolation room, in contrast to the standard hospital room. We noted the predominance of coagulase-negative Staphylococcus spp and Bacillus spp. Staphylococcus aureus and Aspergillus spp, common pathogens in healthcare-associated infections, were notably absent in the protective isolation room. The findings underline the pivotal role of hospital environments in the transmission of healthcare-associated infections.<br><br>CONCLUSION: The protective isolation room demonstrated effective control of microbial contamination, with fewer and less resistant germs. The study highlighted the significance of air treatment systems in preventing the spread of opportunistic infections. Our study underscored the critical role of microbiological cleanliness in preventing nosocomial infections.}, }
@article {pmid38982749, year = {2024}, author = {Schrecengost, A and Rotterová, J and Poláková, K and Čepička, I and Beinart, RA}, title = {Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38982749}, issn = {1751-7370}, support = {//Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award/ ; 1330406//United States National Science Foundation EPSCoR Track II Cooperative Agreement Award/ ; 23-06004S//Czech Science Foundation/ ; OIA-1655221//National Science Foundation EPSCoR/ ; //Vini&#x10d;n&#xe1; Microscopy Core Facility/ ; LM2023050//MEYS CR/ ; 1919588//National Science Foundation Major Research Instrumentation/ ; }, mesh = {*Symbiosis ; *Ciliophora/classification/genetics/physiology ; *Phylogeny ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 18S/genetics ; DNA, Archaeal/genetics/chemistry ; Sequence Analysis, DNA ; Seawater/microbiology/parasitology ; }, abstract = {Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.}, }
@article {pmid38980056, year = {2024}, author = {Henson, MW and Thrash, JC}, title = {Microbial ecology of northern Gulf of Mexico estuarine waters.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0131823}, pmid = {38980056}, issn = {2379-5077}, support = {Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation (SF)/ ; Marine Microbiology Postdoctoral Fellowship//Simons Foundation (SF)/ ; LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (LBR)/ ; Lerner Gray grant//American Museum of Natural History (AMNH)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; LEEC Grant//Louisiana Department of Fish and Wildlife/ ; }, mesh = {Gulf of Mexico ; *Estuaries ; Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology/chemistry ; Louisiana ; Microbiota ; Water Microbiology ; Ecosystem ; Salinity ; }, abstract = {Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.}, }
@article {pmid38980052, year = {2024}, author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH}, title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0057324}, pmid = {38980052}, issn = {2379-5077}, support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; }, abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.<br><br>IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.}, }
@article {pmid38979877, year = {2024}, author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD}, title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13991}, doi = {10.1111/1755-0998.13991}, pmid = {38979877}, issn = {1755-0998}, support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsr&#xe5;det/ ; 101044505/ERC_/European Research Council/International ; }, mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; }, abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.}, }
@article {pmid38974332, year = {2024}, author = {Johnston, JT and Quoc, BN and Abrahamson, B and Candry, P and Ramon, C and Cash, KJ and Saccomano, SC and Samo, TJ and Ye, C and Weber, PK and Winkler, MH and Mayali, X}, title = {Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae086}, pmid = {38974332}, issn = {2730-6151}, abstract = {Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with [13]C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.}, }
@article {pmid38973247, year = {2024}, author = {Akay, C and Ulrich, N and Rocha, U and Ding, C and Adrian, L}, title = {Sequential Anaerobic-Aerobic Treatment Enhances Sulfamethoxazole Removal: From Batch Cultures to Observations in a Large-Scale Wastewater Treatment Plant.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {28}, pages = {12609-12620}, pmid = {38973247}, issn = {1520-5851}, mesh = {*Sulfamethoxazole/metabolism ; *Wastewater/chemistry ; Anaerobiosis ; Waste Disposal, Fluid ; Water Pollutants, Chemical/metabolism ; Aerobiosis ; }, abstract = {Sulfamethoxazole (SMX) passes through conventional wastewater treatment plants (WWTPs) mainly unaltered. Under anoxic conditions sulfate-reducing bacteria can transform SMX but the fate of the transformation products (TPs) and their prevalence in WWTPs remain unknown. Here, we report the anaerobic formation and aerobic degradation of SMX TPs. SMX biotransformation was observed in nitrate- and sulfate-reducing enrichment cultures. We identified 10 SMX TPs predominantly showing alterations in the heterocyclic and N[4]-arylamine moieties. Abiotic oxic incubation of sulfate-reducing culture filtrates led to further degradation of the major anaerobic SMX TPs. Upon reinoculation under oxic conditions, all anaerobically formed TPs, including the secondary TPs, were degraded. In samples collected at different stages of a full-scale municipal WWTP, anaerobically formed SMX TPs were detected at high concentrations in the primary clarifier and digested sludge units, where anoxic conditions were prevalent. Contrarily, their concentrations were lower in oxic zones like the biological treatment and final effluent. Our results suggest that anaerobically formed TPs were eliminated in the aerobic treatment stages, consistent with our observations in batch biotransformation experiments. More generally, our findings highlight the significance of varying redox states determining the fate of SMX and its TPs in engineered environments.}, }
@article {pmid38971962, year = {2024}, author = {Zhang, W and Zhang, F and Wu, Y and Liu, J and Fahad, S and Li, Z and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Powdery Mildew of Xanthium strumarium Caused by Podosphaera xanthii in central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-05-24-1062-PDN}, pmid = {38971962}, issn = {0191-2917}, abstract = {Xanthium strumarium, known as cocklebur, is an annual herb and has been used in traditional Chinese medicine. In October 2020, powdery mildew-like disease signs and symptoms were observed on X. strumarium grown in a crop field, Xinxiang city, Henan Province, China (35.36076° N, 113.93467° E). The specimen (PX-XS2023) was stored in Xinxiang Key Laboratory of Plant Stress Biology. White colonies in irregular or coalesced circular shaped-lesions were abundant on both ad- and abaxial surfaces of leaves and covered up to 99 % of the leaf area. Some of the infected leaves were senesced. More than 70 % of plants (n = 130) exhibited these signs and symptoms. Conidiophores were straight or slightly curved, 55 to 160 × 11 to 13 μm composed of foot-cells, shorter cells and conidia. Conidia were ellipsoid to oval, 29 to 40 × 14 to 20 μm (n = 50), with a length/width ration of 2.0 to 2.5, containing fibrosin bodies. Dark brown to black chasmothecia were found on infected leaves. The appendages were mycelium-shaped and at the base of scattered or gregarious chasmothecia (n = 50, 70 to 120 μm in diameter). Asci were 55 to 80 × 50 to 65 μm (n=30). These morphological characteristics were consistent with those of Podosphaera xanthii (Braun and Cook 2012). The internal transcribed spacer (ITS) region and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) region of the fungus (PX-XS2023) were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were respectively deposited into GenBank (Accession No. MW300956 and PP236083). BLASTn analysis indicated that the sequences were respectively 99.82 % (564/565) and 100% (272/272) identical to P. xanthii (MT260063 and ON075658). The phylogenetic analysis indicated that the strain PX-XS2023 and P. xanthii were clustered into a same branch. Therefore, the causal agent of powdery mildew on X. strumarium was P. xanthii. To conduct pathogenicity assays, mature leaves of five healthy X. strumarium (height in 50 centimeters) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants (Zhu et al. 2020). Five untreated plants served as controls. The controls and inoculated plants were separately maintained in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). Eight days post-inoculation, signs of powdery mildew were detectable on inoculated plants, however, the controls were asymptomatic. Thus, the fungal pathogen was morphologically and molecularly identified and confirmed as P. xanthii. This powdery mildew caused by P. xanthii was previously reported on X. strumarium in Korea, Russia and India (Farr and Rossman, 2021). In addition, P. xanthii was recorded on X. strumarium in Xinjiang Province, China (Tai 1979). However, this is the first report of P. xanthii on X. strumarium in central China, where is around 3000 km away from Xinjiang Province with geographically differences. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce medical value of X. strumarium. Therefore, the identification and confirmation of P. xanthii infecting X. strumarium enhance the knowledge on the hosts of this pathogen in China and will provide fundamental information for disease control in the future.}, }
@article {pmid38969462, year = {2024}, author = {Chen, Y and Zhou, H and Gao, H and Su, Z and Li, X and Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Xing, X and Yang, J and Chen, C and Ma, K and Chen, J}, title = {Comprehensive comparison of water quality risk and microbial ecology between new and old cast iron pipe distribution systems.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {55-66}, doi = {10.1016/j.jes.2023.05.020}, pmid = {38969462}, issn = {1001-0742}, mesh = {*Iron ; *Water Quality ; *Biofilms ; Corrosion ; *Water Supply ; Water Microbiology ; Drinking Water/microbiology/chemistry ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Trihalomethanes/analysis ; }, abstract = {The effects of cast iron pipe corrosion on water quality risk and microbial ecology in drinking water distribution systems (DWDSs) were investigated. It was found that trihalomethane (THMs) concentration and antibiotic resistance genes (ARGs) increased sharply in the old DWDSs. Under the same residual chlorine concentration conditions, the adenosine triphosphate concentration in the effluent of old DWDSs (Eff-old) was significantly higher than that in the effluent of new DWDSs. Moreover, stronger bioflocculation ability and weaker hydrophobicity coexisted in the extracellular polymeric substances of Eff-old, meanwhile, iron particles could be well inserted into the structure of the biofilms to enhance the mechanical strength and stability of the biofilms, hence enhancing the formation of THMs. Old DWDSs significantly influenced the microbial community of bulk water and triggered stronger microbial antioxidant systems response, resulting in higher ARGs abundance. Corroded cast iron pipes induced a unique interaction system of biofilms, chlorine, and corrosion products. Therefore, as the age of cast iron pipes increases, the fluctuation of water quality and microbial ecology should be paid more attention to maintain the safety of tap water.}, }
@article {pmid38969457, year = {2024}, author = {Chen, SC and Musat, F and Richnow, HH and Krüger, M}, title = {Microbial diversity and oil biodegradation potential of northern Barents Sea sediments.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {283-297}, doi = {10.1016/j.jes.2023.12.010}, pmid = {38969457}, issn = {1001-0742}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Biodegradation, Environmental ; Arctic Regions ; *Microbiota ; Petroleum/metabolism ; Bacteria/classification/metabolism/genetics ; Archaea/metabolism/classification/genetics ; Water Pollutants, Chemical/analysis/metabolism ; Biodiversity ; }, abstract = {The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.}, }
@article {pmid38969451, year = {2024}, author = {Ma, B and Zheng, L and Xie, B and Ma, L and Jia, M and Xie, C and Hu, C and Ulbricht, M and Wei, Y}, title = {Sustainable wastewater treatment and reuse in space.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {237-240}, doi = {10.1016/j.jes.2023.08.023}, pmid = {38969451}, issn = {1001-0742}, mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Space Flight ; }, abstract = {Exploring the vast extraterrestrial space is an inevitable trend with continuous human development. Water treatment and reuse are crucial in the limited and closed space that is available in spaceships or long-term use space bases that will be established in the foreseeable future. Dedicated water treatment technologies have experienced iterative development for more than 60 years since the first manned spaceflight was successfully launched. Herein, we briefly review the related wastewater characteristics and the history of water treatment in space stations, and we focus on future challenges and perspectives, aiming at providing insights for optimizing wastewater treatment technologies and closing the water cycle in future.}, }
@article {pmid38968348, year = {2024}, author = {Miettinen, TP and Gomez, AL and Wu, Y and Wu, W and Usherwood, TR and Hwang, Y and Roller, BRK and Polz, MF and Manalis, SR}, title = {Cell size, density, and nutrient dependency of unicellular algal gravitational sinking velocities.}, journal = {Science advances}, volume = {10}, number = {27}, pages = {eadn8356}, pmid = {38968348}, issn = {2375-2548}, mesh = {*Cell Size ; *Nutrients/metabolism ; Gravitation ; Phytoplankton/physiology/metabolism ; Photosynthesis ; Microalgae/metabolism ; }, abstract = {Eukaryotic phytoplankton, also known as algae, form the basis of marine food webs and drive marine carbon sequestration. Algae must regulate their motility and gravitational sinking to balance access to light at the surface and nutrients in deeper layers. However, the regulation of gravitational sinking remains largely unknown, especially in motile species. Here, we quantify gravitational sinking velocities according to Stokes' law in diverse clades of unicellular marine microalgae to reveal the cell size, density, and nutrient dependency of sinking velocities. We identify a motile algal species, Tetraselmis sp., that sinks faster when starved due to a photosynthesis-driven accumulation of carbohydrates and a loss of intracellular water, both of which increase cell density. Moreover, the regulation of cell sinking velocities is connected to proliferation and can respond to multiple nutrients. Overall, our work elucidates how cell size and density respond to environmental conditions to drive the vertical migration of motile algae.}, }
@article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, }
@article {pmid38964855, year = {2024}, author = {Zhao, F and Wang, B and Cui, Q and Wu, Y}, title = {Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae168}, pmid = {38964855}, issn = {1365-2672}, support = {31700117//National Natural Science Foundation of China/ ; 6096//Qufu Normal University/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/metabolism ; *Petroleum/metabolism ; *Surface-Active Agents/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Hydrocarbons/metabolism ; Microbiota ; }, abstract = {AIMS: Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community?<br><br>METHODS AND RESULTS: A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. Pseudomonas aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200&#xa0;mg l-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbon-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide-producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas, and Arcobacter.<br><br>CONCLUSIONS: Culture-based and sequence-based analyses reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.}, }
@article {pmid38962127, year = {2024}, author = {Lange, E and Kranert, L and Krüger, J and Benndorf, D and Heyer, R}, title = {Microbiome modeling: a beginner's guide.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1368377}, pmid = {38962127}, issn = {1664-302X}, abstract = {Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.}, }
@article {pmid38960913, year = {2024}, author = {Bischof, PSP and Bartolomaeus, TUP and Löber, U and Bleidorn, C}, title = {Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {91}, pmid = {38960913}, issn = {1432-184X}, support = {F01KI1909A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Diptera/microbiology ; *Larva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Kelp/microbiology ; }, abstract = {Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.}, }
@article {pmid38960411, year = {2024}, author = {Mafune, KK and Kasson, MT and Winkler, MH}, title = {Building blocks toward sustainable biofertilizers: variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae167}, pmid = {38960411}, issn = {1365-2672}, support = {2021 postdoctoral//Washington Research Foundation/ ; //Mycological Society of America/ ; 2023-67013-4017//National Institute of Food and Agriculture/ ; }, mesh = {*Mycorrhizae/physiology ; *Spores, Fungal/growth &amp; development ; *Hydrogels ; *Azospirillum brasilense/metabolism ; *Fertilizers/analysis ; Alginates ; }, abstract = {AIM: We investigated whether there was interspecies and intraspecies variation in spore germination of 12 strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth-promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads.<br><br>METHODS AND RESULTS: Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2%&#xa0;w/v) to form biodegradable hydrogel beads. One hundred beads from each combination (total of 1200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system.<br><br>CONCLUSIONS: Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant growth-promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.}, }
@article {pmid38959887, year = {2024}, author = {Perruzza, L and Rezzonico Jost, T and Raneri, M and Gargari, G and Palatella, M and De Ponte Conti, B and Seehusen, F and Heckmann, J and Viemann, D and Guglielmetti, S and Grassi, F}, title = {Protection from environmental enteric dysfunction and growth improvement in malnourished newborns by amplification of secretory IgA.}, journal = {Cell reports. Medicine}, volume = {5}, number = {7}, pages = {101639}, pmid = {38959887}, issn = {2666-3791}, mesh = {Animals ; *Immunoglobulin A, Secretory/metabolism ; *Malnutrition/immunology ; Mice ; Female ; *Gastrointestinal Microbiome ; Animals, Newborn ; Humans ; Apyrase/metabolism ; Infant, Newborn ; }, abstract = {Environmental enteric dysfunction (EED) is a condition associated with malnutrition that can progress to malabsorption and villous atrophy. Severe EED results in linear growth stunting, slowed neurocognitive development, and unresponsiveness to oral vaccines. Prenatal exposure to malnutrition and breast feeding by malnourished mothers replicates EED. Pups are characterized by deprivation of secretory IgA (SIgA) and altered development of the gut immune system and microbiota. Extracellular ATP (eATP) released by microbiota limits T follicular helper (Tfh) cell activity and SIgA generation in Peyer's patches (PPs). Administration of a live biotherapeutic releasing the ATP-degrading enzyme apyrase to malnourished pups restores SIgA levels and ameliorates stunted growth. SIgA is instrumental in improving the growth and intestinal immune competence of mice while they are continuously fed a malnourished diet. The analysis of microbiota composition suggests that amplification of endogenous SIgA may exert a dominant function in correcting malnourishment dysbiosis and its consequences on host organisms, irrespective of the actual microbial ecology.}, }
@article {pmid38958675, year = {2024}, author = {Dendooven, L and Pérez-Hernández, V and Navarro-Pérez, G and Tlalmis-Corona, J and Navarro-Noya, YE}, title = {Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. &amp; Cham.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {90}, pmid = {38958675}, issn = {1432-184X}, support = {591213//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; INFR-2015-01-253217//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; }, mesh = {*Seedlings/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Endophytes/classification/isolation &amp; purification/physiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Abies/microbiology ; *Plant Roots/microbiology ; Soil Microbiology ; Biodiversity ; Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. &amp; Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.}, }
@article {pmid38955825, year = {2024}, author = {Pan, H and Wattiez, R and Gillan, D}, title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {257}, pmid = {38955825}, issn = {1432-0991}, support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; }, abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.}, }
@article {pmid38955821, year = {2024}, author = {Weisse, T and Pröschold, T and Kammerlander, B and Sonntag, B and Schicker, L}, title = {Numerical and Thermal Response of the Bacterivorous Ciliate Colpidium kleini, a Species Potentially at Risk of Extinction by Rising Water Temperatures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {89}, pmid = {38955821}, issn = {1432-184X}, support = {P 32714/FWF_/Austrian Science Fund FWF/Austria ; DOC fForte 22883//&#xd6;sterreichischen Akademie der Wissenschaften/ ; 10.55776/P32714//Austrian Science Fund/ ; }, mesh = {*Ciliophora/physiology/growth &amp; development/classification/isolation &amp; purification ; Lakes/microbiology/parasitology ; Temperature ; Phylogeny ; Extinction, Biological ; Bacteria/classification/isolation &amp; purification/genetics ; }, abstract = {We investigated the food-dependent growth and thermal response of the freshwater ciliate Colpidium kleini using numerical response (NR) experiments. This bacterivorous ciliate occurs in lotic water and the pelagial of lakes and ponds. The C. kleini strain used in this work was isolated from a small alpine lake and identified by combining detailed morphological inspections with molecular phylogeny. Specific growth rates (rmax) were measured from 5 to 21 °C. The ciliate did not survive at 22 °C. The threshold bacterial food levels (0.3 - 2.2 × 10[6] bacterial cells mL[-1]) matched the bacterial abundance in the alpine lake from which C. kleini was isolated. The food threshold was notably lower than previously reported for C. kleini and two other Colpidium species. The threshold was similar to levels reported for oligotrich and choreotrich ciliates if expressed in terms of bacterial biomass (0.05 - 0.43 mg C L[-1]). From the NR results, we calculated physiological mortality rates at zero food concentration. The mean mortality (0.55 ± 0.17 d[-1]) of C. kleini was close to the mean estimate obtained for other planktonic ciliates that do not encyst. We used the data obtained by the NR experiments to fit a thermal performance curve (TPC). The TPC yielded a temperature optimum at 17.3 °C for C. kleini, a maximum upper thermal tolerance limit of 21.9 °C, and a thermal safety margin of 4.6 °C. We demonstrated that combining NR with TPC analysis is a powerful tool to predict better a species' fitness in response to temperature and food.}, }
@article {pmid38954336, year = {2024}, author = {Benammar, L and Menasria, T and Dibi, AR}, title = {Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {32}, pages = {44848-44862}, pmid = {38954336}, issn = {1614-7499}, mesh = {*Hot Springs/microbiology ; Algeria ; *Bacteria ; *RNA, Ribosomal, 16S ; Biodiversity ; Archaea ; }, abstract = {Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.}, }
@article {pmid38952448, year = {2024}, author = {Aqueel, R and Badar, A and Ijaz, UZ and Malik, KA}, title = {Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1381883}, pmid = {38952448}, issn = {1664-302X}, abstract = {Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant's ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant's response to viral disease, which may be microbially mediated.}, }
@article {pmid38949619, year = {2024}, author = {Jibrin, MO and Sharma, A and Mavian, CN and Timilsina, S and Kaur, A and Iruegas-Bocardo, F and Potnis, N and Minsavage, GV and Coutinho, TA and Creswell, TC and Egel, DS and Francis, DM and Kebede, M and Miller, SA and Montelongo, MJ and Nikolaeva, E and Pianzzola, MJ and Pruvost, O and Quezado-Duval, AM and Ruhl, GE and Shutt, VM and Maynard, E and Maeso, DC and Siri, MI and Trueman, CL and Salemi, M and Vallad, GE and Roberts, PD and Jones, JB and Goss, EM}, title = {Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen Xanthomonas hortorum pv. gardneri.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {37}, number = {10}, pages = {712-720}, doi = {10.1094/MPMI-04-24-0035-R}, pmid = {38949619}, issn = {0894-0282}, mesh = {*Solanum lycopersicum/microbiology ; *Plant Diseases/microbiology ; *Xanthomonas/genetics/pathogenicity ; *Phylogeny ; *Genetic Variation ; Genome, Bacterial ; }, abstract = {The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid38946903, year = {2024}, author = {Malfent, F and Zehl, M and Kirkegaard, RH and Oberhofer, M and Zotchev, SB}, title = {Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1408479}, pmid = {38946903}, issn = {1664-302X}, abstract = {Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.}, }
@article {pmid38946328, year = {2024}, author = {Langlois, GA}, title = {Past-President address: My journey in microbial ecology-footprints in the sand, island hopping, supply chains, and technology bridges.}, journal = {The Journal of eukaryotic microbiology}, volume = {71}, number = {4}, pages = {e13037}, doi = {10.1111/jeu.13037}, pmid = {38946328}, issn = {1550-7408}, mesh = {*Ecology ; Eukaryota/physiology ; History, 20th Century ; History, 21st Century ; }, abstract = {This paper highlights and honors the connectivity among protistan researchers, using my own research journey as a backdrop, with attention to the supply chain of ideas, supporters, and other influencers who helped to shape and guide my career by sharing their ideas, protocols, skills, and enthusiasm. In looking back at the journey, the supply chain in my career has also included changes in the conceptual framework for my research studies, converging with a continuous flow of ideas and support from colleagues and mentors. To illustrate the complex map of ideas and supporters, this paper will examine technological advances, paradigm shifts in ecological constructs, geographical considerations, breakthroughs in peritrich biology, and the importance of an integrated perspective as we navigate the changing realities of today's scientific challenges.}, }
@article {pmid38946115, year = {2024}, author = {Zayed, N and Vertommen, R and Simoens, K and Bernaerts, K and Boon, N and Srivastava, MG and Braem, A and Van Holm, W and Castro, AB and Teughels, W}, title = {How well do antimicrobial mouth rinses prevent dysbiosis in an in vitro periodontitis biofilm model?.}, journal = {Journal of periodontology}, volume = {95}, number = {9}, pages = {880-891}, doi = {10.1002/JPER.23-0674}, pmid = {38946115}, issn = {1943-3670}, mesh = {*Biofilms/drug effects ; Humans ; *Dysbiosis/prevention &amp; control ; *Mouthwashes/pharmacology/therapeutic use ; *Periodontitis/prevention &amp; control/microbiology ; Microscopy, Electron, Scanning ; Chlorhexidine/pharmacology/analogs &amp; derivatives/therapeutic use ; Interleukin-8 ; In Vitro Techniques ; Anti-Infective Agents/pharmacology/therapeutic use ; Durapatite ; Anti-Infective Agents, Local/pharmacology/therapeutic use ; Microbiota/drug effects ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiosis in the oral microbial communities. Managing oral biofilms is therefore key for preventing these diseases. Management protocols often include over-the-counter antimicrobial mouth rinses, which lack data on their effects on the oral microbiome's ecology, bacterial composition, metabolic activity, and dysbiosis resilience. This study examined the efficacy of antimicrobial mouth rinses to halt dysbiosis in in vitro oral biofilms under periodontitis-simulating conditions.<br><br>METHODS: Multispecies oral biofilms were grown on hydroxyapatite discs (HADs) and rinsed daily with one of six mouth rinses. Positive and negative controls were included. After three rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and visualized using scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis. In addition, human oral keratinocytes were exposed to rinsed biofilms to assess their inflammatory response. All outputs were analyzed for correlation using Spearman coefficient.<br><br>RESULTS: Product-related changes were observed in the rinsed biofilms. Three of the six tested mouth rinses could significantly prevent dysbiosis with &#x2265;30% reduction in pathobiont abundance relative to the control. These biofilms had lower metabolic activity, and the exposed human oral keratinocyte produced less interleukin-8. Interleukin-8 production correlated to both pathobiont quantity and the metabolic activity of the biofilms.<br><br>CONCLUSION: Some mouth rinses could support biofilm resilience and stop dysbiosis evolution in the biofilm model, with a clear product-related effect. Such mouth rinses can be considered for patients under maintenance/supportive periodontal therapy to prevent/delay disease recurrence. Others are more useful for different periodontal therapy stages.}, }
@article {pmid38945268, year = {2024}, author = {Tom, WA and Judy, JV and Kononoff, PJ and Fernando, SC}, title = {Influence of empirically derived filtering parameters, amplicon sequence variant, and operational taxonomic unit pipelines on assessing rumen microbial diversity.}, journal = {Journal of dairy science}, volume = {107}, number = {11}, pages = {9209-9234}, doi = {10.3168/jds.2023-24479}, pmid = {38945268}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; }, abstract = {Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies.}, }
@article {pmid38943017, year = {2024}, author = {Pires, CS and Costa, L and Barbosa, SG and Sequeira, JC and Cachetas, D and Freitas, JP and Martins, G and Machado, AV and Cavaleiro, AJ and Salvador, AF}, title = {Microplastics Biodegradation by Estuarine and Landfill Microbiomes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {88}, pmid = {38943017}, issn = {1432-184X}, support = {UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.01617.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; }, mesh = {*Biodegradation, Environmental ; *Microbiota ; *Microplastics/metabolism ; *Waste Disposal Facilities ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Water Pollutants, Chemical/metabolism ; Polyesters/metabolism ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Estuaries ; Polyethylene/metabolism ; Polyethylene Terephthalates/metabolism ; }, abstract = {Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in environments contaminated with microplastics is crucial for mitigating the effects of plastic pollution. In this work, we evaluated the potential of landfill leachate (LL) and estuarine sediments (ES) to biodegrade polyethylene (PE), polyethylene terephthalate (PET), and polycaprolactone (PCL), under aerobic, anaerobic, thermophilic, and mesophilic conditions. PCL underwent extensive aerobic biodegradation with LL (99 ± 7%) and ES (78 ± 3%) within 50-60 days. Under anaerobic conditions, LL degraded 87 ± 19% of PCL in 60 days, whereas ES showed minimal biodegradation (3 ± 0.3%). PE and PET showed no notable degradation. Metataxonomics results (16S rRNA sequencing) revealed the presence of highly abundant thermophilic microorganisms assigned to Coprothermobacter sp. (6.8% and 28% relative abundance in anaerobic and aerobic incubations, respectively). Coprothermobacter spp. contain genes encoding two enzymes, an esterase and a thermostable monoacylglycerol lipase, that can potentially catalyze PCL hydrolysis. These results suggest that Coprothermobacter sp. may be pivotal in landfill leachate microbiomes for thermophilic PCL biodegradation across varying conditions. The anaerobic microbial community was dominated by hydrogenotrophic methanogens assigned to Methanothermobacter sp. (21%), pointing at possible syntrophic interactions with Coprothermobacter sp. (a H2-producer) during PCL biodegradation. In the aerobic experiments, fungi dominated the eukaryotic microbial community (e.g., Exophiala (41%), Penicillium (17%), and Mucor (18%)), suggesting that aerobic PCL biodegradation by LL involves collaboration between fungi and bacteria. Our findings bring insights on the microbial communities and microbial interactions mediating plastic biodegradation, offering valuable perspectives for plastic pollution mitigation.}, }
@article {pmid38942024, year = {2024}, author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H}, title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.}, journal = {Cell genomics}, volume = {4}, number = {7}, pages = {100586}, pmid = {38942024}, issn = {2666-979X}, mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; }, abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.}, }
@article {pmid38940921, year = {2024}, author = {Picariello, E and De Nicola, F}, title = {Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {86}, pmid = {38940921}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Fagus/microbiology ; *Quercus/microbiology ; *Forests ; *Microbiota ; *Soil/chemistry ; *Seasons ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Biodiversity ; Forestry ; Trees/microbiology ; Ecosystem ; }, abstract = {Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.}, }
@article {pmid38940862, year = {2024}, author = {Ljaljević Grbić, M and Dimkić, I and Janakiev, T and Kosel, J and Tavzes, &#x10c; and Popović, S and Knežević, A and Legan, L and Retko, K and Ropret, P and Unković, N}, title = {Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {87}, pmid = {38940862}, issn = {1432-184X}, support = {451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; }, mesh = {*Biofilms ; *Lichens/microbiology/physiology ; *Calcium Carbonate ; Slovenia ; Ascomycota/physiology ; Mycobiome ; }, abstract = {The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.}, }
@article {pmid38940768, year = {2024}, author = {Baroncelli, R and Cobo-Díaz, JF and Benocci, T and Peng, M and Battaglia, E and Haridas, S and Andreopoulos, W and LaButti, K and Pangilinan, J and Lipzen, A and Koriabine, M and Bauer, D and Le Floch, G and Mäkelä, MR and Drula, E and Henrissat, B and Grigoriev, IV and Crouch, JA and de Vries, RP and Sukno, SA and Thon, MR}, title = {Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38940768}, issn = {2047-217X}, mesh = {*Colletotrichum/genetics/pathogenicity ; *Transcriptome ; *Genome, Fungal ; *Evolution, Molecular ; Phylogeny ; Adaptation, Physiological/genetics ; Gene Expression Profiling/methods ; Plant Diseases/microbiology/genetics ; }, abstract = {BACKGROUND: Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.<br><br>RESULTS: Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.<br><br>CONCLUSIONS: These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.}, }
@article {pmid38940583, year = {2024}, author = {Xie, G and Sun, C and Luo, W and Gong, Y and Tang, X}, title = {Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0071424}, pmid = {38940583}, issn = {1098-5336}, support = {41971062, 42371065//MOST | National Natural Science Foundation of China (NSFC)/ ; WGKQ2022032//West Anhui University ()/ ; }, mesh = {*Lakes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; *Microbiota ; Ecosystem ; Seasons ; }, abstract = {Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.}, }
@article {pmid38939048, year = {2024}, author = {Shi, Q and Sun, L and Gao, J and Li, F and Chen, D and Shi, T and Tan, Y and Chang, H and Liu, X and Kang, J and Lu, F and Huang, Z and Zhao, H}, title = {Effects of sodium lauryl sulfate and postbiotic toothpaste on oral microecology.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2372224}, pmid = {38939048}, issn = {2000-2297}, abstract = {The diversity and delicate balance of the oral microbiome contribute to oral health, with its disruption leading to oral and systemic diseases. Toothpaste includes elements like traditional additives such as sodium lauryl sulfate (SLS) as well as novel postbiotics derived from probiotics, which are commonly employed for maintaining oral hygiene and a healthy oral cavity. However, the response of the oral microbiota to these treatments remains poorly understood. In this study, we systematically investigated the impact of SLS, and toothpaste containing postbiotics (hereafter, postbiotic toothpaste) across three systems: biofilms, animal models, and clinical populations. SLS was found to kill bacteria in both preformed biofilms (mature biofilms) and developing biofilms (immature biofilms), and disturbed the microbial community structure by increasing the number of pathogenic bacteria. SLS also destroyed periodontal tissue, promoted alveolar bone resorption, and enhanced the extent of inflammatory response level. The postbiotic toothpaste favored bacterial homeostasis and the normal development of the two types of biofilms in vitro, and attenuated periodontitis and gingivitis in vivo via modulation of oral microecology. Importantly, the postbiotic toothpaste mitigated the adverse effects of SLS when used in combination, both in vitro and in vivo. Overall, the findings of this study describe the impact of toothpaste components on oral microflora and stress the necessity for obtaining a comprehensive understanding of oral microbial ecology by considering multiple aspects.}, }
@article {pmid38938005, year = {2024}, author = {Chaudhary, DK and Kim, SE and Park, HJ and Kim, KH}, title = {Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {6}, pages = {1260-1269}, pmid = {38938005}, issn = {1738-8872}, mesh = {Animals ; *Penaeidae/microbiology ; *Hepatopancreas/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Republic of Korea ; *Intestines/microbiology ; Phylogeny ; Stomach/microbiology ; Biodiversity ; Aquaculture ; DNA, Bacterial/genetics ; }, abstract = {The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.}, }
@article {pmid38937989, year = {2024}, author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W}, title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {33}, pages = {e2400058}, pmid = {38937989}, issn = {2198-3844}, support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; }, abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.}, }
@article {pmid38936927, year = {2024}, author = {Shen, CL and Wankhade, UD and Shankar, K and Najjar, RS and Feresin, RG and Elmassry, MM and Dufour, JM and Kaur, G and Chintapalli, SV and Piccolo, BD and Dunn, DM and Cao, JJ}, title = {Effects of Statin and Annatto-extracted Tocotrienol Supplementation on Glucose Homeostasis, Bone Microstructure, and Gut Microbiota Composition in Obese Mice.}, journal = {In vivo (Athens, Greece)}, volume = {38}, number = {4}, pages = {1557-1570}, pmid = {38936927}, issn = {1791-7549}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Tocotrienols/pharmacology/administration &amp; dosage ; Mice ; *Homeostasis/drug effects ; *Obesity/drug therapy/metabolism ; Male ; *Dietary Supplements ; *Bone and Bones/drug effects/metabolism/pathology ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; *Diet, High-Fat/adverse effects ; Bixaceae/chemistry ; Mice, Obese ; Plant Extracts/pharmacology/administration &amp; dosage ; Glucose/metabolism ; Mice, Inbred C57BL ; Insulin Resistance ; Blood Glucose ; Disease Models, Animal ; Liver/drug effects/metabolism/pathology ; Biomarkers ; Carotenoids ; }, abstract = {BACKGROUND/AIM: This study examined the effects of tocotrienols (TT) in conjunction with statin on glucose homeostasis, bone microstructure, gut microbiome, and systemic and liver inflammatory markers in obese C57BL/6J mice.<br><br>MATERIALS AND METHODS: Forty male C57BL/6J mice were fed a high-fat diet (HFD) and assigned into four groups in a 2 (no statin vs. 120 mg statin/kg diet)&#xd7;2 (no TT vs. 400 mg TT/kg diet) factorial design for 14 weeks.<br><br>RESULTS: Statin and TT improved glucose tolerance only when each was given alone, and only statin supplementation decreased insulin resistance. Consistently, only statin supplementation decreased serum insulin levels and HOMA-IR. Pancreatic insulin was also increased with statin treatment. Statin and TT, alone or in combination, reduced the levels of serum IL-6, but only TT attenuated the increased serum leptin levels induced by a HFD. Statin supplementation increased bone area/total area and connectivity density at LV-4, while TT supplementation increased bone area/total area and trabecular number, but decreased trabecular separation at the distal femur. Statin supplementation, but not TT, reduced hepatic inflammatory cytokine gene expression. Neither TT supplementation nor statin supplementation statistically altered microbiome species evenness or richness. However, they altered the relative abundance of certain microbiome species. Most notably, both TT and statin supplementation increased the relative abundance of Lachnospiraceae UCG-006.<br><br>CONCLUSION: TT and statin collectively benefit bone microstructure, glucose homeostasis, and microbial ecology in obese mice. Such changes may be, in part, associated with suppression of inflammation in the host.}, }
@article {pmid38936916, year = {2024}, author = {Morikawa, T and Paudel, D and Uehara, O and Ariwansa, D and Kobayashi, Y and Yang, J and Yoshida, K and Abiko, Y}, title = {Effects of Laurus nobilis Leaf Extract (LAURESH[®]) on Oral and Gut Microbiota Diversity in Mice.}, journal = {In vivo (Athens, Greece)}, volume = {38}, number = {4}, pages = {1758-1766}, pmid = {38936916}, issn = {1791-7549}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; Mice ; *Plant Extracts/pharmacology ; *Laurus/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Biodiversity ; Feces/microbiology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Male ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND/AIM: The leaves of Laurus nobilis have been used for culinary purposes for many years and have recently been shown to have beneficial effects on human health by altering microbiota composition. However, the effects of L. nobilis on the diversity of microbiomes in the oral cavity and gut remain unknown. Therefore, in this study, we examined the effects of an extract of L. nobilis on the diversity of microbiomes in the oral cavity and gut in mice.<br><br>MATERIALS AND METHODS: C57BL/6J mice were randomly divided into two groups and fed a standard diet (SD) and a standard diet containing 5% LAURESH[&#xae;], a laurel extract (SDL). After 10 weeks, oral swabs and fecal samples were collected. The bacterial DNA extracted from the oral swabs and feces was used for microbiota analysis using 16S rRNA sequencing. The sequencing data were analyzed using the Quantitative Insights into Microbial Ecology 2 in the DADA2 pipeline and 16S rRNA database.<br><br>RESULTS: The &#x3b1;-diversity of the oral microbiome was significantly greater in the SDL group than in the SD group. The &#x3b2;-diversity of the oral microbiome was also significantly different between the groups. Moreover, the taxonomic abundance analysis showed that five bacteria in the gut were significantly different among the groups. Furthermore, the SDL diet increased the abundance of beneficial gut bacteria, such as Akkermansia sp.<br><br>CONCLUSION: Increased diversity of the oral microbiome and proportion of Akkermansia sp. in the gut microbiome induced by L. nobilis consumption may benefit oral and gut health.}, }
@article {pmid38936824, year = {2024}, author = {Chen, YC and Destouches, L and Cook, A and Fedorec, AJH}, title = {Synthetic microbial ecology: engineering habitats for modular consortia.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae158}, pmid = {38936824}, issn = {1365-2672}, support = {EP/W524335/1//Engineering and Physical Sciences Research Council/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Microbial Consortia ; *Synthetic Biology/methods ; *Microbiota ; *Ecosystem ; Ecology ; }, abstract = {Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.}, }
@article {pmid38935596, year = {2024}, author = {O'Brien, JM and Blais, N and Butler, C and White, N and Bustead, A and Figler, C and Wells, M and Anderson, G and Yuhas, A and Ernakovich, JG}, title = {Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research.}, journal = {PLoS computational biology}, volume = {20}, number = {6}, pages = {e1012093}, pmid = {38935596}, issn = {1553-7358}, mesh = {Arctic Regions ; Humans ; *Indigenous Peoples ; Research Personnel ; }, }
@article {pmid38935504, year = {2024}, author = {Luo, S and Zhang, X and Zhou, X}, title = {Temporospatial dynamics and host specificity of honeybee gut bacteria.}, journal = {Cell reports}, volume = {43}, number = {7}, pages = {114408}, doi = {10.1016/j.celrep.2024.114408}, pmid = {38935504}, issn = {2211-1247}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Host Specificity ; *Bacteria/genetics ; Host Microbial Interactions/physiology ; }, abstract = {Honeybees are important pollinators worldwide, with their gut microbiota playing a crucial role in maintaining their health. The gut bacteria of honeybees consist of primarily five core lineages that are spread through social interactions. Previous studies have provided a basic understanding of the composition and function of the honeybee gut microbiota, with recent advancements focusing on analyzing diversity at the strain level and changes in bacterial functional genes. Research on honeybee gut microbiota across different regions globally has provided insights into microbial ecology. Additionally, recent findings have shed light on the mechanisms of host specificity of honeybee gut bacteria. This review explores the temporospatial dynamics in honeybee gut microbiota, discussing the reasons and mechanisms behind these fluctuations. This synopsis provides insights into host-microbe interactions and is invaluable for honeybee health.}, }
@article {pmid38935220, year = {2024}, author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A}, title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {85}, pmid = {38935220}, issn = {1432-184X}, support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.}, }
@article {pmid38933974, year = {2024}, author = {Rezende, GS and Rocha, FI and Funnicelli, MIG and Malavazi, I and Crauwels, S and Brandao, MM and Cunha, AF}, title = {Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e32283}, pmid = {38933974}, issn = {2405-8440}, abstract = {Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.}, }
@article {pmid38933028, year = {2024}, author = {Stemple, B and Gulliver, D and Sarkar, P and Tinker, K and Bibby, K}, title = {Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1376536}, pmid = {38933028}, issn = {1664-302X}, abstract = {Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.}, }
@article {pmid38932970, year = {2024}, author = {Ponce, MA and Maille, JM and Stoll, I and James, A and Bruce, A and Kim, TN and Scully, ED and Morrison, WR}, title = {Microbial vectoring capacity by internal- and external-infesting stored product insects after varying dispersal periods between novel food patches: An underestimated risk.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11368}, pmid = {38932970}, issn = {2045-7758}, abstract = {Understanding the ability of internal- and external-infesting stored product insects to vector microbes is important for estimating the relative risk that insects pose to postharvest commodities as they move between habitat patches and in the landscape. Thus, the aim of the current study was to evaluate and compare the microbial growth in novel food patches at different dispersal periods by different populations of Sitophilus oryzae (e.g., internal-infesting) and Lasioderma serricorne (e.g., external-infesting). Adults of both species collected from laboratory colonies or field-captured populations were either placed immediately in a novel food patch, or given a dispersal period of 24 or 72 h in a sterilized environment before entering a surrogate food patch. Vectored microbes in new food patches were imaged after 3 or 5 days of foraging, and microbial growth was processed using ImageJ while fungal species were identified through sequencing the ITS4/5 ribosomal subunit. We found that increasing dispersal time resulted in multiple-fold reductions in microbial growth surrogate food patches by L. serricorne but not S. oryzae. This was likely attributable to higher mobility by S. oryzae than L. serricorne. A total of 20 morphospecies were identified from 13 genera among the 59 sequences, with a total of 23% and 16% classified as Aspergillus and Penicillium spp. Our data suggest that there is a persistent risk of microbial contamination by both species, which has important food safety implications at food facilities.}, }
@article {pmid38930577, year = {2024}, author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA}, title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, pmid = {38930577}, issn = {2076-2607}, abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.}, }
@article {pmid38928853, year = {2024}, author = {Tata, A and Massaro, A and Miano, B and Petrin, S and Antonelli, P and Peruzzo, A and Pezzuto, A and Favretti, M and Bragolusi, M and Zacometti, C and Losasso, C and Piro, R}, title = {A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {38928853}, issn = {2304-8158}, support = {RC IZSVe 11/2018//Ministero della Salute/ ; }, abstract = {Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.}, }
@article {pmid38928813, year = {2024}, author = {Vale, ADS and Pereira, CMT and De Dea Lindner, J and Rodrigues, LRS and Kadri, NKE and Pagnoncelli, MGB and Kaur Brar, S and Soccol, CR and Pereira, GVM}, title = {Exploring Microbial Influence on Flavor Development during Coffee Processing in Humid Subtropical Climate through Metagenetic-Metabolomics Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {38928813}, issn = {2304-8158}, support = {440343/2022-4//National Council for Scientific and Technological Development/ ; }, abstract = {Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the resilience and quality of global coffee production. This study aimed to investigate how microbial communities interact and contribute to flavor development in coffee processing within humid subtropical climates. Employing Illumina sequencing for microbial dynamics analysis, and high-performance liquid chromatography (HPLC) integrated with gas chromatography-mass spectrometry (GC-MS) for metabolite assessment, the study revealed intricate microbial diversity and associated metabolic activities. Throughout the fermentation process, dominant microbial species included Enterobacter, Erwinia, Kluyvera, and Pantoea from the prokaryotic group, and Fusarium, Cladosporium, Kurtzmaniella, Leptosphaerulina, Neonectria, and Penicillium from the eukaryotic group. The key metabolites identified were ethanol, and lactic, acetic, and citric acids. Notably, the bacterial community plays a crucial role in flavor development by utilizing metabolic versatility to produce esters and alcohols, while plant-derived metabolites such as caffeine and linalool remain stable throughout the fermentation process. The undirected network analysis revealed 321 interactions among microbial species and key substances during the fermentation process, with Enterobacter, Kluyvera, and Serratia showing strong connections with sugar and various volatile compounds, such as hexanal, benzaldehyde, 3-methylbenzaldehyde, 2-butenal, and 4-heptenal. These interactions, including inhibitory effects by Fusarium and Cladosporium, suggest microbial adaptability to subtropical conditions, potentially influencing fermentation and coffee quality. The sensory analysis showed that the final beverage obtained a score of 80.83 ± 0.39, being classified as a specialty coffee by the Specialty Coffee Association (SCA) metrics. Nonetheless, further enhancements in acidity, body, and aftertaste could lead to a more balanced flavor profile. The findings of this research hold substantial implications for the coffee industry in humid subtropical regions, offering potential strategies to enhance flavor quality and consistency through controlled fermentation practices. Furthermore, this study contributes to the broader understanding of how microbial ecology interplays with environmental factors to influence food and beverage fermentation, a topic of growing interest in the context of climate change and sustainable agriculture.}, }
@article {pmid38927252, year = {2024}, author = {Huang, Y and Chen, Y and Xie, H and Feng, Y and Chen, S and Bao, B}, title = {Effects of Inducible Nitric Oxide Synthase (iNOS) Gene Knockout on the Diversity, Composition, and Function of Gut Microbiota in Adult Zebrafish.}, journal = {Biology}, volume = {13}, number = {6}, pages = {}, pmid = {38927252}, issn = {2079-7737}, support = {2022YFD2400103//the National Key R&amp;D Program of China/ ; 2021N3016//the Regional Development Project of Fujian/ ; }, abstract = {The gut microbiota constitutes a complex ecosystem that has an important impact on host health. In this study, genetically engineered zebrafish with inducible nitric oxide synthase (iNOS or NOS2) knockout were used as a model to investigate the effects of nos2a/nos2b gene single knockout and nos2 gene double knockout on intestinal microbiome composition and function. Extensive 16S rRNA sequencing revealed substantial changes in microbial diversity and specific taxonomic abundances, yet it did not affect the functional structure of the intestinal tissues. Notably, iNOS-deficient zebrafish demonstrated a decrease in Vibrio species and an increase in Aeromonas species, with more pronounced effects observed in double knockouts. Further transcriptomic analysis of the gut in double iNOS knockout zebrafish indicated significant alterations in immune-related and metabolic pathways, including the complement and PPAR signaling pathways. These findings underscore the crucial interplay between host genetics and gut microbiota, indicating that iNOS plays a key role in modulating the gut microbial ecology, host immune system, and metabolic responses.}, }
@article {pmid38926469, year = {2024}, author = {Martin, LC and O'Hare, MA and Ghielmetti, G and Twesigomwe, D and Kerr, TJ and Gumbo, R and Buss, PE and Kitchin, N and Hemmings, SMJ and Miller, MA and Goosen, WJ}, title = {Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14768}, pmid = {38926469}, issn = {2045-2322}, support = {S007355//American Association of Zoo Veterinarians/ ; 86949//National Research Foundation, South Africa/ ; MND200409511840//National Research Foundation/ ; /WT_/Wellcome Trust/United Kingdom ; 222941/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; S005651//American Association of Zoo Veterinarians/ ; PMDS22052113333//National Research Foundation/ ; }, mesh = {Animals ; *Elephants/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Respiratory System/microbiology ; Animals, Zoo/microbiology ; Sequence Analysis, DNA/methods ; Animals, Wild/microbiology ; Phylogeny ; }, abstract = {Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.}, }
@article {pmid38926391, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5412}, pmid = {38926391}, issn = {2041-1723}, support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; }, abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.}, }
@article {pmid38923208, year = {2024}, author = {Bosch, J and Lebre, PH and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Kinetics and pathways of sub-lithic microbial community (hypolithon) development.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13290}, pmid = {38923208}, issn = {1758-2229}, support = {//University of Pretoria/ ; 113308//National Research Foundation/ ; 137954//National Research Foundation/ ; 95565//National Research Foundation/ ; }, mesh = {*Soil Microbiology ; *Cyanobacteria/genetics/isolation &amp; purification/growth &amp; development/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Desert Climate ; Namibia ; Kinetics ; Phylogeny ; DNA, Bacterial/genetics ; Soil/chemistry ; }, abstract = {Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.}, }
@article {pmid38922748, year = {2024}, author = {Pérez-Pazos, E and Beidler, KV and Narayanan, A and Beatty, BH and Maillard, F and Bancos, A and Heckman, KA and Kennedy, PG}, title = {Fungi rather than bacteria drive early mass loss from fungal necromass regardless of particle size.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13280}, pmid = {38922748}, issn = {1758-2229}, support = {SCW1632//Department of Energy Office of Biological and Environmental Research Genomic Science Program/ ; 2038293//National Science Foundation/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development/metabolism ; *Particle Size ; Fungi/growth &amp; development/classification/genetics/physiology ; Soil Microbiology ; Hydrogen-Ion Concentration ; Ascomycota/growth &amp; development/physiology ; }, abstract = {Microbial necromass is increasingly recognized as an important fast-cycling component of the long-term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250-500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal-bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass-infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co-cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.}, }
@article {pmid38922446, year = {2024}, author = {Filek, K and Vuković, BB and Žižek, M and DiBello, A and Kanjer, L and Trotta, A and Corrente, M and Bosak, S}, title = {Correction to: Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {84}, doi = {10.1007/s00248-024-02405-z}, pmid = {38922446}, issn = {1432-184X}, }
@article {pmid38921731, year = {2024}, author = {Wang, C and Defoirdt, T and Rajkovic, A}, title = {The Effect of Caco-2 Cells on Sporulation and Enterotoxin Expression by Foodborne Clostridium perfringens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38921731}, issn = {2076-0817}, support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Special Research Fund of Ghent University/ ; 1506419N//Research Foundation - Flanders/ ; }, mesh = {Humans ; Caco-2 Cells ; *Clostridium perfringens/genetics ; *Enterotoxins/metabolism/genetics ; *Spores, Bacterial/genetics ; *Coculture Techniques ; Clostridium Infections/microbiology/metabolism ; Epithelial Cells/metabolism/microbiology ; Foodborne Diseases/microbiology ; }, abstract = {Clostridium perfringens enterotoxin (Cpe)-producing strains cause gastrointestinal infections in humans and account for the second-largest number of all foodborne outbreaks caused by bacterial toxins. The Cpe toxin is only produced during sporulation; this process might be affected when C. perfringens comes into contact with host cells. The current study determined how the cpe expression levels and spore formation changed over time during co-culture with Caco-2 cells (as a model of intestinal epithelial cells). In co-culture with Caco-2 cells, total C. perfringens cell counts first decreased and then remained more or less stable, whereas spore counts were stable over the whole incubation period. The cpe mRNA level in the co-culture with Caco-2 cells increased more rapidly than in the absence of Caco-2 cells (3.9-fold higher levels in coculture than in the absence of Caco-2 cells after 8 h of incubation). Finally, we found that cpe expression is inhibited by a cue released by Caco-2 cells (8.3-fold lower levels in the presence of supernatants of Caco-2 cells than in the absence of the supernatants after 10 h of incubation); as a consequence, the increased expression in co-culture with Caco-2 cells must be caused by a factor associated with the Caco-2 cells.}, }
@article {pmid38920365, year = {2024}, author = {Givati, S and Forchielli, E and Aharonovich, D and Barak, N and Weissberg, O and Belkin, N and Rahav, E and Segrè, D and Sher, D}, title = {Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0025624}, pmid = {38920365}, issn = {1098-5336}, support = {RGP0020/2016//Human Frontier Science Program (HFSP)/ ; NSFOCE-BSF 1635070//United States-Israel Binational Science Foundation (BSF)/ ; 1786/20//Israel Science Foundation (ISF)/ ; }, mesh = {*Seawater/microbiology ; *Heterotrophic Processes ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Mediterranean Sea ; Microbiota ; Amino Acids/metabolism ; Organic Chemicals/metabolism ; }, abstract = {UNLABELLED: Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.<br><br>IMPORTANCE: A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.}, }
@article {pmid38918384, year = {2024}, author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, &#xc5; and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH}, title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5361}, pmid = {38918384}, issn = {2041-1723}, support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; }, abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.}, }
@article {pmid38918217, year = {2024}, author = {Duong, HL and Paufler, S and Harms, H and Maskow, T and Schlosser, D}, title = {Biocalorimetry-aided monitoring of fungal pretreatment of lignocellulosic agricultural residues.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {394}, pmid = {38918217}, issn = {1432-0614}, support = {911 Program//B&#x1ed9; Gi&#xe1;o d&#x1ee5;c v&#xe0; &#xd0;&#xe0;o t&#x1ea1;o/ ; }, mesh = {*Lignin/metabolism ; *Triticum/microbiology/chemistry ; *Fungi/metabolism ; Fermentation ; Hydrolysis ; Agriculture/methods ; }, abstract = {The present study aimed to investigate whether and how non-invasive biocalorimetric measurements could serve for process monitoring of fungal pretreatment during solid-state fermentation (SSF) of lignocellulosic agricultural residues such as wheat straw. Seven filamentous fungi representing different lignocellulose decay types were employed. Water-soluble sugars being immediately available after fungal pretreatment and those becoming water-extractable after enzymatic digestion of pretreated wheat straw with hydrolysing (hemi)cellulases were considered to constitute the total bioaccessible sugar fraction. The latter was used to indicate the success of pretreatments and linked to corresponding species-specific metabolic heat yield coefficients (YQ/X) derived from metabolic heat flux measurements during fungal wheat straw colonisation. An YQ/X range of about 120 to 140 kJ/g was seemingly optimal for pretreatment upon consideration of all investigated fungi and application of a non-linear Gaussian fitting model. Upon exclusion from analysis of the brown-rot basidiomycete Gloeophyllum trabeum, which differs from all other here investigated fungi in employing extracellular Fenton chemistry for lignocellulose decomposition, a linear relationship where amounts of total bioaccessible sugars were suggested to increase with increasing YQ/X values was obtained. It remains to be elucidated whether an YQ/X range being optimal for fungal pretreatment could firmly be established, or if the sugar accessibility for post-treatment generally increases with increasing YQ/X values as long as "conventional" enzymatic, i.e. (hemi)cellulase-based, lignocellulose decomposition mechanisms are operative. In any case, metabolic heat measurement-derived parameters such as YQ/X values may become very valuable tools supporting the assessment of the suitability of different fungal species for pretreatment of lignocellulosic substrates. KEY POINTS: • Biocalorimetry was used to monitor wheat straw pretreatment with seven filamentous fungi. • Metabolic heat yield coefficients (YQ/X) seem to indicate pretreatment success. • YQ/X values may support the selection of suitable fungal strains for pretreatment.}, }
@article {pmid38917910, year = {2024}, author = {Gao, Y and Heng, S and Wang, J and Liu, Z and Liu, Y and Chen, B and Han, Y and Li, W and Lu, X and Zhen, G}, title = {Bioelectrochemically altering microbial ecology in upflow anaerobic sludge blanket to enhance methanogenesis fed with high-sulfate methanolic wastewater.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {131026}, doi = {10.1016/j.biortech.2024.131026}, pmid = {38917910}, issn = {1873-2976}, mesh = {*Wastewater/microbiology ; *Methanol/metabolism ; *Methane/metabolism ; *Sulfates/metabolism ; *Sewage/microbiology ; Anaerobiosis ; Bioreactors/microbiology ; Electrodes ; }, abstract = {A bioelectrochemical upflow anaerobic sludge blanket (BE-UASB) was constructed and compared with the traditional UASB to investigate the role of bioelectrocatalysis in modulating methanogenesis and sulfidogensis involved within anaerobic treatment of high-sulfate methanolic wastewater (COD/SO4[2-] ratio ≤ 2). Methane production rate for BE-UASB was 1.4 times higher than that of the single UASB, while SO4[2-] removal stabilized at 16.7%. Bioelectrocatalysis selectively enriched key functional anaerobes and stimulated the secretion of extracellular polymeric substances, especially humic acids favoring electron transfer, thereby accelerating the electroactive biofilms development of electrodes. Methanomethylovorans was the dominant genus (35%) to directly convert methanol to CH4. Methanobacterium as CO2 electroreduction methane-producing archaea appeared only on electrodes. Acetobacterium exhibited anode-dependence, which provided acetate for sulfate-reducing bacteria (norank Syntrophobacteraceae and Desulfomicrobium) through synergistic coexistence. This study confirmed that BE-UASB regulated the microbial ecology to achieve efficient removal and energy recovery of high-sulfate methanolic wastewater.}, }
@article {pmid38917500, year = {2024}, author = {Zhang, D and Calmanovici, B and Marican, H and Reisser, J and Summers, S}, title = {The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef.}, journal = {Marine pollution bulletin}, volume = {205}, number = {}, pages = {116651}, doi = {10.1016/j.marpolbul.2024.116651}, pmid = {38917500}, issn = {1879-3363}, mesh = {*Biofilms ; *Plastics ; Australia ; Microbiota ; Seawater/microbiology ; Coral Reefs ; Bacteria ; Waste Products ; }, abstract = {Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.}, }
@article {pmid38916294, year = {2024}, author = {Chadwick, GL and Dury, GA and Nayak, DD}, title = {Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0222023}, pmid = {38916294}, issn = {1098-5336}, support = {//Searle Scholars Program (SSP)/ ; Beckman Young Investigator Award//Arnold and Mabel Beckman Foundation (AMBF)/ ; Simons Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation (PF)/ ; Chan-Zuckerberg Biohub - San Francisco Investigator//Chan Zuckerberg Initiative (CZI)/ ; 5T32GM06698-14//HHS | National Institutes of Health (NIH)/ ; //Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley (MIBRS)/ ; }, mesh = {*Methanosarcina/genetics/enzymology/metabolism ; *Oxidoreductases/metabolism/genetics ; *Transcriptome ; Methane/metabolism ; Archaeal Proteins/genetics/metabolism ; Gene Expression Regulation, Archaeal ; Operon ; }, abstract = {UNLABELLED: Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth.<br><br>IMPORTANCE: Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.}, }
@article {pmid38915372, year = {2024}, author = {Levi, EE and Jeppesen, E and Nejstgaard, JC and Davidson, TA}, title = {Chlorophyll-a determinations in mesocosms under varying nutrient and temperature treatments: in-situ fluorescence sensors versus in-vitro measurements.}, journal = {Open research Europe}, volume = {4}, number = {}, pages = {69}, pmid = {38915372}, issn = {2732-5121}, abstract = {Harmful algal blooms (HABs) are a significant threat to freshwater ecosystems, and monitoring for changes in biomass is therefore important. Fluorescence in-situ sensors enable rapid and high frequency real-time data collection and have been widely used to determine chlorophyll- a (Chla) concentrations that are used as an indicator of the total algal biomass. However, conversion of fluorescence to equivalent-Chla concentrations is often complicated due to biofouling, phytoplankton composition and the type of equipment used. Here, we validated measurements from 24 Chla and 12 phycocyanin (cyanobacteria indicator) fluorescence in-situ sensors (Cyclops-7F, Turner Designs) against spectrophotometrically (in-vitro) determined Chla and tested a data-cleaning procedure for eliminating data errors and impacts of non-photochemical quenching (i.e. light-induced decrease in fluorescence intensity). The test was done across a range of freshwater plankton communities in 24 mesocosms (i.e. experimental tanks) with a 2x3 (high and low nutrient x ambient, IPCC-A2 and IPCC-A2+50% temperature scenarios) factorial design. For most mesocosms (tanks), we found accurate (r [2] ≥ 0.7) calibration of in-situ Chla fluorescence data using simple linear regression. An exception was tanks with high in-situ phycocyanin fluorescence, for which multiple regressions were employed, which increased the explained variance by >10%. Another exception was the low Chla concentration tanks (r [2] < 0.5). Our results also show that the high frequency in-situ fluorescence data recorded the timing of sudden Chla variations, while less frequent in-vitro sampling sometimes missed these or, when recorded, the duration of changes was inaccurately determined. Fluorescence in-situ sensors are particularly useful to detect and quantify sudden phytoplankton biomass variations through high frequency measurements, especially when using appropriate data-cleaning methods and accounting for factors that can impact the fluorescence readings. Nevertheless, corroborating these data with in-vitro Chla assessments would provide additional validation for the early warnings provided by sensor data.}, }
@article {pmid38912052, year = {2024}, author = {Goldman, SL and Sanders, JG and Sprockett, DD and Landers, A and Yan, W and Moeller, AH}, title = {Hackflex library preparation enables low-cost metagenomic profiling.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae075}, pmid = {38912052}, issn = {2730-6151}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; T32 AI145821/AI/NIAID NIH HHS/United States ; }, abstract = {Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.}, }
@article {pmid38910491, year = {2024}, author = {Kommana, G and Hupfer, M and Woodhouse, JN and Grossart, HP and Goldhammer, T}, title = {Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments.}, journal = {Environmental science. Processes &amp; impacts}, volume = {26}, number = {7}, pages = {1227-1244}, doi = {10.1039/d4em00185k}, pmid = {38910491}, issn = {2050-7895}, mesh = {*Geologic Sediments/chemistry ; *Greenhouse Gases/analysis ; *Iron ; Particulate Matter/analysis ; Germany ; Air Pollutants/analysis ; Environmental Monitoring ; Biodegradation, Environmental ; Water Pollutants, Chemical/analysis ; }, abstract = {Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.}, }
@article {pmid38909617, year = {2024}, author = {Kullberg, RFJ and Wikki, I and Haak, BW and Kauko, A and Galenkamp, H and Peters-Sengers, H and Butler, JM and Havulinna, AS and Palmu, J and McDonald, D and Benchraka, C and Abdel-Aziz, MI and Prins, M and Maitland van der Zee, AH and van den Born, BJ and Jousilahti, P and de Vos, WM and Salomaa, V and Knight, R and Lahti, L and Nieuwdorp, M and Niiranen, T and Wiersinga, WJ}, title = {Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies.}, journal = {The Lancet. Microbe}, volume = {5}, number = {9}, pages = {100864}, doi = {10.1016/S2666-5247(24)00079-X}, pmid = {38909617}, issn = {2666-5247}, mesh = {Humans ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Aged ; Finland/epidemiology ; *Butyrates/metabolism ; *RNA, Ribosomal, 16S/genetics/analysis ; Netherlands/epidemiology ; Young Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Adolescent ; Communicable Diseases/microbiology/epidemiology ; Cohort Studies ; Risk Factors ; }, abstract = {BACKGROUND: Microbiota alterations are common in patients hospitalised for severe infections, and preclinical models have shown that anaerobic butyrate-producing gut bacteria protect against systemic infections. However, the relationship between microbiota disruptions and increased susceptibility to severe infections in humans remains unclear. We investigated the relationship between gut microbiota and the risk of future infection-related hospitalisation in two large population-based cohorts.<br><br>METHODS: In this observational microbiome study, gut microbiota were characterised using 16S rRNA gene sequencing in independent population-based cohorts from the Netherlands (HELIUS study; derivation cohort) and Finland (FINRISK 2002 study; validation cohort). HELIUS was conducted in Amsterdam, Netherlands, and included adults (aged 18-70 years at inclusion) who were randomly sampled from the municipality register of Amsterdam. FINRISK 2002 was conducted in six regions in Finland and is a population survey that included a random sample of adults (aged 25-74 years). In both cohorts, participants completed questionnaires, underwent a physical examination, and provided a faecal sample at inclusion (Jan 3, 2013, to Nov 27, 2015, for HELIUS participants and Jan 21 to April 19, 2002, for FINRISK participants. For inclusion in our study, a faecal sample needed to be provided and successfully sequenced, and national registry data needed to be available. Primary predictor variables were microbiota composition, diversity, and relative abundance of butyrate-producing bacteria. Our primary outcome was hospitalisation or mortality due to any infectious disease during 5-7-year follow-up after faecal sample collection, based on national registry data. We examined associations between microbiota and infection risk using microbial ecology and Cox proportional hazards.<br><br>FINDINGS: We profiled gut microbiota from 10&#x2009;699 participants (4248 [39&#xb7;7%] from the derivation cohort and 6451&#xa0;[60&#xb7;3%] from the validation cohort). 602 (5&#xb7;6%) participants (152 [3&#xb7;6%] from the derivation cohort; 450 [7&#xb7;0%] from the validation cohort) were hospitalised or died due to infections during follow-up. Gut microbiota composition of these participants differed from those without hospitalisation for infections (derivation p=0&#xb7;041; validation p=0&#xb7;0002). Specifically, higher relative abundance of butyrate-producing bacteria was associated with a reduced risk of hospitalisation for infections (derivation cohort cause-specific hazard ratio 0&#xb7;75 [95% CI 0&#xb7;60-0&#xb7;94] per 10% increase in butyrate producers, p=0&#xb7;013; validation cohort 0&#xb7;86 [0&#xb7;77-0&#xb7;96] per 10% increase, p=0&#xb7;0077). These associations remained unchanged following adjustment for demographics, lifestyle, antibiotic exposure, and comorbidities.<br><br>INTERPRETATION: Gut microbiota composition, specifically colonisation with butyrate-producing bacteria, was associated with protection against hospitalisation for infectious diseases in the general population across two independent European cohorts. Further studies should investigate whether modulation of the microbiome can reduce the risk of severe infections.<br><br>FUNDING: Amsterdam UMC, Porticus, National Institutes of Health, Netherlands Organisation for Health Research and Development (ZonMw), and Leducq Foundation.}, }
@article {pmid38906896, year = {2024}, author = {Schorn, S and Graf, JS and Littmann, S and Hach, PF and Lavik, G and Speth, DR and Schubert, CJ and Kuypers, MMM and Milucka, J}, title = {Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5293}, pmid = {38906896}, issn = {2041-1723}, mesh = {*Methane/metabolism ; *Lakes/microbiology ; *Oxidation-Reduction ; Anaerobiosis ; Methylococcaceae/metabolism/genetics ; Metagenomics ; Oxygen/metabolism ; }, abstract = {Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d[-1]. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.}, }
@article {pmid38904568, year = {2024}, author = {Ganier, C and Callewaert, C and Matos, TR and Sonkoly, E and Dyring-Andersen, B and Rajan, N}, title = {Young ESDR: Engaging and Nurturing the Next-Generation Skin Research Community.}, journal = {The Journal of investigative dermatology}, volume = {144}, number = {11}, pages = {2349-2350}, doi = {10.1016/j.jid.2024.05.004}, pmid = {38904568}, issn = {1523-1747}, }
@article {pmid38902915, year = {2024}, author = {Kerr, BJ and Anderson, CL and Pearce, SC and Schweer, WP}, title = {Dietary isoacids effects on growth, nitrogen, and energy digestibility, and fecal volatile fatty acids and microbial ecology in finishing pigs.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {38902915}, issn = {1525-3163}, mesh = {Animals ; *Feces/chemistry/microbiology ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fatty Acids, Volatile/metabolism ; Female ; *Nitrogen/metabolism ; *Animal Nutritional Physiological Phenomena ; Swine/growth &amp; development ; Energy Metabolism/drug effects ; }, abstract = {Isoacids are branched ketoacids which when fed to ruminants have been shown to enhance the growth of fiber-digesting organisms. Ninety finishing gilts were individually fed dietary treatments consisting of diet type: corn-soybean meal (CSBM), a diet containing 40% distillers dried grains with solubles (DDGS), or a diet containing 40% sugar beet pulp (SBP); in combination with either no feed additive (CNT), the addition of 0.50% isobutyrate (IB), or the addition of a 0.88% mix of isobutyrate, isovalerate, and 2-methylbutyrate (MX). Gilts consumed an average of 2.171 kg/d over the 28-d trial. On d 26, fresh fecal samples were collected for determination of apparent total tract digestibility (ATTD) of gross energy (GE) and nitrogen (N), determination of fecal volatile fatty acids (VFA), and evaluation of microbial ecology. There was no interaction between diet type and isoacid addition, and no main effect of isoacid or diet type on alpha or Shannon microbial diversity measures (P > 0.05). There was no interaction between isoacid addition and diet type, and no main effect of isoacid addition on microbial beta diversity (P > 0.05), but differences were observed in microbial beta diversity due to diet type (P ≤ 0.05). There was no interaction between diet type and isoacid addition observed in fecal VFA concentrations (P > 0.05), with only minor differences in fecal VFA concentrations noted due to isoacid addition (P ≤ 0.05). The interaction between diet type and isoacid addition on ATTD of dietary GE and N (P ≤ 0.01) was large because the addition of IB did not affect the ATTD of GE or N in pigs fed the CSBM diet, but increased ATTD of GE and N in pigs fed diets containing DDGS and decreased the ATTD of GE and N in pigs fed diets containing SBP. In contrast, adding a blend of isoacids (i.e., MX) reduced the ATTD of GE and N, regardless of diet type. There was no interaction between diet type and isoacid addition, and no effect of isoacid addition was observed on pig performance (P > 0.05). Diet type did not affect average daily gain (P > 0.05), but pigs fed diets containing DDGS or SBP consumed less feed (P = 0.01) and exhibited greater GF ratios compared to pigs fed the low-fiber CSBM diet (P ≤ 0.05). In conclusion, there was little to no effect of isoacid addition on microbial ecology, fecal VFA concentrations, ATTD of GE or N, or pig performance, but the improvement in ATTD of GE and N in pigs fed diets containing DDGS when IB was added warrants further investigation.}, }
@article {pmid38896653, year = {2024}, author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ}, title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38896653}, issn = {1751-7370}, support = {BB/T008741/1//Biotechnology and Biological Sciences Research Council SWBio DTP/ ; DH150169//Royal Society Dorothy Hodgkin Fellowship/ ; NE/S001921/1//Natural Environment Research Council/ ; BB/X010600/1//Biotechnology and Biological Sciences Research Council Discovery Fellowship/ ; }, mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; Pseudomonas aeruginosa/virology/genetics/immunology ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}_{\Delta }$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.}, }
@article {pmid38896454, year = {2024}, author = {Zhang, Y and Quensen, J and Chen, B and Li, H and Tiedje, J and Sun, W and Qian, X}, title = {Paenalcaligenes faecalis sp. nov., a novel species of the family Alcaligenaceae isolated from chicken faeces.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006429}, pmid = {38896454}, issn = {1466-5034}, mesh = {Animals ; *Base Composition ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Chickens/microbiology ; *Feces/microbiology ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Alcaligenaceae/genetics/classification/isolation &amp; purification ; Fatty Acids ; Genome, Bacterial ; }, abstract = {A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04[T], was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761A[T] (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04[T] and P. hominis CCUG 53761A[T] were 76.3 and 18.2 %, respectively. Strain YLCF04[T] has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04[T] represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04[T] (=CCTCC AB 2022359[T]= KCTC 92789[T]).}, }
@article {pmid38895568, year = {2024}, author = {Puente-Sánchez, F and Macías-Pérez, LA and Campbell, KL and Royo-Llonch, M and Balagué, V and Sánchez, P and Tamames, J and Mundy, CJ and Pedrós-Alió, C}, title = {Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11546}, pmid = {38895568}, issn = {2045-7758}, abstract = {Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2-3 μm). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB-dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer.}, }
@article {pmid38894967, year = {2024}, author = {Zou, C and Yi, X and Li, H and Bizic, M and Berman-Frank, I and Gao, K}, title = {Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1396369}, pmid = {38894967}, issn = {1664-302X}, abstract = {The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC[-1] day[-1]) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d[-1] to 0.34 ± 0.02 d[-1], with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.}, }
@article {pmid38892722, year = {2024}, author = {Thompson, RS and Bowers, SJ and Vargas, F and Hopkins, S and Kelley, T and Gonzalez, A and Lowry, CA and Dorrestein, PC and Vitaterna, MH and Turek, FW and Knight, R and Wright, KP and Fleshner, M}, title = {A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892722}, issn = {2072-6643}, support = {N00014-15-1-2809//Office of Naval Research/ ; }, mesh = {Animals ; *Prebiotics ; Male ; *Gastrointestinal Microbiome/drug effects ; *Rats, Sprague-Dawley ; *Oligosaccharides/pharmacology/administration &amp; dosage ; *Glucans ; Rats ; Bile Acids and Salts/metabolism ; Feces/microbiology ; Bacteria/classification/metabolism ; RNA, Ribosomal, 16S ; Diet/methods ; }, abstract = {Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbially modified metabolites over time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides (GOS) and polydextrose (PDX)), compared to a control diet, would consistently impact the gut microbiome and microbially modified bile acids over time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiomes and metabolomes were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered the beta diversity, relative abundance of bacterial genera, and microbially modified bile acids over time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by the prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbially modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites, supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.}, }
@article {pmid38892504, year = {2024}, author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M}, title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892504}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; }, abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).}, }
@article {pmid38891933, year = {2024}, author = {Carpio, LE and Olivares, M and Benítez-Paez, A and Serrano-Candelas, E and Barigye, SJ and Sanz, Y and Gozalbes, R}, title = {Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM).}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38891933}, issn = {1422-0067}, support = {reference INNTAL32/19/002, INNTA3/2021/16 and INNTA3/2022/20//Agencia Valenciana de la innovaci&#xf3;/ ; grant PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities (MCIU)/ ; APOTIP/2021/035//Generalitat Valenciana/ ; CEX2021-001189-S/MCIU/AEI/10.13039/501100011033//Spanish Government MCIU/AEI/ ; }, mesh = {Humans ; Bacteria/metabolism ; Bacterial Proteins/metabolism/chemistry ; Binding Sites ; *Diabetes Mellitus, Type 2/metabolism/drug therapy ; *Dipeptidyl Peptidase 4/metabolism/chemistry ; *Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; }, abstract = {The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.}, }
@article {pmid38890249, year = {2024}, author = {Plewa-Tutaj, K and Krzyściak, P and Dobrzycka, A}, title = {Mycological air contamination level and biodiversity of airborne fungi isolated from the zoological garden air - preliminary research.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {30}, pages = {43066-43079}, pmid = {38890249}, issn = {1614-7499}, support = {2022/06/X/NZ8/00430//National Science Center, Poland/ ; }, mesh = {*Air Microbiology ; *Fungi/isolation &amp; purification/classification ; *Biodiversity ; Animals ; *Environmental Monitoring ; Gardens ; Animals, Zoo/microbiology ; }, abstract = {The aim of this paper was to evaluate the degree of mycological air contamination and determine the taxonomic diversity of airborne fungi residing in the air of 20 different animal facilities in a zoological garden. The concentrations of fungi in the zoological garden were measured using a MAS-100 air sampler. The collected microorganisms were identified using the combination of molecular and morphological methods. The fungal concentration ranged from 50 to 3.65 × 10[4] CFU/m[3] during the whole study. The quantitative analysis of the fungal aerosol showed that the obtained concentration values were lower than the recommended permissible limits (5 × 10[4] CFU/m[3] for fungi). Environmental factors, including temperature and relative humidity, exerted a varying effect on the presence and concentration of isolated fungi. Relative humidity was shown to correlate positively with the concentration of fungal spores in the air of the facilities studied (rho = 0.57, p < 0.0021). In parallel, no significant correlation was established between temperature and total fungal concentration (rho = - 0.1, p < 0.2263). A total of 112 fungal strains belonging to 50 species and 10 genera were isolated. Penicillium was the dominant genera, including 58.9% of total fungal strains, followed by Aspergillus 25.89%, Cladosporium 3.57%, Talaromyces 3.57%, Mucor 1.78%, Schizophyllum 1.78%, Syncephalastrum 0.89%, Alternaria 0.89%, Absidia 0.89%, and Cunninghamella 0.89%. Our preliminary studies provide basic information about the fungal concentrations, as well as their biodiversity in zoological garden. Further studies are needed to generate additional data from long-term sampling in order to increase our understanding of airborne fungal composition in the zoological garden.}, }
@article {pmid38888768, year = {2024}, author = {Sanderson, H and White, AP}, title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2813}, number = {}, pages = {19-37}, pmid = {38888768}, issn = {1940-6029}, mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.}, }
@article {pmid38888737, year = {2024}, author = {Sagar, A and Rai, S and Sharma, S and Perveen, K and Bukhari, NA and Sayyed, RZ and Mastinu, A}, title = {Molecular Characterization Reveals Biodiversity and Biopotential of Rhizobacterial Isolates of Bacillus Spp.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {83}, pmid = {38888737}, issn = {1432-184X}, mesh = {*Bacillus/isolation &amp; purification/genetics/metabolism ; *Soil Microbiology ; *Biodiversity ; India ; Plant Roots/microbiology ; Cicer/microbiology/growth &amp; development ; Solanum lycopersicum/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Phylogeny ; Antibiosis ; Siderophores/metabolism ; Indoleacetic Acids/metabolism ; }, abstract = {Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.}, }
@article {pmid38886127, year = {2024}, author = {Piwosz, K and Villena-Alemany, C and Całkiewicz, J and Mujakić, I and Náhlík, V and Dean, J and Koblížek, M}, title = {Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38886127}, issn = {1574-6941}, support = {2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; }, mesh = {*Carbon/metabolism ; *Phototrophic Processes ; Heterotrophic Processes ; Lakes/microbiology ; Bacteria, Aerobic/metabolism/growth &amp; development ; Light ; Ecosystem ; Bacteria/metabolism/growth &amp; development/genetics ; }, abstract = {Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.}, }
@article {pmid38884913, year = {2024}, author = {Obregón-Gutierrez, P and Aragón, V and Correa-Fiz, F}, title = {Analysis of the Nasal Microbiota in Healthy and Diseased Pigs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2815}, number = {}, pages = {93-113}, pmid = {38884913}, issn = {1940-6029}, mesh = {Animals ; *Microbiota/genetics ; Swine/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nose/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Swine Diseases/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Massive sequencing of a fragment of 16S rRNA gene allows the characterization of bacterial communities in different body sites: the microbiota. Nasal microbiota can be analyzed by DNA extraction from nasal swabs, amplification of the specific fragment of interest, and posterior sequencing. The raw sequences obtained need to go through a computational process to check their quality and then assign the taxonomy. Here, we will describe the complete process from sampling to get the microbial diversity of nasal microbiota in health and disease.}, }
@article {pmid38878412, year = {2024}, author = {Zheng, P and Mao, A and Meng, S and Yu, F and Zhang, S and Lun, J and Li, J and Hu, Z}, title = {Assembly mechanism of microbial community under different seasons in Shantou sea area.}, journal = {Marine pollution bulletin}, volume = {205}, number = {}, pages = {116550}, doi = {10.1016/j.marpolbul.2024.116550}, pmid = {38878412}, issn = {1879-3363}, mesh = {*Seasons ; *Microbiota ; *Seawater/microbiology ; Bacteria/classification ; Phylogeny ; Biodiversity ; China ; Oceans and Seas ; }, abstract = {Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.}, }
@article {pmid38876584, year = {2024}, author = {Kothe, CI and Carøe, C and Mazel, F and Zilber, D and Cruz-Morales, P and Mohellibi, N and Evans, JD}, title = {Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {189}, number = {}, pages = {114490}, doi = {10.1016/j.foodres.2024.114490}, pmid = {38876584}, issn = {1873-7145}, mesh = {*Fermentation ; *Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Taste ; Fermented Foods/microbiology ; Microbiota ; Japan ; Metagenomics ; }, abstract = {Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.}, }
@article {pmid38876281, year = {2024}, author = {Ponce-Jahen, SJ and Valenzuela, EI and Rangel-Mendez, JR and Sánchez-Carrillo, S and Cervantes, FJ}, title = {Anoxic nitrification with carbon-based materials as terminal electron acceptors.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {130961}, doi = {10.1016/j.biortech.2024.130961}, pmid = {38876281}, issn = {1873-2976}, mesh = {*Nitrification ; *Carbon/chemistry ; Electrons ; Graphite/chemistry ; Phylogeny ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Anaerobiosis ; Nitrates/metabolism ; Bacteria/metabolism ; }, abstract = {This study investigates the potential of humic substances (HS) and graphene oxide (GO), as extracellular electron acceptors (EEA) for nitrification, aiming to explore alternatives to sustain this process in wastewater treatment systems. Experimental results demonstrate the conversion of ammonium to nitrate (up to 87 % of conversion) coupled to the reduction of either HS or GO by anaerobic consortia. Electron balance confirmed the contribution of HS and GO to ammonium oxidation. Tracer analysis in incubations performed with [15]NH4[+] demonstrated [15]NO3[-] as the main product with a minor fraction ending as [29]N2. Phylogenetic analysis identified Firmicutes, Euryarchaeota, and Chloroflexi as the microbial lineages potentially involved in anoxic nitrification linked to HS reduction. This study introduces a new avenue for research in which carbon-based materials with electron-accepting capacity may support the anoxic oxidation of ammonium, for instance in bioelectrochemical systems in which carbon-based anodes could support this novel process.}, }
@article {pmid38874336, year = {2024}, author = {Tomazelli, D and Klauberg-Filho, O and Mendes, LW and Goss-Souza, D}, title = {The impact of land-use changes and management intensification on bacterial communities in the last decade: a review.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0030924}, pmid = {38874336}, issn = {1098-5336}, support = {1/CX/CSRD VA/United States ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Brazil ; *Agriculture/methods ; *Microbiota ; Biodiversity ; Soil/chemistry ; }, abstract = {In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.}, }
@article {pmid38873612, year = {2024}, author = {Pulvirenti, F and Giufrè, M and Pentimalli, TM and Camilli, R and Milito, C and Villa, A and Sculco, E and Cerquetti, M and Pantosti, A and Quinti, I}, title = {Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1371118}, pmid = {38873612}, issn = {1664-3224}, mesh = {Humans ; *Common Variable Immunodeficiency/microbiology/immunology/complications ; *Oropharynx/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Respiratory Tract Infections/microbiology/immunology ; *Dysbiosis ; Microbiota ; Prospective Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Acute Disease ; Bacteria/classification/genetics ; Case-Control Studies ; }, abstract = {BACKGROUND: The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited.<br><br>OBJECTIVE: This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections.<br><br>METHODS: Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients.<br><br>RESULTS: Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months.<br><br>CONCLUSIONS: CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.}, }
@article {pmid38873164, year = {2024}, author = {Rodríguez-Cruz, UE and Castelán-Sánchez, HG and Madrigal-Trejo, D and Eguiarte, LE and Souza, V}, title = {Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1369263}, pmid = {38873164}, issn = {1664-302X}, abstract = {A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).}, }
@article {pmid38870896, year = {2024}, author = {de la Cuesta-Zuluaga, J and Boldt, L and Maier, L}, title = {Response, resistance, and recovery of gut bacteria to human-targeted drug exposure.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {6}, pages = {786-793}, doi = {10.1016/j.chom.2024.05.009}, pmid = {38870896}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects ; Xenobiotics/pharmacology ; Symbiosis ; Gastrointestinal Tract/microbiology/drug effects ; Drug Resistance, Bacterial ; Host Microbial Interactions/drug effects ; }, abstract = {Survival strategies of human-associated microbes to drug exposure have been mainly studied in the context of bona fide pathogens exposed to antibiotics. Less well understood are the survival strategies of non-pathogenic microbes and host-associated commensal communities to the variety of drugs and xenobiotics to which humans are exposed. The lifestyle of microbial commensals within complex communities offers a variety of ways to adapt to different drug-induced stresses. Here, we review the responses and survival strategies employed by gut commensals when exposed to drugs-antibiotics and non-antibiotics-at the individual and community level. We also discuss the factors influencing the recovery and establishment of a new community structure following drug exposure. These survival strategies are key to the stability and resilience of the gut microbiome, ultimately influencing the overall health and well-being of the host.}, }
@article {pmid38869727, year = {2024}, author = {Dyczko, D and Krysmann, A and Kolanek, A and Borczyk, B and Kiewra, D}, title = {Bacterial pathogens in Ixodes ricinus collected from lizards Lacerta agilis and Zootoca vivipara in urban areas of Wrocław, SW Poland- preliminary study.}, journal = {Experimental &amp; applied acarology}, volume = {93}, number = {2}, pages = {409-420}, pmid = {38869727}, issn = {1572-9702}, mesh = {Animals ; Female ; Male ; *Anaplasma/isolation &amp; purification/genetics ; *Borrelia/isolation &amp; purification/genetics ; Cities ; *Ixodes/microbiology/physiology ; Larva/microbiology/physiology ; *Lizards/parasitology/microbiology ; Nymph/microbiology/physiology ; Poland ; *Rickettsia/genetics/isolation &amp; purification ; }, abstract = {The aim of this study was to determine the level of infection of Ixodes ricinus ticks with pathogens (Borrelia spp., Rickettsia spp., and Anaplasma spp.) collected from Lacerta agilis and Zootoca vivipara lizards in the urban areas of Wrocław (SW Poland). The study was carried out in July-August 2020. Lizards were caught by a noose attached to a pole or by bare hands, identified by species, and examined for the presence of ticks. Each lizard was then released at the site of capture. Ticks were removed with tweezers, identified by species using keys, and molecular tests were performed for the presence of pathogens. From 28 lizards (17 specimens of Z. vivipara and 11 specimens of L. agilis) a total of 445 ticks, including 321 larvae and 124 nymphs, identified as I. ricinus were collected. A larger number of ticks were obtained from L. agilis compared to Z. vivipara. Molecular tests for the presence of pathogens were performed on 445 specimens of I. ricinus. The nested PCR method for the fla gene allowed the detection of Borrelia spp. in 9.4% of ticks, and it was higher in ticks from L. agilis (12.0%) than from Z. vivipara (1.0%). The RFLP method showed the presence of three species, including two belonging to the B. burgdorferi s.l. complex (B. lusitaniae and B. afzelii), and B. miyamotoi. The overall level of infection of Rickettsia spp. was 19.3%, including 27.2% in ticks collected from Z. vivipara and 17.0% from L. agilis. Sequencing of randomly selected samples confirmed the presence of R. helvetica. DNA of Anaplasma spp. was detected only in one pool of larvae collected from L. agilis, and sample sequencing confirmed the presence of (A) phagocytophilum. The research results indicate the important role of lizards as hosts of ticks and their role in maintaining pathogens in the environment including urban agglomeration as evidenced by the first recorded presence of (B) miyamotoi and (A) phagocytophilum in I. ricinus ticks collected from L. agilis. However, confirmation of the role of sand lizards in maintaining (B) miyamotoi and A. phagocytophilum requires more studies and sampling of lizard tissue.}, }
@article {pmid38868805, year = {2024}, author = {Riello, GBC and da Silva, PM and da Silva Oliveira, FA and de Oliveira, RTG and da Silva, FER and da Frota França, IG and Melo, VMM and Miyajima, F and Pinheiro, RF and Danielle S, M}, title = {Gut Microbiota Composition Correlates with Disease Severity in Myelodysplastic Syndrome.}, journal = {International journal of hematology-oncology and stem cell research}, volume = {18}, number = {2}, pages = {192-201}, pmid = {38868805}, issn = {2008-3009}, abstract = {The myelodysplastic syndrome (MDS) is a heterogeneous group of clonal disorders of hematopoietic progenitor cells related to ineffective hematopoiesis and an increased risk of transformation to acute myelogenous leukemia. MDS is divided into categories, namely lineage dysplasia (MDS-SLD), MDS with ring sideroblasts (MDS-RS), MDS with multilineage dysplasia (MDS-MLD), MDS with excess blasts (MDS-EB). The International Prognostic Classification System (IPSS) ranks the patients as very low, low, intermediate, high, and very high based on disease evolution and survival rates. Evidence points to toll-like receptor (TLR) abnormal signaling as an underlying mechanism of this disease, providing a link between MDS and immune dysfunction. Microbial signals, such as lipopolysaccharides from gram-negative bacteria, can activate or suppress TLRs. Therefore, we hypothesized that MDS patients present gut microbiota alterations associated with disease subtypes and prognosis. To test this hypothesis, we sequenced the 16S rRNA gene from fecal samples of 30 MDS patients and 16 healthy elderly controls. We observed a negative correlation between Prevotella spp. and Akkermansia spp. in MDS patients compared with the control group. High-risk patients presented a significant increase in the genus Prevotella spp. compared to the other risk categories. There was a significant reduction in the abundance of the genus Akkermansia spp. in high-risk patients compared with low- and intermediate-risk. There was a significant decrease in the genus Ruminococcus spp. in MDS-EB patients compared with controls. Our findings show a new association between gut dysbiosis and higher-risk MDS, with a predominance of gram-negative bacteria.}, }
@article {pmid38868511, year = {2024}, author = {Li, M and Hu, J and Wei, Z and Jousset, A and Pommier, T and Yu, X and Xu, Y and Shen, Q}, title = {Synthetic microbial communities: Sandbox and blueprint for soil health enhancement.}, journal = {iMeta}, volume = {3}, number = {1}, pages = {e172}, pmid = {38868511}, issn = {2770-596X}, abstract = {We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.}, }
@article {pmid38867105, year = {2025}, author = {Mahjoubi, M and Cherif, H and Aliyu, H and Chouchane, H and Cappello, S and Neifar, M and Mapelli, F and Souissi, Y and Borin, S and Cowan, DA and Cherif, A}, title = {Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {2}, pages = {299-313}, pmid = {38867105}, issn = {1618-1905}, mesh = {*Brucella/metabolism/genetics/classification/growth &amp; development ; *Surface-Active Agents/metabolism/chemistry ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Polysaccharides, Bacterial/metabolism/chemistry ; Metals, Heavy/metabolism/toxicity ; Genome, Bacterial ; Petroleum/metabolism ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm[-1] generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.}, }
@article {pmid38865907, year = {2024}, author = {Wang, L and Lee, E and Barlaz, MA and de Los Reyes, FL}, title = {Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage.}, journal = {Waste management (New York, N.Y.)}, volume = {186}, number = {}, pages = {77-85}, doi = {10.1016/j.wasman.2024.06.004}, pmid = {38865907}, issn = {1879-2456}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Refuse Disposal/methods ; Solid Waste/analysis ; Bacteria/metabolism/genetics/classification ; Vegetables/microbiology ; Methane/metabolism ; Fruit/microbiology ; Garbage ; Food Loss and Waste ; }, abstract = {A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.}, }
@article {pmid38861460, year = {2024}, author = {Wutkowska, M and Tláskal, V and Bordel, S and Stein, LY and Nweze, JA and Daebeler, A}, title = {Leveraging genome-scale metabolic models to understand aerobic methanotrophs.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38861460}, issn = {1751-7370}, support = {21-17322M//Czech Science Foundation/ ; }, mesh = {*Methane/metabolism ; Oxidation-Reduction ; Aerobiosis ; Metabolic Networks and Pathways/genetics ; Models, Biological ; }, abstract = {Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.}, }
@article {pmid38860973, year = {2024}, author = {Deehan, EC and Zhang, Z and Nguyen, NK and Perez-Muñoz, ME and Cole, J and Riva, A and Berry, D and Prado, CM and Walter, J}, title = {Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2363021}, pmid = {38860973}, issn = {1949-0984}, support = {741623/ERC_/European Research Council/International ; }, mesh = {*Xylans/metabolism ; Humans ; *Feces/microbiology/chemistry ; Male ; Female ; *Dietary Fiber/metabolism ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium longum/metabolism ; Adult ; Dietary Supplements/analysis ; Fermentation ; Aged ; Adaptation, Physiological ; }, abstract = {Dietary fiber supplements are a strategy to close the 'fiber gap' and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa involved in AX fermentation were identified by bioorthogonal non-canonical amino acid tagging. Associations between GI symptoms, fecal microbiota features, and diet history were systematically investigated. AX supplementation increased symptoms during the first three weeks relative to MCC (p < 0.05, Mann-Whitney tests), but subjects 'adapted' with symptoms reverting to baseline levels toward the end of treatment. Symptom adaptations were individualized and correlated with the relative abundance of Bifidobacterium longum at baseline (rs = 0.74, p = 0.002), within the bacterial community that utilized AX (rs = 0.69, p = 0.006), and AX-induced shifts in acetate (rs = 0.54, p = 0.039). Lower baseline consumption of animal-based foods and higher whole grains associated with less severity and better adaptation. These findings suggest that humans do 'adapt' to tolerate efficacious fiber doses, and this process is linked to their microbiome and dietary factors known to interact with gut microbes, providing a basis for the development of strategies for improved tolerance of dietary fibers.}, }
@article {pmid38860825, year = {2024}, author = {Paillet, T and Lamy-Besnier, Q and Figueroa, C and Petit, M-A and Dugat-Bony, E}, title = {Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0020124}, pmid = {38860825}, issn = {2379-5077}, mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/isolation &amp; purification ; Bacteria/virology/genetics/isolation &amp; purification ; Microbiota ; Food Microbiology ; France ; Metagenomics ; Virome ; }, abstract = {The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.}, }
@article {pmid38858788, year = {2024}, author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Thurber, RLV and Peixoto, RS}, title = {Correction: Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {105}, pmid = {38858788}, issn = {2049-2618}, }
@article {pmid38857239, year = {2024}, author = {Martinez-Villegas, L and Lado, P and Klompen, H and Wang, S and Cummings, C and Pesapane, R and Short, SM}, title = {The microbiota of Amblyomma americanum reflects known westward expansion.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0304959}, pmid = {38857239}, issn = {1932-6203}, mesh = {Animals ; *Microbiota ; Female ; Male ; *Amblyomma/microbiology ; United States ; Ixodidae/microbiology ; }, abstract = {Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host's life history and vectorial capacity. Bacterial communities associated with A. americanum may reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick-borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations of A. americanum ticks from the Historical range. Spatial autocorrelation, and particularly the detection of non-selective ecological processes, are indicative of geographic isolation. We also found that prevalence of Ehrlichia chaffeensis, E. ewingii, and Anaplasma phagocytophilum ranged from 3.40-5.11% and did not significantly differ by region. Rickettsia rickettsii was absent from our samples. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion in A. americanum and potentially other tick vectors as well.}, }
@article {pmid38855766, year = {2024}, author = {Tong, L and Jun, L and He, J and Min, Y and Guoqing, D and Yuting, H and Huaxing, Z and Huan, W and Tingshuang, P}, title = {Differences in environmental microbial community responses under rice-crab co-culture and crab monoculture models under cyanobacterial bloom.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1327520}, pmid = {38855766}, issn = {1664-302X}, abstract = {Cyanobacterial blooms (CBs) present significant challenges to Chinese mitten crab (CMC) culture, posing hazards to the aquatic microbial ecology. However, the current focus on the microbial ecological changes within the CMC culture system under the influence of CBs is somewhat insufficient. There's an urgent need to analyze the microbial ecosystem of the CMC culture system under CBs. This study employed 16S rRNA gene amplicon sequencing to investigate the dynamics of the environmental microbial community in both the rice-crab co-culture (RC) and crab monoculture (CM) models. The results revealed that cyanobacteria reached high levels in the CM water in July, while they began to increase in the RC water in August. Notably, OTU147 (uncultured bacterium g_Planktothrix NIVA-CYA 15), identified as the dominant taxon associated with CBs, showed a significant linear relationship with TP, NO2 [-]-N, and the N:P ratio. TP, TN, NO2 [-]-N, and CODMn had a more pronounced impact on the structure of bacterial communities and cyanobacterial taxa in the water. The bacterial community structure involved in carbon metabolism displayed temporal succession in the water. The co-occurrence network of the bacterial community primarily consisted of Chloroflexi, Proteobacteria, and Firnicutes in the sediment, and Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidota in the water. In contrast, the co-occurrence network included different peripheral species in the sediment and water. Keystone species were predominantly represented by OTU22 (uncultured actinobacterium g_ hgcI clade) and OTU12 (uncultured Opitutae bacterium g_ norank) in the RC water, and by OTU25 (uncultured bacterium g_ Limnohabitans) in the CM water. TP, TN, NO2 [-]-N, and CODMn were identified as the primary environmental factors influencing these keystone taxa within the culture water. In conclusion, this study on the microbial ecology of the CMC culture system under the influence of CBs provides valuable insights that can be instrumental in subsequent management efforts.}, }
@article {pmid38852236, year = {2024}, author = {Xu, Y and Yu, Z and Liu, C and Hu, Y and Zhang, J and Liu, J and Chen, X and Liu, J and Wang, G and Liu, X and Jin, J and Li, Y}, title = {Variability in soybean yield responses to elevated atmospheric CO2: Insights from non-structural carbohydrate remobilisation during seed filling.}, journal = {Plant physiology and biochemistry : PPB}, volume = {213}, number = {}, pages = {108802}, doi = {10.1016/j.plaphy.2024.108802}, pmid = {38852236}, issn = {1873-2690}, mesh = {*Glycine max/metabolism/growth &amp; development/drug effects/physiology ; *Carbon Dioxide/metabolism/pharmacology ; *Photosynthesis/drug effects ; *Carbohydrate Metabolism ; *Seeds/metabolism/growth &amp; development/drug effects ; }, abstract = {The increasing atmospheric CO2 concentration (e[CO2]) has mixed effects on soybean most varieties' yield. This study elucidated the effect of e[CO2] on soybean yield and the underlying mechanisms related to photosynthetic capacity, non-structural carbohydrate (NSC) accumulation, and remobilisation. Four soybean cultivars were cultivated in open-top chambers at two CO2 levels. Photosynthesis rates were determined from R2 to R6. Plants were sampled at R5 and R8 to determine carbohydrate concentrations. There were significant variations in yield responses among the soybean cultivars under e[CO2], from no change in DS1 to a 22% increase in SN14. DS1 and SN14 had the smallest and largest increase, respectively, in daily carbon assimilation capacity. Under e[CO2], DS1, MF5, and XHJ had an increase in Ci, at which point the transition from Rubisco-limited to ribulose-1,5-bisphosphate regeneration-limited photosynthesis occurred, in contrast with SN14. Thus, the cultivars might have distinct mechanisms that enhance photosynthesis under e[CO2] conditions. A positive correlation was between daily carbon assimilation response to e[CO2] and soybean yield, emphasising the importance of enhanced photosynthate accumulation before the R5 stage in determining yield response to e[CO2]. E[CO2] significantly influenced NSC accumulation in vegetative organs at R5, with variation among cultivars. There was enhanced NSC remobilisation during seed filling, indicating cultivar-specific responses to the remobilisation of sucrose and soluble sugars, excluding sucrose and starch. A positive correlation was between leaf and stem NSC remobilisation and yield response to e[CO2], emphasising the role of genetic differences in carbohydrate remobilisation mechanisms in determining soybean yield variation under elevated CO2 levels.}, }
@article {pmid38849711, year = {2024}, author = {Doménech-Pascual, A and Carrasco-Barea, L and Gich, F and Boadella, J and Freixinos Campillo, Z and Gómez Cerezo, R and Butturini, A and Romaní, AM}, title = {Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16661}, doi = {10.1111/1462-2920.16661}, pmid = {38849711}, issn = {1462-2920}, support = {PID2021-123735OB-C2/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RTI2018-097950-B-C2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PCI2020-120702-2/AEI/10.13039/501.100.011.033//Agencia Estatal de Investigaci&#xf3;n/ ; 2021 FISDU 00297//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, mesh = {*Droughts ; *Bacteria/metabolism/classification ; *Fungi/metabolism ; *Rivers/microbiology ; *Salinity ; *Plant Stems/microbiology/metabolism ; Ecosystem ; }, abstract = {Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.}, }
@article {pmid38849299, year = {2024}, author = {Papazlatani, C and Garbeva, P and Huerta Lwanga, E}, title = {Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {38849299}, issn = {1574-6968}, mesh = {*Oligochaeta/microbiology/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Soil Pollutants/toxicity ; Soil Microbiology ; }, abstract = {Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.}, }
@article {pmid38844497, year = {2024}, author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS}, title = {Author Correction: Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4830}, doi = {10.1038/s41467-024-49328-4}, pmid = {38844497}, issn = {2041-1723}, }
@article {pmid38842339, year = {2024}, author = {Kortenbosch, HH and van Leuven, F and van den Heuvel, C and Schoustra, SE and Zwaan, BJ and Snelders, E}, title = {Catching some air: a method to spatially quantify aerial triazole resistance in Aspergillus fumigatus.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0027124}, pmid = {38842339}, issn = {1098-5336}, support = {GROEN.2019.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {*Aspergillus fumigatus/drug effects/genetics ; *Drug Resistance, Fungal ; *Air Microbiology ; *Triazoles/pharmacology ; *Antifungal Agents/pharmacology ; Spores, Fungal/drug effects/genetics ; Environmental Monitoring/methods ; }, abstract = {Airborne triazole-resistant spores of the human fungal pathogen Aspergillus fumigatus are a significant human health problem as the agricultural use of triazoles has been selecting for cross-resistance to life-saving clinical triazoles. However, how to quantify exposure to airborne triazole-resistant spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can regionally yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling 12 regions, we demonstrate that there are significant regional differences in airborne CFU numbers, and the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole (∼4 mg/L) and voriconazole (∼2 mg/L). Our efficient and accessible air sampling protocol opens up extensive options for fine-scale spatial sampling and surveillance studies of airborne A. fumigatus.IMPORTANCEAspergillus fumigatus is an opportunistic fungal pathogen that humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, in A. fumigatus can make infections by this fungus untreatable and uncurable. Here, we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping of A. fumigatus TR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen-scientists for large-scale spatial air sampling. Spatial air sampling can open up extensive options for surveillance, health-risk assessment, and the study of landscape-level ecology of A. fumigatus, as well as investigating the environmental drivers of triazole resistance.}, }
@article {pmid38840338, year = {2024}, author = {Olson, EG and Dittoe, DK and Micciche, AC and Stock, DA and Rubinelli, PM and Rothrock, MJ and Ricke, SC}, title = {Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {59}, number = {8}, pages = {448-482}, doi = {10.1080/03601234.2024.2361596}, pmid = {38840338}, issn = {1532-4109}, mesh = {Animals ; *Animal Feed/analysis ; *Poultry/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Chickens/microbiology ; Microbiota ; }, abstract = {Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.}, }
@article {pmid38840053, year = {2024}, author = {Ullah, I and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Fahad, S}, title = {Germination responses of Lens Culiunaris L. seeds to osmotic potentials at cardinal temperatures using hydrothermal time model.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {502}, pmid = {38840053}, issn = {1471-2229}, mesh = {*Germination/physiology ; *Seeds/physiology/growth &amp; development ; *Lens Plant/physiology/growth &amp; development ; *Temperature ; Water/metabolism ; Models, Biological ; Osmotic Pressure ; }, abstract = {BACKGROUND: Lentil is a significant legume that are consumed as a staple food and have a significant economic impact around the world. The purpose of the present research on lentil was to assess the hydrothermal time model's capacity to explain the dynamics of Lens culinaris L. var. Markaz-09 seed germination, as well as to ascertain the germination responses at various sub-optimal temperatures (T) and water potentials (Ψ). In order to study lentil seed germination (SG) behavior at variable water potentials (Ψs) and temperatures (Ts). A lab experiment employing the hydrothermal time model was created. Seeds were germinated at six distinct temperatures: 15 [0]С, 20 [0]С, 25 [0]С, 30 [0]С, 35 [0]С, and 40 [0]С, with five Ψs of 0, -0.3, -0.6, -0.9, and - 1.2 MPa in a PEG-6000 (Polyethylene glycol 6000) solution.<br><br>RESULTS: The results indicated that the agronomic parameters like Germination index (GI), Germination energy (GE), Timson germination index (TGI), were maximum in 25 [0]C at (-0.9&#xa0;MPa) and lowest at 40 [0]C in 0&#xa0;MPa. On other hand, mean germination time (MGT) value was highest at 15 [0]C in -1.2&#xa0;MPa and minimum at 40 [0]C in (-0.6&#xa0;MPa) while Mean germination rate (MGR) was maximum at 40 [0]C in (0&#xa0;MPa) and minimum at 15 [0]C in (-0.6&#xa0;MPa).<br><br>CONCLUSIONS: The HTT model eventually defined the germination response of Lens culinaris L. var. Markaz-09 (Lentil) for all Ts and &#x3a8;s, allowing it to be employed as a predictive tool in Lens culinaris L. var. Markaz-09 (Lentil) seed germination simulation models.}, }
@article {pmid38839775, year = {2024}, author = {Ray, K and Basak, SK and Giri, CK and Kotal, HN and Mandal, A and Chatterjee, K and Saha, S and Biswas, B and Mondal, S and Das, I and Ghosh, A and Bhadury, P and Joshi, R}, title = {Ecological restoration at pilot-scale employing site-specific rationales for small-patch degraded mangroves in Indian Sundarbans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12952}, pmid = {38839775}, issn = {2045-2322}, support = {BT/PR7501/BCE/8/982/2013//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; File No. BT/PR30531/BCE/8/1496/2018//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; EMR/2016/005262//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; }, mesh = {*Wetlands ; India ; *Conservation of Natural Resources/methods ; Ecosystem ; Environmental Restoration and Remediation/methods ; Pilot Projects ; Bayes Theorem ; }, abstract = {To date, degraded mangrove ecosystem restoration accomplished worldwide primarily aligns towards rehabilitation with monotypic plantations, while ecological restoration principles are rarely followed in these interventions. However, researchers admit that most of these initiatives' success rate is not appreciable often. An integrative framework of ecological restoration for degraded mangroves where site-specific observations could be scientifically rationalized, with co-located reference pristine mangroves as the target ecosystem to achieve is currently distinctively lacking. Through this experimental scale study, we studied the suitability of site-specific strategies to ecologically restore degraded mangrove patches vis-à-vis the conventional mono-species plantations in a highly vulnerable mangrove ecosystem in Indian Sundarbans. This comprehensive restoration framework was trialed in small discrete degraded mangrove patches spanning ~ 65 ha. Site-specific key restoration components applied are statistically validated through RDA analyses and Bayesian t-tests. 25 quantifiable metrics evaluate the restoration success of a ~ 3 ha degraded mangrove patch with Ridgeline distribution, Kolmogorov-Smirnov (K-S) tests, and Mahalanobis Distance (D[2]) measure to prove the site's near-equivalence to pristine reference in multiple ecosystem attributes. This restoration intervention irrevocably establishes the greater potential of this framework in the recovery of ecosystem functions and self-sustenance compared to that of predominant monoculture practices for vulnerable mangroves.}, }
@article {pmid38839017, year = {2024}, author = {Ruan, SY and Luo, HW and Tang, XR and Qi, JY}, title = {Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system.}, journal = {The Science of the total environment}, volume = {944}, number = {}, pages = {173722}, doi = {10.1016/j.scitotenv.2024.173722}, pmid = {38839017}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Organic Agriculture/methods ; *Virulence Factors/genetics ; China ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.}, }
@article {pmid38839005, year = {2024}, author = {David, GM and Pimentel, IM and Rehsen, PM and Vermiert, AM and Leese, F and Gessner, MO}, title = {Multiple stressors affecting microbial decomposer and litter decomposition in restored urban streams: Assessing effects of salinization, increased temperature, and reduced flow velocity in a field mesocosm experiment.}, journal = {The Science of the total environment}, volume = {943}, number = {}, pages = {173669}, doi = {10.1016/j.scitotenv.2024.173669}, pmid = {38839005}, issn = {1879-1026}, mesh = {*Rivers/chemistry/microbiology ; *Salinity ; Biodegradation, Environmental ; Ecosystem ; Plant Leaves ; Alnus ; Temperature ; Environmental Monitoring ; }, abstract = {A multitude of anthropogenic stressors impact biological communities and ecosystem processes in urban streams. Prominent among them are salinization, increased temperature, and altered flow regimes, all of which can affect microbial decomposer communities and litter decomposition, a fundamental ecosystem process in streams. Impairments caused by these stressors individually or in combination and recovery of communities and ecosystem processes after release from these stressors are not well understood. To improve our understanding of multiple stressors impacts we performed an outdoor stream mesocosm experiment with 64 experimental units to assess the response of microbial litter decomposers and decomposition. The three stressors we applied in a full-factorial design were increased salinity (NaCl addition, 0.53 mS cm[-1] above ambient), elevated temperature (3.5 °C above ambient), and reduced flow velocity (3.5 vs 14.2 cm s[-1]). After two weeks of stressor exposure (first sampling) and two subsequent weeks of recovery (second sampling), we determined leaf-associated microbial respiration, fungal biomass, and the sporulation activity and community composition of aquatic hyphomycetes in addition to decomposition rates of black alder (Alnus glutinosa) leaves confined in fine-mesh litter bags. Microbial colonization of the litter was accompanied by significant mass loss in all mesocosms. However, there was little indication that mass loss, microbial respiration, fungal biomass, sporulation rate or community composition of aquatic hyphomycetes was strongly affected by either single stressors or their interactions. Two exceptions were temperature effects on sporulation and decomposition rate. Similarly, no notable differences among mesocosms were observed after the recovery phase. These results suggest that microbial decomposers and leaf litter decomposition are either barely impaired by exposure to the tested stressors at the levels applied in our experiment, or that communities in restored urban streams are well adapted to cope with these stressor levels.}, }
@article {pmid38832805, year = {2024}, author = {Freitas, ASd and Zagatto, LFG and Rocha, GS and Pellegrinetti, TA and Alves, LdCM and Lara, VMd and Mandro, JA and Martins, GL and Muniz, AW and Hanada, RE and Würdig Roesch, LF and Tsai, SM}, title = {Bacterial genomes recovered from litter's metagenomes in Amazonian Dark Earths.}, journal = {Microbiology resource announcements}, volume = {13}, number = {7}, pages = {e0042224}, pmid = {38832805}, issn = {2576-098X}, support = {2021/10.626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas (FAPEAM)/ ; 2020/08927-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; }, abstract = {Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).}, }
@article {pmid38831142, year = {2024}, author = {Chen, D and Tian, C and Yuan, H and Zhai, W and Chang, Z}, title = {Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {82}, pmid = {38831142}, issn = {1432-184X}, support = {2023YFD2401704//National Key Research and Development Program of China/ ; CARS-48//Agriculture Research System of China/ ; No.2023TD50//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, mesh = {*Nitrogen/metabolism ; *Aquaculture ; *Denitrification ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Ponds/microbiology ; *Microbiota ; Animals ; *Penaeidae/microbiology ; *Nitrous Oxide/metabolism/analysis ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; }, abstract = {Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.}, }
@article {pmid38830709, year = {2024}, author = {Mugani, R and El Khalloufi, F and Kasada, M and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and Zerrifi, SEA and Herter, SO and Hejjaj, A and Aziz, F and Ouazzani, N and Azevedo, J and Campos, A and Putschew, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B}, title = {Monitoring of toxic cyanobacterial blooms in Lalla Takerkoust reservoir by satellite imagery and microcystin transfer to surrounding farms.}, journal = {Harmful algae}, volume = {135}, number = {}, pages = {102631}, doi = {10.1016/j.hal.2024.102631}, pmid = {38830709}, issn = {1878-1470}, mesh = {*Microcystins/metabolism/analysis ; *Harmful Algal Bloom ; *Microcystis/physiology/growth &amp; development ; *Satellite Imagery ; *Environmental Monitoring/methods ; Cyanobacteria/physiology/growth &amp; development ; Indonesia ; Synechococcus/physiology ; Lakes/microbiology ; }, abstract = {Cyanobacterial harmful algal blooms (CyanoHABs) threaten public health and freshwater ecosystems worldwide. In this study, our main goal was to explore the dynamics of cyanobacterial blooms and how microcystins (MCs) move from the Lalla Takerkoust reservoir to the nearby farms. We used Landsat imagery, molecular analysis, collecting and analyzing physicochemical data, and assessing toxins using HPLC. Our investigation identified two cyanobacterial species responsible for the blooms: Microcystis sp. and Synechococcus sp. Our Microcystis strain produced three MC variants (MC-RR, MC-YR, and MC-LR), with MC-RR exhibiting the highest concentrations in dissolved and intracellular toxins. In contrast, our Synechococcus strain did not produce any detectable toxins. To validate our Normalized Difference Vegetation Index (NDVI) results, we utilized limnological data, including algal cell counts, and quantified MCs in freeze-dried Microcystis bloom samples collected from the reservoir. Our study revealed patterns and trends in cyanobacterial proliferation in the reservoir over 30 years and presented a historical map of the area of cyanobacterial infestation using the NDVI method. The study found that MC-LR accumulates near the water surface due to the buoyancy of Microcystis. The maximum concentration of MC-LR in the reservoir water was 160 µg L[-1]. In contrast, 4 km downstream of the reservoir, the concentration decreased by a factor of 5.39 to 29.63 µgL[-1], indicating a decrease in MC-LR concentration with increasing distance from the bloom source. Similarly, the MC-YR concentration decreased by a factor of 2.98 for the same distance. Interestingly, the MC distribution varied with depth, with MC-LR dominating at the water surface and MC-YR at the reservoir outlet at a water depth of 10 m. Our findings highlight the impact of nutrient concentrations, environmental factors, and transfer processes on bloom dynamics and MC distribution. We emphasize the need for effective management strategies to minimize toxin transfer and ensure public health and safety.}, }
@article {pmid38830413, year = {2024}, author = {Kerfahi, D and Dong, K and Tripathi, B and Adams, JM}, title = {Global comparison shows that soil bacterial communities in extreme pH soils are more structured by deterministic processes.}, journal = {The Science of the total environment}, volume = {942}, number = {}, pages = {173662}, doi = {10.1016/j.scitotenv.2024.173662}, pmid = {38830413}, issn = {1879-1026}, mesh = {*Soil Microbiology ; Hydrogen-Ion Concentration ; *Soil/chemistry ; *Bacteria ; Microbiota ; }, abstract = {A major aim of microbial ecology is the search for basic 'rules' that dominate variation in microbial communities. An earlier comparison of several soil successional series showed that pH explained variation in the relative importance of stochastic versus deterministic processes in bacterial communities. In neutral pH soils, bacterial communities were more strongly influenced by stochastic processes than in low or high pH soils. Here, we took a broad level approach to attempt a more definitive answer of whether soil pH dominates bacterial community structuring using the global database of 237 samples. The beta-NTI showed that at both a global and continental scale, samples with low pH were dominated by deterministic processes, while in samples at around neutral pH, stochastic processes dominated. At high pH, stochasticity dominated on the global scale, but on several continents, the beta-NTI showed determinism predominating. Overall, it appears that bacterial community structuring is strongly and predictably affected by pH, with the most consistent difference observed between determinism at low pH and stochasticity at neutral pH. There is a need for hypothesis testing to explain why this trend exists. It is possible that at low pH, there is a greater selection for consortia to exploit resources, which leads to more predictable, deterministic combinations of species co-occurring. Additionally, the high energy demands for homeostasis and the constraints from the lack of available nutrient resources may impose greater niche-based competition, resulting in more deterministic community structuring at low pH.}, }
@article {pmid38829422, year = {2024}, author = {Jurado, V and Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C}, title = {Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {80}, pmid = {38829422}, issn = {1432-184X}, mesh = {*Caves/microbiology ; *Chiroptera/microbiology/physiology ; Animals ; *Biofilms ; *Fungi/classification/physiology/genetics/isolation &amp; purification ; *Arthropods/microbiology ; *Calcium Sulfate ; Spain ; Biodiversity ; Mycobiome ; Soil Microbiology ; }, abstract = {The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.}, }
@article {pmid38829379, year = {2024}, author = {Gwokyalya, R and Herren, JK and Weldon, CW and Ndlela, S and Gichuhi, J and Ongeso, N and Wairimu, AW and Ekesi, S and Mohamed, SA}, title = {Shaping the Microbial Landscape: Parasitoid-Driven Modifications of Bactrocera dorsalis Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {81}, pmid = {38829379}, issn = {1432-184X}, mesh = {Animals ; *Tephritidae/microbiology/parasitology ; *Wasps/microbiology/physiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Larva/microbiology/parasitology/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; Fungi/genetics/physiology ; Host-Parasite Interactions ; Microbiota ; Dysbiosis/microbiology/parasitology ; }, abstract = {Koinobiont endoparasitoids regulate the physiology of their hosts through altering host immuno-metabolic responses, processes which function in tandem to shape the composition of the microbiota of these hosts. Here, we employed 16S rRNA and ITS amplicon sequencing to investigate whether parasitization by the parasitoid wasps, Diachasmimorpha longicaudata (Ashmaed) (Hymenoptera: Braconidae) and Psyttalia cosyrae (Wilkinson) (Hymenoptera: Braconidae), induces gut dysbiosis and differentially alter the gut microbial (bacteria and fungi) communities of an important horticultural pest, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). We further investigated the composition of bacterial communities of adult D. longicaudata and P. cosyrae to ascertain whether the adult parasitoids and parasitized host larvae share microbial taxa through transmission. We demonstrated that parasitism by D. longicaudata induced significant gut perturbations, resulting in the colonization and increased relative abundance of pathogenic gut bacteria. Some pathogenic bacteria like Stenotrophomonas and Morganella were detected in both the guts of D. longicaudata-parasitized B. dorsalis larvae and adult D. longicaudata wasps, suggesting a horizontal transfer of microbes from the parasitoid to the host. The bacterial community of P. cosyrae adult wasps was dominated by Arsenophonus nasoniae, whereas that of D. longicaudata adults was dominated by Paucibater spp. and Pseudomonas spp. Parasitization by either parasitoid wasp was associated with an overall reduction in fungal diversity and evenness. These findings indicate that unlike P. cosyrae which is avirulent to B. dorsalis, parasitization by D. longicaudata induces shifts in the gut bacteriome of B. dorsalis larvae to a pathobiont-dominated community. This mechanism possibly enhances its virulence against the pest, further supporting its candidacy as an effective biocontrol agent of this frugivorous tephritid fruit fly pest.}, }
@article {pmid38828615, year = {2024}, author = {Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG}, title = {Improved Visualization of Oral Microbial Consortia.}, journal = {Journal of dental research}, volume = {103}, number = {13}, pages = {1421-1427}, pmid = {38828615}, issn = {1544-0591}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 GM126257/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biofilms ; Humans ; *Microbial Consortia ; *Tongue/microbiology ; In Situ Hybridization, Fluorescence/methods ; Actinomyces ; Streptococcus salivarius ; }, abstract = {Bacteria on the tongue dorsum (TD) form consortia tens to hundreds of microns in diameter organized around a core of epithelial cells. Whole-mount preparations have been instrumental in revealing their organization and specific microbial associations. However, their thickness and intricate 3-dimensional complexity present challenges for a comprehensive spatial analysis. To overcome these challenges, we employed a complementary approach: embedding in hydrophilic plastic followed by sectioning and postsectioning labeling. Samples were labeled by hybridization with multiplexed fluorescent oligonucleotide probes and visualized by spectral imaging and linear unmixing. Application of this strategy to TD biofilms improved the visualization of bacteria that were difficult to resolve in whole-mount imaging. Actinomyces, previously detected as patches, became resolved at the single-cell level. The filamentous taxa Leptotrichia and Lachnospiraceae, located at the core of the consortium, were regularly visualized whereas previously they were rarely detected when using whole mounts. Streptococcus salivarius, heterogeneously detected in whole mounts, were regularly and homogenously observed. Two-dimensional images provide valuable information about the organization of bacterial biofilms. However, they offer only a single plane of view for objects that can extend to hundreds of microns in thickness, and information obtained from such images may not always reflect the complexity of a 3-dimensional object. We combined serial physical sectioning with optical sectioning to facilitate the 3-dimensional reconstruction of consortia, spanning over 100 µm in thickness. Our work showcases the use of hydrophilic plastic embedding and sectioning for examining the structure of TD biofilms through spectral imaging fluorescence in situ hybridization. The result was improved visualization of important members of the human oral microbiome. This technique serves as a complementary method to the previously employed whole-mount analysis, offering its own set of advantages and limitations. Addressing the spatial complexity of bacterial consortia demands a multifaceted approach for a comprehensive and effective analysis.}, }
@article {pmid38827504, year = {2024}, author = {Gupta, VVSR and Tiedje, JM}, title = {Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales.}, journal = {mLife}, volume = {3}, number = {1}, pages = {21-41}, pmid = {38827504}, issn = {2770-100X}, abstract = {The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.}, }
@article {pmid38827283, year = {2024}, author = {Viladomat Jasso, M and García-Ulloa, M and Zapata-Peñasco, I and Eguiarte, LE and Souza, V}, title = {Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17412}, pmid = {38827283}, issn = {2167-8359}, mesh = {*Metagenomics ; Archaea/genetics/classification ; Mexico ; Bacteria/genetics/classification ; Ecosystem ; Microbiota/genetics ; Metagenome ; Geologic Sediments/microbiology ; }, abstract = {Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.}, }
@article {pmid38825932, year = {2024}, author = {Li, SQ and Song, Y and Zhou, F and Chen, MY and Chen, LG and Zhou, JP}, title = {[Primary biliary cholangitis and autoimmune hepatitis overlap syndrome complicated with skin and soft tissue infection of lower limb during corticosteroids treatment: a case report].}, journal = {Zhonghua nei ke za zhi}, volume = {63}, number = {6}, pages = {618-620}, doi = {10.3760/cma.j.cn112138-20231030-00263}, pmid = {38825932}, issn = {0578-1426}, mesh = {Humans ; Adrenal Cortex Hormones/adverse effects ; Cholangitis/chemically induced ; *Hepatitis, Autoimmune/etiology/drug therapy ; Liver Cirrhosis, Biliary/drug therapy/complications ; Lower Extremity ; }, }
@article {pmid38820701, year = {2024}, author = {Wang, Z and Fu, X and Kuramae, EE}, title = {Insight into farming native microbiome by bioinoculant in soil-plant system.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127776}, doi = {10.1016/j.micres.2024.127776}, pmid = {38820701}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Soil/chemistry ; *Agriculture/methods ; Bacteria/classification/metabolism/isolation &amp; purification/genetics ; Crops, Agricultural/microbiology ; Plants/microbiology ; Microbial Interactions ; }, abstract = {Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.}, }
@article {pmid38819559, year = {2024}, author = {Sanchez, FB and Sato Guima, SE and Setubal, JC}, title = {How to Obtain and Compare Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {135-163}, pmid = {38819559}, issn = {1940-6029}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.}, }
@article {pmid38819147, year = {2024}, author = {Sumner, DY}, title = {Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0009324}, pmid = {38819147}, issn = {1098-5336}, mesh = {*Earth, Planet ; *Atmosphere/chemistry ; *Carbon Isotopes/analysis/metabolism ; Oxygen/metabolism ; Methane/metabolism ; Bacteria/metabolism/genetics/classification ; Cyanobacteria/metabolism/genetics ; }, abstract = {The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves [13]C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of [12]C into organic carbon and CH4. Extreme and variable [13]C enrichments in carbonates were caused by [13]C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly [13]C enriched. Thus, the loss of extreme [13]C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.}, }
@article {pmid38819146, year = {2024}, author = {Tang, S and Wu, G and Liu, Y and Xue, B and Zhang, S and Zhang, W and Jia, Y and Xie, Q and Liang, C and Wang, L and Heng, H and Wei, W and Shi, X and Hu, Y and Yang, J and Zhao, L and Wang, X and Zhao, L and Yuan, H}, title = {Guild-level signature of gut microbiome for diabetic kidney disease.}, journal = {mBio}, volume = {15}, number = {7}, pages = {e0073524}, pmid = {38819146}, issn = {2150-7511}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetic Nephropathies/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Metagenomics ; Adult ; Aged ; *Metagenome ; }, abstract = {UNLABELLED: Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest classification model established with the 54 HQMAGs was also applicable for classifying patients with end-stage renal disease and healthy subjects in an independent data set. Therefore, this genome-level, guild-based microbial analysis strategy may identify DKD patients with different severity at an earlier stage to guide clinical interventions.<br><br>IMPORTANCE: Traditionally, microbiome research has been constrained by the reliance on taxonomic classifications that may not reflect the functional dynamics or the ecological interactions within microbial communities. By transcending these limitations with a genome-centric and guild-based analysis, our study sheds light on the intricate and specific interactions between microbial strains and diabetic kidney disease (DKD). We have unveiled two distinct microbial guilds with opposite influences on host health, which may redefine our understanding of microbial contributions to disease progression. The implications of our findings extend beyond mere association, providing potential pathways for intervention and opening new avenues for patient stratification in clinical settings. This work paves the way for a paradigm shift in microbiome research in DKD and potentially other chronic kidney diseases, from a focus on taxonomy to a more nuanced view of microbial ecology and function that is more closely aligned with clinical outcomes.}, }
@article {pmid38818274, year = {2023}, author = {Fu, Y and Dou, Q and Smalla, K and Wang, Y and Johnson, TA and Brandt, KK and Mei, Z and Liao, M and Hashsham, SA and Schäffer, A and Smidt, H and Zhang, T and Li, H and Stedtfeld, R and Sheng, H and Chai, B and Virta, M and Jiang, X and Wang, F and Zhu, YG and Tiedje, JM}, title = {Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes.}, journal = {mLife}, volume = {2}, number = {4}, pages = {350-364}, pmid = {38818274}, issn = {2770-100X}, abstract = {The emergence and rapid spread of antimicrobial resistance is of global public health concern. The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes (ARGs). In this review, we describe the reservoirs of gut ARGs and their dynamics in both animals and humans, use the One Health perspective to track the transmission of ARG-containing bacteria between humans, animals, and the environment, and assess the impact of antimicrobial resistance on human health and socioeconomic development. The gut resistome can evolve in an environment subject to various selective pressures, including antibiotic administration and environmental and lifestyle factors (e.g., diet, age, gender, and living conditions), and interventions through probiotics. Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance. With the help of effective measures taken at the national, local, personal, and intestinal management, it will also result in preventing or minimizing the spread of infectious diseases. This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.}, }
@article {pmid38818270, year = {2023}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics.}, journal = {mLife}, volume = {2}, number = {4}, pages = {378-388}, pmid = {38818270}, issn = {2770-100X}, abstract = {Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste-activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long-term operation. In this study, we found that short-term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%-9.0%, whereas higher levels (30-200 particles/g sludge) suppressed methanogenesis by 15.2%-30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long-term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long-term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.}, }
@article {pmid38817815, year = {2023}, author = {Wu, L and Yang, Y and Ning, D and Gao, Q and Yin, H and Xiao, N and Zhou, BY and Chen, S and He, Q and Zhou, J}, title = {Assessing mechanisms for microbial taxa and community dynamics using process models.}, journal = {mLife}, volume = {2}, number = {3}, pages = {239-252}, pmid = {38817815}, issn = {2770-100X}, abstract = {Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.}, }
@article {pmid38816803, year = {2024}, author = {Saeed, S and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Khan, MA and Fahad, S}, title = {Salicylic acid and Tocopherol improve wheat (Triticum aestivum L.) Physio-biochemical and agronomic features grown in deep sowing stress: a way forward towards sustainable production.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {477}, pmid = {38816803}, issn = {1471-2229}, mesh = {*Triticum/growth &amp; development/metabolism/drug effects ; *Salicylic Acid/pharmacology/metabolism ; *Tocopherols/metabolism ; *Germination/drug effects ; Seeds/drug effects/growth &amp; development ; Antioxidants/metabolism ; Stress, Physiological ; Sustainable Development ; Chlorophyll/metabolism ; }, abstract = {BACKGROUND: The rate of germination and other physiological characteristics of seeds that are germinating are impacted by deep sowing. Based on the results of earlier studies, conclusions were drawn that deep sowing altered the physio-biochemical and agronomic characteristics of wheat (Triticum aestivum L.).<br><br>RESULTS: In this study, seeds of wheat were sown at 2 (control) and 6&#xa0;cm depth and the impact of exogenously applied salicylic acid and tocopherol (Vitamin-E) on its physio-biochemical and agronomic features was assessed. As a result, seeds grown at 2&#xa0;cm depth witnessed an increase in mean germination time, germination percentage, germination rate index, germination energy, and seed vigor index. In contrast, 6&#xa0;cm deep sowing resulted in negatively affecting all the aforementioned agronomic characteristics. In addition, deep planting led to a rise in MDA, glutathione reductase, and antioxidants enzymes including APX, POD, and SOD concentration. Moreover, the concentration of chlorophyll a, b, carotenoids, proline, protein, sugar, hydrogen peroxide, and agronomic attributes was boosted significantly with exogenously applied salicylic acid and tocopherol under deep sowing stress.<br><br>CONCLUSIONS: The results of the study showed that the depth of seed sowing has an impact on agronomic and physio-biochemical characteristics and that the negative effects of deep sowing stress can be reduced by applying salicylic acid and tocopherol to the leaves.}, }
@article {pmid38816227, year = {2024}, author = {Carrillo-Barragan, P}, title = {Clean your own house first: integrating sustainability into microbiology labs.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38816227}, issn = {1574-6941}, support = {//University of Basel/ ; }, mesh = {*Laboratories ; Environmental Microbiology ; Sustainable Development ; Microbiology ; Conservation of Natural Resources ; }, abstract = {Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.}, }
@article {pmid38814337, year = {2024}, author = {Filek, K and Vuković, BB and Žižek, M and Kanjer, L and Trotta, A and Di Bello, A and Corrente, M and Bosak, S}, title = {Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {79}, pmid = {38814337}, issn = {1432-184X}, support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; }, mesh = {Animals ; *Turtles/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Microbiota ; Cloaca/microbiology ; Mycobiome ; Biodiversity ; Gastrointestinal Microbiome ; Biofilms ; }, abstract = {Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads' cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.}, }
@article {pmid38814057, year = {2024}, author = {Chen, M and Grégoire, DS and Bain, JG and Blowes, DW and Hug, LA}, title = {Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0014324}, pmid = {38814057}, issn = {1098-5336}, support = {ORF-RE09-061//Ontario Research Fund - Research Excellence/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; //Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Mining ; *Sulfur/metabolism ; *Iron/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Copper/metabolism/analysis ; *Nickel/metabolism ; Ontario ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Biodegradation, Environmental ; }, abstract = {The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.}, }
@article {pmid38812552, year = {2024}, author = {Zhu, W and Chang, L and Zhang, M and Chen, Q and Sui, L and Shen, C and Jiang, J}, title = {Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors.}, journal = {iScience}, volume = {27}, number = {6}, pages = {109907}, pmid = {38812552}, issn = {2589-0042}, abstract = {Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.}, }
@article {pmid38812371, year = {2024}, author = {Liu, J and Wu, Y and Zhang, W and Fahad, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Podosphaera xanthii Causing Powdery Mildew on Salvia farinacea in Central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-24-0591-PDN}, pmid = {38812371}, issn = {0191-2917}, abstract = {Salvia farinacea, commonly referred as mealycup sage, is a perennial herbaceous plant belonging to the Salvia genus of the Lamiaceae family. It originates from the Mediterranean region, North America, and Europe and is globally cultivated due to its appealing and captivating flowers. Moreover, mealycup sage is utilized as traditional Chinese medicinal plant for treatment of cardiovascular diseases (Li et al. 2018). In October 2023, powdery mildew-like symptoms were observed on Salvia farinacea plants cultivated in a garden located in Xinxiang City, Henan Province, China (113.93, 35.29). The leaves were covered with white and thin masses of mycelia, conidiophores and conidia of the fungus. About 100 plants were checked and 90 % were infected. There were a large number of white colonies with irregular or continuous round lesions on the adaxial and abaxial surfaces of the leaves, covering approximately 80% of the leaf area. The slightly or straight curved conidiophores (n = 30) were 46 to 145× 8 to 11 μm in size and consisted of foot cells, shorter cells and conidia. The ellipsoidal to oval conidia (n = 30), containing fibrosin bodies, were 24 to 35 × 12 to 19 μm in size and had a length/width ratio of 1.8 to 2.1. No chasmothecia were observed on leaves. These morphological features were consistent with those of Podosphaera xanthii (Braun and Cook 2012). Following the previously described method (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022a), the sequences of ITS and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3' ; ITS4 5'-TCCTCCGCTTATTGATATGC-3') and PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), and the resulting sequences were uploaded in GenBank (Accession No. OR761885 and PP236082, respectively). BLASTn analysis showed that the sequence shared 560/565 (99%) and 272/272 (100%) homology with P. xanthii (MW301281) on Impatiens balsamina (Zhu et al. 2022b) and with P. xanthii (ON075658) on Cucumis melo (Bradshaw et al. 2022), respectively. The phylogenetic analysis clearly illustrated that the collected isolate of P. xanthii clustered in the same clade. The pathogenicity was tested according to the method previously described (Zhu et al. 2021). The fungus was inoculated onto the leaf surfaces of three healthy plants by blowing conidia from infected leaves with pressurized air. Non-inoculated plants were treated as control. Both the control and inoculated plants were separately placed in growth chambers under 60% humidity; light/dark, 16 h/8 h; and a temperature of 18°C. After a period of 12-15 days, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. Therefore, the fungal pathogen was identified and confirmed as P. xanthii (isolate PXSF202310). Previously, P. xanthii was reported on Impatiens balsamina and S. farinacea from China and Korea (Zhu et al. 2021; Choi et al. 2022). As far as we know, this is the first documentation of P. xanthii on S. farinacea in central China. The presence of P. xanthii can lead to a deterioration in plant health and stunted growth, thereby negatively impacting both the decorative and medicinal value of S. farinacea. The recognition of P. xanthii on S. farinacea enhances our comprehension of this pathogen hosts and provides fundamental information for forthcoming disease control studies.}, }
@article {pmid38812269, year = {2024}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Munoz, F and Tenllado, &#xc1; and Vinyeta, M and Le Roux, X and Vasseur, F}, title = {Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {620-635}, doi = {10.1111/nph.19870}, pmid = {38812269}, issn = {1469-8137}, support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft/ ; ERC-StG-2014-639706-CONSTRAINTS/ERC_/European Research Council/International ; ERC-StG-2020-949843/ERC_/European Research Council/International ; }, mesh = {*Arabidopsis/genetics/metabolism/microbiology ; *Nitrogen Cycle ; *Soil Microbiology ; *Biomass ; Nitrogen/metabolism ; Soil/chemistry ; Genotype ; Nitrification ; Denitrification ; Ecosystem ; }, abstract = {In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.}, }
@article {pmid38811807, year = {2024}, author = {Eliette, AS and Elodie, B and Arnaud, M and Tiffany, R and Aymé, S and Pascal, P}, title = {Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12375}, pmid = {38811807}, issn = {2045-2322}, support = {773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; }, mesh = {*Soil Microbiology ; *Listeria monocytogenes/physiology ; Humans ; *Microbiota ; Klebsiella pneumoniae/physiology ; Temperature ; Biodiversity ; }, abstract = {Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.}, }
@article {pmid38810265, year = {2024}, author = {Li, C and Wang, L and Tong, C and Li, H and Qin, Z and Zeng, X and Chang, Y and Li, M and Yang, Q}, title = {Molecular Insights into the Defense of Dioscorea opposita Cultivar Tiegun Callus Against Pathogenic and Endophytic Fungal Infection Through Transcriptome Analysis.}, journal = {Phytopathology}, volume = {114}, number = {8}, pages = {1893-1903}, doi = {10.1094/PHYTO-04-24-0125-R}, pmid = {38810265}, issn = {0031-949X}, mesh = {*Dioscorea/microbiology/genetics ; *Alternaria/physiology/pathogenicity ; *Plant Diseases/microbiology/immunology ; *Endophytes/physiology/genetics ; Penicillium/genetics/physiology/pathogenicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; }, abstract = {Dioscorea opposita cultivar Tiegun is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of Tiegun were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, whereas P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase, peroxidase, and catalase; thus, the degree of damage to the callus caused by P. halotolerans was weaker than that caused by A. alternata. RNA sequencing analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism, and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.}, }
@article {pmid38808529, year = {2024}, author = {Demircan, T and Gül, S and Taşçı, EA}, title = {Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {6}, pages = {291-302}, doi = {10.1089/omi.2024.0075}, pmid = {38808529}, issn = {1557-8100}, mesh = {Animals ; *Regeneration ; *Microbiota/genetics ; *Ambystoma mexicanum/microbiology/physiology ; *RNA, Ribosomal, 16S/genetics ; *Extremities/microbiology ; Phylogeny ; }, abstract = {The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.}, }
@article {pmid38806848, year = {2024}, author = {Banchi, E and Manna, V and Muggia, L and Celussi, M}, title = {Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {78}, pmid = {38806848}, issn = {1432-184X}, mesh = {*Seawater/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; *RNA, Ribosomal, 18S/genetics/analysis ; Mycobiome ; DNA, Fungal/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA, Ribosomal Spacer/genetics/analysis ; Ascomycota/genetics/classification/isolation &amp; purification ; }, abstract = {Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.}, }
@article {pmid38806738, year = {2024}, author = {Wissner, JL and Parada-Fabián, JC and Márquez-Velázquez, NA and Escobedo-Hinojosa, W and Gaudêncio, SP and Prieto-Davó, A}, title = {Diversity and Bioprospection of Gram-positive Bacteria Derived from a Mayan Sinkhole.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {77}, pmid = {38806738}, issn = {1432-184X}, support = {POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; LA/P/0140/2020//FCT-Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia, IP/ ; PAIP 5000-9149//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico, Facultad de Qu&#xed;mica/ ; A1-S-10785//Consejo Nacional de Ciencia Humanidades y Tecnolog&#xed;a (CONAHCyT) Ciencia B&#xe1;sica/ ; }, mesh = {*Geologic Sediments/microbiology ; Mexico ; *Biodiversity ; *Gram-Positive Bacteria/isolation &amp; purification/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; Bioprospecting ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Seawater/microbiology ; }, abstract = {Water-filled sinkholes known locally as cenotes, found on the Yucatán Peninsula, have remarkable biodiversity. The primary objective of this study was to explore the biotechnological potential of Gram-positive cultivable bacteria obtained from sediment samples collected at the coastal cenote Pol-Ac in Yucatán, Mexico. Specifically, the investigation aimed to assess production of hydrolytic enzymes and antimicrobial compounds. 16 S rRNA gene sequencing led to the identification of 49 Gram-positive bacterial isolates belonging to the phyla Bacillota (n = 29) and Actinomycetota (n = 20) divided into the common genera Bacillus and Streptomyces, as well as the genera Virgibacillus, Halobacillus, Metabacillus, Solibacillus, Neobacillus, Rossellomorea, Nocardiopsis and Corynebacterium. With growth at 55ºC, 21 of the 49 strains were classified as moderately thermotolerant. All strains were classified as halotolerant and 24 were dependent on marine water for growth. Screening for six extracellular hydrolytic enzymes revealed gelatinase, amylase, lipase, cellulase, protease and chitinase activities in 93.9%, 67.3%, 63.3%, 59.2%, 59.2% and 38.8%, of isolated strains, respectively. The genes for polyketide synthases type I, were detected in 24 of the strains. Of 18 strains that achieved > 25% inhibition of growth in the bacterial pathogen Staphylococcus aureus ATCC 6538, 4 also inhibited growth in Escherichia coli ATCC 35,218. Isolates Streptomyces sp. NCA_378 and Bacillus sp. NCA_374 demonstrated 50-75% growth inhibition against at least one of the two pathogens tested, along with significant enzymatic activity across all six extracellular enzymes. This is the first comprehensive report on the biotechnological potential of Gram-positive bacteria isolated from sediments in the cenotes of the Yucatán Peninsula.}, }
@article {pmid38805423, year = {2024}, author = {Fournier, C and Fiedler, A and Weidele, M and Kautz, H and Schleheck, D}, title = {Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303937}, pmid = {38805423}, issn = {1932-6203}, mesh = {*Filtration/instrumentation/methods ; *Plankton/genetics ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Lakes/microbiology ; Phylogeny ; Biomass ; }, abstract = {Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.}, }
@article {pmid38804464, year = {2024}, author = {Lappan, R and Thakar, J and Molares Moncayo, L and Besser, A and Bradley, JA and Goordial, J and Trembath-Reichert, E and Greening, C}, title = {The atmosphere: a transport medium or an active microbial ecosystem?.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38804464}, issn = {1751-7370}, support = {RGY0058/2022//Human Frontier Science Program/ ; }, mesh = {*Atmosphere ; *Ecosystem ; Microbiota ; Air Microbiology ; Biodiversity ; Bacteria/metabolism/classification/growth &amp; development ; }, abstract = {The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.}, }
@article {pmid38804108, year = {2024}, author = {Ochoa-Hueso, R and Eldridge, DJ and Berdugo, M and Trivedi, P and Sokoya, B and Cano-Díaz, C and Abades, S and Alfaro, F and Bamigboye, AR and Bastida, F and Blanco-Pastor, JL and de Los Rios, A and Durán, J and Geisen, S and Grebenc, T and Illán, JG and Liu, YR and Makhalanyane, TP and Mamet, S and Molina-Montenegro, MA and Moreno, JL and Nahberger, TU and Peñaloza-Bojacá, GF and Plaza, C and Rey, A and Rodríguez, A and Siebe, C and Singh, BK and Teixido, AL and Torres-Díaz, C and Wang, L and Wang, J and Wang, J and Zaady, E and Zhou, X and Zhou, XQ and Tedersoo, L and Delgado-Baquerizo, M}, title = {Unearthing the soil-borne microbiome of land plants.}, journal = {Global change biology}, volume = {30}, number = {5}, pages = {e17295}, doi = {10.1111/gcb.17295}, pmid = {38804108}, issn = {1365-2486}, support = {LRB17\1019//British Ecological Society/ ; J4-1766//Slovenian Research Agency/ ; GOPC-CA-20-0001//Junta de Andaluc&#xed;a/ ; P20_00323//Junta de Andaluc&#xed;a/ ; EMC21_00207//Junta de Andaluc&#xed;a/ ; GO2022-01//Junta de Andaluc&#xed;a/ ; PID2019-106004RA-I00//Spanish Ministry of Science and Innovation/ ; PID2020-115813RA-I00//Spanish Ministry of Science and Innovation/ ; TED2021-130908B-C41//Spanish Ministry of Science and Innovation/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Embryophyta ; Biodiversity ; Soil/chemistry ; }, abstract = {Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.}, }
@article {pmid38804043, year = {2024}, author = {Owens, LA and Thurber, MI and Goldberg, TL}, title = {CRISPR-Cas9-mediated host signal reduction for 18S metabarcoding of host-associated eukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13980}, pmid = {38804043}, issn = {1755-0998}, support = {R01 AG049395/AG/NIA NIH HHS/United States ; R37 AG049395/AG/NIA NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; 1R21AI163592-01/HI/NHLBI NIH HHS/United States ; T32AI007414/HI/NHLBI NIH HHS/United States ; 1R01AG049395-01/HI/NHLBI NIH HHS/United States ; R21 AI163592/AI/NIAID NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; *Eukaryota/genetics ; *DNA Barcoding, Taxonomic/methods ; *RNA, Ribosomal, 18S/genetics ; Metagenomics/methods ; Humans ; Animals ; }, abstract = {Metabarcoding-based methods for identification of host-associated eukaryotes have the potential to revolutionize parasitology and microbial ecology, yet significant technical challenges remain. In particular, highly abundant host reads can mask the presence of less-abundant target organisms, especially for sample types rich in host DNA (e.g., blood and tissues). Here, we present a new CRISPR-Cas9-mediated approach designed to reduce host signal by selective amplicon digestion, thus enriching clinical samples for eukaryotic endosymbiont sequences during metabarcoding. Our method achieves a nearly 76% increased efficiency in host signal reduction compared with no treatment and a nearly 60% increased efficiency in host signal reduction compared with the most commonly used published method. Furthermore, the application of our method to clinical samples allows for the detection of parasite infections that would otherwise have been missed.}, }
@article {pmid38802328, year = {2024}, author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM}, title = {Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {23}, pages = {10216-10226}, doi = {10.1021/acs.est.3c10423}, pmid = {38802328}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.}, }
@article {pmid38801800, year = {2024}, author = {Oesterle, I and Ayeni, KI and Ezekiel, CN and Berry, D and Rompel, A and Warth, B}, title = {Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome.}, journal = {Environment international}, volume = {188}, number = {}, pages = {108766}, doi = {10.1016/j.envint.2024.108766}, pmid = {38801800}, issn = {1873-6750}, support = {P 32326/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Nigeria ; *Milk, Human/chemistry/microbiology ; Infant ; Female ; *Feces/microbiology/chemistry ; Exposome ; Xenobiotics/analysis ; Infant, Newborn ; RNA, Ribosomal, 16S ; Environmental Pollutants/analysis ; Adult ; Male ; }, abstract = {Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants' diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.}, }
@article {pmid38801423, year = {2024}, author = {Ramírez-Pool, JA and Calderón-Pérez, B and Ruiz-Medrano, R and Ortiz-Castro, R and Xoconostle-Cazares, B}, title = {Bacillus Strains as Effective Biocontrol Agents Against Phytopathogenic Bacteria and Promoters of Plant Growth.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {76}, pmid = {38801423}, issn = {1432-184X}, mesh = {*Bacillus/physiology ; *Arabidopsis/microbiology/growth &amp; development ; *Plant Diseases/prevention &amp; control/microbiology ; Quorum Sensing ; Chromobacterium/physiology/growth &amp; development ; Biological Control Agents/pharmacology ; Plant Development ; Seedlings/microbiology/growth &amp; development ; Soil Microbiology ; }, abstract = {Modern crop production relies on the application of chemical pesticides and fertilizers causing environmental and economic challenges. In response, less environmentally impactful alternatives have emerged such as the use of beneficial microorganisms. These microorganisms, particularly plant growth-promoting bacteria (PGPB), have demonstrated their ability to enhance plant growth, protect against various stresses, and reduce the need for chemical inputs. Among the PGPB, Bacillus species have garnered attention due to their adaptability and commercial potential. Recent reports have highlighted Bacillus strains as biocontrol agents against phytopathogenic bacteria while concurrently promoting plant growth. We also examined Bacillus plant growth-promoting abilities in Arabidopsis thaliana seedlings. In this study, we assessed the potential of various Bacillus strains to control diverse phytopathogenic bacteria and inhibit quorum sensing using Chromobacterium violaceum as a model system. In conclusion, our results suggest that bacteria of the genus Bacillus hold significant potential for biotechnological applications. This includes developments aimed at reducing agrochemical use, promoting sustainable agriculture, and enhancing crop yield and protection.}, }
@article {pmid38801001, year = {2024}, author = {Timmis, K and Hallsworth, JE and McGenity, TJ and Armstrong, R and Colom, MF and Karahan, ZC and Chavarría, M and Bernal, P and Boyd, ES and Ramos, JL and Kaltenpoth, M and Pruzzo, C and Clarke, G and López-Garcia, P and Yakimov, MM and Perlmutter, J and Greening, C and Eloe-Fadrosh, E and Verstraete, W and Nunes, OC and Kotsyurbenko, O and Nikel, PI and Scavone, P and Häggblom, MM and Lavigne, R and Le Roux, F and Timmis, JK and Parro, V and Michán, C and García, JL and Casadevall, A and Payne, SM and Frey, J and Koren, O and Prosser, JI and Lahti, L and Lal, R and Anand, S and Sood, U and Offre, P and Bryce, CC and Mswaka, AY and Jores, J and Kaçar, B and Blank, LM and Maaßen, N and Pope, PB and Banciu, HL and Armitage, J and Lee, SY and Wang, F and Makhalanyane, TP and Gilbert, JA and Wood, TK and Vasiljevic, B and Soberón, M and Udaondo, Z and Rojo, F and Tamang, JP and Giraud, T and Ropars, J and Ezeji, T and Müller, V and Danbara, H and Averhoff, B and Sessitsch, A and Partida-Martínez, LP and Huang, W and Molin, S and Junier, P and Amils, R and Wu, XL and Ron, E and Erten, H and de Martinis, ECP and Rapoport, A and Öpik, M and Pokatong, WDR and Stairs, C and Amoozegar, MA and Serna, JG}, title = {A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society.}, journal = {Microbial biotechnology}, volume = {17}, number = {5}, pages = {e14456}, pmid = {38801001}, issn = {1751-7915}, mesh = {*Microbiology/education ; Humans ; Biotechnology ; }, abstract = {EXECUTIVE SUMMARY: Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient.<br><br>ABSTRACT: The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.}, }
@article {pmid38799067, year = {2024}, author = {Vargas-Sánchez, M and Alcocer, J and Puche, E and Sánchez-Carrillo, S}, title = {Abiotic processes control carbon dioxide dynamics in temperate karst lakes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17393}, pmid = {38799067}, issn = {2167-8359}, mesh = {*Lakes/chemistry ; *Carbon Dioxide/analysis/metabolism ; Spain ; *Seasons ; Environmental Monitoring/methods ; Carbon Cycle ; Phytoplankton/metabolism ; }, abstract = {Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ[13]C-DIC, δ[13]C-CO2 in lake waters, and δ[13]C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36-2.26 µmol L[-1]). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ[13]C-DIC signatures below -12‰ confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ[13]C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ[13]C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO3[2-] ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth's surface but seem essential in the CO2 dynamics at a global scale.}, }
@article {pmid38798771, year = {2024}, author = {Mahalak, KK and Liu, L and Bobokalonov, J and Narrowe, AB and Firrman, J and Bittinger, K and Hu, W and Jones, SM and Moustafa, AM}, title = {Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1304045}, pmid = {38798771}, issn = {2296-861X}, abstract = {INTRODUCTION: Studies have shown that a diet high in fiber and prebiotics has a positive impact on human health due largely to the fermentation of these compounds by the gut microbiota. One underutilized source of fiber may be rice bran, a waste product of rice processing that is used most frequently as an additive to livestock feed but may be a good source of fibers and other phenolic compounds as a human diet supplement. Previous studies focused on specific compounds extracted from rice bran showed that soluble fibers extracted from rice bran can improve glucose response and reduce weight gain in mouse models. However, less is known about changes in the human gut microbiota in response to regular rice bran consumption.<br><br>METHODS: In this study, we used a Simulator of the Human Intestinal Microbial Ecology (SHIME&#xae;) to cultivate the human gut microbiota of 3 different donors in conditions containing either soluble or insoluble fiber fractions from rice bran. Using 16S rRNA amplicon sequencing and targeted metabolomics via Gas Chromatography-Mass Spectrometry, we explored how gut microbial communities developed provided different supplemental fiber sources.<br><br>RESULTS: We found that insoluble and soluble fiber fractions increased short-chain fatty acid production, indicating that both fractions were fermented. However, there were differences in response between donors, for example the gut microbiota from donor 1 increased acetic acid production with both fiber types compared with control; whereas for donors 2 and 3, butanoic acid production increased with ISF and SF supplementation. Both soluble and insoluble rice bran fractions increased the abundance of Bifidobacterium and Lachnospiraceae taxa.<br><br>DISCUSSION: Overall, analysis of the effect of soluble and insoluble rice bran fractions on the human in vitro gut microbiota and the metabolites produced revealed individually variant responses to these prebiotics.}, }
@article {pmid38798271, year = {2024}, author = {Almeida-Silva, F and Prost-Boxoen, L and Van de Peer, Y}, title = {hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {811-819}, pmid = {38798271}, issn = {1469-8137}, support = {833522/ERC_/European Research Council/International ; 833522//H2020 European Research Council/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; }, mesh = {*Software ; *Hybridization, Genetic ; *Gene Expression Profiling ; *Oryza/genetics ; *Transcriptome/genetics ; Gossypium/genetics ; Hybrid Vigor/genetics ; Gene Expression Regulation, Plant ; Plant Roots/genetics ; Polyploidy ; }, abstract = {Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).}, }
@article {pmid38794902, year = {2024}, author = {Fricker, AD and Yao, T and Lindemann, SR and Flores, GE}, title = {Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38794902}, issn = {1574-6941}, support = {SC1 GM136546/GM/NIGMS NIH HHS/United States ; SC1GM136546/NH/NIH HHS/United States ; }, mesh = {Humans ; *Mucins/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbial Consortia ; *Fermentation ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Akkermansia/metabolism ; Desulfovibrio/metabolism/genetics/classification ; Bacteroides/metabolism/genetics/classification/growth &amp; development ; }, abstract = {Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.}, }
@article {pmid38792792, year = {2024}, author = {Jiao, F and Qian, L and Wu, J and Zhang, D and Zhang, J and Wang, M and Sui, X and Zhang, X}, title = {Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792792}, issn = {2076-2607}, support = {LBH-Q21167//Heilongjiang Province Postdoctoral Research Start-up Fund Project/ ; }, abstract = {To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.}, }
@article {pmid38790992, year = {2024}, author = {Roszkowska, P and Klimczak, E and Ostrycharz, E and Rączka, A and Wojciechowska-Koszko, I and Dybus, A and Cheng, YH and Yu, YH and Mazgaj, S and Hukowska-Szematowicz, B}, title = {Small Intestinal Bacterial Overgrowth (SIBO) and Twelve Groups of Related Diseases-Current State of Knowledge.}, journal = {Biomedicines}, volume = {12}, number = {5}, pages = {}, pmid = {38790992}, issn = {2227-9059}, abstract = {The human gut microbiota creates a complex microbial ecosystem, characterized by its high population density, wide diversity, and complex interactions. Any imbalance of the intestinal microbiome, whether qualitative or quantitative, may have serious consequences for human health, including small intestinal bacterial overgrowth (SIBO). SIBO is defined as an increase in the number of bacteria (10[3]-10[5] CFU/mL), an alteration in the bacterial composition, or both in the small intestine. The PubMed, Science Direct, Web of Science, EMBASE, and Medline databases were searched for studies on SIBO and related diseases. These diseases were divided into 12 groups: (1) gastrointestinal disorders; (2) autoimmune disease; (3) cardiovascular system disease; (4) metabolic disease; (5) endocrine disorders; (6) nephrological disorders; (7) dermatological diseases; (8) neurological diseases (9); developmental disorders; (10) mental disorders; (11) genetic diseases; and (12) gastrointestinal cancer. The purpose of this comprehensive review is to present the current state of knowledge on the relationships between SIBO and these 12 disease groups, taking into account risk factors and the causal context. This review fills the evidence gap on SIBO and presents a biological-medical approach to the problem, clearly showing the groups and diseases having a proven relationship with SIBO, as well as indicating groups within which research should continue to be expanded.}, }
@article {pmid38790880, year = {2024}, author = {Ding, Y and Wang, L and Wang, H and Li, H}, title = {Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {38790880}, issn = {2304-8158}, support = {LYNJ202110//research and application of key technologies for sustainable development of wine industry/ ; }, abstract = {The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.}, }
@article {pmid38790838, year = {2024}, author = {Ayed, L and M'hir, S and Nuzzolese, D and Di Cagno, R and Filannino, P}, title = {Harnessing the Health and Techno-Functional Potential of Lactic Acid Bacteria: A Comprehensive Review.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {38790838}, issn = {2304-8158}, abstract = {This review examines the techno-functional properties of lactic acid bacteria (LABs) in the food industry, focusing on their potential health benefits. We discuss current findings related to the techno-functionality of LAB, which includes acidification, proteolytic and lipolytic features, and a variety of other biochemical activities. These activities include the production of antimicrobial compounds and the synthesis of exopolysaccharides that improve food safety and consumer sensory experience. LABs are also known for their antioxidant abilities, which help reduce oxidative reactions in foods and improve their functional properties. In addition, LABs' role as probiotics is known for their promising effects on gut health, immune system modulation, cholesterol control, and general wellbeing. Despite these advantages, several challenges hinder the effective production and use of probiotic LABs, such as maintaining strain viability during storage and transport as well as ensuring their efficacy in the gastrointestinal tract. Our review identifies these critical barriers and suggests avenues for future research.}, }
@article {pmid38788571, year = {2024}, author = {Liu, J and Zhao, R and Feng, J and Fu, W and Cao, L and Zhang, J and Lei, Y and Liang, J and Lin, L and Li, X and Li, B}, title = {Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134613}, doi = {10.1016/j.jhazmat.2024.134613}, pmid = {38788571}, issn = {1873-3336}, mesh = {*Drinking Water/microbiology ; *Bacteria/classification/genetics/metabolism ; *Water Purification/methods ; *Water Microbiology ; Halogenation ; Filtration ; Biodiversity ; Water Supply ; }, abstract = {Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.}, }
@article {pmid38786909, year = {2024}, author = {Jawień, P and Pfitzner, WP and Schaffner, F and Kiewra, D}, title = {Mosquitoes (Diptera: Culicidae) of Poland: An Update of Species Diversity and Current Challenges.}, journal = {Insects}, volume = {15}, number = {5}, pages = {}, pmid = {38786909}, issn = {2075-4450}, abstract = {This article presents the current state of knowledge of mosquito species (Diptera: Culicidae) occurring in Poland. In comparison to the most recently published checklists (1999 and 2007), which listed 47 mosquito species, four species (Aedes japonicus, Anopheles daciae, Anopheles hyrcanus, and Anopheles petragnani) are added to the Polish fauna. Our new checklist of Polish mosquito fauna includes 51 species of mosquitoes from five genera: Aedes (30), Anopheles (8), Coquillettidia (1), Culiseta (7), and Culex (5). Aspects of the ecology and biology of the Polish mosquito fauna, with particular emphasis on newly recorded species, are discussed.}, }
@article {pmid38786897, year = {2024}, author = {Dyczko, D and Plewa-Tutaj, K and Kiewra, D}, title = {Entomopathogenic Fungi in Forest Habitats of Ixodes ricinus.}, journal = {Insects}, volume = {15}, number = {5}, pages = {}, pmid = {38786897}, issn = {2075-4450}, abstract = {(1) Background: In addition to the microclimate, host availability, and tick microbiota, soil environmental microorganisms can affect tick populations. This study aimed to (1) determine the presence and diversity of entomopathogenic fungi (EF) in forests, where ticks are abundant, and (2) estimate the effectiveness of the isolated EF strains against Ixodes ricinus. (2) Methods: EF were isolated using the trap insect method from soil collected from tick sites. A bioassay was used to estimate the effectiveness of EF against ticks. (3) Results: The presence of EF was found in all tested forest habitat types. A total of 53 strains belonging to the genera Metarhizium, Beauveria, and Isaria were isolated. All the six strains subjected to the bioassay showed potential efficacy against both adult and nymphal stages of I. ricinus; however, the strains differed in their effectiveness. The most effective isolate against I. ricinus was the soil environmental strain of Metarhizium anisopliae. (4) Conclusion: The study indicates that tick habitats can be the source of entomopathogenic fungi, which have a lethal effect on ticks, as demonstrated in preliminary laboratory tests with I. ricinus. However, for practical use, extensive field tests and further research on application methods and long-term effects are necessary to develop effective and sustainable tick management strategies.}, }
@article {pmid38782346, year = {2024}, author = {Liu, Y and Delgado-Baquerizo, M and Bing, H and Wang, Y and Wang, J and Chen, J and Qiu, S and Zhu, H and Wu, Y and Fang, L and Chang, R}, title = {Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights.}, journal = {Environmental research}, volume = {255}, number = {}, pages = {119206}, doi = {10.1016/j.envres.2024.119206}, pmid = {38782346}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Microbiota ; Tibet ; Soil/chemistry ; Global Warming ; Ecosystem ; Altitude ; Climate Change ; }, abstract = {Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.}, }
@article {pmid38781750, year = {2024}, author = {Bouchali, R and Mandon, C and Danty-Berger, E and Géloën, A and Marjolet, L and Youenou, B and Pozzi, ACM and Vareilles, S and Galia, W and Kouyi, GL and Toussaint, JY and Cournoyer, B}, title = {Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns.}, journal = {International journal of hygiene and environmental health}, volume = {260}, number = {}, pages = {114391}, doi = {10.1016/j.ijheh.2024.114391}, pmid = {38781750}, issn = {1618-131X}, mesh = {*Rain ; Humans ; *Microbiota ; *Water Microbiology ; *Cities ; *Bacteria/isolation &amp; purification/classification/genetics ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.}, }
@article {pmid38780093, year = {2024}, author = {Beaver, RC and Neufeld, JD}, title = {Microbial ecology of the deep terrestrial subsurface.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38780093}, issn = {1751-7370}, support = {//Nuclear Waste Management Organization/ ; //Ontario Research Fund: Research Excellence/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Archaea/classification/isolation &amp; purification/metabolism ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; *Soil Microbiology ; Microbiota ; Ecosystem ; }, abstract = {The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.}, }
@article {pmid38779669, year = {2024}, author = {Kou, Z and Liu, K and Qiao, Z and Wang, Y and Li, Y and Li, Y and Yu, X and Han, W}, title = {The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1407439}, pmid = {38779669}, issn = {1664-3224}, mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; Humans ; *Gastrointestinal Microbiome ; Mouth/microbiology ; Microbiota ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.<br><br>METHODS: A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.<br><br>RESULTS: A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, Prevotella, Streptococcus, Actinomyces, and Veillonella of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that Haemophilus, Lactobacillus, and Pseudomonas were increased, but Veillonella, Prevotella, Actinomyces, Porphyromonas, and Atopobium were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of Haemophilus, Lactobacillus and Pseudomonas genera exhibited an increase, whereas Actinomyces and Porphyromonas showed a decrease in the airway microbiota of AECOPD compared to HC. And Lachnospira of intestine microbiota in SCOPD was reduced at the genus level.<br><br>CONCLUSION: The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.<br><br>PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.}, }
@article {pmid38779326, year = {2024}, author = {Mellouk, A and Mahmood, T and Jlali, M and Vieco-Saiz, N and Michel, V and Cozannet, P and Ozbek, S and Mercier, Y and Devillard, E and Consuegra, J}, title = {Potential of guar gum as a leaky gut model in broilers: Digestibility, performance, and microbiota responses.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {17}, number = {}, pages = {177-187}, pmid = {38779326}, issn = {2405-6383}, abstract = {Diet is a major modulator of animal resilience and its three pillars: host's immune response, gut microbiota, and intestinal barrier. In the present study, we endeavour to delineate a challenging condition aimed to degrade these pillars and elucidate its impact on broiler performance and nutrient digestibility. To attain this objective, we opted to use guar gum (GG) as a source of galactomannan. A series of three in vivo experiments were conducted employing conventional or semi-purified diets, supplemented with or without GG during the grower phase (14-28 d). Our findings demonstrate a substantial decline in animal performance metrics such as body weight (reduced by 29%, P < 0.001), feed intake (decreased by 12%, P < 0.001), and feed conversion ratio (up to 58% increase, P < 0.001) in the presence of GG at 2%. The supplementation of a semi-purified diet with incremental doses of GG resulted in a linear reduction (P < 0.001) in the apparent total tract digestibility of dry matter and apparent metabolisable energy. Additionally, a marked reduction in ileal endogenous losses, as well as apparent and standardised digestibility of all amino acids with varying proportions (P < 0.05), was observed. These alterations were accompanied by disrupted gut integrity assessed by fluorescein isothiocyanate-dextran (FITC-d) (P < 0.001) as well as an inflammatory status characterised by elevated levels of acute-phase proteins, namely orosomucoid and serum amyloid A in the sera (P = 0.03), and increased mRNA expression levels of IL-1, IL-6, IL-8, Inos, and K203 genes in the ileum, along with a decrease in IgA levels in the gut lumen (P < 0.05). Microbial ecology and activity were characterised by reduced diversity and richness (Shannon index, P = 0.005) in the presence of GG. Consequently, our results revealed diminished levels of short-chain fatty acids (P = 0.01) and their producer genera, such as Clostridium_XIVa and Blautia, in the gut caeca, coupled with excessive accumulation of lactate (17-fold increase, P < 0.01) in the presence of GG at 2%. In addition to providing a more comprehensive characterisation of the GG supplementation as a leaky gut model, our results substantiate a thorough understanding of the intricate adjustments and interplay between the intestinal barrier, immune response, and microbiota. Furthermore, they underscore the significance of feed components in modulating these dynamics.}, }
@article {pmid38779128, year = {2024}, author = {Eckmann, CA and Bachy, C and Wittmers, F and Strauss, J and Blanco-Bercial, L and Vergin, KL and Parsons, RJ and Kudela, RM and Johnson, R and Bolaños, LM and Giovannoni, SJ and Carlson, CA and Worden, AZ}, title = {Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {266}, pmid = {38779128}, issn = {2662-4435}, abstract = {Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46 ± 24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.}, }
@article {pmid38775958, year = {2024}, author = {Starr, K and Montesanto, F and Perisho, E and Aluthge, N and Pegg, M and Fernando, SC}, title = {Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {75}, pmid = {38775958}, issn = {1432-184X}, support = {20-121 &amp; 18-176//Nebraska Environmental Trust/ ; 20-121 &amp; 18-176//Nebraska Environmental Trust/ ; NC 1189//National Institute of Food and Agriculture/ ; 2022-33522-38219//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics ; *Cyprinidae/microbiology ; *Rivers/microbiology ; RNA, Ribosomal, 16S/genetics ; Nebraska ; }, abstract = {The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.}, }
@article {pmid38773211, year = {2024}, author = {Fischer, FC and Schulze-Makuch, D and Heinz, J}, title = {Microbial preference for chlorate over perchlorate under simulated shallow subsurface Mars-like conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11537}, pmid = {38773211}, issn = {2045-2322}, support = {455070607//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Perchlorates/metabolism ; *Mars ; *Chlorates/metabolism ; *Extraterrestrial Environment ; Aspergillus niger/metabolism ; Saccharomycetales/metabolism ; Water/chemistry ; Microbial Viability ; }, abstract = {The Martian surface and shallow subsurface lacks stable liquid water, yet hygroscopic salts in the regolith may enable the transient formation of liquid brines. This study investigated the combined impact of water scarcity, UV exposure, and regolith depth on microbial survival under Mars-like environmental conditions. Both vegetative cells of Debaryomyces hansenii and Planococcus halocryophilus, alongside with spores of Aspergillus niger, were exposed to an experimental chamber simulating Martian environmental conditions (constant temperatures of about - 11 °C, low pressure of approximately 6 mbar, a CO2 atmosphere, and 2 h of daily UV irradiation). We evaluated colony-forming units (CFU) and water content at three different regolith depths before and after exposure periods of 3 and 7 days, respectively. Each organism was tested under three conditions: one without the addition of salts to the regolith, one containing sodium chlorate, and one with sodium perchlorate. Our results reveal that the residual water content after the exposure experiments increased with regolith depth, along with the organism survival rates in chlorate-containing and salt-free samples. The survival rates of the three organisms in perchlorate-containing regolith were consistently lower for all organisms and depths compared to chlorate, with the most significant difference being observed at a depth of 10-12 cm, which corresponds to the depth with the highest residual water content. The postulated reason for this is an increase in the salt concentration at this depth due to the freezing of water, showing that for these organisms, perchlorate brines are more toxic than chlorate brines under the experimental conditions. This underscores the significance of chlorate salts when considering the habitability of Martian environments.}, }
@article {pmid38773116, year = {2024}, author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ}, title = {Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4339}, pmid = {38773116}, issn = {2041-1723}, support = {201706990001//China Scholarship Council (CSC)/ ; E032-2017-01 55851//CONCYTEC | Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (Cienciactiva)/ ; }, mesh = {*Nicotiana/immunology/microbiology/genetics/metabolism ; *Plant Proteins/metabolism/genetics ; *Plant Immunity/genetics ; *Protein Serine-Threonine Kinases/metabolism/genetics ; *Plant Diseases/microbiology/immunology ; Phytophthora/pathogenicity ; Protein Kinases/metabolism/genetics ; Phosphorylation ; Gene Expression Regulation, Plant ; Reactive Oxygen Species/metabolism ; Signal Transduction ; }, abstract = {Cell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, -7, and -8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.}, }
@article {pmid38772810, year = {2024}, author = {Zai, X and Cordovez, V and Zhu, F and Zhao, M and Diao, X and Zhang, F and Raaijmakers, JM and Song, C}, title = {C4 cereal and biofuel crop microbiomes.}, journal = {Trends in microbiology}, volume = {32}, number = {11}, pages = {1119-1131}, doi = {10.1016/j.tim.2024.04.008}, pmid = {38772810}, issn = {1878-4380}, mesh = {*Biofuels/microbiology ; *Microbiota/physiology ; *Edible Grain/microbiology ; *Crops, Agricultural/microbiology ; Setaria Plant/genetics/microbiology ; Climate Change ; }, abstract = {Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.}, }
@article {pmid38771894, year = {2024}, author = {Van Hee, S and Alınç, T and Weldegergis, BT and Dicke, M and Colazza, S and Peri, E and Jacquemyn, H and Cusumano, A and Lievens, B}, title = {Differential effects of plant-beneficial fungi on the attraction of the egg parasitoid Trissolcus basalis in response to Nezara viridula egg deposition.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0304220}, pmid = {38771894}, issn = {1932-6203}, mesh = {Animals ; *Beauveria/physiology ; *Capsicum/parasitology/microbiology ; *Wasps/physiology ; *Oviposition ; Volatile Organic Compounds/metabolism ; Female ; Trichoderma/physiology ; Host-Parasite Interactions ; Ovum ; Herbivory ; }, abstract = {There is increasing evidence that plant-associated microorganisms play important roles in defending plants against insect herbivores through both direct and indirect mechanisms. While previous research has shown that these microbes can modify the behaviour and performance of insect herbivores and their natural enemies, little is known about their effect on egg parasitoids which utilize oviposition-induced plant volatiles to locate their hosts. In this study, we investigated how root inoculation of sweet pepper (Capsicum annuum) with the plant-beneficial fungi Beauveria bassiana ARSEF 3097 or Trichoderma harzianum T22 influences the olfactory behaviour of the egg parasitoid Trissolcus basalis following egg deposition by its host Nezara viridula. Olfactometer assays showed that inoculation by T. harzianum significantly enhanced the attraction of the egg parasitoid, while B. bassiana had the opposite effect. However, no variation was observed in the chemical composition of plant volatiles. Additionally, fitness-related traits of the parasitoids (wasp body size) were not altered by any of the two fungi, suggesting that fungal inoculation did not indirectly affect host quality. Altogether, our results indicate that plant inoculation with T. harzianum T22 can be used to enhance attraction of egg parasitoids, which could be a promising strategy in manipulating early plant responses against pest species and improving sustainable crop protection. From a more fundamental point of view, our findings highlight the importance of taking into account the role of microorganisms when studying the intricate interactions between plants, herbivores and their associated egg parasitoids.}, }
@article {pmid38771538, year = {2024}, author = {Song, S and Sun, Z and Xu, G and Xu, H}, title = {Continuous warming drives the colonization dynamics of periphytic ciliate fauna in marine environments.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {25}, pages = {37326-37336}, pmid = {38771538}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; }, mesh = {*Ciliophora/physiology ; *Global Warming ; *Ecosystem ; Temperature ; }, abstract = {In order to evaluate the influence of global warming on the ecosystem processes in marine environments, the changes in colonization dynamics of periphytic microbiota were studied using the periphytic ciliate communities as the test organism fauna under a continuous warming gradient of 22℃ (control), 25℃, 28℃, 31℃, and 34 ℃. The results demonstrated that (1) the test ciliate communities generally showed a similar temporal pattern in within the colonization process under the water temperatures from 22 up to 28℃; however, (2) the colonization dynamics were significantly changed, and the fitness of colonization curves to the MacArthur-Wilson model equation was failed under the temperature increased by 6 ℃, and (3) the loading or assimilative capacity of the test aquatic ecosystem was decreased with the increase of water temperature. Therefore, this study suggests that continuous warming may significantly drive the colonization dynamics of periphytic ciliates in marine ecosystems.}, }
@article {pmid38771339, year = {2024}, author = {Jiao, Y and Zhang, G and Ai, X and Wang, X}, title = {Comparison of the Effects of LDPE and PBAT Film Residues on Soil Microbial Ecology.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {185}, pmid = {38771339}, issn = {1432-0991}, support = {52200109//National Natural Science Foundation of China/ ; 202102310278//State Scholarship Fund and the Key R&amp;D and Promotion Project of Henan Province/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Polyethylene/chemistry ; Polyesters/metabolism ; Soil/chemistry ; Soil Pollutants/analysis ; Microbiota ; }, abstract = {The plastic film is extensively applied with limited recycling, leading to the long-run residue accumulation in soil, which offers a distinctive habitat for microorganisms, and creates a plastisphere. In this study, traditional low-density polyethylene (LDPE) plastic film and biodegradable polybutylene adipate terephthalate (PBAT) plastic film materials were selected to test their effects on soil microbial ecology. Based on high-throughput sequencing, compared to the soil environment, the alpha-diversity of bacterial communities in plastisphere was lower, and the abundance of Actinobacteria increased. Plastic film residues, as bacterial habitats, exhibited greater heterogeneity and harbor unique bacterial communities. The communities were distinguished between plastisphere and soil environment by means of a random-forest (RF) machine-learning model. Prominent distinctions emerged among bacterial functions between soil environment and plastisphere, especially regarding organics degradation. The neutral model and null model indicated that the constitution of bacterial communities was dominated by random processes except in LDPE plastisphere. The bacterial co-occurrence network of the plastisphere exhibited higher complexity and modularity. This study contributes to our comprehending of characteristics of plastisphere bacterial communities in soil environment and the associated ecological risks of plastic film residues accumulation.}, }
@article {pmid38771320, year = {2024}, author = {Wang, Y and Zou, Q}, title = {Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {74}, pmid = {38771320}, issn = {1432-184X}, support = {62102269, 62373080//National Natural Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/genetics/classification/physiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Adaptation, Physiological ; Ecosystem ; Bacterial Physiological Phenomena ; }, abstract = {Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.}, }
@article {pmid38765607, year = {2024}, author = {Wu, S and Qu, Z and Chen, D and Wu, H and Caiyin, Q and Qiao, J}, title = {Deciphering and designing microbial communities by genome-scale metabolic modelling.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {1990-2000}, pmid = {38765607}, issn = {2001-0370}, abstract = {Microbial communities are shaped by the complex interactions among organisms and the environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the complexity and ecological properties of various microbial communities, revealing their intricate interactions. Many researchers have modified GEMs for the microbial communities based on specific needs. Thus, GEMs need to be comprehensively summarized to better understand the trends in their development. In this review, we summarized the key developments in deciphering and designing microbial communities using different GEMs. A timeline of selected highlights in GEMs indicated that this area is evolving from the single-strain level to the microbial community level. Then, we outlined a framework for constructing GEMs of microbial communities. We also summarized the models and resources of static and dynamic community-level GEMs. We focused on the role of external environmental and intracellular resources in shaping the assembly of microbial communities. Finally, we discussed the key challenges and future directions of GEMs, focusing on the integration of GEMs with quorum sensing mechanisms, microbial ecology interactions, machine learning algorithms, and automatic modeling, all of which contribute to consortia-based applications in different fields.}, }
@article {pmid38763283, year = {2024}, author = {Liu, S and Shi, Y and Chen, J and Zhang, Z and Cao, H and Li, W and Ye, M}, title = {Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic.}, journal = {Environmental research}, volume = {253}, number = {}, pages = {119153}, doi = {10.1016/j.envres.2024.119153}, pmid = {38763283}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/genetics/classification/drug effects ; China ; Stochastic Processes ; Microbiota/drug effects ; }, abstract = {Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.}, }
@article {pmid38762502, year = {2024}, author = {Awala, SI and Gwak, JH and Kim, Y and Jung, MY and Dunfield, PF and Wagner, M and Rhee, SK}, title = {Nitrous oxide respiration in acidophilic methanotrophs.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4226}, pmid = {38762502}, issn = {2041-1723}, mesh = {*Nitrous Oxide/metabolism ; *Methane/metabolism ; Hydrogen-Ion Concentration ; Oxidoreductases/metabolism/genetics ; Oxygen/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Methanol/metabolism ; Hydrogen/metabolism ; Oxygenases/metabolism/genetics ; }, abstract = {Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.}, }
@article {pmid38762482, year = {2024}, author = {Min, K and Glowacki, AJ and Bosma, ML and McGuire, JA and Tian, S and McAdoo, K and DelSasso, A and Fourre, T and Gambogi, RJ and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {578}, pmid = {38762482}, issn = {1472-6831}, mesh = {Humans ; *Mouthwashes/therapeutic use ; *Oils, Volatile/therapeutic use/pharmacology ; *Dental Plaque/microbiology ; *Microbiota/drug effects ; Adult ; *Gingivitis/microbiology/prevention &amp; control ; Male ; Female ; Anti-Infective Agents, Local/therapeutic use ; Salicylates/therapeutic use ; Young Adult ; Middle Aged ; Drug Combinations ; Terpenes ; }, abstract = {BACKGROUND: The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome.<br><br>METHODS: In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE&#xae; Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards.<br><br>RESULTS: Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use.<br><br>CONCLUSIONS: By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.}, }
@article {pmid38761763, year = {2024}, author = {Wang, Z and Lü, C and Wang, Y and Gomes, RL and Clarke, CJ and Gomes, HI}, title = {Zero-valent iron (ZVI) facilitated in-situ selenium (Se) immobilization and its recovery by magnetic separation: Mechanisms and implications for microbial ecology.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134591}, doi = {10.1016/j.jhazmat.2024.134591}, pmid = {38761763}, issn = {1873-3336}, mesh = {*Selenium/chemistry ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; *Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/genetics ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Magnetic Phenomena ; }, abstract = {Selenium (Se(VI)) is environmentally toxic. One of the most popular reducing agents for Se(VI) remediation is zero-valent iron (ZVI). However, most ZVI studies were carried out in water matrices, and the recovery of reduced Se has not been investigated. A water-sediment system constructed using natural sediment was employed here to study in-situ Se remediation and recovery. A combined effect of ZVI and unacclimated microorganisms from natural sediment was found in Se(VI) removal in the water phase with a removal efficiency of 92.7 ± 1.1% within 7 d when 10 mg L[-1] Se(VI) was present. Soluble Se(VI) was removed from the water and precipitated to the sediment phase (74.8 ± 0.1%), which was enhanced by the addition of ZVI (83.3 ± 0.3%). The recovery proportion of the immobilized Se was 34.2 ± 0.1% and 92.5 ± 0.2% through wet and dry magnetic separation with 1 g L[-1] ZVI added, respectively. The 16 s rRNA sequencing revealed the variations in the microbial communities in response to ZVI and Se, which the magnetic separation could potentially mitigate in the long term. This study provides a novel technique to achieve in-situ Se remediation and recovery by combining ZVI reduction and magnetic separation.}, }
@article {pmid38760758, year = {2024}, author = {Min, K and Bosma, ML and John, G and McGuire, JA and DelSasso, A and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {575}, pmid = {38760758}, issn = {1472-6831}, mesh = {Humans ; *Dental Plaque/microbiology ; *Gingivitis/microbiology ; *Mouthwashes/therapeutic use ; Female ; *Microbiota/drug effects ; Adult ; *Toothbrushing/methods ; Male ; *Dental Devices, Home Care ; Single-Blind Method ; Middle Aged ; Salicylates/therapeutic use ; Drug Combinations ; Terpenes/therapeutic use/pharmacology ; Bacterial Load/drug effects ; Anti-Infective Agents, Local/therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Translational microbiome research using next-generation DNA sequencing is challenging due to the semi-qualitative nature of relative abundance data. A novel method for quantitative analysis was applied in this 12-week clinical trial to understand the mechanical vs. chemotherapeutic actions of brushing, flossing, and mouthrinsing against the supragingival dental plaque microbiome. Enumeration of viable bacteria using vPCR was also applied on supragingival plaque for validation and on subgingival plaque to evaluate interventional effects below the gingival margin.<br><br>METHODS: Subjects with gingivitis were enrolled in a single center, examiner-blind, virtually supervised, parallel group controlled clinical trial. Subjects with gingivitis were randomized into brushing only (B); brushing and flossing (BF); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Antiseptic (BA); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BZ); or brushing, flossing, and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BFZ). All subjects brushed twice daily for 1&#xa0;min with a sodium monofluorophosphate toothpaste and a soft-bristled toothbrush. Subjects who flossed used unflavored waxed dental floss once daily. Subjects assigned to mouthrinses rinsed twice daily. Plaque specimens were collected at the baseline visit and after 4 and 12 weeks of intervention. Bacterial cell number quantification was achieved by adding reference amounts of DNA controls to plaque samples prior to DNA extraction, followed by shallow shotgun metagenome sequencing.<br><br>RESULTS: 286 subjects completed the trial. The metagenomic data for supragingival plaque showed significant reductions in Shannon-Weaver diversity, species richness, and total and categorical bacterial abundances (commensal, gingivitis, and malodor) after 4 and 12 weeks for the BA, BZ, and BFZ groups compared to the B group, while no significant differences were observed between the B and BF groups. Supragingival plaque vPCR further validated these results, and subgingival plaque vPCR demonstrated significant efficacy for the BFZ intervention only.<br><br>CONCLUSIONS: This publication reports on a successful application of a quantitative method of microbiome analysis in a clinical trial demonstrating the sustained and superior efficacy of essential oil mouthrinses at controlling dental plaque compared to mechanical methods. The quantitative microbiological data in this trial also reinforce the safety and mechanism of action of EO mouthrinses against plaque microbial ecology and highlights the importance of elevating EO mouthrinsing as an integral part of an oral hygiene regimen.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 31/10/2022. The registration number is NCT05600231.}, }
@article {pmid38758374, year = {2024}, author = {Nie, X and Zhao, Z and Zhang, X and Bastías, DA and Nan, Z and Li, C}, title = {Endophytes Alleviate Drought-Derived Oxidative Damage in Achnatherum inebrians Plants Through Increasing Antioxidants and Regulating Host Stress Responses.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {73}, pmid = {38758374}, issn = {1432-184X}, support = {31772665//The National Nature Science Foundation of China/ ; jbky-2022-ey21//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Endophytes/metabolism/physiology ; *Antioxidants/metabolism ; *Oxidative Stress ; *Droughts ; *Epichloe/physiology/genetics/metabolism ; Gene Expression Regulation, Plant ; Stress, Physiological ; }, abstract = {Endophytes generally increase antioxidant contents of plants subjected to environmental stresses. However, the mechanisms by which endophytes alter the accumulation of antioxidants in plant tissues are not entirely clear. We hypothesized that, in stress situations, endophytes would simultaneously reduce oxidative damage and increase antioxidant contents of plants and that the accumulation of antioxidants would be a consequence of the endophyte ability to regulate the expression of plant antioxidant genes. We investigated the effects of the fungal endophyte Epichloë gansuensis (C.J. Li &amp; Nan) on oxidative damage, antioxidant contents, and expression of representative genes associated with antioxidant pathways in Achnatherum inebrians (Hance) Keng plants subjected to low (15%) and high (60%) soil moisture conditions. Gene expression levels were measured using RNA-seq. As expected, the endophyte reduced the oxidative damage by 17.55% and increased the antioxidant contents by 53.14% (on average) in plants subjected to low soil moisture. In line with the accumulation of antioxidants in plant tissues, the endophyte increased the expression of most plant genes associated with the biosynthesis of antioxidants (e.g., MIOX, crtB, gpx) while it reduced the expression of plant genes related to the metabolization of antioxidants (e.g., GST, PRODH, ALDH). Our findings suggest that endophyte ability of increasing antioxidant contents in plants may reduce the oxidative damage caused by stresses and that the fungal regulation of plant antioxidants would partly explain the accumulation of these compounds in plant tissues.}, }
@article {pmid38756954, year = {2024}, author = {Wang, F and Xiang, L and Sze-Yin Leung, K and Elsner, M and Zhang, Y and Guo, Y and Pan, B and Sun, H and An, T and Ying, G and Brooks, BW and Hou, D and Helbling, DE and Sun, J and Qiu, H and Vogel, TM and Zhang, W and Gao, Y and Simpson, MJ and Luo, Y and Chang, SX and Su, G and Wong, BM and Fu, TM and Zhu, D and Jobst, KJ and Ge, C and Coulon, F and Harindintwali, JD and Zeng, X and Wang, H and Fu, Y and Wei, Z and Lohmann, R and Chen, C and Song, Y and Sanchez-Cid, C and Wang, Y and El-Naggar, A and Yao, Y and Huang, Y and Cheuk-Fung Law, J and Gu, C and Shen, H and Gao, Y and Qin, C and Li, H and Zhang, T and Corcoll, N and Liu, M and Alessi, DS and Li, H and Brandt, KK and Pico, Y and Gu, C and Guo, J and Su, J and Corvini, P and Ye, M and Rocha-Santos, T and He, H and Yang, Y and Tong, M and Zhang, W and Suanon, F and Brahushi, F and Wang, Z and Hashsham, SA and Virta, M and Yuan, Q and Jiang, G and Tremblay, LA and Bu, Q and Wu, J and Peijnenburg, W and Topp, E and Cao, X and Jiang, X and Zheng, M and Zhang, T and Luo, Y and Zhu, L and Li, X and Barceló, D and Chen, J and Xing, B and Amelung, W and Cai, Z and Naidu, R and Shen, Q and Pawliszyn, J and Zhu, YG and Schaeffer, A and Rillig, MC and Wu, F and Yu, G and Tiedje, JM}, title = {Emerging contaminants: A One Health perspective.}, journal = {Innovation (Cambridge (Mass.))}, volume = {5}, number = {4}, pages = {100612}, pmid = {38756954}, issn = {2666-6758}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES027706/ES/NIEHS NIH HHS/United States ; }, abstract = {Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.}, }
@article {pmid38756730, year = {2024}, author = {Akashi, M and Takemura, M and Suzuki, S}, title = {Continuous year-round isolation of giant viruses from brackish shoreline soils.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1402690}, pmid = {38756730}, issn = {1664-302X}, abstract = {Giant viruses, categorized under Nucleocytoviricota, are believed to exist ubiquitously in natural environments. However, comprehensive reports on isolated giant viruses remain scarce, with limited information available on unrecoverable strains, viral proliferation sites, and natural hosts. Previously, the author highlighted Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. styx, isolated from brackish water soil, as potential hotspots for giant virus multiplication. This study presents findings from nearly a year of monthly sampling within the same brackish water region after isolating the three aforementioned strains. This report details the recurrent isolation of a wide range of giant viruses. Each month, four soil samples were randomly collected from an approximately 5 × 10 m plot, comprising three soil samples and one water sample containing sediment from the riverbed. Acanthamoeba castellanii was used as a host for virus isolation. These efforts consistently yielded at least one viral species per month, culminating in a total of 55 giant virus isolates. The most frequently isolated species was Mimiviridae (24 isolates), followed by Marseilleviridae (23 isolates), Pandoravirus (6 isolates), and singular isolates of Pithovirus and Cedratvirus. Notably, viruses were not consistently isolated from any of the four samples every month, with certain sites yielding no viruses. Cluster analysis based on isolate numbers revealed that soil samples from May and water and sediment samples from January produced the highest number of viral strains. These findings underscore brackish coastal soil as a significant site for isolating numerous giant viruses, highlighting the non-uniform distribution along coastlines.}, }
@article {pmid38755460, year = {2024}, author = {Flores-Almaraz, VS and Truong, C and Hernández-Oaxaca, D and Reyes-Galindo, V and Mastretta-Yanes, A and Jaramillo-Correa, JP and Salas-Lizana, R}, title = {Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {72}, pmid = {38755460}, issn = {1432-184X}, support = {grant 778409//CONAHCyT Becas Nacionales/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; }, mesh = {*Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Plant Leaves/microbiology ; Mexico ; *Air Pollution/adverse effects ; Ozone ; Stress, Physiological ; Cities ; }, abstract = {Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. &amp; Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.}, }
@article {pmid38755154, year = {2024}, author = {Schmider, T and Hestnes, AG and Brzykcy, J and Schmidt, H and Schintlmeister, A and Roller, BRK and Teran, EJ and Söllinger, A and Schmidt, O and Polz, MF and Richter, A and Svenning, MM and Tveit, AT}, title = {Physiological basis for atmospheric methane oxidation and methanotrophic growth on air.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4151}, pmid = {38755154}, issn = {2041-1723}, support = {295910//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 315129//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; }, mesh = {*Methane/metabolism ; *Oxidation-Reduction ; *Carbon Monoxide/metabolism ; *Hydrogen/metabolism ; Atmosphere/chemistry ; Air ; Nitrogen/metabolism ; Greenhouse Gases/metabolism ; }, abstract = {Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.}, }
@article {pmid38755019, year = {2024}, author = {Vaccalluzzo, A and Pino, A and Grimaldi, RL and Caggia, C and Cianci, S and Randazzo, CL}, title = {Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) is an effective strategy for managing vaginal dysbiosis, rising the lactobacilli population.}, journal = {Journal of applied microbiology}, volume = {135}, number = {5}, pages = {}, doi = {10.1093/jambio/lxae110}, pmid = {38755019}, issn = {1365-2672}, support = {//Uriach/ ; }, mesh = {Female ; Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Lacticaseibacillus rhamnosus ; *Dysbiosis/microbiology ; *Vagina/microbiology ; Adult ; Middle Aged ; Young Adult ; Quality of Life ; Lactobacillus ; Vaginosis, Bacterial/microbiology/drug therapy ; }, abstract = {AIM: The present study is a single-centre, randomized, controlled clinical trial aimed to evaluate the effectiveness of the probiotic Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) strain, orally administrated, to treat vaginal dysbiosis.<br><br>METHODS AND RESULTS: Overall, 80 women, with signs and symptoms of vaginal dysbiosis, were enrolled and allocated to the treatment group (A, n=60), who took 1 capsule of the probiotic strain for 10 consecutive days, or the non-treatment group (B, n=20), who did not receive any treatment. Clinical (vaginal signs and symptoms; pH of the vaginal fluid; Amsel criteria; Nugent score; Lactobacillary grade) and microbiological examinations were performed at baseline (T0), 10 days (T1), and 30 (T2) days after the oral administration of the probiotic TOM 22.8 strain. The latter resulted in a restoration of the physiological pH, accompanied by remission or attenuation of clinical signs and symptoms as well as the improvement of the quality of life (QoL). Microbiological data revealed a significant reduction of potentially pathogenic bacteria.<br><br>CONCLUSION: The administration of the L. rhamnosus TOM 22.8 probiotic strain could be proposed as an effective strategy for the treatment of vaginal dysbiosis.}, }
@article {pmid38754710, year = {2024}, author = {Thomé, PC and Wolinska, J and Van Den Wyngaert, S and Reñé, A and Ilicic, D and Agha, R and Grossart, HP and Garcés, E and Monaghan, MT and Strassert, JFH}, title = {Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum.}, journal = {Molecular phylogenetics and evolution}, volume = {197}, number = {}, pages = {108103}, doi = {10.1016/j.ympev.2024.108103}, pmid = {38754710}, issn = {1095-9513}, mesh = {*Phylogeny ; *Chytridiomycota/genetics/classification ; *Phytoplankton/genetics/classification ; Genomics ; }, abstract = {Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.}, }
@article {pmid38754295, year = {2024}, author = {Verstraete, W}, title = {Nitrogen and me - How little did we, and do we know about "stikstof - azote - nitrogen"?.}, journal = {Water research}, volume = {258}, number = {}, pages = {121687}, doi = {10.1016/j.watres.2024.121687}, pmid = {38754295}, issn = {1879-2448}, mesh = {Humans ; *Agriculture ; Fertilizers ; History, 20th Century ; *Nitrogen ; }, abstract = {This retrospective article reflects on the complex and evolving relationship between humans and nitrogen over several decades. Raised on a Flemish farm, the author's early experiences with nitrogen in agriculture - both its benefits and dangers - laid the foundation for a lifelong interest in this element. The article traverses a broad range of topics related to nitrogen, highlighting its critical role in various historical, agricultural, environmental, and industrial contexts. The narrative begins with a historical overview of nitrogen's role in agriculture and warfare. The development of industrial processes like the Haber and Ostwald methods transformed nitrogen into a key ingredient for both fertilizers and explosives. The dual nature of nitrogen - as a life-giver in agriculture and a destructive component in warfare and also in biodiversity - is an important theme. The article delves into the environmental impacts of nitrogen, particularly in the context of modern agriculture and industrialization. Issues like fertilization, water contamination, and the challenges of managing nitrogenous waste highlight the complex interplay between human activities and environmental health. Technological advancements are explored, including the development of bioaugmentation methods and the potential of genetic engineering in optimizing nitrogen fixation. Throughout the narrative, personal anecdotes are weaved with scientific information, offering a unique perspective on the historical and contemporary challenges of managing nitrogen. The discussion extends to the broader implications of nitrogen management in the context of sustainability, climate change, and global food security and its overall regulatory space. All these considerations call for a re-evaluation of our relationship with nitrogen, advocating for innovative solutions and systemic thinking to address the multifaceted challenges posed by this essential, yet often problematic element.}, }
@article {pmid38752760, year = {2024}, author = {Barnett, SE and Shade, A}, title = {Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0019824}, pmid = {38752760}, issn = {2576-098X}, support = {1749544//National Science Foundation (NSF)/ ; }, abstract = {We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.}, }
@article {pmid38750737, year = {2024}, author = {Kaijser, W and Lorenz, AW and Brauer, VS and Burfeid-Castellanos, A and David, GM and Nuy, JK and Baikova, D and Beszteri, B and Gillmann, SM and Kiesel, J and Mayombo, NAS and Peters, K and Rettig, K and Rolauffs, P and Haase, P and Hering, D}, title = {Differential associations of five riverine organism groups with multiple stressors.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173105}, doi = {10.1016/j.scitotenv.2024.173105}, pmid = {38750737}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; *Environmental Monitoring ; Animals ; *Biodiversity ; Fungi ; Diatoms/physiology ; Invertebrates/physiology ; Fishes ; Bacteria/classification ; Water Pollutants, Chemical/analysis ; }, abstract = {The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.}, }
@article {pmid38750646, year = {2024}, author = {Huusko, K and Manninen, OH and Myrsky, E and Stark, S}, title = {Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties.}, journal = {The New phytologist}, volume = {243}, number = {1}, pages = {407-422}, doi = {10.1111/nph.19808}, pmid = {38750646}, issn = {1469-8137}, support = {323504//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/physiology ; *Bacteria/classification ; *Tundra ; Finland ; Chemical Phenomena ; Plants/microbiology ; }, abstract = {Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.}, }
@article {pmid38749545, year = {2024}, author = {Sato, Y}, title = {Transcriptome analysis: a powerful tool to understand individual microbial behaviors and interactions in ecosystems.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {88}, number = {8}, pages = {850-856}, doi = {10.1093/bbb/zbae064}, pmid = {38749545}, issn = {1347-6947}, support = {17H04716//Japan Society for the Promotion of Science/ ; JPMJFR2174//Japan Science and Technology Agency/ ; }, mesh = {*Ecosystem ; *Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Transcriptome ; Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Microbial Interactions/genetics ; Metagenome ; }, abstract = {Transcriptome analysis is a powerful tool for studying microbial ecology, especially individual microbial functions in an ecosystem and their interactions. With the development of high-throughput sequencing technology, great progress has been made in analytical methods for microbial communities in natural environments. 16S rRNA gene amplicon sequencing (ie microbial community structure analysis) and shotgun metagenome analysis have been widely used to determine the composition and potential metabolic capability of microorganisms in target environments without requiring culture. However, even if the types of microorganisms present and their genes are known, it is difficult to determine what they are doing in an ecosystem. Gene expression analysis (transcriptome analysis; RNA-seq) is a powerful tool to address these issues. The history and basic information of gene expression analysis, as well as examples of studies using this method to analyze microbial ecosystems, are presented.}, }
@article {pmid38749241, year = {2024}, author = {Kutralam-Muniasamy, G and Shruti, VC and Pérez-Guevara, F}, title = {Plastisphere-hosted viruses: A review of interactions, behavior, and effects.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134533}, doi = {10.1016/j.jhazmat.2024.134533}, pmid = {38749241}, issn = {1873-3336}, mesh = {*Viruses ; Plastics ; Virus Physiological Phenomena ; Biofilms ; Ecosystem ; Microplastics ; }, abstract = {Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.}, }
@article {pmid38748252, year = {2024}, author = {Perez-Bou, L and Gonzalez-Martinez, A and Cabrera, JJ and Juarez-Jimenez, B and Rodelas, B and Gonzalez-Lopez, J and Correa-Galeote, D}, title = {Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {71}, pmid = {38748252}, issn = {1432-184X}, mesh = {*DNA Primers/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Wastewater/microbiology ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; }, abstract = {The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R[2] > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.}, }
@article {pmid38747602, year = {2024}, author = {Sudo, M and Osvatic, J and Taylor, JD and Dufour, SC and Prathep, A and Wilkins, LGE and Rattei, T and Yuen, B and Petersen, JM}, title = {SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0113523}, pmid = {38747602}, issn = {2379-5077}, support = {VRG14-021//Vienna Science and Technology Fund (WWTF)/ ; DOC 69/FWF_/Austrian Science Fund FWF/Austria ; 802494//EC | European Research Council (ERC)/ ; Grant-DOI 10.55776/DOC69//Austrian Science Fund (FWF) DocFunds/ ; 10.55776/COE7//University of Vienna/ ; SEP-210693430//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {Animals ; Adaptation, Physiological/genetics ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Hydrothermal Vents/microbiology ; Multigene Family ; *Oxidation-Reduction ; Phylogeny ; *Sulfides/metabolism ; Sulfur/metabolism ; *Symbiosis/genetics ; Bivalvia ; }, abstract = {Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.}, }
@article {pmid38747384, year = {2024}, author = {Tanabe, TS and Bach, E and D'Ermo, G and Mohr, MG and Hager, N and Pfeiffer, N and Guiral, M and Dahl, C}, title = {A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex.}, journal = {Protein science : a publication of the Protein Society}, volume = {33}, number = {6}, pages = {e5014}, pmid = {38747384}, issn = {1469-896X}, support = {57388731//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; 40444VM//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; //Studienstiftung des Deutschen Volkes/ ; 351/13-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfurtransferases/metabolism/chemistry/genetics ; *Oxidoreductases/metabolism/chemistry ; *Bacterial Proteins/metabolism/chemistry/genetics ; }, abstract = {A heterodisulfide reductase-like complex (sHdr) and novel lipoate-binding proteins (LbpAs) are central players of a wide-spread pathway of dissimilatory sulfur oxidation. Bioinformatic analysis demonstrate that the cytoplasmic sHdr-LbpA systems are always accompanied by sets of sulfur transferases (DsrE proteins, TusA, and rhodaneses). The exact composition of these sets may vary depending on the organism and sHdr system type. To enable generalizations, we studied model sulfur oxidizers from distant bacterial phyla, that is, Aquificota and Pseudomonadota. DsrE3C of the chemoorganotrophic Alphaproteobacterium Hyphomicrobium denitrificans and DsrE3B from the Gammaproteobacteria Thioalkalivibrio sp. K90mix, an obligate chemolithotroph, and Thiorhodospira sibirica, an obligate photolithotroph, are homotrimers that donate sulfur to TusA. Additionally, the hyphomicrobial rhodanese-like protein Rhd442 exchanges sulfur with both TusA and DsrE3C. The latter is essential for sulfur oxidation in Hm. denitrificans. TusA from Aquifex aeolicus (AqTusA) interacts physiologically with AqDsrE, AqLbpA, and AqsHdr proteins. This is particularly significant as it establishes a direct link between sulfur transferases and the sHdr-LbpA complex that oxidizes sulfane sulfur to sulfite. In vivo, it is unlikely that there is a strict unidirectional transfer between the sulfur-binding enzymes studied. Rather, the sulfur transferases form a network, each with a pool of bound sulfur. Sulfur flux can then be shifted in one direction or the other depending on metabolic requirements. A single pair of sulfur-binding proteins with a preferred transfer direction, such as a DsrE3-type protein towards TusA, may be sufficient to push sulfur into the sink where it is further metabolized or needed.}, }
@article {pmid38746754, year = {2024}, author = {Shan, Z and Chen, H and Deng, Y and He, D and Ren, L}, title = {An abrupt regime shift of bacterioplankton community from weak to strong thermal pollution in a subtropical bay.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1395583}, pmid = {38746754}, issn = {1664-302X}, abstract = {Thermal pollution from the cooling system of the nuclear power plants greatly changes the environmental and the ecological conditions of the receiving marine water body, but we know little about their impact on the steady-state transition of marine bacterioplankton communities. In this study, we used high-throughput sequencing based on the 16S rRNA gene to investigate the impact of the thermal pollution on the bacterioplankton communities in a subtropical bay (the Daya Bay). We observed that thermal pollution from the cooling system of the nuclear power plant caused a pronounced thermal gradient ranging from 19.6°C to 24.12°C over the whole Daya Bay. A temperature difference of 4.5°C between the northern and southern parts of the bay led to a regime shift in the bacterioplankton community structure. In the three typical scenarios of regime shifts, the steady-state transition of bacterioplankton community structure in response to temperature increasing was more likely consistent with an abrupt regime shift rather than a smooth regime or a discontinuous regime model. Water temperature was a decisive factor on the regime shift of bacterioplankton community structure. High temperature significantly decreased bacterioplankton diversity and shifted its community compositions. Cyanobium and Synechococcus of Cyanobacteria, NS5 marine group of Bacteroidota, and Vibrio of Gammaproteobacteria were found that favored high temperature environments. Furthermore, the increased water temperature significantly altered the community assembly of bacterioplankton in Daya Bay, with a substantial decrease in the proportion of drift and others, and a marked increase in the proportion of homogeneous selection. In summary, we proposed that seawater temperature increasing induced by the thermal pollution resulted in an abrupt regime shift of bacterioplankton community in winter subtropical bay. Our research might broad our understanding of marine microbial ecology under future conditions of global warming.}, }
@article {pmid38746391, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: Coverage-based Analysis for Identification of Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38746391}, issn = {2692-8205}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid38740585, year = {2024}, author = {Bin, X and Wang, P and Shen, Y and Xiang, X and Jafir, M and Wan, X}, title = {Investigation of Fungal Community Structure in the Gut of the Stag Beetle Dorcus hopei (Coleoptera; Lucanidae): Comparisons Among Developmental Stages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {70}, pmid = {38740585}, issn = {1432-184X}, support = {31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Coleoptera/microbiology/growth &amp; development ; *Larva/growth &amp; development/microbiology ; *Fungi/genetics/classification/physiology ; *Gastrointestinal Microbiome ; Pupa/growth &amp; development/microbiology ; Mycobiome ; Biodiversity ; Symbiosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Stag beetles, recognized as common saproxylic insects, are valued for their vibrant coloration and distinctive morphology. These beetles play a crucial ecological role in decomposition and nutrient cycling, serving as a vital functional component in ecosystem functioning. Although previous studies have confirmed that stag beetles are predominantly fungivores, the fluctuations in their intestinal fungal communities at different developmental stages remain poorly understood. In the current study, high-throughput sequencing was employed to investigate the dynamic changes within intestinal fungal communities at various developmental stages in the stag beetle Dorcus hopei. Results showed that microbial diversity was higher during the larval stage than during the pupal and adult stages. Furthermore, significant differences were identified in the composition of the intestinal fungal communities across the larval, pupal, and adult stages, suggesting that developmental transitions may be crucial factors contributing to variations in fungal community composition and diversity. Dominant genera included Candida, Scheffersomyces, Phaeoacremonium, and Trichosporon. Functional predictions indicated a greater diversity and relative abundance of endosymbiotic fungi in the larval gut, suggesting a potential dependency of larvae on beneficial gut fungi for nutrient acquisition. Additionally, the application of abundance-based β-null deviation and niche width analyses revealed that the adult gut exerted a stronger selection pressure on its fungal community, favoring certain taxa. This selection process culminates in a more robust co-occurrence network of fungal communities within the adult gut, thereby enhancing their adaptability to environmental fluctuations. This study advances our understanding of the intestinal fungal community structure in stag beetles, providing a crucial theoretical foundation for the development of saproxylic beetle resources, biomass energy utilization, plastic degradation strategies, and beetle conservation efforts.}, }
@article {pmid38740197, year = {2024}, author = {Ibrahim, SS and Ionescu, D and Grossart, HP}, title = {Tapping into fungal potential: Biodegradation of plastic and rubber by potent Fungi.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173188}, doi = {10.1016/j.scitotenv.2024.173188}, pmid = {38740197}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Fungi/metabolism ; *Rubber/metabolism ; Polyurethanes ; }, abstract = {Plastic polymers are present in most aspects of routine daily life. Their increasing leakage into the environment poses a threat to environmental, animal, and human health. These polymers are often resistant to microbial degradation and are predicted to remain in the environment for tens to hundreds of years. Fungi have been shown to degrade complex polymers and are considered good candidates for bioremediation (biological pollutant reduction) of plastics. Therefore, we screened 18 selected fungal strains for their ability to degrade polyurethane (PU), polyethylene (PE), and tire rubber. As a proxy for plastic polymer mineralization, we quantified O2 consumption and CO2 production in an enclosed biodegradation system providing plastic as the sole carbon source. In contrast to most studies we demonstrated that the tested fungi attach to, and colonize the different plastic polymers without any pretreatment of the plastics and in the absence of sugars, which were suggested essential for priming the degradation process. Functional polymer groups identified by Fourier-transform infrared spectroscopy (FTIR), and changes in fungal morphology as seen in light and scanning electron microscopy (SEM) were used as indicators of fungal adaptation to growth on PU as a substrate. Thereby, SEM analysis revealed new morphological structures and deformation of the cell wall of several fungal strains when colonizing PU and utilizing this plastic polymer for cell growth. Strains of Fusarium, Penicillium, Botryotinia cinerea EN41, and Trichoderma demonstrated a high potential to degrade PU, rubber, and PE. Growing on PU, over 90 % of the O2 was consumed in <14 days with 300-500 ppm of CO2 generated in parallel. Our study highlights a high bioremediation potential of some fungal strains to efficiently degrade plastic polymers, largely dependent on plastic type.}, }
@article {pmid38739959, year = {2024}, author = {Kazmi, SSUH and Tayyab, M and Pastorino, P and Barcelò, D and Yaseen, ZM and Grossart, HP and Khan, ZH and Li, G}, title = {Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134574}, doi = {10.1016/j.jhazmat.2024.134574}, pmid = {38739959}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects/genetics ; Animals ; *Transcriptome/drug effects ; Nanoparticles/toxicity/chemistry ; }, abstract = {The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.}, }
@article {pmid38736980, year = {2024}, author = {Ahmad, R and Liaquat, M and Sammi, S and Al-Hawadi, JS and Jahangir, M and Mumtaz, A and Khan, I and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Adnan, M and Sadiq, A and Rahman, TU and Asghari, BH and Fahad, S}, title = {Physicochemical and nutritional profiles of wild adlay (Coix lacryma-jobi Linn) accessions by GC, FTIR, and spectrophotometer.}, journal = {Food chemistry: X}, volume = {22}, number = {}, pages = {101418}, pmid = {38736980}, issn = {2590-1575}, abstract = {Purpose of current study was to determine physicochemical, triglyceride composition, and functional groups of wild adlay accessions (brown, black, yellow, grey, green, off white, and purple) to find out its scope as cereal crop. Triglycerides, minerals and functional groups were determined through Gas chromatography, spectrophotometer and Fourier Transform Infrared (FTIR) spectrophotometer respectively. Results revealed variation among bulk densities, specific densities, percent empty spaces, and corresponding grain counts per 10 g of sample are useful in distinguishing brown, black, yellow, grey, green, off white, and purple wild adlay accessions. Specific density and grain count per 10 g sample was significantly related. No statistical relationship exists among the pronounced physical characteristics. Brown adlay expressed the highest protein, fat, and fiber contents 15.82%, 4.76% and 2.37% respectively. Protein, fat, ash, and fiber percent contents were found comparable to cultivated adlay. Spectrophotometric analysis revealed macro elements including phosphorus, potassium, calcium, and sodium in the range 0.3% - 2.2% and micro elements boron, iron, copper, zinc, and manganese in the range 1.6 mg/kg - 20.8 mg/kg. Gas chromatography showed polyunsaturated fatty acids (PUFA) constitute the primary fraction (39% ± 7.2) of wild adlay triglycerides. Linoleic and palmitic acids were present as prominent fatty acids, 43.5% ±1.4 and 26.3% ±1.4 respectively. Infra-red frequencies distinguished functional groups in narrow band and fingerprint region of protein in association with out of plane region leading to structural differences among adlay accessions. Comparison of major distinguishing vibrational frequencies among different flours indicated black adlay containing highest functional groups appeared promising for varietal development.}, }
@article {pmid38734822, year = {2024}, author = {Breedt, G and Korsten, L and Gokul, JK}, title = {Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {170}, pmid = {38734822}, issn = {1432-0991}, mesh = {*Triticum/microbiology/growth &amp; development ; *Phosphates/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Fertilizers/analysis ; Paenibacillus/metabolism/genetics/growth &amp; development ; Phosphorus/metabolism ; }, abstract = {As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.}, }
@article {pmid38733792, year = {2024}, author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N}, title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.}, journal = {Current opinion in microbiology}, volume = {79}, number = {}, pages = {102486}, doi = {10.1016/j.mib.2024.102486}, pmid = {38733792}, issn = {1879-0364}, mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; }, abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.}, }
@article {pmid38730059, year = {2024}, author = {Kimura, K and Okuro, T}, title = {Cyanobacterial Biocrust on Biomineralized Soil Mitigates Freeze-Thaw Effects and Preserves Structure and Ecological Functions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {69}, pmid = {38730059}, issn = {1432-184X}, support = {JPMJSA1906//Science and Technology Research Partnership for Sustainable Development/ ; JP22H01310//Japan Society for the Promotion of Science/ ; JPMEERF20205001//Environment Research and Technology Development Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Freezing ; *Cyanobacteria/metabolism/chemistry ; Carbonates/chemistry/metabolism ; Ecosystem ; Sporosarcina/metabolism/growth &amp; development ; }, abstract = {Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological functions of the two tools persist when these methods are combined and subjected to freeze-thaw (FT) cycles. We hypothesized a synergetic interaction between MICP treatment and biocrust under FT cycles, which would allow both components to retain their ecological functions. We grew cyanobacterial (Nostoc commune) biocrusts on bare soil and on MICP (Sporosarcina pasteurii)-treated soil, subjecting them to repeated FT cycles simulating the Mongolian climate. Generalized linear modeling revealed that FT cycling did not affect physical structure or related functions but could increase the productivity and reduce the nutrient condition of the crust. The results confirm the high tolerance of MICP-treated soil and biocrust to FT cycling. MICP treatment + biocrust maintained higher total carbohydrate content under FT stress. Our study indicates that biocrust on biomineralized soil has a robust enough structure to endure FT cycling during spring and autumn and to promote restoration of degraded lands.}, }
@article {pmid38729708, year = {2024}, author = {Garcia-Gutierrez, E and Monteoliva García, G and Bodea, I and Cotter, PD and Iguaz, A and Garre, A}, title = {A secondary model for the effect of pH on the variability in growth fitness of Listeria innocua strains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {186}, number = {}, pages = {114314}, doi = {10.1016/j.foodres.2024.114314}, pmid = {38729708}, issn = {1873-7145}, mesh = {*Listeria/growth &amp; development/classification ; Hydrogen-Ion Concentration ; *Food Microbiology ; Models, Biological ; Colony Count, Microbial ; Risk Assessment ; }, abstract = {Variability in microbial growth is a keystone of modern Quantitative Microbiological Risk Assessment (QMRA). However, there are still significant knowledge gaps on how to model variability, with the most common assumption being that variability is constant. This is implemented by an error term (with constant variance) added on top of the secondary growth model (for the square root of the growth rate). However, this may go against microbial ecology principles, where differences in growth fitness among bacterial strains would be more prominent in the vicinity of the growth limits than at optimal growth conditions. This study coins the term "secondary models for variability", evaluating whether they should be considered in QMRA instead of the constant strain variability hypothesis. For this, 21 strains of Listeria innocua were used as case study, estimating their growth rate by the two-fold dilution method at pH between 5 and 10. Estimates of between-strain variability and experimental uncertainty were obtained for each pH using mixed-effects models, showing the lowest variability at optimal growth conditions, increasing towards the growth limits. Nonetheless, the experimental uncertainty also increased towards the extremes, evidencing the need to analyze both sources of variance independently. A secondary model was thus proposed, relating strain variability and pH conditions. Although the modelling approach certainly has some limitations that would need further experimental validation, it is an important step towards improving the description of variability in QMRA, being the first model of this type in the field.}, }
@article {pmid38728984, year = {2024}, author = {Yuan, Y and Zhang, G and Fang, H and Peng, S and Xia, Y and Wang, F}, title = {The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations.}, journal = {Journal of environmental management}, volume = {359}, number = {}, pages = {121107}, doi = {10.1016/j.jenvman.2024.121107}, pmid = {38728984}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; Ecology ; Corrosion ; Microbiota ; }, abstract = {Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.}, }
@article {pmid38728226, year = {2024}, author = {Ma, T and Rothschild, J and Halabeya, F and Zilman, A and Milstein, JN}, title = {Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {20}, pages = {e2322321121}, pmid = {38728226}, issn = {1091-6490}, support = {RGPIN-2019-06520//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; RGPIN-2022-04909//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 207-2019-2020-Q4-00576//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Escherichia coli/physiology ; Models, Biological ; Biodiversity ; Ecosystem ; }, abstract = {Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.}, }
@article {pmid38727217, year = {2024}, author = {Thomas, MJN and Brockhurst, MA and Coyte, KZ}, title = {What makes a temperate phage an effective bacterial weapon?.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0103623}, pmid = {38727217}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/T014342/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 220243/Z/20/Z//Wellcome Trust (WT)/ ; 226047/Z/22/Z//Wellcome Trust (WT)/ ; }, mesh = {*Lysogeny ; *Pseudomonas aeruginosa/virology ; Bacteriophages/genetics/physiology ; }, abstract = {UNLABELLED: Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly.<br><br>IMPORTANCE: Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.}, }
@article {pmid38726295, year = {2024}, author = {Casero, JJD and Rovedder, APM and Vargas, LK}, title = {Editorial: Plant-microbe interactions in forest ecosystems, volume II.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1414383}, pmid = {38726295}, issn = {1664-462X}, }
@article {pmid38724726, year = {2024}, author = {Bobonis, J and Yang, ALJ and Voogdt, CGP and Typas, A}, title = {TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems.}, journal = {Nature protocols}, volume = {19}, number = {8}, pages = {2231-2249}, pmid = {38724726}, issn = {1750-2799}, mesh = {*Toxin-Antitoxin Systems/genetics ; *Escherichia coli/genetics ; Bacterial Toxins/genetics/metabolism ; Bacteriophages/genetics ; High-Throughput Screening Assays/methods ; Conjugation, Genetic ; }, abstract = {Toxin-antitoxin systems (TAs) are abundant in bacterial chromosomes and can arrest growth under stress, but usually remain inactive. TAs have been increasingly implicated in halting the growth of infected bacteria from bacteriophages or foreign genetic elements[1,2] to protect the population (abortive infection, Abi). The vast diversity and abundance of TAs and other Abi systems[3] suggest they play an important immunity role, yet what allows them to sense attack remains largely enigmatic. Here, we describe a method called toxin activation-inhibition conjugation (TAC-TIC), which we used to identify gene products that trigger or block the toxicity of phage-defending tripartite retron-TAs[4]. TAC-TIC employs high-density arrayed mobilizable gene-overexpression libraries, which are transferred into cells carrying the full TA system or only its toxic component, on inducible vectors. The double-plasmid transconjugants are then pinned on inducer-containing agar plates and their colony fitness is quantified to identify gene products that trigger a TA to inhibit growth (TAC), or that block it from acting (TIC). TAC-TIC is optimized for the Singer ROTOR pinning robot, but can also be used with other robots or manual pinners, and allows screening tens of thousands of genes against any TA or Abi (with toxicity) within a week. Finally, we present a dual conjugation donor/cloning strain (Escherichia coli DATC), which accelerates the construction of TAC-TIC gene-donor libraries from phages, enabling the use of TAC-TIC for identifying TA triggers and antidefense mechanisms in phage genomes.}, }
@article {pmid38723661, year = {2024}, author = {Tschitschko, B and Esti, M and Philippi, M and Kidane, AT and Littmann, S and Kitzinger, K and Speth, DR and Li, S and Kraberg, A and Tienken, D and Marchant, HK and Kartal, B and Milucka, J and Mohr, W and Kuypers, MMM}, title = {Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean.}, journal = {Nature}, volume = {630}, number = {8018}, pages = {899-904}, pmid = {38723661}, issn = {1476-4687}, mesh = {Carbon/metabolism ; *Diatoms/metabolism/physiology ; *Nitrogen/metabolism ; *Nitrogen Fixation ; *Oceans and Seas ; Photosynthesis ; Phylogeny ; *Rhizobium/classification/metabolism/physiology ; *Seawater/microbiology/chemistry ; *Symbiosis ; Cyanobacteria/isolation &amp; purification/metabolism ; Atlantic Ocean ; }, abstract = {Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean[1] and has a key role in fuelling the biological carbon pump[2]. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea[3-5]. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land[6]. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.}, }
@article {pmid38722447, year = {2024}, author = {Hu, Y and Cai, J and Song, Y and Li, G and Gong, Y and Jiang, X and Tang, X and Shao, K and Gao, G}, title = {Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {68}, pmid = {38722447}, issn = {1432-184X}, support = {2019YFA0607100//Key Technologies Research and Development Program/ ; U2003205//National Natural Science Foundation of China/ ; 2022xjkk1504//The third Xinjiang Scientific Expedition/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; China ; *DNA, Bacterial/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.}, }
@article {pmid38722171, year = {2024}, author = {Stice, SP and Jan, H-H and Chen, H-C and Nwosu, L and Shin, GY and Weaver, S and Coutinho, T and Kvitko, BH and Baltrus, DA}, title = {Erratum for Stice et al., "Pantailocins: phage-derived bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes".}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0062924}, doi = {10.1128/aem.00629-24}, pmid = {38722171}, issn = {1098-5336}, }
@article {pmid38718505, year = {2024}, author = {Liu, S and Zhang, Z and Zhao, C and Zhang, M and Han, F and Hao, J and Wang, X and Shan, X and Zhou, W}, title = {Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134460}, doi = {10.1016/j.jhazmat.2024.134460}, pmid = {38718505}, issn = {1873-3336}, mesh = {*Parabens/chemistry/toxicity ; *Biofilms/drug effects ; Bacteria/drug effects ; Density Functional Theory ; Quorum Sensing/drug effects ; }, abstract = {Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. ENVIRONMENTAL IMPLICATION: Parabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.}, }
@article {pmid38714759, year = {2024}, author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R}, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.}, journal = {Nature microbiology}, volume = {9}, number = {5}, pages = {1152-1156}, pmid = {38714759}, issn = {2058-5276}, support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; }, mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; }, }
@article {pmid38712704, year = {2024}, author = {Vandermaesen, J and Daly, AJ and Mawarda, PC and Baetens, JM and De Baets, B and Boon, N and Springael, D}, title = {Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship.}, journal = {Ecology letters}, volume = {27}, number = {5}, pages = {e14433}, doi = {10.1111/ele.14433}, pmid = {38712704}, issn = {1461-0248}, support = {266039//EU FP7/ ; G0D0322N//Fonds Wetenschappelijk Onderzoek/ ; BELSPO P7/25//Belgian Science Policy (BELSPO)/ ; }, mesh = {*Microbiota ; Benzamides ; Microbial Interactions ; Phyllobacteriaceae/physiology ; Groundwater/microbiology ; Biodiversity ; }, abstract = {The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.}, }
@article {pmid38712077, year = {2024}, author = {Letourneau, J and Carrion, VM and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA}, title = {Interplay between particle size and microbial ecology in the gut microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38712077}, issn = {2692-8205}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; R01 DK128611/DK/NIDDK NIH HHS/United States ; }, abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Surprisingly, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that mammalian and human gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion, and that the microbiomes of individuals vary in this capacity. These new insights also suggest FPS in humans to be governed by processes beyond those found in other mammals and emphasize the importance of gut microbiota in shaping their own abiotic environment.}, }
@article {pmid38711157, year = {2024}, author = {Jurburg, SD and Blowes, SA and Shade, A and Eisenhauer, N and Chase, JM}, title = {Synthesis of recovery patterns in microbial communities across environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {79}, pmid = {38711157}, issn = {2049-2618}, support = {FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Microbiota ; *Soil Microbiology ; *Bayes Theorem ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Mammals/microbiology ; Biodiversity ; Water Microbiology ; }, abstract = {BACKGROUND: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.<br><br>RESULTS: To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50&#xa0;days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.<br><br>CONCLUSIONS: This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.}, }
@article {pmid38710359, year = {2024}, author = {Lambert, S and Vercauteren, M and Catarino, AI and Li, Y and Van Landuyt, J and Boon, N and Everaert, G and De Rijcke, M and Janssen, CR and Asselman, J}, title = {Aerosolization of micro- and nanoplastics via sea spray: Investigating the role of polymer type, size, and concentration, and potential implications for human exposure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124105}, doi = {10.1016/j.envpol.2024.124105}, pmid = {38710359}, issn = {1873-6424}, mesh = {*Aerosols ; Humans ; *Microplastics/analysis ; *Seawater/chemistry ; *Plastics ; *Particle Size ; Polymers/chemistry ; Air Pollutants/analysis ; Inhalation Exposure/statistics &amp; numerical data ; Environmental Monitoring/methods ; Environmental Exposure ; Nanoparticles ; }, abstract = {Micro- and nanoplastics (MNPs) can enter the atmosphere via sea spray aerosols (SSAs), but the effects of plastic characteristics on the aerosolization process are unclear. Furthermore, the importance of the transport of MNPs via these SSAs as a possible new exposure route for human health remains unknown. The aim of this study was two-fold: (1) to examine if a selection of factors affects aerosolization processes of MNPs, and (2) to estimate human exposure to MNPs via aerosols inhalation. A laboratory-based bubble bursting mechanism, simulating the aerosolization process at sea, was used to investigate the influence of MNP as well as seawater characteristics. To determine the potential human exposure to microplastics via inhalation of SSAs, the results of the laboratory experiments were extrapolated to the field based on sea surface microplastic concentrations and the volume of inhaled aerosols. Enrichment seemed to be influenced by MNP size, concentration and polymer type. With higher enrichment for smaller particles and denser polymers. Experiments with different concentrations showed a larger range of variability but nonetheless lower concentrations seemed to result in higher enrichment, presumably due to lower aggregation. In addition to the MNP characteristics, the type of seawater used seemed to influence the aerosolization process. Our human exposure estimate to microplastic via inhalation of sea spray aerosols shows that in comparison with reported inhaled concentrations in urban and indoor environments, this exposure route seems negligible for microplastics. Following the business-as-usual scenario on plastic production, the daily plastic inhalation in coastal areas in 2100 is estimated to increase but remain far below 1 particle per day. This study shows that aerosolization of MNPs is a new plastic transport pathway to be considered, but in terms of human exposure it seems negligible compared to other more important sources of MNPs, based on current reported environmental concentrations.}, }
@article {pmid38708804, year = {2024}, author = {Burr, DJ and Drauschke, J and Kanevche, K and Kümmel, S and Stryhanyuk, H and Heberle, J and Perfumo, A and Elsaesser, A}, title = {Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {20}, number = {36}, pages = {e2400289}, doi = {10.1002/smll.202400289}, pmid = {38708804}, issn = {1613-6829}, support = {462858357//Deutsche Forschungsgemeinschaft/ ; Freigeist//Volkswagen Foundation/ ; 50WB1623//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; 50WB2023//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; }, mesh = {Spectroscopy, Fourier Transform Infrared/methods ; *Carbon Isotopes/chemistry ; Microscopy, Atomic Force ; Isotope Labeling/methods ; Nanotechnology/methods ; Escherichia coli/metabolism/growth &amp; development ; Glucose/metabolism ; }, abstract = {This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of [13]C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of [13]C-[13]C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.}, }
@article {pmid38707845, year = {2024}, author = {Rivas-Santisteban, J and Yubero, P and Robaina-Estévez, S and González, JM and Tamames, J and Pedrós-Alió, C}, title = {Quantifying microbial guilds.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae042}, pmid = {38707845}, issn = {2730-6151}, abstract = {The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.}, }
@article {pmid38706006, year = {2024}, author = {Liew, KJ and Shahar, S and Shamsir, MS and Shaharuddin, NB and Liang, CH and Chan, KG and Pointing, SB and Sani, RK and Goh, KM}, title = {Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {29}, pmid = {38706006}, issn = {2524-6372}, support = {FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; 4J549//UTM QuickWin grant/ ; 4J549//UTM QuickWin grant/ ; T2EP30123-0028//Singapore Ministry of Education ARC Tier 2 fund/ ; 1736255, 1849206, and 1920954//National Science Foundation/ ; }, abstract = {BACKGROUND: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.<br><br>RESULTS: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.<br><br>CONCLUSIONS: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.}, }
@article {pmid38705066, year = {2024}, author = {Shao, YH and Wu, JH and Chen, HW}, title = {Comammox Nitrospira cooperate with anammox bacteria in a partial nitritation-anammox membrane bioreactor treating low-strength ammonium wastewater at high loadings.}, journal = {Water research}, volume = {257}, number = {}, pages = {121698}, doi = {10.1016/j.watres.2024.121698}, pmid = {38705066}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology ; *Ammonium Compounds/metabolism ; Bacteria/metabolism ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; }, abstract = {Research has revealed that comammox Nitrospira and anammox bacteria engage in dynamic interactions in partial nitritation-anammox reactors, where they compete for ammonium and nitrite or comammox Nitrospria supply nitrite to anammox bacteria. However, two gaps in the literature are present: the know-how to manipulate the interactions to foster a stable and symbiotic relationship and the assessment of how effective this partnership is for treating low-strength ammonium wastewater at high hydraulic loads. In this study, we employed a membrane bioreactor designed to treat synthetic ammonium wastewater at a concentration of 60 mg N/L, reaching a peak loading of 0.36 g N/L/day by gradually reducing the hydraulic retention time to 4 hr. Throughout the experiment, the reactor achieved an approximately 80 % nitrogen removal rate through strategically adjusting intermittent aeration at every stage. Notably, the genera Ca. Kuenena, Nitrosomonas, and Nitrospira collectively constituted approximately 40 % of the microbial community. Under superior intermittent aeration conditions, the expression of comammox amoA was consistently higher than that of Nitrospira nxrB and AOB amoA in the biofilm, despite the higher abundance of Nitrosomonas than comammox Nitrospira, implying that the biofilm environment is favorable for fostering cooperation between comammox and anammox bacteria. We then assessed the in situ activity of comammox Nitrospira in the reactor by selectively suppressing Nitrosomonas using 1-octyne, thereby confirming that comammox Nitrospira played the primary role in facilitating the nitritation (33.1 % of input ammonium) rather than complete nitrification (7.3 % of input ammonium). Kinetic analysis revealed a specific ammonia-oxidizing rate 5.3 times higher than the nitrite-oxidizing rate in the genus Nitrospira, underscoring their critical role in supplying nitrite. These findings provide novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping the management of nitrogen cycling in engineered environments, and aiding the development of microbial ecology-driven wastewater treatment technologies.}, }
@article {pmid38703220, year = {2024}, author = {Zhao, L and Zhang, S and Xiao, R and Zhang, C and Lyu, Z and Zhang, F}, title = {Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {67}, pmid = {38703220}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Microbiome ; Humans ; Phylogeny ; Biodiversity ; Anti-Bacterial Agents/pharmacology ; Pesticides ; }, abstract = {Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.}, }
@article {pmid38702804, year = {2024}, author = {Das, R and Mishra, P and Mishra, B and Jha, R}, title = {Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {62}, pmid = {38702804}, issn = {1674-9782}, abstract = {BACKGROUND: Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17[th] embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.<br><br>RESULTS: The results were considered significantly different at P&#x2009;<&#x2009;0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d&#xa0;21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto&#xa0;1&#xa0;in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.<br><br>CONCLUSION: In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.}, }
@article {pmid38700528, year = {2024}, author = {Purahong, W and Ji, L and Wu, YT}, title = {Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {66}, pmid = {38700528}, issn = {1432-184X}, support = {MOST 107-2311-B-020-002//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Mycobiome ; *Wood/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Forests ; Tropical Climate ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Biodiversity ; }, abstract = {Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.}, }
@article {pmid38700397, year = {2024}, author = {Havlena, ZE and Hose, LD and DuChene, HR and Baker, GM and Powell, JD and Labrado, AL and Brunner, B and Jones, DS}, title = {Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA.}, journal = {Geobiology}, volume = {22}, number = {3}, pages = {e12594}, doi = {10.1111/gbi.12594}, pmid = {38700397}, issn = {1472-4669}, support = {80NSSC20K0619//NASA Exobiology/ ; //Rocky Mountain Association of Geologists/ ; }, mesh = {*Caves/microbiology ; *Minerals/analysis ; *Bacteria/classification/metabolism ; Nevada ; Archaea/metabolism ; Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics ; Sulfuric Acids ; Phylogeny ; Microbiota ; Calcium Sulfate/chemistry ; Microscopy, Electron, Scanning ; }, abstract = {Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ[34]SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.}, }
@article {pmid38697936, year = {2024}, author = {Nair, GR and Kooverjee, BB and de Scally, S and Cowan, DA and Makhalanyane, TP}, title = {Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38697936}, issn = {1574-6941}, support = {UID 110717//National Research Foundation of South Africa/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/enzymology/metabolism ; *Nutrients/metabolism ; *Soil/chemistry ; *Microbiota ; *Carbon/metabolism ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.}, }
@article {pmid38697548, year = {2024}, author = {Hendry, MJ and Kirk, L and Warner, J and Shaw, S and Peyton, BM and Schmeling, E and Barbour, SL}, title = {Selenate bioreduction in a large in situ field trial.}, journal = {The Science of the total environment}, volume = {933}, number = {}, pages = {172869}, doi = {10.1016/j.scitotenv.2024.172869}, pmid = {38697548}, issn = {1879-1026}, mesh = {*Water Pollutants, Chemical/metabolism/analysis ; *Selenic Acid/metabolism ; *Biodegradation, Environmental ; British Columbia ; Coal Mining ; Selenium/metabolism/analysis ; Mining ; }, abstract = {Removing selenium (Se) from mine effluent is a common challenge. A long-term, in situ experiment was conducted to bioremediate large volumes (up to 7500 m[c] d[-1]) of Se(VI)-contaminated water (mean 87 μg L[-1]) by injecting the water into a saturated waste rock fill (SRF) at a coal mining operation in Elk Valley, British Columbia, Canada. To stimulate/maintain biofilm growth in the SRF, labile organic carbon (methanol) and nutrients were added to the water prior to its injection. A conservative tracer (Br[-]) was also added to track the migration of injected water across the SRF, identify wells with minimal dilution and used to quantify the extent of bioreduction. The evolution of the Se species through the SRF was monitored in time and space for 201 d. Selenium concentrations of <3.8 μg L[-1] were attained in monitoring wells located 38 m from the injection wells after 114 to 141 d of operation. Concentrations of Se species in water samples from complementary long-term (351-498 d) column experiments using influent Se(VI) concentrations of 1.0 mg L[-1] were consistent with the results of the in situ experiment. Solid samples collected at the completion of the column experiments confirmed the presence of indigenous Se-reducing bacteria and that the sequestered Se was present as insoluble Se(0), likely in Se-S ring compounds. Based on the success of this ongoing bioremediation experiment, this technology is being applied at other mine sites.}, }
@article {pmid38696469, year = {2024}, author = {Freilich, MA and Poirier, C and Dever, M and Alou-Font, E and Allen, J and Cabornero, A and Sudek, L and Choi, CJ and Ruiz, S and Pascual, A and Farrar, JT and Johnston, TMS and D'Asaro, EA and Worden, AZ and Mahadevan, A}, title = {3D intrusions transport active surface microbial assemblages to the dark ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {19}, pages = {e2319937121}, pmid = {38696469}, issn = {1091-6490}, support = {N00014-16-1-3130//DOD | USN | Office of Naval Research (ONR)/ ; GBMF 3788//Gordon and Betty Moore Foundation (GBMF)/ ; Dimensions 2230811//National Science Foundation (NSF)/ ; N/A//DOD | National Defense Science and Engineering Graduate (NDSEG)/ ; Martin Fellowship//MIT | Environmental Solutions Initiative, Massachusetts Institute of Technology (ESI)/ ; Montrym Fund//MIT | Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology (EAPS, MIT)/ ; N00014-18-1-2416//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2139//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2431//DOD | USN | Office of Naval Research (ONR)/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism ; *Oceans and Seas ; Carbon/metabolism ; Carbon Cycle ; Chlorophyll/metabolism ; Ecosystem ; Phytoplankton/metabolism ; Seasons ; Biomass ; Microbiota/physiology ; Oxygen/metabolism ; }, abstract = {Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.}, }
@article {pmid38695873, year = {2024}, author = {Roh, H and Kannimuthu, D}, title = {Genomic and Transcriptomic Diversification of Flagellin Genes Provides Insight into Environmental Adaptation and Phylogeographic Characteristics in Aeromonas hydrophila.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {65}, pmid = {38695873}, issn = {1432-184X}, mesh = {*Flagellin/genetics ; *Aeromonas hydrophila/genetics/physiology ; *Transcriptome ; Phylogeography ; Adaptation, Physiological/genetics ; Phylogeny ; Biofilms/growth &amp; development ; }, abstract = {Aeromonas hydrophila is an opportunistic motile pathogen with a broad host range, infecting both terrestrial and aquatic animals. Environmental and geographical conditions exert selective pressure on both geno- and phenotypes of pathogens. Flagellin, directly exposed to external environments and containing important immunogenic epitopes, may display significant variability in response to external conditions. In this study, we conducted a comparative analysis of ~ 150 A. hydrophila genomes, leading to the identification of six subunits of the flagellin gene (fla-1 to fla-4, flaA, and flaB). Individual strains harbored different composition of flagellin subunits and copies. The composition of subunits showed distinct patterns depending on environmental sources. Strains from aquatic environments were mainly comprised of fla-1 to fla-4 subunits, while terrestrial strains predominated in groups harboring flaA and flaB subunits. Each flagellin showed varying levels of expression, with flaA and flaB demonstrating significantly higher expression compared to others. One of the chemotaxis pathways that control flagellin movement through a two-component system was significantly upregulated in flaA(+ 1)/flaB(+ 1) group, whereas flaA and flaB showed different transcriptomic expressions. The genes positively correlated with flaA expression were relevant to biofilm formation and bacterial chemotaxis, but flaB showed a negative correlation with the genes in ABC transporters and quorum sensing pathway. However, the expression patterns of fla-2 to fla-4 were identical. This suggests various types of flagellin subunits may have different biological functions. The composition and expression levels of flagellin subunits could provide valuable insights into the adaptation of A. hydrophila and the differences among strains in response to various external environments.}, }
@article {pmid38694807, year = {2024}, author = {Sumithra, TG and Sharma, SRK and Suresh, G and Gop, AP and Surya, S and Gomathi, P and Anil, MK and Sajina, KA and Reshma, KJ and Ebeneezar, S and Narasimapallavan, I and Gopalakrishnan, A}, title = {Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1356828}, pmid = {38694807}, issn = {1664-302X}, abstract = {INTRODUCTION: Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii.<br><br>METHODS: The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed.<br><br>RESULTS: A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, &#x2264;10 DPH (days post-hatching) and&#x2009;>&#x2009;10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations.<br><br>CONCLUSION: The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.}, }
@article {pmid38694752, year = {2024}, author = {Brame, JE and Liddicoat, C and Abbott, CA and Edwards, RA and Robinson, JM and Gauthier, NE and Breed, MF}, title = {The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.}, journal = {Ecology and evolution}, volume = {14}, number = {5}, pages = {e11239}, pmid = {38694752}, issn = {2045-7758}, abstract = {Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.}, }
@article {pmid38691424, year = {2024}, author = {Xiong, X and Othmer, HG and Harcombe, WR}, title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38691424}, issn = {1751-7370}, support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; }, mesh = {*Escherichia coli/drug effects/genetics/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.}, }
@article {pmid38691215, year = {2024}, author = {Tokash-Peters, AG and Niyonzima, JD and Kayirangwa, M and Muhayimana, S and Tokash, IW and Jabon, JD and Lopez, SG and Kearns, PJ and Woodhams, DC}, title = {Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {64}, pmid = {38691215}, issn = {1432-184X}, support = {DGE 1249946//Directorate for Biological Sciences/ ; 1950051//Directorate for Biological Sciences/ ; 1947684//National Science Foundation/ ; 1947684//National Science Foundation/ ; }, mesh = {Rwanda ; Animals ; *Microbiota ; *Culicidae/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; Mosquito Vectors/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Serratia/genetics/isolation &amp; purification/classification ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.}, }
@article {pmid38691135, year = {2024}, author = {Salem, MA and Nour El-Din, HT and Hashem, AM and Aziz, RK}, title = {Genome-Scale Investigation of the Regulation of azoR Expression in Escherichia coli Using Computational Analysis and Transposon Mutagenesis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {63}, pmid = {38691135}, issn = {1432-184X}, mesh = {*DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; *Escherichia coli Proteins/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Nitroreductases/genetics/metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Mutagenesis ; Genome, Bacterial ; Computational Biology ; Mutagenesis, Insertional ; }, abstract = {Bacterial azoreductases are enzymes that catalyze the reduction of ingested or industrial azo dyes. Although azoreductase genes have been well identified and characterized, the regulation of their expression has not been systematically investigated. To determine how different factors affect the expression of azoR, we extracted and analyzed transcriptional data from the Gene Expression Omnibus (GEO) resource, then confirmed computational predictions by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results showed that azoR expression was lower with higher glucose concentration, agitation speed, and incubation temperature, but higher at higher culture densities. Co-expression and clustering analysis indicated ten genes with similar expression patterns to azoR: melA, tpx, yhbW, yciK, fdnG, fpr, nfsA, nfsB, rutF, and chrR (yieF). In parallel, constructing a random transposon library in E. coli K-12 and screening 4320 of its colonies for altered methyl red (MR)-decolorizing activity identified another set of seven genes potentially involved in azoR regulation. Among these genes, arsC, relA, plsY, and trmM were confirmed as potential azoR regulators based on the phenotypic decolorization activity of their transposon mutants, and the expression of arsC and relA was confirmed, by qRT-PCR, to significantly increase in E. coli K-12 in response to different MR concentrations. Finally, the significant decrease in azoR transcription upon transposon insertion in arsC and relA (as compared to its expression in wild-type E. coli) suggests their probable involvement in azoR regulation. In conclusion, combining in silico analysis and random transposon mutagenesis suggested a set of potential regulators of azoR in E. coli.}, }
@article {pmid38690316, year = {2024}, author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C}, title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110421}, pmid = {38690316}, issn = {2352-3409}, abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.}, }
@article {pmid38688974, year = {2024}, author = {Morigasaki, S and Matsui, M and Ohtsu, I and Doi, Y and Kawano, Y and Nakai, R and Iwasaki, W and Hayashi, H and Takaya, N}, title = {Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9896}, pmid = {38688974}, issn = {2045-2322}, support = {JP19H05688//Japan Society for the Promotion of Science/ ; JP19H05683//Japan Society for the Promotion of Science/ ; JP19H05679//Japan Society for the Promotion of Science/ ; }, mesh = {*Fagopyrum ; *Soil Microbiology ; *Fertilizers ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Microbiota ; Nitrogen/metabolism/analysis ; Agriculture/methods ; }, abstract = {This study integrated bacterial community and soil chemicals to characterize the soil ecosystem in an open upland field managed by six controlled fertilizer programs using the minimum amount of pesticides. Amplicon sequencing the 16S rRNA gene revealed that inorganic nitrogen fertilizer and compost altered the diversity and structure of the soil bacterial community throughout buckwheat (Fagopyrum esculentum Moench 'Hitachiakisoba') cultivation. The bacterial community comprised three clusters that contained bacteria that are prevalent in soils fertilized with nitrogen (cluster 1, 340 taxa), without nitrogen and compost (cluster 2, 234 taxa), and with compost-fertilized (cluster 3, 296 taxa). Cluster 2 contained more taxa in Actinobacteriota and less in Acidobacteriota, and cluster 3 contained more taxa in Gemmatimonadota compared with the other clusters. The most frequent taxa in cluster 1 were within the Chloroflexi phylum. The bacterial community structure correlated with soil chemical properties including pH, total organic carbon, SO4[2-], soluble Ca[2+]. A co-occurrence network of bacterial taxa and chemicals identified key bacterial groups comprising the center of a community network that determined topology and dynamics of the network. Temporal dynamics of the bacterial community structure indicated that Burkholderiales were associated with buckwheat ripening, indicating plant-bacteria interaction in the ecosystem.}, }
@article {pmid38688113, year = {2024}, author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P}, title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {211}, number = {}, pages = {108639}, doi = {10.1016/j.plaphy.2024.108639}, pmid = {38688113}, issn = {1873-2690}, mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.}, }
@article {pmid38685217, year = {2024}, author = {Liu, Z and Zhang, J and Fan, C and Sun, S and An, X and Sun, Y and Gao, T and Zhang, D}, title = {Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum.}, journal = {Pesticide biochemistry and physiology}, volume = {201}, number = {}, pages = {105875}, doi = {10.1016/j.pestbp.2024.105875}, pmid = {38685217}, issn = {1095-9939}, mesh = {*Fusarium/genetics/physiology ; *Cucumis sativus/microbiology ; *Rhizosphere ; *Bacillus subtilis/genetics/physiology/metabolism ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Aluminum Silicates ; Plant Roots/microbiology ; }, abstract = {Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.}, }
@article {pmid38684474, year = {2024}, author = {Cohen, Y and Johnke, J and Abed-Rabbo, A and Pasternak, Z and Chatzinotas, A and Jurkevitch, E}, title = {Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38684474}, issn = {1574-6941}, support = {CH 731/2-1//Deutsche Forschungsgemeinschaft/ ; 1583/12//Israel Science Foundation/ ; }, mesh = {*Sewage/microbiology ; *Microbiota ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; Bdellovibrio/genetics/metabolism ; }, abstract = {Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.}, }
@article {pmid38683238, year = {2024}, author = {Cowan, DA and Albers, SV and Antranikian, G and Atomi, H and Averhoff, B and Basen, M and Driessen, AJM and Jebbar, M and Kelman, Z and Kerou, M and Littlechild, J and Müller, V and Schönheit, P and Siebers, B and Vorgias, K}, title = {Extremophiles in a changing world.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {2}, pages = {26}, pmid = {38683238}, issn = {1433-4909}, mesh = {*Extremophiles/metabolism/physiology ; Sustainable Development ; Adaptation, Physiological ; Extreme Environments ; Biotechnology ; }, abstract = {Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.}, }
@article {pmid38683223, year = {2024}, author = {Kunzler, M and Schlechter, RO and Schreiber, L and Remus-Emsermann, MNP}, title = {Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {62}, pmid = {38683223}, issn = {1432-184X}, mesh = {*Pantoea/genetics/metabolism/physiology/growth &amp; development ; *Pseudomonas/metabolism/genetics/growth &amp; development/physiology ; *Surface-Active Agents/metabolism ; }, abstract = {Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.}, }
@article {pmid38682902, year = {2024}, author = {Song, H-S and Lee, N-R and Kessell, AK and McCullough, HC and Park, S-Y and Zhou, K and Lee, D-Y}, title = {Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0130523}, pmid = {38682902}, issn = {2379-5077}, support = {2020R1A2C2007192//National Research Foundation of Korea (NRF)/ ; 32136-05-1- HD050//MAFRA | Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; //Nebraska Tobacco Settlement Biomedical Research Development Fund (NTSBRDF)/ ; 2125155//National Science Foundation (NSF)/ ; 2021R1F1A1064592//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Microbial Interactions/physiology ; Kinetics ; *Escherichia coli/metabolism ; Models, Biological ; Environment ; }, abstract = {Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.}, }
@article {pmid38680790, year = {2024}, author = {García, FM and Guerrero, SIB and la Peña, CG and Gutiérrez, DRA and Rodríguez, QKS and Herrera, CAM and Paniagua, FV and Velásquez, CD and Montoya, AC and Núñez, LMV}, title = {Bacteria in the blood of healthy stray dogs infested by ticks in northern Mexico.}, journal = {Journal of advanced veterinary and animal research}, volume = {11}, number = {1}, pages = {132-138}, pmid = {38680790}, issn = {2311-7710}, abstract = {OBJECTIVE: The objectives of this study were to determine the richness, abundance, and diversity of bacteria in stray dogs (Canis lupus familiaris) infested by ticks in Comarca Lagunera, northern Mexico, and to establish their pathogenic and or/zoonotic potential.<br><br>MATERIALS AND METHODS: Blood samples from 12 dogs were collected, and their deoxyribonucleic acid was extracted. The V3-V4 region of the 16S ribosomal ribunocleic acid gene was amplified by polymerase chain reaction. Next-generation sequencing (NGS) was performed on a MiSeq Illumina platform, and the data were analyzed using quantitative insights into microbial ecology.<br><br>RESULTS: The operational taxonomic units resulted in 23 phyla, 54 classes, 89 orders, 189 families, 586 genera, and 620 bacterial species; among them, 64 species and/or bacterial genera with pathogenic or zoonotic potential were identified, some of which have been reported in the literature as relevant to public health (Anaplasma phagocytophilum, Brucella spp., Clostridium spp., Corynebacterium affermentants, Cutibacterium spp., Dietzia spp., Ehrlichia canis, Fusobacterium necrophorum, Leptotrichia spp., Mycobacterium spp., Paracoccus spp., and Roseomonas gilardii).<br><br>CONCLUSION: This research offers relevant information on the prevalence of tick-borne diseases as well as other potential zoonotic diseases in the blood of stray dogs parasitized by ticks in northern Mexico. New molecular biology and massive NGS techniques may play an important role in the study and documentation of bacterial profiles from animals in close proximity to humans.}, }
@article {pmid38679176, year = {2024}, author = {Guo, Z and Ma, XS and Ni, SQ}, title = {Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding.}, journal = {Chemosphere}, volume = {358}, number = {}, pages = {142093}, doi = {10.1016/j.chemosphere.2024.142093}, pmid = {38679176}, issn = {1879-1298}, mesh = {*Nitrogen/metabolism ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *Oxidation-Reduction ; *Nitrogen Cycle ; Nitrification ; Ecosystem ; }, abstract = {COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4[+] to NO3[-] alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.}, }
@article {pmid38678007, year = {2024}, author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z}, title = {The role of rhizosphere phages in soil health.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38678007}, issn = {1574-6941}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; 42325704//National Natural Science Foundation of China/ ; //Nanjing Agricultural University/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteriophages/genetics ; *Microbiota ; *Bacteria/virology/genetics ; Gene Transfer, Horizontal ; Plants/microbiology/virology ; Ecosystem ; }, abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.}, }
@article {pmid38676557, year = {2024}, author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M}, title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38676557}, issn = {1751-7370}, support = {T 1218//Austrian Science Fund/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Phylogeny ; *Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Metagenome ; }, abstract = {Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification-the aerobic oxidation of ammonia to nitrite and further to nitrate-and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.}, }
@article {pmid38675977, year = {2024}, author = {Król, N and Chitimia-Dobler, L and Dobler, G and Kiewra, D and Czułowska, A and Obiegala, A and Zajkowska, J and Juretzek, T and Pfeffer, M}, title = {Identification of New Microfoci and Genetic Characterization of Tick-Borne Encephalitis Virus Isolates from Eastern Germany and Western Poland.}, journal = {Viruses}, volume = {16}, number = {4}, pages = {}, pmid = {38675977}, issn = {1999-4915}, support = {61508669//Pfizer (Germany)/ ; }, mesh = {*Encephalitis Viruses, Tick-Borne/genetics/classification/isolation &amp; purification ; Animals ; Poland ; Germany/epidemiology ; *Phylogeny ; *Encephalitis, Tick-Borne/virology/epidemiology ; Humans ; Ixodes/virology ; }, abstract = {(1) Background: Tick-borne encephalitis (TBE) is the most important tick-borne viral disease in Eurasia, although effective vaccines are available. Caused by the tick-borne encephalitis virus (TBEV, syn. Orthoflavivirus encephalitidis), in Europe, it is transmitted by ticks like Ixodes ricinus and Dermacentor reticulatus. TBEV circulates in natural foci, making it endemic to specific regions, such as southern Germany and northeastern Poland. Our study aimed to identify new TBEV natural foci and genetically characterize strains in ticks in previously nonendemic areas in Eastern Germany and Western Poland. (2) Methods: Ticks were collected from vegetation in areas reported by TBE patients. After identification, ticks were tested for TBEV in pools of a maximum of 10 specimens using real-time RT-PCR. From the positive TBEV samples, E genes were sequenced. (3) Results: Among 8400 ticks from 19 sites, I. ricinus (n = 4784; 56.9%) was predominant, followed by D. reticulatus (n = 3506; 41.7%), Haemaphysalis concinna (n = 108; 1.3%), and I. frontalis (n = 2; <0.1%). TBEV was detected in 19 pools originating in six sites. The phylogenetic analyses revealed that TBEV strains from Germany and Poland clustered with other German strains, as well as those from Finland and Estonia. (4) Conclusions: Although there are still only a few cases are reported from these areas, people spending much time outdoors should consider TBE vaccination.}, }
@article {pmid38674735, year = {2024}, author = {Isokpehi, RD and Kim, Y and Krejci, SE and Trivedi, VD}, title = {Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674735}, issn = {2076-2607}, support = {U41 HG006941/HG/NHGRI NIH HHS/United States ; U41HG006941/NH/NIH HHS/United States ; }, abstract = {Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.}, }
@article {pmid38674704, year = {2024}, author = {Wang, H and Pijl, A and Liu, B and Wamelink, W and Korthals, GW and Costa, OYA and Kuramae, EE}, title = {A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674704}, issn = {2076-2607}, abstract = {Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.}, }
@article {pmid38672854, year = {2024}, author = {Daval, C and Tran, T and Verdier, F and Martin, A and Alexandre, H and Grandvalet, C and Tourdot-Maréchal, R}, title = {Identification of Key Parameters Inducing Microbial Modulation during Backslopped Kombucha Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {38672854}, issn = {2304-8158}, support = {PO FEDER-FSE Bourgogne 2014/2020//European Regional Development Fund/ ; }, abstract = {The aim of this study was to assess the impact of production parameters on the reproducibility of kombucha fermentation over several production cycles based on backslopping. Six conditions with varying oxygen accessibility (specific interface surface) and initial acidity (through the inoculation rate) of the cultures were carried out and compared to an original kombucha consortium and a synthetic consortium assembled from yeasts and bacteria isolated from the original culture. Output parameters monitored were microbial populations, biofilm weight, key physico-chemical parameters and metabolites. Results highlighted the existence of phases in microbial dynamics as backslopping cycles progressed. The transitions between phases occurred faster for the synthetic consortium compared to the original kombucha. This led to microbial dynamics and fermentative kinetics that were reproducible over several cycles but that could also deviate and shift abruptly to different behaviors. These changes were mainly induced by an increase in the Saccharomyces cerevisiae population, associated with an intensification of sucrose hydrolysis, sugar consumption and an increase in ethanol content, without any significant acceleration in the rate of acidification. The study suggests that the reproducibility of kombucha fermentations relies on high biodiversity to slow down the modulations of microbial dynamics induced by the sustained rhythm of backslopping cycles.}, }
@article {pmid38670213, year = {2024}, author = {Sun, Y and Du, P and Li, H and Zhou, K and Shou, L and Chen, J and Meng Li, }, title = {Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {119011}, doi = {10.1016/j.envres.2024.119011}, pmid = {38670213}, issn = {1096-0953}, mesh = {*Estuaries ; China ; *Nitrogen/metabolism/analysis ; *Oxygen/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S ; Nitrogen Cycle ; }, abstract = {It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO4[3-], and distance offshore (p < 0.05). Water depth, NH4[+], and PO4[3-] were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3[-] (or NO2[-]) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.}, }
@article {pmid38668461, year = {2024}, author = {Takács, E and Lázár, D and Siakwa, A and Klátyik, S and Mörtl, M and Kocsányi, L and Barócsi, A and Lenk, S and Lengyel, E and Székács, A}, title = {Ecotoxicological Evaluation of Safener and Antimicrobial Additives in Isoxaflutole-Based Herbicide Formulations.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668461}, issn = {2305-6304}, support = {NVKP_16-1-2016-0049//Hungarian National Research, Development and Innovation Office within the National Com-petitiveness and Excellence Program/ ; NKFIH-3524-1/2022//National Research, Development and Innovation Fund by the Hungarian Ministry of Culture and Innovation/ ; TKP2021-NVA-22//Thematic Excellence Program 2021, National Defense, National Security Sub-Program/ ; }, abstract = {The environmental load by isoxaflutole and its formulated herbicide products has increasingly become apparent because, after the ban of atrazine, isoxaflutole has become its replacement active ingredient (a.i.). Obtaining information regarding the fate of this a.i. in environmental matrices and its ecotoxicological effects on aquatic organisms is essential for the risk assessment of the herbicide. In this study, the effects of Merlin Flexx- and Merlin WG75 formulated isoxaflutole-based herbicide products and two selected additives (cyprosulfamide safener and 1,2-benzisothiazol-3(2H)-one antimicrobial agent) were investigated on Raphidocelis subcapitata in growth inhibition assays. In ecotoxicological tests, two conventional (optical density and chlorophyll-a content) and two induced fluorescence-based (Fv*/Fp: efficiency of the photosystem PSII and Rfd* changes in the observed ratio of fluorescence decrease) endpoints were determined by UV-spectrophotometer and by our FluoroMeter Module, respectively. Furthermore, dissipation of isoxaflutole alone and in its formulated products was examined by an HPLC-UV method. In ecotoxicological assays, the fluorescence-based Rfd* was observed as the most sensitive endpoint. In this study, the effects of the safener cyprosulfamide and the antimicrobial agent 1,2-benzisothiazol-3(2H)-one on R. subcapitata is firstly reported. The results indicated that the isoxaflutole-equivalent toxicity of the mixture of the isoxaflutole-safener-antimicrobial agent triggered lower toxicity (EC50 = 2.81 ± 0.22 mg/L) compared to the individual effect of the a.i. (EC50 = 0.02 ± 0.00 mg/L). The Merlin Flexx formulation (EC50 = 27.04 ± 1.41 mg/L) was found to be approximately 50-fold less toxic than Merlin WG75, which can be explained by the different chemical characteristics and quantity of additives in them. The additives influenced the dissipation of the a.i. in Z8 medium, as the DT50 value decreased by approximately 1.2- and 3.5-fold under light and dark conditions, respectively.}, }
@article {pmid38668249, year = {2024}, author = {Plewa-Tutaj, K and Twarużek, M and Kosicki, R and Soszczyńska, E}, title = {Analysis of Mycotoxins and Cytotoxicity of Airborne Molds Isolated from the Zoological Garden-Screening Research.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {4}, pages = {}, pmid = {38668249}, issn = {2076-0817}, support = {DEC390 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; }, mesh = {*Mycotoxins/toxicity/analysis ; *Air Microbiology ; *Penicillium/isolation &amp; purification/metabolism ; *Aspergillus/isolation &amp; purification/metabolism ; Animals ; Fungi/isolation &amp; purification/drug effects/genetics ; Chromatography, High Pressure Liquid ; Animals, Zoo/microbiology ; Gardens ; Tandem Mass Spectrometry ; }, abstract = {OBJECTIVE: The objective of this paper was to assess the airborne mold contamination, secondary metabolite profiles, and cytotoxicity of the dominant fungal species isolated from the air in selected rooms at a Zoological Garden.<br><br>MATERIALS AND METHODS: Fungal concentrations were measured with MAS-100 air samplers. The collected airborne fungi were identified using a combination of morphological and molecular methods. The cytotoxicity of 84 strains belonging to two Penicillium and Aspergillus genera was determined using the quantitative colorimetric MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium salt) assay. The mycotoxins were detected using high-performance liquid chromatography (HPLC) with a mass spectrometry detector.<br><br>RESULTS: The ITS gene was amplified and sequenced to identify the 132 species. For mycotoxicological and cytotoxicity analyses, 52 Penicillium isolates and 32 Aspergillus representatives were selected. Cytotoxicity was confirmed in 97.6% of cases analyzed. Using the LC-MS/MS method, 42 out of 84 strains produced at least one of the following toxins: ochratoxin A, ochratoxin B, patulin, gliotoxin, roquefortine C, griseofulvin, sterigmatocystin, fumonisin B2, moniliformin, and mycophenolic acid.<br><br>CONCLUSIONS: Analytical methods for assessing the presence of mycotoxins in fungal isolates collected directly from the air have proven to be an effective tool. Our research provides new information on the occurrence of potentially toxin-producing molds within a zoo.}, }
@article {pmid38665977, year = {2023}, author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, &#x17d; and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ}, title = {Fungal Planet description sheets: 1550-1613.}, journal = {Persoonia}, volume = {51}, number = {}, pages = {280-417}, pmid = {38665977}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.}, }
@article {pmid38664322, year = {2024}, author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L}, title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {6}, pages = {63}, pmid = {38664322}, issn = {1522-9602}, support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; }, abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.}, }
@article {pmid38663208, year = {2024}, author = {Ceballos-Escalera, A and Pous, N and Bañeras, L and Balaguer, MD and Puig, S}, title = {Advancing towards electro-bioremediation scaling-up: On-site pilot plant for successful nitrate-contaminated groundwater treatment.}, journal = {Water research}, volume = {256}, number = {}, pages = {121618}, doi = {10.1016/j.watres.2024.121618}, pmid = {38663208}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Water Pollutants, Chemical ; Pilot Projects ; *Water Purification/methods ; Denitrification ; Spain ; Bioreactors ; }, abstract = {The potential of nitrate electro-bioremediation has been fully demonstrated at the laboratory scale, although it has not yet been fully implemented due to the challenges associated with scaling-up bioelectrochemical reactors and their on-site operation. This study describes the initial start-up and subsequent stable operation of an electro-bioremediation pilot plant for the treatment of nitrate-contaminated groundwater on-site (Navata site, Spain). The pilot plant was operated under continuous flow mode for 3 months, producing an effluent suitable for drinking water in terms of nitrates and nitrites (<50 mg NO3[-] L[-1]; 0 mg NO2[-] L[-1]). A maximum nitrate removal rate of 0.9 ± 0.1 kg NO3[-] m[-3] d[-1] (efficiency 82 ± 18 %) was achieved at a cathodic hydraulic retention time (HRTcat) of 2.0 h with a competitive energy consumption of 4.3 ± 0.4 kWh kg[-1] NO3[-]. Under these conditions, the techno-economic analysis estimated an operational cost of 0.40 € m[-3]. Simultaneously, microbiological analyses revealed structural heterogeneity in the reactor, with denitrification functionality concentrated predominantly from the centre to the upper section of the reactor. The most abundant groups were Pseudomonadaceae, Rhizobiaceae, Gallionellaceae, and Xanthomonadaceae. In conclusion, this pilot plant represents a significant advancement in implementing this technology on a larger scale, validating its effectiveness in terms of nitrate removal and cost-effectiveness. Moreover, the results validate the electro-bioremediation in a real environment and encourage further investigation of its potential as a water treatment.}, }
@article {pmid38662665, year = {2024}, author = {Hulatt, CJ and Suzuki, H and Détain, A and Wijffels, RH and Leya, T and Posewitz, MC}, title = {The genome of the Arctic snow alga Limnomonas spitsbergensis (Chlamydomonadales).}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, pmid = {38662665}, issn = {2160-1836}, support = {749910//Marie Sk&#x142;odowska-Curie Individual Fellowship/ ; //European Union's Horizon 2020/ ; //Posewitz lab/ ; //Colorado School of Mines/ ; //National Center for Genome Resources/ ; NN9634K//UNINETT Sigma-2 Compute Infrastructure/ ; }, mesh = {Arctic Regions ; *Snow/microbiology ; *Molecular Sequence Annotation ; Phylogeny ; Chlorophyta/genetics ; Genomics/methods ; }, abstract = {Snow algae are a diverse group of extremophilic microeukaryotes found on melting polar and alpine snowfields. They play an important role in the microbial ecology of the cryosphere, and their propagation on snow and ice surfaces may in part accelerate climate-induced melting of these systems. High-quality snow algae genomes are needed for studies on their unique physiology, adaptive mechanisms, and genome evolution under multiple forms of stress, including cold temperatures and intense sunlight. Here, we assembled and annotated the genome of Limnomonas spitsbergensis, a cryophilic biciliate green alga originally isolated from melting snow on Svalbard, in the Arctic. The L. spitsbergensis genome assembly is based primarily on the use of PacBio long reads and secondly Illumina short reads, with an assembly size of 260.248 Mb in 124 contigs. A combination of 3 alternative annotation strategies was used including protein homology, RNA-seq evidence, and PacBio full-length transcript isoforms. The best merged set of annotations identified 18,277 protein-coding genes, which were 95.2% complete based on Benchmarking Universal Single-Copy Orthologs analysis. We also provide the annotated mitogenome, which is a relatively large 77.942 kb circular mapping sequence containing extensive repeats. The L. spitsbergensis genome will provide a new resource for research on snow algae adaptation, behavior, and natural selection in unique, low-temperature terrestrial environments that are under threat from climate change.}, }
@article {pmid38662575, year = {2024}, author = {Liu, X and Salles, JF}, title = {Bridging ecological assembly process and community stability upon bacterial invasions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38662575}, issn = {1751-7370}, mesh = {*Soil Microbiology ; *Escherichia coli/genetics ; *Microbiota ; Ecosystem ; Microbial Interactions ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.}, }
@article {pmid38662080, year = {2024}, author = {Ezhumalai, G and Arun, M and Manavalan, A and Rajkumar, R and Heese, K}, title = {A Holistic Approach to Circular Bioeconomy Through the Sustainable Utilization of Microalgal Biomass for Biofuel and Other Value-Added Products.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {61}, pmid = {38662080}, issn = {1432-184X}, mesh = {*Microalgae/metabolism/growth &amp; development ; *Biofuels ; *Biomass ; Cyanobacteria/metabolism ; Seaweed/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Emissions from transportation and industry primarily cause global warming, leading to floods, glacier melt, and rising seas. Widespread greenhouse gas emissions and resulting global warming pose significant risks to the environment, economy, and society. The need for alternative fuels drives the development of third-generation feedstocks: microalgae, seaweed, and cyanobacteria. These microalgae offer traits like rapid growth, high lipid content, non-competition with human food, and growth on non-arable land using brackish or waste water, making them promising for biofuel. These unique phototrophic organisms use sunlight, water, and carbon dioxide (CO2) to produce biofuels, biochemicals, and more. This review delves into the realm of microalgal biofuels, exploring contemporary methodologies employed for lipid extraction, significant value-added products, and the challenges inherent in their commercial-scale production. While the cost of microalgae bioproducts remains high, utilizing wastewater nutrients for cultivation could substantially cut production costs. Furthermore, this review summarizes the significance of biocircular economy approaches, which encompass the utilization of microalgal biomass as a feed supplement and biofertilizer, and biosorption of heavy metals and dyes. Besides, the discussion extends to the in-depth analysis and future prospects on the commercial potential of biofuel within the context of sustainable development. An economically efficient microalgae biorefinery should prioritize affordable nutrient inputs, efficient harvesting techniques, and the generation of valuable by-products.}, }
@article {pmid38661241, year = {2024}, author = {Xiong, H and Zhang, X and Zeng, H and Xie, S and Yi, S}, title = {Experience of diet in patients with inflammatory bowel disease: A thematic synthesis of qualitative studies.}, journal = {Journal of clinical nursing}, volume = {33}, number = {8}, pages = {3283-3293}, doi = {10.1111/jocn.17186}, pmid = {38661241}, issn = {1365-2702}, mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy/psychology ; *Qualitative Research ; *Diet/psychology/methods ; Adult ; Male ; Female ; Middle Aged ; }, abstract = {AIM: To synthesise the dietary expesriences of patients with inflammatory bowel disease by reviewing relevant qualitative studies.<br><br>BACKGROUND: Diet plays a crucial role in the development and progression of inflammatory bowel disease (IBD). There is no specific diet that can be recommended for all patients. We conducted a synthesis of qualitative studies to gain a comprehensive understanding of the dietary management experience of patients with IBD, aiming to provide better dietary guidance in the future.<br><br>DESIGN: A qualitative synthesis was conducted following the Thomas and Harden method and reported following the ENTREQ statement.<br><br>METHODS: Qualitative studies were systematically searched in five electronic databases: PubMed, PsycINFO, Embase, CINAHL, and Web of Science. There was no time limit for publication, and all database searches were up to 10 May, 2023. The Joanna Briggs Institute Qualitative Assessment and Review Instrument was utilised to appraise the quality of the included studies. Data for inclusion in articles were extracted and analysed using a thematic synthesis method.<br><br>RESULTS: Six studies involving 119 patients were eventually included. The studies were conducted in six different countries. Four major themes were identified: the diet of patients with IBD is completely different from the normal one; manage symptoms and live with the disease by modifying diet; psychological adjustment to eating (be frustrated; worried and afraid; feel ashamed; growth and resilience); barriers and challenges (barriers from perceived social support; conflicts between diet and nutrition; challenges from food hedonism and cravings).<br><br>CONCLUSIONS: Patients with IBD highlighted the distinction between their diet and the normal diet. Dietary modifications were used as a way to manage symptoms and live with the disease. In addition to physical symptoms, patients experienced diet-related psychological changes. Dietary modifications in patients with IBD encounters difficulties and challenges, necessitating prompt guidance and intervention. (1) The implementation of dietary modifications in patients with IBD encounters numerous obstacles and complexities, necessitating prompt guidance and intervention.<br><br>No patient or public contribution.<br><br>REGISTRATION: The protocol was registered with PROSPERO (CRD42023391545).}, }
@article {pmid38660030, year = {2024}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Dimitrov, MR and Cantarella, H and Kuramae, EE}, title = {Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.}, journal = {MethodsX}, volume = {12}, number = {}, pages = {102699}, pmid = {38660030}, issn = {2215-0161}, abstract = {In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).}, }
@article {pmid38659931, year = {2024}, author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M}, title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38659931}, issn = {2692-8205}, support = {K08 DK110532/DK/NIDDK NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; R01 AI171100/AI/NIAID NIH HHS/United States ; }, abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.}, }
@article {pmid38658559, year = {2024}, author = {Chen, KH and Feng, J and Bodelier, PLE and Yang, Z and Huang, Q and Delgado-Baquerizo, M and Cai, P and Tan, W and Liu, YR}, title = {Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3471}, pmid = {38658559}, issn = {2041-1723}, support = {32071595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371731//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Oryza/metabolism/microbiology ; *Denitrification ; *Soil Microbiology ; *Oxidation-Reduction ; China ; *Soil/chemistry ; Aerobiosis ; Bacteria/metabolism/genetics/classification ; Nitrous Oxide/metabolism ; Phylogeny ; Carbon Isotopes/metabolism ; Metagenome ; }, abstract = {Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and [13]CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, [13]CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating [13]C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of [13]C-metagenome-assembled genomes and [13]C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.}, }
@article {pmid38658525, year = {2024}, author = {Arthofer, P and Panhölzl, F and Delafont, V and Hay, A and Reipert, S and Cyran, N and Wienkoop, S and Willemsen, A and Sifaoui, I and Arberas-Jiménez, I and Schulz, F and Lorenzo-Morales, J and Horn, M}, title = {A giant virus infecting the amoeboflagellate Naegleria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3307}, pmid = {38658525}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; 101039843//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 891572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; P37198-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, mesh = {*Genome, Viral/genetics ; *Giant Viruses/genetics/classification/ultrastructure/isolation &amp; purification/physiology ; *Naegleria/genetics/virology ; Naegleria fowleri/genetics/isolation &amp; purification ; Phylogeny ; Humans ; }, abstract = {Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.}, }
@article {pmid38657743, year = {2024}, author = {Atasoy, M and Scott, WT and Regueira, A and Mauricio-Iglesias, M and Schaap, PJ and Smidt, H}, title = {Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches.}, journal = {Biotechnology advances}, volume = {73}, number = {}, pages = {108363}, doi = {10.1016/j.biotechadv.2024.108363}, pmid = {38657743}, issn = {1873-1899}, mesh = {Bioreactors/microbiology ; *Fatty Acids, Volatile/metabolism ; Kinetics ; *Metabolic Networks and Pathways ; Models, Biological ; *Microbiota ; }, abstract = {In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.}, }
@article {pmid38657507, year = {2024}, author = {Fu, Y and Jia, F and Su, J and Xu, X and Zhang, Y and Li, X and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM and Wang, F}, title = {Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134252}, doi = {10.1016/j.jhazmat.2024.134252}, pmid = {38657507}, issn = {1873-3336}, mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Diet ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.}, }
@article {pmid38657451, year = {2024}, author = {Guo, D and Tian, K and Peng, X and Liu, S and Xu, X and Tian, W}, title = {Cadmium/zinc stresses and plant cultivation influenced soil microflora: a pot experiment conducted in field.}, journal = {Ecotoxicology and environmental safety}, volume = {277}, number = {}, pages = {116384}, doi = {10.1016/j.ecoenv.2024.116384}, pmid = {38657451}, issn = {1090-2414}, mesh = {*Soil Microbiology ; *Cadmium/toxicity ; *Zinc/toxicity ; *Soil Pollutants/toxicity ; *Rhizosphere ; *Biodegradation, Environmental ; *Fungi/drug effects ; *Bacteria/drug effects/genetics ; Soil/chemistry ; Microbiota/drug effects ; Metals, Heavy/toxicity ; Stress, Physiological ; }, abstract = {It's of great challenge to address for heavy metal-contaminated soil. Once the farmland is contaminated with heavy metals, the microbial ecology of the plant rhizosphere will change, which in turn impacts crop productivity and quality. However, few studies have explored the effects of heavy metals on plant rhizosphere microbes in farmland and the role that plant cultivation plays in such a phytoremediation practice. In this study, the impacts of comfrey (Symphytum officinale L.) cultivation and the stresses of cadmium/zinc (Cd/Zn) on rhizosphere soil microflora were examined. Microbial DNA was collected from soils to evaluate the prevalence of bacteria and fungi communities in rhizosphere soils. High-throughput 16 S rRNA sequencing was used to determine the diversity of the bacterial and fungal communities. The results showed that growing comfrey on polluted soils reduced the levels of Cd and Zn from the vertical profile. Both the comfrey growth and Cd/Zn stresses affected the community of rhizosphere microorganisms (bacteria or fungi). Additionally, the analysis of PCoA and NMDS indicated that the cultivation of comfrey significantly changed the bacterial composition and structure of unpolluted soil. Comfrey cultivation in polluted and unpolluted soils did not result in much variance in the fungi's species composition, but the fungal compositions of the two-type soils were noticeably different. This work provided a better understanding of the impacts of Cd/Zn stresses and comfrey cultivation on rhizosphere microbial community, as well as new insight into phytoremediation of heavy metal-contaminated soils.}, }
@article {pmid38655503, year = {2024}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Arens, F and Airo, A and Ganzert, L and Zamorano, P and Schulze-Makuch, D and Wagner, D}, title = {Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis.}, journal = {PNAS nexus}, volume = {3}, number = {4}, pages = {pgae123}, pmid = {38655503}, issn = {2752-6542}, abstract = {Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.}, }
@article {pmid38654537, year = {2024}, author = {Zhu 朱墨, M and Zhang, W and Duan, X and Yan, S and Cai, Y and Gong, S and Fahad, S and Qiu, Z}, title = {Biocontrol Potential of Cladosporium sphaerospermum Against the Wheat Powdery Mildew Fungus Blumeria graminis f. sp. tritici.}, journal = {Plant disease}, volume = {108}, number = {10}, pages = {2983-2988}, doi = {10.1094/PDIS-02-24-0433-SC}, pmid = {38654537}, issn = {0191-2917}, mesh = {*Ascomycota/physiology ; *Cladosporium/physiology ; *Triticum/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Spores, Fungal/physiology ; Pest Control, Biological ; Biomass ; }, abstract = {Cladosporium spp. are known to be mycoparasites and inhibit phytopathogenic fungi. However, so far, little information is available on the impact of Cladosporium spp. on powdery mildews. Based on the morphological characteristics and molecular analysis, C. sphaerospermum was identified as a mycoparasite on the wheat powdery mildew fungus Blumeria graminis f. sp. tritici (Bgt), recently named B. graminis s. str. C. sphaerospermum was capable of preventing colony formation and conidial distribution of Bgt. The biomasses of Bgt notably decreased by 1.3, 2.2, 3.6, and 3.8 times at 2, 4, 6, and 8 days postinoculation (dpi), respectively. In addition, biomasses of C. sphaerospermum at 2, 4, 6, and 8 dpi significantly increased to 5.6, 13.9, 18.2, and 67.3 times, respectively. In vitro, C. sphaerospermum exudates significantly impaired appressorial formation of Bgt. Thus, C. sphaerospermum acts as a potential biological control agent by suppressing the formation, distribution, and development of Bgt conidia and is a viable alternative for managing the wheat powdery mildew. These results suggest that C. sphaerospermum is an antagonistic parasite of the wheat powdery mildew fungus and, hence, provide new knowledge about the biological control of phytopathogenic fungi.}, }
@article {pmid38653968, year = {2024}, author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS}, title = {Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3421}, pmid = {38653968}, issn = {2041-1723}, support = {PZ00P3_193240//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Fresh Water/microbiology ; *Phylogeny ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Evolution, Molecular ; Genome Size ; Proteome/genetics/metabolism ; }, abstract = {The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.}, }
@article {pmid38653406, year = {2024}, author = {Wu, T and Ding, J and Zhao, YJ and Ding, L and Zang, Y and Sun, HJ and Zhong, L and Pang, JW and Li, Y and Ren, NQ and Yang, SS}, title = {Microplastics shaped performance, microbial ecology and community assembly in simultaneous nitrification, denitrification and phosphorus removal process.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172651}, doi = {10.1016/j.scitotenv.2024.172651}, pmid = {38653406}, issn = {1879-1026}, mesh = {*Nitrification ; *Denitrification ; *Phosphorus/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; *Waste Disposal, Fluid/methods ; *Microplastics ; Wastewater ; Microbiota ; }, abstract = {The widespread use of microplastics (MPs) has led to an increase in their discharge to wastewater treatment plants. However, the knowledge of impact of MPs on macro-performance and micro-ecology in simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) systems is limited, hampering the understanding of potential risks posed by MPs. This study firstly comprehensively investigated the performance, species interactions, and community assembly under polystyrene (PS) and polyvinyl chloride (PVC) exposure in SNDPR systems. The results showed under PS (1, 10 mg/L) and PVC (1, 10 mg/L) exposure, total nitrogen removal was reduced by 3.38-10.15 %. PS and PVC restrained the specific rates of nitrite and nitrate reduction (SNIRR, SNRR), as well as the activities of nitrite and nitrate reductase enzymes (NIR, NR). The specific ammonia oxidation rate (SAOR) and activity of ammonia oxidase enzyme (AMO) were reduced only at 10 mg/L PVC. PS and PVC enhanced the size of co-occurrence networks, niche breadth, and number of key species while decreasing microbial cooperation by 5.85-13.48 %. Heterogeneous selection dominated microbial community assembly, and PS and PVC strengthened the contribution of stochastic processes. PICRUSt prediction further revealed some important pathways were blocked by PS and PVC. Together, the reduced TN removal under PS and PVC exposure can be attributed to the inhibition of SAOR, SNRR, and SNIRR, the restrained activities of NIR, NR, and AMO, the changes in species interactions and community assembly mechanisms, and the suppression of some essential metabolic pathways. This paper offers a new perspective on comprehending the effects of MPs on SNDPR systems.}, }
@article {pmid38651910, year = {2024}, author = {Rodríguez-Ramos, J and Nicora, CD and Purvine, SO and Borton, MA and McGivern, BB and Hoyt, DW and Lipton, MS and Wrighton, KC}, title = {Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0003324}, pmid = {38651910}, issn = {2576-098X}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; Award 1781//Joint Genome Institute Large-scale sequencing award/ ; DE-AC05-76RL01830//Office of Biological and Environmental Research/ ; DE-SC0018170//Subsurface Biogeochemical Research program/ ; }, abstract = {Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.}, }
@article {pmid38648266, year = {2024}, author = {Ramoneda, J and Fan, K and Lucas, JM and Chu, H and Bissett, A and Strickland, MS and Fierer, N}, title = {Ecological relevance of flagellar motility in soil bacterial communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38648266}, issn = {1751-7370}, support = {P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; 2131837//US National Science Foundation/ ; }, mesh = {*Flagella/genetics/physiology ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Soil/chemistry ; Metagenome ; Genome, Bacterial ; }, abstract = {Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.}, }
@article {pmid38648112, year = {2024}, author = {Temple, C and Blouin, AG and Boezen, D and Botermans, M and Durant, L and De Jonghe, K and de Koning, P and Goedefroit, T and Minet, L and Steyer, S and Verdin, E and Zwart, M and Massart, S}, title = {Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems.}, journal = {Phytopathology}, volume = {114}, number = {7}, pages = {1680-1688}, doi = {10.1094/PHYTO-06-23-0194-R}, pmid = {38648112}, issn = {0031-949X}, mesh = {*Plant Diseases/virology ; *Hemiptera/virology ; *Vegetables/virology ; Solanum lycopersicum/virology ; Animals ; Switzerland ; Insect Vectors/virology ; Crops, Agricultural/virology ; Host Specificity ; }, abstract = {In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.}, }
@article {pmid38647288, year = {2024}, author = {Waegenaar, F and García-Timermans, C and Van Landuyt, J and De Gusseme, B and Boon, N}, title = {Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0004224}, pmid = {38647288}, issn = {1098-5336}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; S006221N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Enterobacteriaceae/physiology/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Quality ; Water Purification ; Water Microbiology ; Water Supply ; }, abstract = {UNLABELLED: Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.<br><br>IMPORTANCE: The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.}, }
@article {pmid38646773, year = {2024}, author = {Weng, LY and Luan, DD and Zhou, DP and Guo, QG and Wang, GZ and Zhang, JL}, title = {Improving crop health by synthetic microbial communities: Progress and prospects.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {3}, pages = {847-857}, doi = {10.13287/j.1001-9332.202403.028}, pmid = {38646773}, issn = {1001-9332}, mesh = {*Crops, Agricultural/growth &amp; development/microbiology ; *Microbiota ; *Rhizosphere ; Soil Microbiology ; Synthetic Biology/methods ; Agriculture/methods ; }, abstract = {Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.}, }
@article {pmid38643981, year = {2024}, author = {Haller, F and Jimenez, K and Baumgartner, M and Lang, M and Klotz, A and Jambrich, M and Busslinger, G and Müllauer, L and Khare, V and Gasche, C}, title = {Nfe2l2/NRF2 Deletion Attenuates Tumorigenesis and Increases Bacterial Diversity in a Mouse Model of Lynch Syndrome.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {17}, number = {7}, pages = {311-324}, doi = {10.1158/1940-6207.CAPR-23-0478}, pmid = {38643981}, issn = {1940-6215}, support = {P32302FW//Austrian Science Fund (FWF)/ ; }, mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology/metabolism ; *MutS Homolog 2 Protein/genetics/metabolism ; Humans ; *Mice, Inbred C57BL ; *Disease Models, Animal ; Carcinogenesis/genetics/pathology ; Mice, Knockout ; Female ; Intestinal Mucosa/pathology/metabolism/microbiology ; Male ; }, abstract = {Lynch syndrome (LS) is the most prevalent heritable form of colorectal cancer. Its early onset and high lifetime risk for colorectal cancer emphasize the necessity for effective chemoprevention. NFE2L2 (NRF2) is often considered a potential druggable target, and many chemopreventive compounds induce NRF2. However, although NRF2 counteracts oxidative stress, it is also overexpressed in colorectal cancer and may promote tumorigenesis. In this study, we evaluated the role of NRF2 in the prevention of LS-associated neoplasia. We found increased levels of NRF2 in intestinal epithelia of mice with intestinal epithelium-specific Msh2 deletion (MSH2ΔIEC) compared with C57BL/6 (wild-type) mice, as well as an increase in downstream NRF2 targets NAD(P)H dehydrogenase (quinone 1) and glutamate-cysteine ligase catalytic subunit. Likewise, NRF2 levels were increased in human MSH2-deficient LS tumors compared with healthy human controls. In silico analysis of a publicly accessible RNA sequencing LS dataset also found an increase in downstream NRF2 targets. Upon crossing MSH2ΔIEC with Nrf2null (MSH2ΔIECNrf2null) mice, we unexpectedly found reduced tumorigenesis in MSH2ΔIECNrf2null mice compared with MSH2ΔIEC mice after 40 weeks, which occurred despite an increase in oxidative damage in MSH2ΔIECNrf2null mice. The loss of NRF2 impaired proliferation as seen by Ki67 intestinal staining and in organoid cultures. This was accompanied by diminished WNT/β-catenin signaling, but apoptosis was unaffected. Microbial α-diversity increased over time with the loss of NRF2 based upon 16S rRNA gene amplicon sequencing of murine fecal samples. Altogether, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. Activation of NRF2 may not be a feasible strategy for chemoprevention in LS. Prevention Relevance: Patients with LS have an early onset and high lifetime risk for colorectal cancer. In this study, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. This suggests that NRF2 may not be a tumor suppressor in this specific context.}, }
@article {pmid38643524, year = {2024}, author = {Mishra, S and Zhang, X and Yang, X}, title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.}, journal = {Microbiological research}, volume = {284}, number = {}, pages = {127726}, doi = {10.1016/j.micres.2024.127726}, pmid = {38643524}, issn = {1618-0623}, mesh = {Bacteria/genetics/classification/metabolism ; Metagenomics ; Microbiota/physiology ; *Plant Development ; *Plant Roots/microbiology ; *Plants/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.}, }
@article {pmid38642761, year = {2024}, author = {Wu, WF and Li, XY and Chen, SC and Jin, BJ and Wu, CY and Li, G and Sun, CL and Zhu, YG and Lin, XY}, title = {Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172622}, doi = {10.1016/j.scitotenv.2024.172622}, pmid = {38642761}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Fertilizers ; *Nitrogen ; *Fungi/physiology ; Mycobiome ; Agriculture ; Microbiota ; Plant Leaves/microbiology ; }, abstract = {The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.}, }
@article {pmid38638900, year = {2024}, author = {Yang, W and Li, X and Yan, H and Sun, Y and Wu, D and Du, Y and Luo, Y}, title = {Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1379566}, pmid = {38638900}, issn = {1664-302X}, abstract = {INTRODUCTION: At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.<br><br>METHODS: The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.<br><br>RESULTS: First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.<br><br>DISCUSSION: Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.}, }
@article {pmid38638570, year = {2024}, author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F}, title = {Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation.}, journal = {iScience}, volume = {27}, number = {5}, pages = {109596}, pmid = {38638570}, issn = {2589-0042}, abstract = {The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.}, }
@article {pmid38636749, year = {2024}, author = {Xu, Y and Niu, C and Liang, S and Guo, J and Li, K and Zhang, J and Li, J and Jin, Y and Bai, J and Dai, J and Lu, C}, title = {An inulin-based glycovesicle for pathogen-targeted drug delivery to ameliorate salmonellosis.}, journal = {International journal of biological macromolecules}, volume = {267}, number = {Pt 2}, pages = {131656}, doi = {10.1016/j.ijbiomac.2024.131656}, pmid = {38636749}, issn = {1879-0003}, mesh = {Animals ; *Inulin/pharmacology/chemistry ; Mice ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Salmonella Infections/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Drug Delivery Systems ; Levofloxacin/pharmacology ; Micelles ; Drug Carriers/chemistry ; Nanoparticles/chemistry ; }, abstract = {The gut microbiota plays a significant role in the pathogenesis and remission of inflammatory bowel disease. However, conventional antibiotic therapies may alter microbial ecology and lead to dysbiosis of the gut microbiome, which greatly limits therapeutic efficacy. To address this challenge, novel nanomicelles that couple inulin with levofloxacin via disulfide bonds for the treatment of salmonellosis were developed in this study. Owing to their H2S-responsiveness, the nanomicelles can target the inflamed colon and rapidly release levofloxacin to selectively fight against enteric pathogens. Moreover, the embedded inulin can serve as prebiotic fiber to increase the amount of Bifidobacteria and Lactobacilli in mice with salmonellosis, thus maintaining the intestinal mechanical barrier and regulating the balance of the intestinal flora. Therefore, multifunctional nanomicelles had a better curative effect than pure levofloxacin on ameliorating inflammation in vivo. The pathogen-targeted glycovesicle represents a promising drug delivery platform to maximize the efficacy of antibacterial drugs for the treatment of inflammatory bowel disease.}, }
@article {pmid38636461, year = {2024}, author = {Zafar, H and Saier, MH}, title = {An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes.}, journal = {Microbial physiology}, volume = {34}, number = {1}, pages = {133-141}, pmid = {38636461}, issn = {2673-1673}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/metabolism/pathogenicity ; Animals ; Biological Transport ; Bacterial Proteins/metabolism ; Host Microbial Interactions/physiology ; Carrier Proteins/metabolism ; Gastrointestinal Tract/microbiology ; }, abstract = {BACKGROUND: The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.<br><br>SUMMARY: This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.<br><br>KEY MESSAGES: Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.}, }
@article {pmid38634861, year = {2024}, author = {Lee, HJ and Whang, KS}, title = {Falsiroseomonas oryziterrae sp. nov., and Falsiroseomonas oryzae sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.006349}, pmid = {38634861}, issn = {1466-5034}, mesh = {*Oryza ; Base Composition ; Cardiolipins ; Fatty Acids/chemistry ; Phosphatidylethanolamines ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Amino Acids ; Nucleotides ; Phosphatidylcholines ; Phosphatidylglycerols ; Soil ; }, abstract = {Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4[T], NPKOSM-8 and MO-31[T], were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4[T] and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302[T] (96.1-97.8 %), Falsiroseomonas wooponensis WW53[T] (95.51-96.3 %) and Falsiroseomonas bella CQN31[T] (96.0-96.5 %), respectively. The genomes of strains NPKOSM-4[T] and MO-31[T] consisted of 4 632 875 and 6 455 771 bps, respectively, with 72.0 and 72.1 mol% G+C content. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains NPKOSM-4[T] and MO-31[T] and type strains of Falsiroseomonas species were lower than the cut-offs (≥95 % for ANI, ≥95-96 % for AAI and ≥ 70 % for dDDH) required to define a bacterial species. The major fatty acids of strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] were C18 : 1 ω7c and C18 : 1 2-OH (<10 %) and the predominant quinone was Q-10. The polar lipids of strain NPKOSM-4[T] were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and three unidentified aminolipids. The polar lipid profiles of strain MO-31[T] contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. Based on their distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] are considered to represent two novel species of the genus Falsiroseomonas, for which the names Falsiroseomonas oryziterrae sp. nov. [to accommodate strains NPKOSM-4[T] (= KACC 22135[T]=JCM 34745[T]), NPKOSM-8 (=KACC 22134=JCM 34746)] and Falsiroseomonas oryzae sp. nov. [to accommodate strain MO-31[T] (= KACC 22465[T]=JCM 35532[T])] are proposed.}, }
@article {pmid38634692, year = {2024}, author = {Zimmermann, J and Piecyk, A and Sieber, M and Petersen, C and Johnke, J and Moitinho-Silva, L and Künzel, S and Bluhm, L and Traulsen, A and Kaleta, C and Schulenburg, H}, title = {Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life.}, journal = {mBio}, volume = {15}, number = {5}, pages = {e0001224}, pmid = {38634692}, issn = {2150-7511}, support = {261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Host Microbial Interactions ; Gastrointestinal Tract/microbiology ; Microbiota ; }, abstract = {UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.<br><br>IMPORTANCE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.}, }
@article {pmid38634606, year = {2024}, author = {Vandepol, NS and Shade, A}, title = {Is everything everywhere? A hands-on activity to engage undergraduates with key concepts in quantitative microbial biogeography.}, journal = {Journal of microbiology &amp; biology education}, volume = {25}, number = {2}, pages = {e0017023}, pmid = {38634606}, issn = {1935-7877}, support = {1749544//National Science Foundation/ ; //The Michigan State University Certification in College Teaching within the Graduate School in partnership with the College of Natural Sciences/ ; //The French Centre National de la Recherche Scientifique (CNRS)/ ; }, abstract = {The ubiquity and ease with which microbial cells disperse over space is a key concept in microbiology, especially in microbial ecology. The phenomenon prompted Baas Becking's famous "everything is everywhere" statement that now acts as the null hypothesis in studies that test the dispersal limitation of microbial taxa. Despite covering the content in lectures, exam performance indicated that the concepts of dispersal and biogeography challenged undergraduate students in an upper-level Microbial Ecology course. Therefore, we iteratively designed a hands-on classroom activity to supplement the lecture content and reinforce fundamental microbial dispersal and biogeography concepts while also building quantitative reasoning and teamwork skills. In a class period soon after the lecture, the students formed three-to-five-person teams to engage in the activity, which included a hands-on dispersal simulation and worksheet to guide discussion. The simulation involved stepwise neutral immigration or emigration and then environmental selection on a random community of microbial taxa represented by craft poms. The students recorded the results at each step as microbial community data. A field guide was provided to identify the taxonomy based on the pom phenotype and a reference to each taxon's preferred environmental niches. The worksheet guided a reflection of student observations during the simulation. It also sharpened quantitative thinking by prompting the students to summarize and visualize their and other teams' microbial community data and then to compare the observed community distributions to the idealized expectation given only selection without dispersal. We found that the activity improved student performance on exam questions and general student satisfaction and comfort with the biogeography concepts. Activity instructions and a list of needed materials are included for instructors to reproduce for their classrooms.}, }
@article {pmid38632086, year = {2024}, author = {Chen, H and Zwaenepoel, A and Van de Peer, Y}, title = {wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {5}, pages = {}, pmid = {38632086}, issn = {1367-4811}, support = {3G032219//Research Foundation-Flanders/ ; //Ghent University/ ; }, mesh = {*Polyploidy ; *Genome, Plant ; *Gene Duplication ; *Phylogeny ; Evolution, Molecular ; Software ; Genomics/methods ; }, abstract = {MOTIVATION: Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant.<br><br>RESULTS: Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes.<br><br>wgd v2 is open source and available at https://github.com/heche-psb/wgd.}, }
@article {pmid38631226, year = {2024}, author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B}, title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.}, journal = {Marine environmental research}, volume = {198}, number = {}, pages = {106497}, doi = {10.1016/j.marenvres.2024.106497}, pmid = {38631226}, issn = {1879-0291}, mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Carbon/metabolism ; Salts ; Methane/metabolism ; }, abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.}, }
@article {pmid38630182, year = {2024}, author = {Nithyapriya, S and Sundaram, L and Eswaran, SUD and Perveen, K and Alshaikh, NA and Sayyed, RZ and Mastinu, A}, title = {Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {60}, pmid = {38630182}, issn = {1432-184X}, support = {RSP2024R358//King Saud University/ ; }, mesh = {*Arachis ; Deferoxamine ; *Pseudomonas fluorescens ; India ; RNA, Ribosomal, 16S/genetics ; Nutrients ; Siderophores ; Iron ; Soil ; }, abstract = {Microorganisms produce siderophores, which are low-molecular-weight iron chelators when iron availability is limited. The present analyzed the role of LNPF1 as multifarious PGPR for improving growth parameters and nutrient content in peanut and soil nutrients. Such multifarious PGPR strains can be used as effective bioinoculants for peanut farming. In this work, rhizosphere bacteria from Zea mays and Arachis hypogaea plants in the Salem area of Tamil Nadu, India, were isolated and tested for biochemical attributes and characteristics that stimulate plant growth, such as the production of hydrogen cyanide, ammonia (6 µg/mL), indole acetic acid (76.35 µg/mL), and solubilizing phosphate (520 µg/mL). The 16S rRNA gene sequences identified the isolate LNPF1 as Pseudomonas fluorescens with a similarity percentage of 99% with Pseudomonas sp. Isolate LNPF1 was evaluated for the production of siderophore. Siderophore-rich supernatant using a Sep Pack C18 column and Amberlite-400 Resin Column (λmax 264) produced 298 mg/L and 50 mg/L of siderophore, respectively. The characterization of purified siderophore by TLC, HPLC, FTIR, and 2D-NMR analysis identified the compound as desferrioxamine, a hydroxamate siderophore. A pot culture experiment determined the potential of LNPF1 to improve iron and oil content and photosynthetic pigments in Arachis hypogaea L. and improve soil nutrient content. Inoculation of A. hypogea seeds with LNPF1 improved plant growth parameters such as leaf length (60%), shoot length (22%), root length (54.68%), fresh weight (47.28%), dry weight (37%), and number of nuts (66.66) compared to the control (untreated seeds). This inoculation also improved leaf iron content (43.42), short iron content (38.38%), seed iron (46.72%), seed oil (31.68%), carotenoid (64.40%), and total chlorophyll content (98.%) compared to control (untreated seeds). Bacterized seeds showed a substantial increase in nodulation (61.65%) and weight of individual nodules (95.97) vis-à-vis control. The results of the present study indicated that P. fluorescens might be utilized as a potential bioinoculant to improve growth, iron content, oil content, number of nuts and nodules of Arachishypogaea L., and enrich soil nutrients.}, }
@article {pmid38629830, year = {2024}, author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM}, title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.}, journal = {Microbiology resource announcements}, volume = {13}, number = {5}, pages = {e0116123}, pmid = {38629830}, issn = {2576-098X}, abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.}, }
@article {pmid38628677, year = {2024}, author = {Kim, M and Park, T and Park, C and Baek, YC and Cho, A and Lee, HG and Kim, E and Bok, EY and Jung, YH and Hur, TY and Do, YJ}, title = {Impact of rumen cannulation surgery on rumen microbiota composition in Hanwoo steers.}, journal = {Journal of animal science and technology}, volume = {66}, number = {2}, pages = {353-365}, pmid = {38628677}, issn = {2055-0391}, abstract = {Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.}, }
@article {pmid38627476, year = {2024}, author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT}, title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8798}, pmid = {38627476}, issn = {2045-2322}, support = {2136146//National Science Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; }, abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.}, }
@article {pmid38626537, year = {2024}, author = {Ali, A and Wang, N and Wang, Q and Xu, G and Xu, H}, title = {An approach to evaluating seasonal responses to acute toxicity of antibiotic nitrofurazone on periphytic ciliated protist communities in marine environments.}, journal = {European journal of protistology}, volume = {94}, number = {}, pages = {126081}, doi = {10.1016/j.ejop.2024.126081}, pmid = {38626537}, issn = {1618-0429}, mesh = {*Seasons ; *Nitrofurazone/pharmacology ; *Ciliophora/drug effects ; China ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; Seawater ; }, abstract = {Periphytic protists including ciliates are the primary components of microbial communities in which they play a vital role in the progression of food webs by moving resources from lower to higher trophic levels. However, the toxic effects of veterinary antibiotics on periphytic protists across four seasons are minimally understood. Therefore, in this study, a 1-year survey was conducted with the antibiotic nitrofurazone (NFZ) applied at concentrations of 0.0, 1.5, 3.0, 6.0, and 12.0 mg/L. Samples of protist communities were collected using microscope glass slides during four seasons in the coastal waters of the Yellow Sea, Qingdao, northern China. The abundance of protists dropped with an increase in NFZ concentrations, and almost all species were dead at a concentration of 12.0 mg/L. The 12 h-LC50 values of NFZ for the protist biota were similar among the four seasons, despite significant seasonal variability in the community structure. The present results suggest that the periphytic protist biota may be used as a biomarker for assessing the ecotoxicity of NFZ in marine environments regardless of the year season.}, }
@article {pmid38625060, year = {2024}, author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC}, title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38625060}, issn = {1751-7370}, support = {/NASA/NASA/United States ; //Astrobiology Early Career Collaboration Award/ ; //High Meadows Environmental Institute at Princeton University/ ; //Walbridge Fund Graduate Award/ ; G110-21-W8189//W.M. Keck Foundation/ ; 1170995//National Fund for Scientific and Technological Development/ ; //National Science Foundation/ ; 2121637//Frontier Research in Earth Sciences/ ; 2151015//Division of Ocean Sciences/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Desert Climate ; *Hot Springs/microbiology ; *Oxidation-Reduction ; Carbon Monoxide/metabolism ; Hydrogen/metabolism ; Microbiota ; Altitude ; Soil/chemistry ; }, abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.}, }
@article {pmid38624181, year = {2024}, author = {Manck, LE and Coale, TH and Stephens, BM and Forsch, KO and Aluwihare, LI and Dupont, CL and Allen, AE and Barbeau, KA}, title = {Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38624181}, issn = {1751-7370}, support = {OCE-1026607//NSF/ ; DGE-1144086//NSF/ ; 729162//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-1558453//NSF/ ; OCE-1756884//NSF/ ; 970820//Simons Collaboration on Principles of Microbial Ecosystems/ ; OCE-1558841//NSF/ ; }, mesh = {*Iron/metabolism ; *Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; California ; *Heterotrophic Processes ; Microbiota ; }, abstract = {Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.}, }
@article {pmid38622815, year = {2024}, author = {Riquelme Del Río, B and Sepulveda-Jauregui, A and Salas-Rabaza, JA and Mackenzie, R and Thalasso, F}, title = {Fine-Scale Spatial Variability of Greenhouse Gas Emissions From a Subantarctic Peatland Bog.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {17}, pages = {7393-7402}, pmid = {38622815}, issn = {1520-5851}, mesh = {*Greenhouse Gases/analysis ; *Wetlands ; *Methane/analysis ; Carbon Dioxide/analysis ; Soil/chemistry ; Ecosystem ; Sphagnopsida ; Environmental Monitoring ; }, abstract = {Peatlands are recognized as crucial greenhouse gas sources and sinks and have been extensively studied. Their emissions exhibit high spatial heterogeneity when measured on site using flux chambers. However, the mechanism by which this spatial variability behaves on a very fine scale remains unclear. This study investigates the fine-scale spatial variability of greenhouse gas emissions from a subantarctic Sphagnum peatland bog. Using a recently developed skirt chamber, methane emissions and ecosystem respiration (as carbon dioxide) were measured at a submeter scale resolution, at five specific 3 × 3 m plots, which were examined across the site throughout a single campaign during the Austral summer season. The results indicated that methane fluxes were significantly less homogeneously distributed compared with ecosystem respiration. Furthermore, we established that the spatial variation scale, i.e., the minimum spatial domain over which notable changes in methane emissions and ecosystem respiration occur, was <0.56 m[2]. Factors such as ground height relative to the water table and vegetation coverage were analyzed. It was observed that Tetroncium magellanicum exhibited a notable correlation with higher methane fluxes, likely because of the aerenchymatous nature of this species, facilitating gas transport. This study advances understanding of gas exchange patterns in peatlands but also emphasizes the need for further efforts for characterizing spatial dynamics at a very fine scale for precise greenhouse gas budget assessment.}, }
@article {pmid38621490, year = {2024}, author = {Cheng, J and Robles-Lecompte, A and McKenna, AM and Chang, NB}, title = {Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system.}, journal = {Chemosphere}, volume = {357}, number = {}, pages = {142042}, doi = {10.1016/j.chemosphere.2024.142042}, pmid = {38621490}, issn = {1879-1298}, mesh = {*Nitrogen/metabolism ; *Filtration/methods ; Water Pollutants, Chemical/metabolism/analysis ; Water Purification/methods ; Biodegradation, Environmental ; Denitrification ; Adsorption ; Microbiota ; Florida ; Aluminum Oxide/chemistry ; Waste Disposal, Fluid/methods ; }, abstract = {The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.}, }
@article {pmid38619794, year = {2024}, author = {Van Holm, W and Zayed, N and Lauwens, K and Saghi, M and Axelsson, J and Aktan, MK and Braem, A and Simoens, K and Vanbrabant, L and Proost, P and Van Holm, B and Maes, P and Boon, N and Bernaerts, K and Teughels, W}, title = {Oral Biofilm Composition, Dissemination to Keratinocytes, and Inflammatory Attenuation Depend on Probiotic and Synbiotic Strain Specificity.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {38619794}, issn = {1867-1314}, support = {C24/17/086//KU Leuven/ ; C16/17/010//KU Leuven/ ; C16/17/010//KU Leuven/ ; C24/17/086//KU Leuven/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Several inflammatory diseases are characterized by a disruption in the equilibrium between the host and its microbiome. Due to the increase in resistance, the use of antibiotics for the widespread, nonspecific killing of microorganisms is at risk. Pro-microbial approaches focused on stimulating or introducing beneficial species antagonistic toward pathobionts may be a viable alternative for restoring the host-microbiome equilibrium. Unfortunately, not all potential probiotic or synbiotic species and even subspecies (to strain level) are equally effective for the designated pathology, leading to conflicting accounts of their efficacy. To assess the extent of these species- and strain-specific effects, 13 probiotic candidates were evaluated for their probiotic and synbiotic potential with glycerol on in vitro oral biofilms, dissemination from biofilms to keratinocytes, and anti-inflammatory activity. Species- and strain-specific effects and efficacies were observed in how they functioned as probiotics or synbiotics by influencing oral pathobionts and commensals within biofilms and affected the dissemination of pathobionts to keratinocytes, ranging from ineffective strains to strains that reduced pathobionts by 3 + log. In addition, a minority of the candidates exhibited the ability to mitigate the inflammatory response of LPS-stimulated monocytes. For a comprehensive assessment of probiotic therapy for oral health, a judicious selection of fully characterized probiotic strains that are specifically tailored to the designated pathology is required. This approach aims to challenge the prevailing perception of probiotics, shifting the focus away from "form over function." Rather than using unproven, hypothetical probiotic strains from known genera or species, one should choose strains that are actually functional in resolving the desired pathology before labelling them probiotics.}, }
@article {pmid38619730, year = {2024}, author = {Zhu, H and Li, S and Wu, Z and Xiong, X and Lin, P and Liu, B and He, D and Liu, G}, title = {Diversity Patterns of Eukaryotic Phytoplankton in the Medog Section of the Yarlung Zangbo River.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {59}, pmid = {38619730}, issn = {1432-184X}, mesh = {*Ecosystem ; *Rivers ; Biodiversity ; Biomass ; Phytoplankton ; }, abstract = {As one of the important biodiversity conservation areas in China, the ecosystem in the lower reaches of the Yarlung Zangbo River is fragile, and is particularly sensitive to global changes. To reveal the diversity pattern of phytoplankton, the metabarcode sequencing was employed in the Medog section of the lower reaches of the Yarlung Zangbo River during autumn 2019 in present study. The phytoplankton assemblies can be significantly divided into the main stem and the tributaries; there are significant differences in the phytoplankton biomass, alpha and beta diversity between the main stem and the tributaries. While both the main stem and the tributaries are affected by dispersal limitation, the phytoplankton assemblages in the entire lower reaches are primarily influenced by heterogeneous selection. Community dissimilarity and assembly process were significantly correlated with turbidity, electrical conductivity, and nitrogen nutrition. The tributaries were the main source of the increase in phytoplankton diversity in the lower reaches of the Yarlung Zangbo River. Such diversity pattern of phytoplankton in the lower reach may be caused by the special habitat in Medog, that is, the excessive flow velocity, and the significant spatial heterogeneity in physical and chemical factors between stem and tributaries. Based on the results and conclusions obtained in present study, continuous long-term monitoring is essential to assess and quantify the impact of global changes on phytoplankton.}, }
@article {pmid38618866, year = {2024}, author = {Zha, Z and Wang, R and Wang, Q and Chen, F and Ye, Z and Li, Y}, title = {A fast and efficient liquid chromatography-tandem mass spectrometry method for measuring l- and d-amino acids in the urine of patients with immunoglobulin A nephropathy.}, journal = {Biomedical chromatography : BMC}, volume = {38}, number = {6}, pages = {e5866}, doi = {10.1002/bmc.5866}, pmid = {38618866}, issn = {1099-0801}, support = {82170716//National Science Foundation of China/ ; 81870333//National Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; //College Science and Technology Innovation Project of Shanxi Education Department/ ; }, mesh = {Humans ; *Tandem Mass Spectrometry/methods ; *Amino Acids/urine ; *Glomerulonephritis, IGA/urine ; Chromatography, Liquid/methods ; Male ; Adult ; Female ; Middle Aged ; Reproducibility of Results ; Biomarkers/urine ; Stereoisomerism ; Linear Models ; Case-Control Studies ; Young Adult ; }, abstract = {Immunoglobulin nephropathy (IgAN) stands as the most prevalent primary glomerular nephropathy globally, typically diagnosed through an invasive renal biopsy. Emerging research suggests the significant involvement of chiral amino acids in kidney disease progression. This study introduces a nonderivative LC-tandem mass spectrometry approach, offering efficient separation outcomes within 15 min for identifying chiral amino acids in human urine samples. Subsequently, using this method, the analysis of l- and d-amino acids in the urine of both patients with IgAN and healthy individuals was conducted. Fourteen d-amino acids and 20 l-amino acids were identified in the urine samples obtained from 17 patients with IgAN and 21 healthy individuals. The results indicated notable variances in the concentrations of both l- and d-amino acids between the IgAN and healthy control groups. In contrast to the healthy group, the IgAN group exhibited higher mean urine concentrations of most l-amino acids and lower concentrations of d-amino acids. Furthermore, correlations between amino acids and clinical markers were investigated. These results propose a novel method for monitoring trace amino acids in urine samples and introduce a new concept for potential markers of IgAN.}, }
@article {pmid38617439, year = {2024}, author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K}, title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2339158}, pmid = {38617439}, issn = {2000-2297}, abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.<br><br>METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).<br><br>RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of &#x3b1;-diversity (p&#x2009;<&#x2009;0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in &#x3b2;-diversity between H. pylori-positive and negative child specimens (p&#x2009;<&#x2009;0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p&#x2009;<&#x2009;0.01 and p&#x2009;<&#x2009;0.05, respectively).<br><br>CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.}, }
@article {pmid38613756, year = {2024}, author = {Costa, JL and Silva, LG and Veras, STS and Gavazza, S and Florencio, L and Motteran, F and Kato, MT}, title = {Use of nitrate, sulphate, and iron (III) as electron acceptors to improve the anaerobic degradation of linear alkylbenzene sulfonate: effects on removal potential and microbiota diversification.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38613756}, issn = {1614-7499}, support = {APQ-0603-3.07/14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; CAPES-PrInt//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; finance code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; process number 88887.467533/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Linear alkylbenzene sulfonate (LAS) is a synthetic anionic surfactant that is found in certain amounts in wastewaters and even in water bodies, despite its known biodegradability. This study aimed to assess the influence of nitrate, sulphate, and iron (III) on LAS anaerobic degradation and biomass microbial diversity. Batch reactors were inoculated with anaerobic biomass, nutrients, LAS (20 mg L[-1]), one of the three electron acceptors, and ethanol (40 mg L[-1]) as a co-substrate. The control treatments, with and without co-substrate, showed limited LAS biodegradation efficiencies of 10 ± 2% and 0%, respectively. However, when nitrate and iron (III) were present without co-substrate, biodegradation efficiencies of 53 ± 4% and 75 ± 3% were achieved, respectively, which were the highest levels observed. Clostridium spp. was prominent in all treatments, while Alkaliphilus spp. and Bacillus spp. thrived in the presence of iron, which had the most significant effect on LAS biodegradation. Those microorganisms were identified as crucial in affecting the LAS anaerobic degradation. The experiments revealed that the presence of electron acceptors fostered the development of a more specialised microbiota, especially those involved in the LAS biodegradation. A mutual interaction between the processes of degradation and adsorption was also shown.}, }
@article {pmid38613638, year = {2024}, author = {Cai, Y and Chen, Z and Chen, E and Zhang, D and Wei, T and Sun, M and Lian, Y}, title = {Succinic Acid Ameliorates Concanavalin A-Induced Hepatitis by Altering the Inflammatory Microenvironment and Expression of BCL-2 Family Proteins.}, journal = {Inflammation}, volume = {47}, number = {6}, pages = {2000-2012}, pmid = {38613638}, issn = {1573-2576}, support = {2021J05278//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//The Health Science Foundation of Fujian Youth Program/ ; 82303109//National Natural Science Foundation of China/ ; 2022J05299//Natural Science Foundation of Fujian Province, China/ ; 2021B002//Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China/ ; }, mesh = {Animals ; *Concanavalin A/toxicity ; *Succinic Acid/pharmacology ; Mice ; *Hepatitis, Autoimmune/drug therapy/metabolism/pathology ; *Proto-Oncogene Proteins c-bcl-2/metabolism ; *Apoptosis/drug effects ; Liver/drug effects/pathology/metabolism ; Male ; Cellular Microenvironment/drug effects ; Kupffer Cells/drug effects/metabolism ; Chemical and Drug Induced Liver Injury/drug therapy/metabolism/pathology ; Inflammation/drug therapy/metabolism ; }, abstract = {Autoimmune hepatitis (AIH) is a severe immune-mediated inflammatory liver disease that currently lacks feasible drug treatment methods. Our study aimed to evaluate the protective effect of succinic acid against AIH and provide a reliable method for the clinical treatment of AIH. We performed an in vivo study of the effects of succinic acid on concanavalin A (ConA)-induced liver injury in mice. We examined liver transaminase levels, performed hematoxylin and eosin (HE) staining, and observed apoptotic phenotypes in mice. We performed flow cytometry to detect changes in the number of neutrophils and monocytes, and used liposomes to eliminate the liver Kupffer cells and evaluate their role. We performed bioinformatics analysis, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blotting to detect mitochondrial apoptosis-induced changes in proteins from the B-cell lymphoma 2(Bcl-2) family. Succinic acid ameliorated ConA-induced AIH in a concentration-dependent manner, as reflected in the survival curve. HE and TUNEL staining and terminal deoxynucleotidyl transferase dUTP nick end labeling revealed decreased alanine transaminase and aspartate aminotransferase levels, and reduced liver inflammation and apoptosis. RT-qPCR and enzyme-linked immunosorbent assay revealed that succinic acid significantly reduced liver pro-inflammatory cytokine levels. Flow cytometry revealed significantly decreased levels of liver neutrophils. Moreover, the protective effect of succinic acid disappeared after the Kupffer cells were eliminated, confirming their important role in the effect. Bioinformatics analysis, RT-qPCR, and western blotting showed that succinic acid-induced changes in proteins from the Bcl-2 family involved mitochondrial apoptosis, indicating the molecular mechanism underlying the protective effect of succinic acid. Succinic acid ameliorated ConA-induced liver injury by regulating immune balance, inhibiting pro-inflammatory factors, and promoting anti-apoptotic proteins in the liver. This study provides novel insights into the biological functions and therapeutic potential of succinic acid in the treatment of autoimmune liver injury.}, }
@article {pmid38606974, year = {2024}, author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS}, title = {Localization and symbiotic status of probiotics in the coral holobiont.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0026124}, pmid = {38606974}, issn = {2379-5077}, support = {FCC/1/1976-40-01,BAS/1/1095-01-0//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis/physiology ; Animals ; *Probiotics/pharmacology ; In Situ Hybridization, Fluorescence ; Halomonas/physiology ; Microbiota/physiology ; }, abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.<br><br>IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.}, }
@article {pmid38602612, year = {2024}, author = {Xie, Y and Fan, Y and Su, M and Wang, Y and Zhang, G}, title = {Characteristics of the oral microbiota in patients with primary Sjögren's syndrome.}, journal = {Clinical rheumatology}, volume = {43}, number = {6}, pages = {1939-1947}, pmid = {38602612}, issn = {1434-9949}, support = {2019-106-21//Shantou Medical Health Science and Technology Plan/ ; A2019244//Medical Science Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Female ; Middle Aged ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; High-Throughput Nucleotide Sequencing ; Dental Plaque/microbiology ; Dental Caries/microbiology ; }, abstract = {OBJECTIVE: Primary Sjögren's syndrome (pSS) is an autoimmune disease with unknown etiology that is considered to be related to environmental and genetic factors. The aim of this study was to clarify the oral microflora characteristics of pSS patients and to reveal the connection between oral bacterial composition and dental caries using a high-throughput sequencing technique.<br><br>METHODS: Thirty-five pSS patients and 20 healthy controls were enrolled in this study. We collected saliva and plaque samples from pSS patients and saliva samples from healthy controls. We used 16S ribosomal DNA (16S rDNA) high-throughput sequencing targeting the V3-V4 hypervariable region to determine the composition and structure of the microbiota in the three sample sets. Finally, bioinformatics analyses, including the diversity of the microbiota, species differences, and functional prediction were performed.<br><br>RESULTS: In the alpha diversity and beta diversity analysis, the Chao1 (P&#x2009;<&#x2009;0.01), observed species (P&#x2009;<&#x2009;0.01), and PD whole tree indices (P&#x2009;<&#x2009;0.01) were significantly lower in the saliva and plaque samples of pSS patients than in the saliva samples of healthy controls, but the Shannon (P&#x2009;<&#x2009;0.01) and Simpson indices (P&#x2009;<&#x2009;0.01) were significantly higher in the healthy controls, and their total diversity significantly differed. In the main flora composition at the genus level (top 10), we identified Prevotella and Veillonella as more enriched in the saliva of pSS patients and Fusobacterium, Actinomyces, and Leptotrichia as more enriched in the plaque of pSS patients. Predictive functional analysis showed that the oral microbiota of pSS patients was related to translation, metabolism of cofactors and vitamins, and nucleotide metabolism.<br><br>CONCLUSIONS: The oral microbial ecology of patients with pSS is dysregulated, resulting in a decrease in overall diversity. Prevotella and Veillonella may be related to pSS, while Fusobacterium, Actinomyces, and Leptotrichia may be related to dental caries in pSS patients. Key Points &#x2022; This study revealed differences in the oral microbial composition of patients with pSS compared to healthy controls. &#x2022; We included a plaque group of pSS patients to identify the microbiota related to pSS and dental caries. &#x2022; Prevotella and Veillonella may contribute to pSS, and Fusobacterium, Actinomyces, and Leptotrichia are associated with dental caries in pSS patients.}, }
@article {pmid38602532, year = {2024}, author = {Xing, H and Chen, W and Liu, Y and Cahill, JF}, title = {Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {58}, pmid = {38602532}, issn = {1432-184X}, support = {31670531 and 32071645//National Natural Science Foundation of China/ ; 2022JBGS04 and 2023JBGS06//Research Project of Baishanzu National Park/ ; }, mesh = {China ; Forests ; Gamma Rays ; *Microbiota ; *Mycorrhizae ; Soil ; }, abstract = {Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.}, }
@article {pmid38602492, year = {2024}, author = {Machushynets, NV and Al Ayed, K and Terlouw, BR and Du, C and Buijs, NP and Willemse, J and Elsayed, SS and Schill, J and Trebosc, V and Pieren, M and Alexander, FM and Cochrane, SA and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP}, title = {Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity.}, journal = {ACS chemical biology}, volume = {19}, number = {5}, pages = {1106-1115}, pmid = {38602492}, issn = {1554-8937}, mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Pseudomonas aeruginosa/drug effects ; Humans ; *Microbial Sensitivity Tests ; Host Specificity ; Drug Discovery ; Lipopeptides/pharmacology/chemistry ; Peptides ; }, abstract = {The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.}, }
@article {pmid38598334, year = {2024}, author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C}, title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114078}, doi = {10.1016/j.celrep.2024.114078}, pmid = {38598334}, issn = {2211-1247}, mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; }, abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.}, }
@article {pmid38593340, year = {2024}, author = {Suárez-Moo, P and Prieto-Davó, A}, title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.}, journal = {MicrobiologyOpen}, volume = {13}, number = {2}, pages = {e1407}, pmid = {38593340}, issn = {2045-8827}, support = {//Consejo Nacional de Humanidades Ciencias y Tecnolog&#xed;as (CONAHCYT), M&#xe9;xico project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; }, mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; }, abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.}, }
@article {pmid38593079, year = {2024}, author = {Zhong, Q and Liao, B and Liu, J and Shen, W and Wang, J and Wei, L and Ma, Y and Dong, PT and Bor, B and McLean, JS and Chang, Y and Shi, W and Cen, L and Wu, M and Liu, J and Li, Y and He, X and Le, S}, title = {Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {16}, pages = {e2319790121}, pmid = {38593079}, issn = {1091-6490}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM110243/GM/NIGMS NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; R01 GM124378/GM/NIGMS NIH HHS/United States ; R01 AI152421/AI/NIAID NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; R01 AI132818/AI/NIAID NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; S10 OD023603/OD/NIH HHS/United States ; }, mesh = {Humans ; *Bacteriophages/physiology ; Symbiosis ; Bacteria/genetics ; }, abstract = {Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.}, }
@article {pmid38591008, year = {2024}, author = {Kang, M and Liu, L and Grossart, HP}, title = {Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake.}, journal = {iScience}, volume = {27}, number = {4}, pages = {109520}, pmid = {38591008}, issn = {2589-0042}, abstract = {Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.}, }
@article {pmid38589480, year = {2024}, author = {Sanchis Pla, L and van Gestel, J}, title = {Exploring the microbial savanna: predator-prey interactions in the soil.}, journal = {Molecular systems biology}, volume = {20}, number = {5}, pages = {477-480}, pmid = {38589480}, issn = {1744-4292}, support = {101116560//ERC Starting Grant/ ; }, mesh = {*Soil Microbiology ; Grassland ; Animals ; Food Chain ; Predatory Behavior ; Soil/chemistry ; }, abstract = {Soils host complex multi-trophic communities with diverse, mostly microbial, predator and prey species, including numerous bacterivorous protists and bacterial prey. The molecular mechanisms underlying microbial predator-prey interactions have thus far mainly been explored using reductionist methods, outside the soil environment and independent from the broader life history strategies that microbes display in soils. In this Comment, we advocate for an integrative research approach, combining molecular systems biology and microbial ecology, to investigate how predator-prey interactions shape microbial life history strategies and thereby population dynamics in natural soil communities.}, }
@article {pmid38587642, year = {2024}, author = {Srinivasan, S and Jnana, A and Murali, TS}, title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {56}, pmid = {38587642}, issn = {1432-184X}, support = {CRG/2022/003227//Science and Engineering Research Board/ ; }, mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; }, abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.}, }
@article {pmid38587527, year = {2024}, author = {Garcia Mendez, DF and Egan, S and Wist, J and Holmes, E and Sanabria, J}, title = {Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {57}, pmid = {38587527}, issn = {1432-184X}, support = {FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bioreactors ; Feces ; }, abstract = {Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter".}, }
@article {pmid38585661, year = {2024}, author = {Hill, LJ and Messias, CSMA and Vilela, CLS and Garritano, AN and Villela, HDM and do Carmo, FL and Thomas, T and Peixoto, RS}, title = {Bacteria associated with the in hospite Symbiodiniaceae's phycosphere.}, journal = {iScience}, volume = {27}, number = {4}, pages = {109531}, pmid = {38585661}, issn = {2589-0042}, abstract = {Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.}, }
@article {pmid38585291, year = {2023}, author = {Hobusch, U and Scheuch, M and Heuckmann, B and Hodžić, A and Hobusch, GM and Rammel, C and Pfeffer, A and Lengauer, V and Froehlich, DE}, title = {One Health Education Nexus: enhancing synergy among science-, school-, and teacher education beyond academic silos.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1337748}, pmid = {38585291}, issn = {2296-2565}, mesh = {Humans ; Ecosystem ; *One Health ; *Teacher Training ; Students ; Schools ; Health Education ; Educational Status ; }, abstract = {INTRODUCTION: The fact that the daily lives of billions of people were affected by the medical, social, and political aspects of the SARS-CoV-2 pandemic shows the need to anchor the understanding of One Health in society. Hence, promoting awareness and deepening the understanding of the interrelation between human health, animal health, and ecosystems must be accomplished through quality education, as advocated by UN Sustainable Development Goal 4. The often-questioned and discussed measures taken by governments to control the global pandemic between 2020 and 2023 can be seen as an opportunity to meet the educational needs of civil society solutions in multi-stakeholder settings between public, universities, and schools.<br><br>METHODS: This paper focuses on the integration of One Health principles in educational frameworks, particularly within the context of the higher education teaching framework "Teaching Clinic." This master-level course in the domain of pre-service teacher education serves as a potent vehicle for facilitating One Health Education, bridging the gap between research, higher education, and schools. Through the presentation of two case studies, this article demonstrates how the Teaching Clinic approach fosters interdisciplinary perspectives and provides a dynamic learning environment for pre-service teachers, as well as for pupils involved in the educational process.<br><br>RESULTS: In both cases, the integration of educational One Health school teaching-learning settings effectively enhanced pupils' understanding of complex topics and engaged them in active learning experiences. Pre-service teachers played a crucial role in developing, implementing, and evaluating these interventions. In Case I, pupils demonstrated proficiency in analyzing data and evaluating mathematical models, while in Case II, the chosen instructional approach facilitated One Health knowledge acquisition and enjoyment among pupils. These results underscore the potential of the One Health Teaching Clinic as a valuable educational framework for enhancing teaching and learning outcomes for pre-service teachers and fostering pupil engagement in socio-scientific One Health-related topics.<br><br>DISCUSSION: The discussion delves into the significance of breaking down disciplinary silos and the crucial role of teacher education in promoting a holistic approach to education, emphasizing the intersectionality of One Health Education and Education for Sustainable Development. This article underpins the significance of collaborative efforts across multiple (scientific) disciplines and across secondary and tertiary education levels to reach a nexus. Moreover, it emphasizes the alignment of this approach with the 2030 Agenda, Education for Sustainable Development, and Sustainable Development Goals, highlighting the potential for collective action toward a more sustainable future.}, }
@article {pmid38581683, year = {2024}, author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G}, title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114046}, doi = {10.1016/j.celrep.2024.114046}, pmid = {38581683}, issn = {2211-1247}, support = {/ERC_/European Research Council/International ; }, mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; }, abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.}, }
@article {pmid38581020, year = {2024}, author = {Douillard, FP and Derman, Y and Jian, C and Korpela, K and Saxén, H and Salonen, A and de Vos, WM and Korkeala, H and Lindström, M}, title = {Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism.}, journal = {Gut pathogens}, volume = {16}, number = {1}, pages = {20}, pmid = {38581020}, issn = {1757-4749}, abstract = {BACKGROUND: Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.<br><br>CASE PRESENTATION: To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.<br><br>CONCLUSION: This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.}, }
@article {pmid38579997, year = {2024}, author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L}, title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.}, journal = {Environmental research}, volume = {252}, number = {Pt 1}, pages = {118861}, doi = {10.1016/j.envres.2024.118861}, pmid = {38579997}, issn = {1096-0953}, mesh = {*Metals, Heavy/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Bacteria/genetics/drug effects ; }, abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.}, }
@article {pmid38578091, year = {2024}, author = {Morrison, BH and Jones, JL and Dzwonkowski, B and Krause, JW}, title = {Tracking Vibrio: population dynamics and ecology of Vibrio parahaemolyticus and V. vulnificus in an Alabama estuary.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0367423}, pmid = {38578091}, issn = {2165-0497}, support = {U19 FD005923/FD/FDA HHS/United States ; #5U19FD005923-04//HHS | U.S. Food and Drug Administration (FDA)/ ; }, mesh = {*Vibrio parahaemolyticus/isolation &amp; purification/growth &amp; development ; *Vibrio vulnificus/isolation &amp; purification/growth &amp; development ; *Estuaries ; Alabama ; Population Dynamics ; Salinity ; Vibrio Infections/microbiology/epidemiology ; Seawater/microbiology ; Water Microbiology ; }, abstract = {UNLABELLED: Vibrio is a genus of halophilic, gram-negative bacteria found in estuaries around the globe. Integral parts of coastal cultures often involve contact with vectors of pathogenic Vibrio spp. (e.g., consuming raw shellfish). High rates of mortality from certain Vibrio spp. infections demonstrate the need for an improved understanding of Vibrio spp. dynamics in estuarine regions. Our study assessed meteorological, hydrographic, and biological correlates of Vibrio parahaemolyticus and V. vulnificus at 10 sites in the Eastern Mississippi Sound System (EMSS) from April to October 2019. During the sampling period, median abundances of V. parahaemolyticus and V. vulnificus were 2.31 log MPN/L and 2.90 log MPN/L, respectively. Vibrio spp. dynamics were largely driven by site-based variation, with sites closest to freshwater inputs having the highest abundances. The E-W wind scalar, which affects Ekman transport, was a novel Vibrio spp. correlate observed. A potential salinity effect on bacterial-particle associations was identified, where V. vulnificus was associated with larger particles in conditions outside of their optimal salinity. Additionally, V. vulnificus abundances were correlated to those of harmful algal species that did not dominate community chlorophyll. Correlates from this study may be used to inform the next iteration of regionally predictive Vibrio models and may lend additional insight to Vibrio spp. ecology in similar systems.<br><br>IMPORTANCE: Vibrio spp. are bacteria found in estuaries worldwide; some species can cause illness and infections in humans. Relationships between Vibrio spp. abundance, salinity, and temperature are well documented, but correlations to other environmental parameters are less understood. This study identifies unique correlates (e.g., E-W wind scalar and harmful algal species) that could potentially inform the next iteration of predictive Vibrio models for the EMSS region. Additionally, these correlates may allow existing environmental monitoring efforts to be leveraged in providing data inputs for future Vibrio risk models. An observed correlation between salinity and V. vulnificus/particle-size associations suggests that predicted environmental changes may affect the abundance of Vibrio spp. in certain reservoirs, which may alter which vectors present the greatest vibrio risk.}, }
@article {pmid38575035, year = {2024}, author = {Zheng, W and Wu, Q and Guo, X and Zhou, P and Wu, J and Yan, W}, title = {Rocky desertification succession alters soil microbial communities and survival strategies in the karst context.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172171}, doi = {10.1016/j.scitotenv.2024.172171}, pmid = {38575035}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Microbiota ; *Fungi ; *Soil/chemistry ; Archaea/genetics/physiology ; Ecosystem ; Conservation of Natural Resources ; }, abstract = {Rocky desertification is one of the most ecological problems in the karst context. Although extensive research has been conducted to explore how to restore and protect, the responses of soil fungi and archaea to rocky desertification succession remain limited. Here, four grades of rocky desertification in a karst ecosystem were selected, amplicon sequencing analysis was conducted to investigate fungal and archaeal community adaptation in response to rocky desertification succession. Our findings revealed that the diversity and community structure of fungi and archaea in soils declined with the aggravation of rocky desertification. As the rocky desertification succession intensified, microbial interactions shifted from cooperation to competition. Microbial survival strategies were K-strategist and r-strategist dominated in the early and late stages of succession, respectively. Additionally, the driving factors affecting microorganisms have shifted from vegetation diversity to soil properties as the intensification of rocky desertification. Collectively, our study highlighted that plant diversity and soil properties play important roles on soil microbiomes in fragile karst ecosystems and that environmental factors induced by human activities might still be the dominant factor exacerbating rocky desertification, which could significantly enrich our understanding of microbial ecology within karst ecosystems.}, }
@article {pmid38574431, year = {2024}, author = {Cunha, ICMD and Silva, AVRD and Boleta, EHM and Pellegrinetti, TA and Zagatto, LFG and Zagatto, SDSS and Chaves, MG and Mendes, R and Patreze, CM and Tsai, SM and Mendes, LW}, title = {The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127706}, doi = {10.1016/j.micres.2024.127706}, pmid = {38574431}, issn = {1618-0623}, mesh = {*Rhizosphere ; Plants/microbiology ; Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Phenotype ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.}, }
@article {pmid38571798, year = {2024}, author = {Rani, V and Horváth, Z and Nejstgaard, JC and Fierpasz, &#xc1; and Pálffy, K and Vad, CF}, title = {Food density drives diet shift of the invasive mysid shrimp, Limnomysis benedeni.}, journal = {Ecology and evolution}, volume = {14}, number = {4}, pages = {e11202}, pmid = {38571798}, issn = {2045-7758}, abstract = {Understanding the diet preferences and food selection of invasive species is crucial to better predict their impact on community structure and ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian invasive mysid shrimp, is one of the most successful invaders in numerous European river and lake ecosystems. While existing studies suggest potentially strong trophic impact due to high predation pressure on native plankton communities, little is known of its food selectivity between phyto- and zooplankton, under different food concentrations. Here, we therefore investigated the feeding selectivity of L. benedeni on two commonly occurring prey organisms in freshwaters, the small rotifer zooplankton Brachionus calyciflorus together with the microphytoplankton Cryptomonas sp. present in increasing densities. Our results demonstrated a clear shift in food selection, with L. benedeni switching from B. calyciflorus to Cryptomonas sp. already when the two prey species were provided in equal biomasses. Different functional responses were observed for the two food types, indicating somewhat different foraging mechanisms for each food type. These findings provide experimental evidence on the feeding flexibility of invasive mysid shrimps and potential implications for trophic interactions in invaded ecosystems.}, }
@article {pmid38567263, year = {2023}, author = {Crous, PW and Osieck, ER and Shivas, RG and Tan, YP and Bishop-Hurley, SL and Esteve-Raventós, F and Larsson, E and Luangsa-Ard, JJ and Pancorbo, F and Balashov, S and Baseia, IG and Boekhout, T and Chandranayaka, S and Cowan, DA and Cruz, RHSF and Czachura, P and De la Peña-Lastra, S and Dovana, F and Drury, B and Fell, J and Flakus, A and Fotedar, R and Jurjević, &#x17d; and Kolecka, A and Mack, J and Maggs-Kölling, G and Mahadevakumar, S and Mateos, A and Mongkolsamrit, S and Noisripoom, W and Plaza, M and Overy, DP and Piątek, M and Sandoval-Denis, M and Vauras, J and Wingfield, MJ and Abell, SE and Ahmadpour, A and Akulov, A and Alavi, F and Alavi, Z and Altés, A and Alvarado, P and Anand, G and Ashtekar, N and Assyov, B and Banc-Prandi, G and Barbosa, KD and Barreto, GG and Bellanger, JM and Bezerra, JL and Bhat, DJ and Bilański, P and Bose, T and Bozok, F and Chaves, J and Costa-Rezende, DH and Danteswari, C and Darmostuk, V and Delgado, G and Denman, S and Eichmeier, A and Etayo, J and Eyssartier, G and Faulwetter, S and Ganga, KGG and Ghosta, Y and Goh, J and Góis, JS and Gramaje, D and Granit, L and Groenewald, M and Gulden, G and Gusmão, LFP and Hammerbacher, A and Heidarian, Z and Hywel-Jones, N and Jankowiak, R and Kaliyaperumal, M and Kaygusuz, O and Kezo, K and Khonsanit, A and Kumar, S and Kuo, CH and Læssøe, T and Latha, KPD and Loizides, M and Luo, SM and Maciá-Vicente, JG and Manimohan, P and Marbach, PAS and Marinho, P and Marney, TS and Marques, G and Martín, MP and Miller, AN and Mondello, F and Moreno, G and Mufeeda, KT and Mun, HY and Nau, T and Nkomo, T and Okrasińska, A and Oliveira, JPAF and Oliveira, RL and Ortiz, DA and Pawłowska, J and Pérez-De-Gregorio, M&#xc0; and Podile, AR and Portugal, A and Privitera, N and Rajeshkumar, KC and Rauf, I and Rian, B and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodriguez-Flakus, P and Romero-Gordillo, M and Saar, I and Saba, M and Santos, CD and Sarma, PVSRN and Siquier, JL and Sleiman, S and Spetik, M and Sridhar, KR and Stryjak-Bogacka, M and Szczepańska, K and Taşkın, H and Tennakoon, DS and Thanakitpipattana, D and Trovão, J and Türkekul, I and van Iperen, AL and van 't Hof, P and Vasquez, G and Visagie, CM and Wingfield, BD and Wong, PTW and Yang, WX and Yarar, M and Yarden, O and Yilmaz, N and Zhang, N and Zhu, YN and Groenewald, JZ}, title = {Fungal Planet description sheets: 1478-1549.}, journal = {Persoonia}, volume = {50}, number = {}, pages = {158-310}, pmid = {38567263}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.}, }
@article {pmid38562743, year = {2024}, author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA}, title = {Microbial determinants of dementia risk in subjects of Mexican descent with type 2 diabetes living in South Texas.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38562743}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; T32 AG067952/AG/NIA NIH HHS/United States ; UL1 TR001439/TR/NCATS NIH HHS/United States ; }, abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and dementia, including Alzheimer's Disease (AD), yet the underlying mechanisms remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the predisposing APOE-e4 variant and an absence of the phenotype among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. Here, in a small clinical trial, we show dysbiosis of the human gut microbiome could contribute to neuroinflammation and risk for AD in this population. Divergent Gastrointestinal Symptom Rating Scale (GSRS) responses, despite no differences in expressed dietary preferences, provided the first evidence for altered gut microbial ecology among T2D subjects (sT2D) versus population-matched healthy controls (HC). Metataxonomic 16S rRNA sequencing of participant stool revealed a decrease in alpha diversity of sT2D versus HC gut communities and identified BMI as a driver of gut community structure. Linear discriminant analysis effect size (LEfSe) identified a significant decrease in the relative abundance of the short-chain fatty acid-producing taxa Lachnospiraceae, Faecalibacterium, and Alistipes and an increase in pathobionts Escherichia-Shigella, Enterobacter, and Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. These results suggest characterization of the gut microbiome of individuals with T2D could identify key actors among "disease state" microbiota which may increase risk for or accelerate the onset of neurodegeneration. Furthermore, they identify candidate microbiome-targeted approaches for prevention and treatment of neuroinflammation in AD.}, }
@article {pmid38562476, year = {2024}, author = {Zhang, R and Zhang, H and Yang, C and Li, H and Wu, J}, title = {Effects of water stress on nutrients and enzyme activity in rhizosphere soils of greenhouse grape.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1376849}, pmid = {38562476}, issn = {1664-302X}, abstract = {In grape cultivation, incorrect water regulation will lead to significant water wastage, which in turn will change soil structure and disrupt soil nutrient cycling processes. This study aimed to investigate the effects of different water regulation treatments [by setting moderate water stress (W1), mild water stress (W2), and adequate water availability (CK)] on soil physical-chemical properties and enzyme activity in greenhouse grape during the growing season. The result showed that the W2 treatment had a negative impact on the build-up of dissolved organic carbon (DOC), nitrate nitrogen (NO3-N), and available phosphorus (AP). Throughout the reproductive period, the W1 and W2 treatments decreased the soil's microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) contents, and MBC was more vulnerable to water stress. During the growth period, the trends of urease, catalase, and sucrase activities in different soil depth were ranked as 10-20 cm > 0-10 cm > 20-40 cm. The urease activity in 0-10 cm soil was suppressed by both W1 and W2 treatments, while the invertase activity in various soil layers under W1 treatment differed substantially. The W1 treatment also reduced the catalase activity in the 20-40 cm soil layer in the grape growth season. These findings suggested that W2 treatment can conserve water and enhance microbial ecology of greenhouse grape soils. Therefore, W2 treatment was the most effective water regulation measure for local greenhouse grape cultivation.}, }
@article {pmid38562261, year = {2024}, author = {Zünd, JN and Plüss, S and Mujezinovic, D and Menzi, C and von Bieberstein, PR and de Wouters, T and Lacroix, C and Leventhal, GE and Pugin, B}, title = {A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae035}, pmid = {38562261}, issn = {2730-6151}, abstract = {The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.}, }
@article {pmid38555787, year = {2024}, author = {Mugani, R and El Khalloufi, F and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and El Amrani Zerrifi, S and Hejjaj, A and Ouazzani, N and Campos, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B}, title = {Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies.}, journal = {Water research}, volume = {255}, number = {}, pages = {121497}, doi = {10.1016/j.watres.2024.121497}, pmid = {38555787}, issn = {1879-2448}, mesh = {*Microcystins/metabolism ; *Water Purification/methods ; Biodegradation, Environmental ; *Plankton/metabolism ; Bibliometrics ; Bacteria/metabolism ; }, abstract = {Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.}, }
@article {pmid38555472, year = {2024}, author = {Pan, J and Zhang, Z and Li, Y and Yu, J and You, Z and Li, C and Wang, S and Zhu, M and Ren, F and Zhang, X and Sun, Y and Wang, S}, title = {A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38555472}, issn = {1477-4054}, support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 62325308//National Science Fund for Distinguished Young Scholars of China/ ; 32170114//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Deep Learning ; Pattern Recognition, Automated ; Neural Networks, Computer ; Algorithms ; Bacteria ; }, abstract = {Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.}, }
@article {pmid38555095, year = {2024}, author = {Brame, JE and Warbrick, I and Heke, D and Liddicoat, C and Breed, MF}, title = {Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort.}, journal = {Environmental research}, volume = {252}, number = {Pt 1}, pages = {118814}, doi = {10.1016/j.envres.2024.118814}, pmid = {38555095}, issn = {1096-0953}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Air Microbiology ; Air Pollutants/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Cohort Studies ; Cross-Over Studies ; Environmental Exposure ; Maori People ; *Microbiota ; New Zealand ; *Nose/microbiology ; Parks, Recreational ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.}, }
@article {pmid38554019, year = {2024}, author = {Hohagen, M and Sánchez, L and Herbst, AJ and Kählig, H and Shin, JW and Berry, D and Del Favero, G and Kleitz, F}, title = {MANNosylation of Mesoporous Silica Nanoparticles Modifies TLR4 Localization and NF-κB Translocation in T24 Bladder Cancer Cells.}, journal = {Advanced healthcare materials}, volume = {13}, number = {17}, pages = {e2304150}, pmid = {38554019}, issn = {2192-2659}, support = {//University of Vienna/ ; IBS-R004//Institute for Basic Science/ ; }, mesh = {Humans ; *Toll-Like Receptor 4/metabolism ; *Silicon Dioxide/chemistry ; *Nanoparticles/chemistry ; *NF-kappa B/metabolism ; *Urinary Bladder Neoplasms/metabolism/pathology ; *Mannose/chemistry ; Cell Line, Tumor ; Bacterial Adhesion/drug effects ; Caveolin 1/metabolism ; Porosity ; Lipopolysaccharides ; }, abstract = {D-mannose is widely used as non-antibiotic treatment for bacterial urinary tract infections. This application is based on a well-studied mechanism of binding to the type 1 bacterial pili and, therefore, blocking bacteria adhesion to the uroepithelial cells. To implement D-mannose into carrier systems, the mechanism of action of the sugar in the bladder environment is also relevant and requires investigation. Herein, two different MANNosylation strategies using mesoporous silica nanoparticles (MSNs) are described. The impact of different chemical linkers on bacterial adhesion and bladder cell response is studied via confocal microscopy imaging of the MSN interactions with the respective organisms. Cytotoxicity is assessed and the expression of Toll-like receptor 4 (TLR4) and caveolin-1 (CAV-1), in the presence or absence of simulated infection with bacterial lipopolysaccharide (LPS), is evaluated using the human urinary bladder cancer cell line T24. Further, localisation of the transcription factor NF-κB due to the MANNosylated materials is examined over time. The results show that MANNosylation modifies bacterial adhesion to the nanomaterials and significantly affects TLR4, caveolin-1, and NF-κB in bladder cells. These elements are essential components of the inflammatory cascade/pathogens response during urinary tract infections. These findings demonstrate that MANNosylation is a versatile tool to design hybrid nanocarriers for targeted biomedical applications.}, }
@article {pmid38553666, year = {2024}, author = {Ma, ZS}, title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {137}, pmid = {38553666}, issn = {1471-2105}, mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus &amp; Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.<br><br>RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.<br><br>CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.}, }
@article {pmid38552803, year = {2024}, author = {Petra de Oliveira Barros, V and Macedo Silva, JR and Maciel Melo, VM and Terceiro, PS and Nunes de Oliveira, I and Duarte de Freitas, J and Francisco da Silva Moura, O and Xavier de Araújo-Júnior, J and Erlanny da Silva Rodrigues, E and Maraschin, M and Thompson, FL and Landell, MF}, title = {Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B.}, journal = {Chemosphere}, volume = {355}, number = {}, pages = {141807}, doi = {10.1016/j.chemosphere.2024.141807}, pmid = {38552803}, issn = {1879-1298}, mesh = {*Yarrowia/metabolism ; Surface-Active Agents/chemistry ; Kerosene ; *Petroleum/analysis ; Hydrocarbons/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; }, abstract = {The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.}, }
@article {pmid38549428, year = {2024}, author = {Männistö, MK and Ahonen, SHK and Ganzert, L and Tiirola, M and Stark, S and Häggblom, MM}, title = {Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38549428}, issn = {1574-6941}, support = {252323//Academy of Finland/ ; OCE 2129351//National Science Foundation/ ; }, mesh = {*Ecosystem ; *Mycobiome ; Snow ; Tundra ; Bacteria/genetics ; Soil/chemistry ; Seasons ; Climate Change ; Nutrients ; Arctic Regions ; }, abstract = {Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.}, }
@article {pmid38549276, year = {2024}, author = {Gao, J and Chen, L and Wang, J and Zhao, W and Zhang, J and Qin, Z and Wang, M and Chen, X and Li, M and Yang, Q}, title = {Response of the Symbiotic Microbial Community of Dioscorea opposita Cultivar Tiegun to Root-Knot Nematode Infection.}, journal = {Plant disease}, volume = {108}, number = {8}, pages = {2472-2483}, doi = {10.1094/PDIS-01-24-0169-RE}, pmid = {38549276}, issn = {0191-2917}, mesh = {Animals ; *Dioscorea/microbiology/parasitology ; *Plant Roots/microbiology/parasitology ; *Plant Diseases/parasitology/microbiology ; *Soil Microbiology ; *Symbiosis ; *Tylenchoidea/physiology ; *Rhizosphere ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; Nematoda/physiology/microbiology ; }, abstract = {Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial α-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.}, }
@article {pmid38548725, year = {2024}, author = {Giordano, N and Gaudin, M and Trottier, C and Delage, E and Nef, C and Bowler, C and Chaffron, S}, title = {Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2721}, pmid = {38548725}, issn = {2041-1723}, support = {862923//European Commission (EC)/ ; }, mesh = {*Ecosystem ; Phylogeny ; *Bacteria/genetics ; Aquatic Organisms/genetics ; Oceans and Seas ; }, abstract = {Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.}, }
@article {pmid38548158, year = {2024}, author = {Yang, S and Zuo, J and Grossart, HP and Dai, G and Liu, J and Song, L and Gan, N}, title = {Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {348}, number = {}, pages = {123878}, doi = {10.1016/j.envpol.2024.123878}, pmid = {38548158}, issn = {1873-6424}, mesh = {Microcystins/metabolism ; Reproducibility of Results ; *Cyanobacteria/metabolism ; *Microcystis/metabolism ; Biomass ; }, abstract = {Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.}, }
@article {pmid38547998, year = {2024}, author = {Li, Y and Schütte, W and Dekeukeleire, M and Janssen, C and Boon, N and Asselman, J and Lebeer, S and Spacova, I and De Rijcke, M}, title = {The immunostimulatory activity of sea spray aerosols: bacteria and endotoxins activate TLR4, TLR2/6, NF-κB and IRF in human cells.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {171969}, doi = {10.1016/j.scitotenv.2024.171969}, pmid = {38547998}, issn = {1879-1026}, mesh = {Humans ; *NF-kappa B/metabolism ; *Aerosols ; *Endotoxins ; Toll-Like Receptor 4/metabolism ; Interferon Regulatory Factors/metabolism ; Toll-Like Receptor 2/metabolism ; Bacteria ; Air Pollutants ; Belgium ; Immunity, Innate ; }, abstract = {Frequent exposure to sea spray aerosols (SSA) containing marine microorganisms and bioactive compounds may influence human health. However, little is known about potential immunostimulation by SSA exposure. This study focuses on the effects of marine bacteria and endotoxins in SSA on several receptors and transcription factors known to play a key role in the human innate immune system. SSA samples were collected in the field (Ostend, Belgium) or generated in the lab using a marine aerosol reference tank (MART). Samples were characterized by their sodium contents, total bacterial counts, and endotoxin concentrations. Human reporter cells were exposed to SSA to investigate the activation of toll-like receptor 4 (TLR4) in HEK-Blue hTLR4 cells and TLR2/6 in HEK-Blue hTLR2/6 cells, as well as the activation of nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRF) in THP1-Dual monocytes. These responses were then correlated to the total bacterial counts and endotoxin concentrations to explore dose-effect relationships. Field SSA contained from 3.0 × 10[3] to 6.0 × 10[5] bacteria/m[3] air (averaging 2.0 ± 1.9 × 10[5] bacteria/m[3] air) and an endotoxin concentration ranging from 7 to 1217 EU/m[3] air (averaging 389 ± 434 EU/m[3] air). In contrast, MART SSA exhibited elevated levels of total bacterial count (from 2.0 × 10[5] to 2.4 × 10[6], averaging 7.3 ± 5.5 × 10[5] cells/m[3] air) and endotoxin concentration from 536 to 2191 (averaging 1310 ± 513 EU/m[3] air). SSA samples differentially activated TLR4, TLR2/6, NF-κB and IRF. These immune responses correlated dose-dependently with the total bacterial counts, endotoxin levels, or both. This study sheds light on the immunostimulatory potential of SSA and its underlying mechanisms, highlighting the need for further research to deepen our understanding of the health implications of SSA exposure.}, }
@article {pmid38546802, year = {2024}, author = {Stephenson, MM and Coleman, ME and Azzolina, NA}, title = {Trends in Burdens of Disease by Transmission Source (USA, 2005-2020) and Hazard Identification for Foods: Focus on Milkborne Disease.}, journal = {Journal of epidemiology and global health}, volume = {14}, number = {3}, pages = {787-816}, pmid = {38546802}, issn = {2210-6014}, mesh = {Humans ; *Foodborne Diseases/epidemiology ; United States/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Animals ; *Milk/microbiology ; Cost of Illness ; Hazard Analysis and Critical Control Points/methods ; Food Microbiology ; }, abstract = {BACKGROUND: Robust solutions to global, national, and regional burdens of communicable and non-communicable diseases, particularly related to diet, demand interdisciplinary or transdisciplinary collaborations to effectively inform risk analysis and policy decisions.<br><br>OBJECTIVE: U.S. outbreak data for 2005-2020 from all transmission sources were analyzed for trends in the burden of infectious disease and foodborne outbreaks.<br><br>METHODS: Outbreak data from 58 Microsoft Access[&#xae;] data tables were structured using systematic queries and pivot tables for analysis by transmission source, pathogen, and date. Trends were examined using graphical representations, smoothing splines, Spearman's rho rank correlations, and non-parametric testing for trend. Hazard Identification was conducted based on the number and severity of illnesses.<br><br>RESULTS: The evidence does not support increasing trends in the burden of infectious foodborne disease, though strongly increasing trends were observed for other transmission sources. Morbidity and mortality were dominated by person-to-person transmission; foodborne and other transmission sources accounted for small portions of the disease burden. Foods representing the greatest hazards associated with the four major foodborne bacterial diseases were identified. Fatal foodborne disease was dominated by fruits, vegetables, peanut butter, and pasteurized dairy.<br><br>CONCLUSION: The available evidence conflicts with assumptions of zero risk for pasteurized milk and increasing trends in the burden of illness for raw milk. For future evidence-based risk management, transdisciplinary risk analysis methodologies are essential to balance both communicable and non-communicable diseases and both food safety and food security, considering scientific, sustainable, economic, cultural, social, and political factors to support health and wellness for humans and ecosystems.}, }
@article {pmid38544331, year = {2024}, author = {Wang, C and Defoirdt, T and Rajkovic, A}, title = {The impact of indole and mucin on sporulation, biofilm formation, and enterotoxin production in foodborne Clostridium perfringens.}, journal = {Journal of applied microbiology}, volume = {135}, number = {4}, pages = {}, doi = {10.1093/jambio/lxae083}, pmid = {38544331}, issn = {1365-2672}, support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Ghent University/ ; 1506419N//Research Foundation Flanders/ ; }, mesh = {*Clostridium perfringens/genetics ; *Enterotoxins/genetics ; Mucins/metabolism ; Spores, Bacterial ; Biofilms ; }, abstract = {AIMS: Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact Clostridium perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.<br><br>METHODS AND RESULTS: There was no impact on growth of Cl. perfringens for up to 400&#xa0;&#xb5;M indole and 240&#xa0;mg/l mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of Cl. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased Cl. perfringens enterotoxin levels in mucin-treated Cl. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significantly increased biofilm formation of Cl. perfringens, although the effect size was relatively small (less than 1.5 fold).<br><br>CONCLUSION: These results indicate that Cl. perfringens can sense its presence in a host environment by responding to mucin, and thereby markedly increased enterotoxin production.}, }
@article {pmid38543583, year = {2024}, author = {Pandey, S and Blache, A and Achouak, W}, title = {Insights into Bacterial Extracellular Vesicle Biogenesis, Functions, and Implications in Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543583}, issn = {2076-2607}, abstract = {Plant-microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria and their importance in plant defense, and paves the way for future research in this exciting field.}, }
@article {pmid38543493, year = {2024}, author = {Heczko, P}, title = {Editorial for Special Issue "Effects of Probiotics on Health".}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543493}, issn = {2076-2607}, abstract = {Since 1987, when Professor Sherwood Gorbach discovered, characterized, and commercialized the first probiotic Lactobacillus rhamnosus GG, a total of over 17,000 publications have been indexed in PubMed under "probiotic" and "health", which is an extensive amount of research on the specific bacteria and yeasts defined as "live microorganisms that, when administered in adequate amounts, exert a health benefit on the host" [...].}, }
@article {pmid38543484, year = {2024}, author = {Rosa-Masegosa, A and Rodriguez-Sanchez, A and Gorrasi, S and Fenice, M and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B}, title = {Microbial Ecology of Granular Biofilm Technologies for Wastewater Treatment: A Review.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543484}, issn = {2076-2607}, abstract = {Nowadays, the discharge of wastewater is a global concern due to the damage caused to human and environmental health. Wastewater treatment has progressed to provide environmentally and economically sustainable technologies. The biological treatment of wastewater is one of the fundamental bases of this field, and the employment of new technologies based on granular biofilm systems is demonstrating success in tackling the environmental issues derived from the discharge of wastewater. The granular-conforming microorganisms must be evaluated as functional entities because their activities and functions for removing pollutants are interconnected with the surrounding microbiota. The deep knowledge of microbial communities allows for the improvement in system operation, as the proliferation of microorganisms in charge of metabolic roles could be modified by adjustments to operational conditions. This is why engineering must consider the intrinsic microbiological aspects of biological wastewater treatment systems to obtain the most effective performance. This review provides an extensive view of the microbial ecology of biological wastewater treatment technologies based on granular biofilms for mitigating water pollution.}, }
@article {pmid38543271, year = {2024}, author = {Srivastava, MG and Kamarudin, NHN and Aktan, MK and Zheng, K and Zayed, N and Yongabi, D and Wagner, P and Teughels, W and Boccaccini, AR and Braem, A}, title = {pH-Triggered Controlled Release of Chlorhexidine Using Chitosan-Coated Titanium Silica Composite for Dental Infection Prevention.}, journal = {Pharmaceutics}, volume = {16}, number = {3}, pages = {}, pmid = {38543271}, issn = {1999-4923}, support = {STG/17/024, C32/18/059//KU Leuven/ ; }, abstract = {Peri-implantitis is a growing pathological concern for dental implants which aggravates the occurrence of revision surgeries. This increases the burden on both hospitals and the patients themselves. Research is now focused on the development of materials and accompanying implants designed to resist biofilm formation. To enhance this endeavor, a smart method of biofilm inhibition coupled with limiting toxicity to the host cells is crucial. Therefore, this research aims to establish a proof-of-concept for the pH-triggered release of chlorhexidine (CHX), an antiseptic commonly used in mouth rinses, from a titanium (Ti) substrate to inhibit biofilm formation on its surface. To this end, a macroporous Ti matrix is filled with mesoporous silica (together referred to as Ti/SiO2), which acts as a diffusion barrier for CHX from the CHX feed side to the release side. To limit release to acidic conditions, the release side of Ti/SiO2 is coated with crosslinked chitosan (CS), a pH-responsive and antimicrobial natural polymer. Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM/EDX) and Fourier transform infrared (FTIR) spectroscopy confirmed successful CS film formation and crosslinking on the Ti/SiO2 disks. The presence of the CS coating reduced CHX release by 33% as compared to non-coated Ti/SiO2 disks, thus reducing the antiseptic exposure to the environment in normal conditions. Simultaneous differential scanning calorimetry and thermogravimetric analyzer (SDT) results highlighted the thermal stability of the crosslinked CS films. Quartz crystal microbalance with dissipation monitoring (QCM-D) indicated a clear pH response for crosslinked CS coatings in an acidic medium. This pH response also influenced CHX release through a Ti/SiO2/CS disk where the CHX release was higher than the average trend in the neutral medium. Finally, the antimicrobial study revealed a significant reduction in biofilm formation for the CS-coated samples compared to the control sample using viability quantitative polymerase chain reaction (v-qPCR) measurements, which were also corroborated using SEM imaging. Overall, this study investigates the smart triggered release of pharmaceutical agents aimed at inhibiting biofilm formation, with potential applicability to implant-like structures.}, }
@article {pmid38542054, year = {2024}, author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX}, title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, pmid = {38542054}, issn = {1422-0067}, support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; }, mesh = {*Ecosystem ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Extracellular Vesicles ; Genes, Bacterial ; }, abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.}, }
@article {pmid38539868, year = {2024}, author = {M'hir, S and Ayed, L and De Pasquale, I and Fanizza, E and Tlais, AZA and Comparelli, R and Verni, M and Latronico, R and Gobbetti, M and Di Cagno, R and Filannino, P}, title = {Comparison of Milk Kefirs Obtained from Cow's, Ewe's and Goat's Milk: Antioxidant Role of Microbial-Derived Exopolysaccharides.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38539868}, issn = {2076-3921}, abstract = {Different types of milk are used in the production of milk kefir, but little information is available on the release of potentially antioxidant exopolysaccharides (EPS). The aim of this study was to investigate whether the microbial dynamics and EPS release are dependent on the milk substrate. In our study, the inoculated microbial consortium was driven differently by each type of milk (cow, ewe, and goat). This was evident in the sugar consumption, organic acid production, free amino release, and EPS production. The amount and the composition of the secreted EPS varied depending on the milk type, with implications for the structure and functional properties of the EPS. The low EPS yield in ewe's milk was associated with a higher lactic acid production and thus with the use of carbon sources oriented towards energy production. Depending on the milk used as substrate, the EPS showed different monosaccharide and FT-IR profiles, microstructures, and surface morphologies. These differences affected the antiradical properties and reducing power of the EPS. In particular, EPS extracted from cow's milk had a higher antioxidant activity than other milk types, and the antioxidant activity was concentration dependent.}, }
@article {pmid38539229, year = {2024}, author = {Villena-Alemany, C and Mujakić, I and Fecskeová, LK and Woodhouse, J and Auladell, A and Dean, J and Hanusová, M and Socha, M and Gazulla, CR and Ruscheweyh, HJ and Sunagawa, S and Silva Kavagutti, V and Andrei, A&#x15e; and Grossart, HP and Ghai, R and Koblížek, M and Piwosz, K}, title = {Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {65}, pmid = {38539229}, issn = {2049-2618}, support = {19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 2021/03/Y/NZ8/00076//Polska Akademia Nauk/ ; }, mesh = {*Phototrophic Processes ; *Lakes/microbiology ; Bacteria/genetics ; Biomass ; Bacteria, Aerobic/genetics/metabolism ; Phytoplankton/genetics ; }, abstract = {BACKGROUND: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.<br><br>RESULTS: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment.<br><br>CONCLUSIONS: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.}, }
@article {pmid38537828, year = {2024}, author = {Madge Pimentel, I and Baikova, D and Buchner, D and Burfeid Castellanos, A and David, GM and Deep, A and Doliwa, A and Hadžiomerović, U and Mayombo, NAS and Prati, S and Spyra, MA and Vermiert, AM and Beisser, D and Dunthorn, M and Piggott, JJ and Sures, B and Tiegs, SD and Leese, F and Beermann, AJ}, title = {Assessing the response of an urban stream ecosystem to salinization under different flow regimes.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171849}, doi = {10.1016/j.scitotenv.2024.171849}, pmid = {38537828}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; *Rivers ; Invertebrates/physiology ; Fresh Water ; Sodium Chloride ; }, abstract = {Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.}, }
@article {pmid38537819, year = {2024}, author = {Tobias-Hünefeldt, SP and van Beusekom, JEE and Russnak, V and Dähnke, K and Streit, WR and Grossart, HP}, title = {Seasonality, rather than estuarine gradient or particle suspension/sinking dynamics, determines estuarine carbon distributions.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171962}, doi = {10.1016/j.scitotenv.2024.171962}, pmid = {38537819}, issn = {1879-1026}, mesh = {*Carbon/analysis ; Dissolved Organic Matter ; *Greenhouse Gases/analysis ; Estuaries ; Particulate Matter/analysis ; Rivers ; }, abstract = {Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. However, how estuarine gradients affect sinking/suspended particles, and dissolved organic matter dynamic interactions remains unexplored. We fractionated suspended/sinking particles to assess and characterise carbon fate differences. We investigated bacterial colonisation (SYBR Green I) and exopolymer concentrations (TEP/CSP) with microscopy staining techniques. C/H/N and dry weight analysis identified particle composition differences. Meanwhile, nutrient and carbon analysis, and excitation and emission matrix evaluations with a subsequent parallel factor (PARAFAC) analysis characterised dissolved organic matter. The lack of clear salinity driven patterns in our study are presumably due to strong mixing forces and high particle heterogeneity along the estuary, with only density differences between suspended and sinking particles. Elbe estuary particles' organic portion is made up of marine-like (sinking) and terrestrial-like (suspended) signatures. Salinity did not have a significant role in microbial degradation and carbon composition, although brackish estuary portions were more biologically active. Indicative of increased degradation rates, leading to decreased greenhouse gas emissions, which are especially relevant for estuaries, with their disproportionate greenhouse gas emissions. Bacterial colonisation decreased seawards, indicative of decreased degradation, and shifts in microbial community composition and functions. Our findings span diverse strands of research, concerning steady carbon contributions from both marine and terrestrial sources, carbon aromaticity, humification index, and bioavailability. Their integration highlights the importance of the Elbe estuary as a model system, providing robust information for future policy decisions affecting dissolved and particulate matter dynamics within the Elbe Estuary.}, }
@article {pmid38537644, year = {2024}, author = {Kawa, D and Thiombiano, B and Shimels, MZ and Taylor, T and Walmsley, A and Vahldick, HE and Rybka, D and Leite, MFA and Musa, Z and Bucksch, A and Dini-Andreote, F and Schilder, M and Chen, AJ and Daksa, J and Etalo, DW and Tessema, T and Kuramae, EE and Raaijmakers, JM and Bouwmeester, H and Brady, SM}, title = {The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {113971}, pmid = {38537644}, issn = {2211-1247}, mesh = {*Sorghum/microbiology/metabolism ; *Striga/physiology ; *Plant Roots/microbiology/metabolism/parasitology ; *Microbiota ; *Soil Microbiology ; Metabolome ; Plant Diseases/microbiology/parasitology ; }, abstract = {Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.}, }
@article {pmid38537571, year = {2024}, author = {Jing, J and Garbeva, P and Raaijmakers, JM and Medema, MH}, title = {Strategies for tailoring functional microbial synthetic communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38537571}, issn = {1751-7370}, mesh = {*Microbiota ; Soil/chemistry ; Soil Microbiology ; Microbial Interactions ; }, abstract = {Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.}, }
@article {pmid38535593, year = {2024}, author = {Cristino, S and Pascale, MR and Marino, F and Derelitto, C and Salaris, S and Orsini, M and Squarzoni, S and Grottola, A and Girolamini, L}, title = {Characterization of a Novel Species of Legionella Isolated from a Healthcare Facility: Legionella resiliens sp. nov.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38535593}, issn = {2076-0817}, mesh = {*Legionella/genetics/isolation &amp; purification ; *Phylogeny ; Fatty Acids/analysis ; Water Microbiology ; Health Facilities ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Base Composition/genetics ; Bacterial Typing Techniques ; Humans ; Whole Genome Sequencing ; }, abstract = {Two Legionella-like isolates, 8cVS16[T] and 9fVS26, were isolated from a water distribution system (WDS) in a healthcare facility. Cells were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, motile, and exhibited a blue-white fluorescence under Wood's lamp at 365 nm. The strains grew in a range of 32-37 °C on BCYE with L-cysteine (Cys+), GVPC, and MWY agar medium, with a positive reaction for oxidase, catalase, and gelatinase. The dominant fatty acids were summed features 3 (C16:1ω7c/C16:1ω6c) (27.7%), C16:0 iso (17.5%), and C16:0 (16.3%), and Q13 as the major ubiquinone. The mip and rpoB gene sequences showed a similarity of 96.7% and 92.4%, with L. anisa (ATCC 35292[T]). The whole genomes sequencing (WGS) performed displayed a GC content of 38.21 mol% for both. The digital DNA-DNA hybridization (dDDH) analysis demonstrated the separation of the two strains from the phylogenetically most related L. anisa (ATCC 35292[T]), with ≤43% DNA-DNA relatedness. The Average Nucleotide Identity (ANI) between the two strains and L. anisa (ATCC 35292[T]) was 90.74%, confirming that the two isolates represent a novel species of the genus Legionella. The name proposed for this species is Legionella resiliens sp. nov., with 8cVS16[T] (=DSM 114356[T] = CCUG 76627[T]) as the type strain.}, }
@article {pmid38531380, year = {2024}, author = {Skinner, JP and Palar, S and Allen, C and Raderstorf, A and Blake, P and Morán Reyes, A and Berg, RN and Muse, C and Robles, A and Hamdan, N and Chu, MY and Delgado, AG}, title = {Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {14}, pages = {6274-6283}, pmid = {38531380}, issn = {1520-5851}, mesh = {*Trichloroethylene/metabolism ; Acetylene/metabolism ; Biodegradation, Environmental ; Bacteria/metabolism ; Biomass ; *Groundwater ; }, abstract = {Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v[-1]) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.}, }
@article {pmid38530469, year = {2024}, author = {Maraci, &#xd6; and Antonatou-Papaioannou, A and Jünemann, S and Schneeberger, K and Schulze, M and Scheffler, I and Caspers, BA}, title = {Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {55}, pmid = {38530469}, issn = {1432-184X}, support = {SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Male ; Female ; Odorants ; Smell ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Bacteria ; Pheromones/metabolism ; *Microbiota/genetics ; }, abstract = {Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.}, }
@article {pmid38528797, year = {2024}, author = {Avila Santos, AP and de Almeida, BLS and Bonidia, RP and Stadler, PF and Stefanic, P and Mandic-Mulec, I and Rocha, U and Sanches, DS and de Carvalho, ACPLF}, title = {BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.}, journal = {RNA biology}, volume = {21}, number = {1}, pages = {1-12}, pmid = {38528797}, issn = {1555-8584}, support = {2023/00264-0//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior [CAPES] - Universidade de S&#xe3;o Paulo [USP]/ ; 109981//Canada&#x2019;s International Development Research Centre [IDRC]/ ; J1-4411//ARIS project/ ; }, mesh = {*Deep Learning ; RNA, Untranslated/genetics ; Algorithms ; RNA ; Neural Networks, Computer ; }, abstract = {The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.}, }
@article {pmid38526664, year = {2024}, author = {Roy, R and Paul, P and Chakraborty, P and Malik, M and Das, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Sarkar, S and Das Gupta, A and Tribedi, P}, title = {Cuminaldehyde and Tobramycin Forestall the Biofilm Threats of Staphylococcus aureus: A Combinatorial Strategy to Evade the Biofilm Challenges.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {11}, pages = {7588-7613}, pmid = {38526664}, issn = {1559-0291}, support = {R&amp;D/2020/F2//The Neotia University/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Tobramycin/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; *Benzaldehydes/pharmacology ; *Cymenes/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Xanthophylls/pharmacology ; Humans ; }, abstract = {Staphylococcus aureus, an opportunistic Gram-positive pathogen, is known for causing various infections in humans, primarily by forming biofilms. The biofilm-induced antibiotic resistance has been considered a significant medical threat. Combinatorial therapy has been considered a reliable approach to combat antibiotic resistance by using multiple antimicrobial agents simultaneously, targeting bacteria through different mechanisms of action. To this end, we examined the effects of two molecules, cuminaldehyde (a natural compound) and tobramycin (an antibiotic), individually and in combination, against staphylococcal biofilm. Our experimental observations demonstrated that cuminaldehyde (20 μg/mL) in combination with tobramycin (0.05 μg/mL) exhibited efficient reduction in biofilm formation compared to their individual treatments (p < 0.01). Additionally, the combination showed an additive interaction (fractional inhibitory concentration value 0.66) against S. aureus. Further analysis revealed that the effective combination accelerated the buildup of reactive oxygen species (ROS) and increased the membrane permeability of the bacteria. Our findings also specified that the cuminaldehyde in combination with tobramycin efficiently reduced biofilm-associated pathogenicity factors of S. aureus, including fibrinogen clumping ability, hemolysis property, and staphyloxanthin production. The selected concentrations of tobramycin and cuminaldehyde demonstrated promising activity against the biofilm development of S. aureus on catheter models without exerting antimicrobial effects. In conclusion, the combination of tobramycin and cuminaldehyde presented a successful strategy for combating staphylococcal biofilm-related healthcare threats. This combinatorial approach holds the potential for controlling biofilm-associated infections caused by S. aureus.}, }
@article {pmid38524670, year = {2023}, author = {Yount, TA and Murtha, AN and Cecere, AG and Miyashiro, TI}, title = {Quorum sensing facilitates interpopulation signaling by Vibrio fischeri within the light organ of Euprymna scolopes.}, journal = {Israel journal of chemistry}, volume = {63}, number = {5-6}, pages = {}, pmid = {38524670}, issn = {0021-2148}, support = {R01 GM129133/GM/NIGMS NIH HHS/United States ; }, abstract = {Quorum sensing is an intercellular signaling mechanism that enables bacterial cells to coordinate population-level behaviors. How quorum sensing functions in natural habitats remains poorly understood. Vibrio fischeri is a bacterial symbiont of the Hawaiian bobtail squid Euprymna scolopes and depends on LuxI/LuxR quorum sensing to produce the symbiotic trait of bioluminescence. A previous study demonstrated that animals emit light when co-colonized by a Δlux mutant, which lacks several genes within the lux operon that are necessary for bioluminescence production, and a LuxI[-] mutant, which cannot synthesize the quorum signaling molecule N-3-oxohexanoyl-homoserine lactone. Here, we build upon that observation and show that populations of LuxI[-] feature elevated promoter activity for the lux operon. We find that population structures comprising of Δlux and LuxI[-] are attenuated within the squid, but a wild-type strain enables the LuxI[-] strain type to be maintained in vivo. These experimental results support a model of interpopulation signaling, which provides basic insight into how quorum sensing functions within the natural habitats found within a host.}, }
@article {pmid38521905, year = {2024}, author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y}, title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {300}, pmid = {38521905}, issn = {1479-5876}, support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; }, mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.<br><br>METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.<br><br>RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.<br><br>CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.}, }
@article {pmid38519354, year = {2024}, author = {,  and Jurburg, SD and Álvarez Blanco, MJ and Chatzinotas, A and Kazem, A and König-Ries, B and Babin, D and Smalla, K and Cerecetto, V and Fernandez-Gnecco, G and Covacevich, F and Viruel, E and Bernaschina, Y and Leoni, C and Garaycochea, S and Terra, JA and Fresia, P and Figuerola, ELM and Wall, LG and Covelli, JM and Agnello, AC and Nieto, EE and Festa, S and Dominici, LE and Allegrini, M and Zabaloy, MC and Morales, ME and Erijman, L and Coniglio, A and Cassán, FD and Nievas, S and Roldán, DM and Menes, R and Jauri, PV and Marrero, CS and Massa, AM and Revetria, MAM and Fernández-Scavino, A and Pereira-Mora, L and Martínez, S and Frene, JP}, title = {Datathons: fostering equitability in data reuse in ecology.}, journal = {Trends in microbiology}, volume = {32}, number = {5}, pages = {415-418}, doi = {10.1016/j.tim.2024.02.010}, pmid = {38519354}, issn = {1878-4380}, mesh = {Argentina ; *Biodiversity ; *Ecology ; *Microbiota ; Uruguay ; }, abstract = {Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.}, }
@article {pmid38518769, year = {2024}, author = {Pristner, M and Wasinger, D and Seki, D and Klebermaß-Schrehof, K and Berger, A and Berry, D and Wisgrill, L and Warth, B}, title = {Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury.}, journal = {Cell reports. Medicine}, volume = {5}, number = {4}, pages = {101480}, pmid = {38518769}, issn = {2666-3791}, mesh = {Infant, Newborn ; Infant ; Humans ; *Infant, Extremely Premature ; Chromatography, Liquid/methods ; *Bile Acids and Salts ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; }, abstract = {The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.}, }
@article {pmid38516656, year = {2024}, author = {Brait, N and Hackl, T and Morel, C and Exbrayat, A and Gutierrez, S and Lequime, S}, title = {A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead088}, pmid = {38516656}, issn = {2057-1577}, abstract = {Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.}, }
@article {pmid38514851, year = {2024}, author = {Silva, DEO and Costa, RM and Campos, JR and Rocha, SMB and de Araujo Pereira, AP and Melo, VMM and Oliveira, FAS and de Alcantara Neto, F and Mendes, LW and Araujo, ASF}, title = {Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6845}, pmid = {38514851}, issn = {2045-2322}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics ; Brazil ; *Bacteria/genetics ; Acidobacteria/genetics ; Soil Microbiology ; }, abstract = {Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.}, }
@article {pmid38512483, year = {2024}, author = {Zhan, Y and Wang, E and Zhou, Y and He, G and Lv, P and Wang, L and Zhou, T and Miao, X and Chen, C and Li, Q}, title = {Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {54}, pmid = {38512483}, issn = {1432-184X}, mesh = {Soil/chemistry ; *Panax ; Agriculture/methods ; *Microbiota ; *Mycobiome ; Soil Microbiology ; }, abstract = {Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.}, }
@article {pmid38509266, year = {2024}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica.}, journal = {Mycorrhiza}, volume = {34}, number = {1-2}, pages = {119-130}, pmid = {38509266}, issn = {1432-1890}, support = {JP22H02382//Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Mycorrhizae/genetics ; Soil/chemistry ; Ecosystem ; *Cryptomeria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; Trees ; DNA, Fungal/genetics ; Fungi/genetics ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.}, }
@article {pmid38508742, year = {2024}, author = {Nishimura, Y and Yamada, K and Okazaki, Y and Ogata, H}, title = {DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics.}, journal = {Microbes and environments}, volume = {39}, number = {1}, pages = {}, pmid = {38508742}, issn = {1347-4405}, mesh = {*Software ; *User-Computer Interface ; Sequence Alignment ; Genomics ; Genome ; }, abstract = {With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), a web server that provides versatile functionality for comparative genomics with an intuitive interface. It allows the user to perform the highly customizable visualization of a synteny map by simply uploading nucleotide sequences of interest, ranging from a specific region to the whole genome landscape of microorganisms and viruses. DiGAlign will serve a wide range of biological researchers, particularly experimental biologists, with multifaceted features that allow the rapid characterization of genomic sequences of interest and the generation of a publication-ready figure.}, }
@article {pmid38508273, year = {2024}, author = {O'Donnell, C and Thorn, C and Roskam, E and Friel, R and Kirwan, SF and Waters, SM and O'Flaherty, V}, title = {Novel oxidising feed additives reduce in vitro methane emissions using the rumen simulation technique.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171808}, doi = {10.1016/j.scitotenv.2024.171808}, pmid = {38508273}, issn = {1879-1026}, mesh = {Animals ; Female ; *Rumen ; *Propionates/metabolism ; Methane/metabolism ; Magnesium Oxide/metabolism ; Diet ; Silage/analysis ; Ruminants ; Acetates/metabolism ; Oxygen/metabolism ; Animal Feed/analysis ; Fermentation ; Digestion ; Lactation ; }, abstract = {Enteric methane (CH4) produced by ruminant livestock is a potent greenhouse gas and represents significant energy loss for the animal. The novel application of oxidising compounds as antimethanogenic agents with future potential to be included in ruminant feeds, was assessed across two separate experiments in this study. Low concentrations of oxidising agents, namely urea hydrogen peroxide (UHP) with and without potassium iodide (KI), and magnesium peroxide (MgO2), were investigated for their effects on CH4 production, total gas production (TGP), volatile fatty acid (VFA) profiles, and nutrient disappearance in vitro using the rumen simulation technique. In both experiments, the in vitro diet consisted of 50:50 grass silage:concentrate on a dry matter basis. Treatment concentrations were based on the amount of oxygen delivered and expressed in terms of fold concentration. In Experiment 1, four treatments were tested (Control, 1× UHP + KI, 1× UHP, and 0.5× UHP + KI), and six treatments were assessed in Experiment 2 (Control, 0.5× UHP + KI, 0.5× UHP, 0.25× UHP + KI, 0.25× UHP, and 0.12× MgO2). All treatments in this study had a reducing effect on CH4 parameters. A dose-dependent reduction of TGP and CH4 parameters was observed, where treatments delivering higher levels of oxygen resulted in greater CH4 suppression. 1× UHP + KI reduced TGP by 28 % (p = 0.611), CH4% by 64 % (p = 0.075) and CH4 mmol/g digestible organic matter by 71 % (p = 0.037). 0.12× MgO2 reduced CH4 volume by 25 % (p > 0.05) without affecting any other parameters. Acetate-to-propionate ratios were reduced by treatments in both experiments (p < 0.01). Molar proportions of acetate and butyrate were reduced, while propionate and valerate were increased in UHP treatments. High concentrations of UHP affected the degradation of neutral detergent fibre in the forage substrate. Future in vitro work should investigate alternative slow-release oxygen sources aimed at prolonging CH4 suppression.}, }
@article {pmid38508106, year = {2024}, author = {Luo, Y and Pang, J and Pan, S and Wang, J and Jiang, X and Xu, Q and Zhang, H and Ruan, C and Ren, J and Zhang, C and Shi, J}, title = {Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron effectively reduces Cr(VI) and shifts soil microbiota.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {134058}, doi = {10.1016/j.jhazmat.2024.134058}, pmid = {38508106}, issn = {1873-3336}, mesh = {*Chromium/analysis/metabolism ; *Environmental Restoration and Remediation ; Iron ; *Penicillium ; Soil ; Urease ; *Water Pollutants, Chemical/analysis ; }, abstract = {Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg[-1] using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg[-1] within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.}, }
@article {pmid38507071, year = {2024}, author = {Martin-Pozas, T and Nováková, A and Jurado, V and Cuezva, S and Fernandez-Cortes, A and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {53}, pmid = {38507071}, issn = {1432-184X}, support = {PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Fungi/genetics ; Spain/epidemiology ; *Ecosystem ; Caves/microbiology ; Disease Outbreaks ; }, abstract = {Castañar is a cave with strict visitor control measures since it was open to public visits in 2003. However, in recent years, the cave suffered two fungal outbreaks, the first in 2008 and controlled by cleaning the contaminated sediments and subsequent closure of the cave until 2014. The cave was reopened but limited to a maximum of 450 visitors/year. Despite these restrictions on visit, the cave experienced a second outbreak in 2021, originating from the installation of a steel grating walkway, aiming at protecting the ground sediments from the visitors' footsteps. Here, we conducted an analysis using Next-Generation Sequencing and culture-dependent techniques to investigate the fungal communities related to the second outbreak and compare with those present before the cave suffered the outbreak. The results show that the most abundant fungi involved in the 2021 outbreak were already detected in 2020, and even in 2008 and 2009, although the main species that originating both outbreaks were different, likely due to the different carbon sources introduced into the cave.}, }
@article {pmid38502221, year = {2024}, author = {Saati-Santamaría, Z and Flores-Félix, JD and Igual, JM and Velázquez, E and García-Fraile, P and Martínez-Molina, E}, title = {Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host.}, journal = {Journal of molecular evolution}, volume = {92}, number = {2}, pages = {169-180}, pmid = {38502221}, issn = {1432-1432}, support = {SA293P18//Junta de Castilla y Le&#xf3;n/ ; }, mesh = {*Fatty Acids ; Phylogeny ; *Plants/genetics ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {The bacterial strain SECRCQ15[T] was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15[T], we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15[T] genome. We also found that singletons of F. quinoae SECRCQ15[T] are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.}, }
@article {pmid38500703, year = {2024}, author = {Dreyling, L and Penone, C and Schenk, NV and Schmitt, I and Dal Grande, F}, title = {Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae012}, pmid = {38500703}, issn = {2730-6151}, abstract = {Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.}, }
@article {pmid38499207, year = {2024}, author = {Kodama, T and Takehara, T}, title = {Molecular Genealogy of Metabolic-associated Hepatocellular Carcinoma.}, journal = {Seminars in liver disease}, volume = {44}, number = {2}, pages = {147-158}, pmid = {38499207}, issn = {1098-8971}, support = {JP23ama221410,JP23ck0106793,JP23fk0210131//Japan Agency for Medical Research and Development/ ; JP23ama221410//Japan Agency for Medical Research and Development/ ; JP23ck0106793//Japan Agency for Medical Research and Development/ ; JP23fk0210131//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/genetics ; *Liver Neoplasms/genetics ; *Tumor Microenvironment ; *Genetic Predisposition to Disease ; Animals ; Non-alcoholic Fatty Liver Disease/genetics ; Lipid Metabolism/genetics ; Insulin Resistance ; Membrane Proteins/genetics ; Diabetes Mellitus, Type 2/genetics ; Oxidative Stress ; Obesity/genetics/complications ; Risk Factors ; Polymorphism, Single Nucleotide ; Acyltransferases/genetics ; Adaptor Proteins, Signal Transducing ; Phospholipases A2, Calcium-Independent ; }, abstract = {This review examines the latest epidemiological and molecular pathogenic findings of metabolic-associated hepatocellular carcinoma (HCC). Its increasing prevalence is a significant concern and reflects the growing burden of obesity and metabolic diseases, including metabolic dysfunction-associated steatotic liver disease, formerly known as nonalcoholic fatty liver disease, and type 2 diabetes. Metabolic-associated HCC has unique molecular abnormality and distinctive gene expression patterns implicating aberrations in bile acid, fatty acid metabolism, oxidative stress, and proinflammatory pathways. Furthermore, a notable frequency of single nucleotide polymorphisms in genes such as patatin-like phospholipase domain-containing 3, transmembrane 6 superfamily member 2, glucokinase regulator, and membrane-bound O-acyltransferase domain-containing 7 has been observed. The tumor immune microenvironment of metabolic-associated HCC is characterized by unique phenotypes of macrophages, neutrophils, and T lymphocytes. Additionally, the pathogenesis of metabolic-associated HCC is influenced by abnormal lipid metabolism, insulin resistance, and dysbiosis. In conclusion, deciphering the intricate interactions among metabolic processes, genetic predispositions, inflammatory responses, immune regulation, and microbial ecology is imperative for the development of novel therapeutic and preventative measures against metabolic-associated HCC.}, }
@article {pmid38498218, year = {2024}, author = {Greipel, E and Nagy, K and Csákvári, E and Dér, L and Galajda, P and Kutasi, J}, title = {Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {52}, pmid = {38498218}, issn = {1432-184X}, mesh = {*Azospirillum brasilense ; *Scenedesmus/metabolism ; Microfluidics ; Oxaloacetic Acid/metabolism ; Plant Growth Regulators/metabolism ; Plants/metabolism ; }, abstract = {The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.}, }
@article {pmid38497641, year = {2024}, author = {Dean, CJ and Peña-Mosca, F and Ray, T and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Godden, S and Heins, B and Pinedo, P and Machado, VS and Caixeta, LS and Noyes, NR}, title = {Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0223423}, pmid = {38497641}, issn = {1098-5336}, mesh = {Female ; Cattle ; Animals ; Staphylococcus aureus/genetics ; Metagenome ; Case-Control Studies ; *Mastitis, Bovine/epidemiology/microbiology ; *Staphylococcal Infections/epidemiology/veterinary/microbiology ; Milk/microbiology ; Mammary Glands, Animal/microbiology ; }, abstract = {UNLABELLED: The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).<br><br>IMPORTANCE: Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.}, }
@article {pmid38494494, year = {2024}, author = {Liu, X and Salles, JF}, title = {Lose-lose consequences of bacterial community-driven invasions in soil.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {57}, pmid = {38494494}, issn = {2049-2618}, mesh = {*Soil ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.<br><br>RESULTS: Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~&#x2009;5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.<br><br>CONCLUSIONS: Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.}, }
@article {pmid38493536, year = {2024}, author = {Mekonnen, YT and Savini, F and Indio, V and Seguino, A and Giacometti, F and Serraino, A and Candela, M and De Cesare, A}, title = {Systematic review on microbiome-related nutritional interventions interfering with the colonization of foodborne pathogens in broiler gut to prevent contamination of poultry meat.}, journal = {Poultry science}, volume = {103}, number = {5}, pages = {103607}, pmid = {38493536}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Poultry Diseases/prevention &amp; control/microbiology ; Meat/analysis ; Probiotics/administration &amp; dosage/pharmacology ; Animal Feed/analysis ; Food Microbiology ; Foodborne Diseases/veterinary/prevention &amp; control/microbiology ; Diet/veterinary ; }, abstract = {This systematic review aimed to compile the available body of knowledge about microbiome-related nutritional interventions contributing to improve the chicken health and having an impact on the reduction of colonization by foodborne pathogens in the gut. Original research articles published between 2012 and 2022 were systematically searched in Scopus and PubMed. A total of 1,948 articles were retrieved and 140 fulfilled the inclusion criteria. Overall, 73 papers described 99 interventions against colonization by Escherichia coli and related organisms; 10 papers described 15 interventions against Campylobacter spp.; 36 papers described 54 interventions against Salmonella; 40 papers described 54 interventions against Clostridium perfringens. A total of 197 microbiome-related interventions were identified as effective against one or more of the listed pathogens and included probiotics (n = 80), prebiotics (n = 23), phytobiotics (n = 25), synbiotics (n = 12), organic acids (n = 12), enzymes (n = 4), essential oils (n = 14) and combination of these (n = 27). The identified interventions were mostly administered in the feed (173/197) or through oral gavage (11/197), in the drinking water (7/197), in ovo (2/197), intra amniotic (2/197), in fresh or reused litter (1/197) or both in the feed and water (1/197). The interventions enhanced the beneficial microbial communities in the broiler gut as Lactic acid bacteria, mostly Lactobacillus spp., or modulated multiple microbial populations. The mechanisms promoting the fighting against colonization by foodborne pathogens included competitive exclusion, production of short chain fatty acids, decrease of gut pH, restoration of the microbiome after dysbiosis events, promotion of a more stable microbial ecology, expression of genes improving the integrity of intestinal mucosa, enhancing of mucin production and improvement of host immune response. All the studies extracted from the literature described in vivo trials but performed on a limited number of animals under experimental settings. Moreover, they detailed the effect of the intervention on the chicken gut without details on further impact on poultry meat safety.}, }
@article {pmid38493186, year = {2024}, author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L}, title = {Data-driven prediction of colonization outcomes for complex microbial communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2406}, pmid = {38493186}, issn = {2041-1723}, support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; K25 HL166208/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Feces/microbiology ; *Enterococcus faecium ; Microbial Interactions ; Enterococcus faecalis ; }, abstract = {Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.}, }
@article {pmid38492828, year = {2024}, author = {Malik, M and Das, S and Chakraborty, P and Paul, P and Roy, R and Das Gupta, A and Sarkar, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Tribedi, P}, title = {Application of cuminaldehyde and ciprofloxacin for the effective control of biofilm assembly of Pseudomonas aeruginosa: A combinatorial study.}, journal = {Microbial pathogenesis}, volume = {190}, number = {}, pages = {106624}, doi = {10.1016/j.micpath.2024.106624}, pmid = {38492828}, issn = {1096-1208}, mesh = {*Biofilms/drug effects ; *Ciprofloxacin/pharmacology ; *Pseudomonas aeruginosa/drug effects/physiology ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Benzaldehydes/pharmacology ; *Reactive Oxygen Species/metabolism ; Virulence Factors ; Cymenes/pharmacology ; Drug Synergism ; Cell Membrane Permeability/drug effects ; Humans ; }, abstract = {Pseudomonas aeruginosa is widely associated with biofilm-mediated antibiotic resistant chronic and acute infections which constitute a persistent healthcare challenges. Addressing this threat requires exploration of novel therapeutic strategies involving the combination of natural compounds and conventional antibiotics. Hence, our study has focused on two compounds; cuminaldehyde and ciprofloxacin, which were strategically combined to target the biofilm challenge of P. aeruginosa. The minimum inhibitory concentration (MIC) of cuminaldehyde and ciprofloxacin was found to be 400 μg/mL and 0.4 μg/mL, respectively. Moreover, the fractional inhibitory concentration index (FICI = 0.62) indicated an additive interaction prevailed between cuminaldehyde and ciprofloxacin. Subsequently, sub-MIC doses of cuminaldehyde (25 μg/mL) and ciprofloxacin (0.05 μg/mL) were selected for an array of antibiofilm assays which confirmed their biofilm inhibitory potential without exhibiting any antimicrobial activity. Furthermore, selected doses of the mentioned compounds could manage biofilm on catheter surface by inhibiting and disintegrating existing biofilm. Additionally, the test combination of the mentioned compounds reduced virulence factors secretion, accumulated reactive oxygen species and increased cell-membrane permeability. Thus, the combination of cuminaldehyde and ciprofloxacin demonstrates potential in combating biofilm-associated Pseudomonal threats.}, }
@article {pmid38492604, year = {2024}, author = {Zhao, S and Zheng, Q and Wang, H and Fan, X}, title = {Nitrogen in landfills: Sources, environmental impacts and novel treatment approaches.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171725}, doi = {10.1016/j.scitotenv.2024.171725}, pmid = {38492604}, issn = {1879-1026}, abstract = {Nitrogen (N) accumulation in landfills is a pressing environmental concern due to its diverse sources and significant environmental impacts. However, there is relatively limited attention and research focus on N in landfills as it is overshadowed by other more prominent pollutants. This study comprehensively examines the sources of N in landfills, including food waste contributing to 390 million tons of N annually, industrial discharges, and sewage treatment plant effluents. The environmental impacts of N in landfills are primarily manifested in N2O emissions and leachate with high N concentrations. To address these challenges, this study presents various mitigation and management strategies, including N2O reduction measures and novel NH4[+] removal techniques, such as electrochemical technologies, membrane separation processes, algae-based process, and other advanced oxidation processes. However, a more in-depth understanding of the complexities of N cycling in landfills is required, due to the lack of long-term monitoring data and the presence of intricate interactions and feedback mechanisms. To ultimately achieve optimized N management and minimized adverse environmental impacts in landfill settings, future prospects should emphasize advancements in monitoring and modeling technologies, enhanced understanding of microbial ecology, implementation of circular economy principles, application of innovative treatment technologies, and comprehensive landfill design and planning.}, }
@article {pmid38491554, year = {2024}, author = {Xu, G and Zhao, S and Rogers, MJ and Chen, C and He, J}, title = {Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {54}, pmid = {38491554}, issn = {2049-2618}, support = {R-302-000-198720//Ng Teng Fong Charitable Foundation (NTFCF)/ ; MOE-00003301//The Ministry of Education, Singapore/ ; }, mesh = {Humans ; *Polychlorinated Biphenyls/analysis ; Sewage ; *Chloroflexi/genetics ; Prevalence ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; *Environmental Pollutants/analysis ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.<br><br>RESULTS: Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.<br><br>CONCLUSIONS: Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.}, }
@article {pmid38488929, year = {2024}, author = {Dayang Najwa, AB and Elexson, N and Dalene, L and Teng, ST}, title = {Vibrio Species and Cyanobacteria: Understanding Their Association in Local Shrimp Farm Using Canonical Correspondence Analysis (CCA).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {51}, pmid = {38488929}, issn = {1432-184X}, mesh = {Animals ; *Vibrio ; *Cyanobacteria ; Ponds ; Water ; Aquaculture ; *Vibrio parahaemolyticus ; *Penaeidae/microbiology ; }, abstract = {In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from pond A (n = 6), pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in pond A, pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14-7.64), while cyanobacteria correlated with pH, salinity (17.4-24 ppt), and temperature (30.8-31.5 °C), with salinity as the most influential factor. This suggests that factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.}, }
@article {pmid38488280, year = {2024}, author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0401723}, pmid = {38488280}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Aggregatibacter/physiology ; Phylogeny ; *Ecosystem ; *Haemophilus/genetics ; Mouth ; }, abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.<br><br>IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.}, }
@article {pmid38485445, year = {2024}, author = {Harris, TD and Reinl, KL and Azarderakhsh, M and Berger, SA and Berman, MC and Bizic, M and Bhattacharya, R and Burnet, SH and Cianci-Gaskill, JA and Domis, LNS and Elfferich, I and Ger, KA and Grossart, HF and Ibelings, BW and Ionescu, D and Kouhanestani, ZM and Mauch, J and McElarney, YR and Nava, V and North, RL and Ogashawara, I and Paule-Mercado, MCA and Soria-Píriz, S and Sun, X and Trout-Haney, JV and Weyhenmeyer, GA and Yokota, K and Zhan, Q}, title = {What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors.}, journal = {Harmful algae}, volume = {133}, number = {}, pages = {102599}, doi = {10.1016/j.hal.2024.102599}, pmid = {38485445}, issn = {1878-1470}, mesh = {*Cyanobacteria/physiology ; *Harmful Algal Bloom ; }, abstract = {Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies.}, }
@article {pmid38485438, year = {2024}, author = {Woodhouse, JN and Burford, MA and Neilan, BA and Jex, A and Tichkule, S and Sivonen, K and Fewer, DP and Grossart, HP and Willis, A}, title = {Long-term stability of the genome structure of the cyanobacterium, Dolichospermum in a deep German lake.}, journal = {Harmful algae}, volume = {133}, number = {}, pages = {102600}, doi = {10.1016/j.hal.2024.102600}, pmid = {38485438}, issn = {1878-1470}, support = {/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics ; Phytoplankton ; Biomass ; Phosphorus ; }, abstract = {Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations.}, }
@article {pmid38484962, year = {2024}, author = {Fang, X and Colina Blanco, AE and Christl, I and Le Bars, M and Straub, D and Kleindienst, S and Planer-Friedrich, B and Zhao, FJ and Kappler, A and Kretzschmar, R}, title = {Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {347}, number = {}, pages = {123786}, doi = {10.1016/j.envpol.2024.123786}, pmid = {38484962}, issn = {1873-6424}, mesh = {Cadmium/analysis ; *Arsenic/analysis ; Calcium Carbonate ; Soil ; *Oryza ; Sulfates ; Clay ; Sulfur Oxides ; Sand ; *Soil Pollutants/analysis ; *Oxides ; *Calcium Compounds ; }, abstract = {Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding. To study the unknown effects of combined sulfate and limestone amendment under intermittent flooding for simultaneously decreasing As and Cd in rice, we performed a pot experiment using an acidic sandy loam paddy soil. We also included a clay loam paddy soil to study the role of soil texture in low-As rice production under intermittent flooding. We found that liming not only decreased rice Cd concentrations but also greatly decreased dimethylarsenate (DMA) accumulation in rice. We hypothesize that this is due to suppressed sulfate reduction, As methylation, and As thiolation by liming in the sulfate-amended soil and a higher share of deprotonated DMA at higher pH which is taken up less readily than protonated DMA. Decreased gene abundance of potential soil sulfate-reducers by liming further supported our hypothesis. Combined sulfate and limestone amendment to the acidic sandy loam soil produced rice with 43% lower inorganic As, 72% lower DMA, and 68% lower Cd compared to the control soil without amendment. A tradeoff between soil aeration and water availability was observed for the clay loam soil, suggesting difficulties to decrease As in rice while avoiding plant water stress under intermittent flooding in fine-textured soils. Our results suggest that combining sulfate amendment, liming, and intermittent flooding can help to secure rice safety when the presence of both As and Cd in coarse-textured soils is of concern.}, }
@article {pmid38483479, year = {2024}, author = {Mermans, F and De Baets, H and García-Timermans, C and Teughels, W and Boon, N}, title = {Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0393123}, pmid = {38483479}, issn = {2165-0497}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {Humans ; *Cephalothin ; Flow Cytometry ; Cost-Benefit Analysis ; *Anti-Infective Agents/pharmacology ; Drug Development ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.}, }
@article {pmid38481338, year = {2024}, author = {Sun, J and Zhao, J and Liu, M and Li, J and Cheng, J and Li, W and Yuan, M and Xiao, S and Xue, C}, title = {SreC-dependent adaption to host iron environments regulates the transition of trophic stages and developmental processes of Curvularia lunata.}, journal = {Molecular plant pathology}, volume = {25}, number = {3}, pages = {e13444}, pmid = {38481338}, issn = {1364-3703}, support = {31271992//National Natural Science Foundation of China/ ; 2022JH2/101300168//Liaoning Provincial Applied Basic Program/ ; }, mesh = {*Iron/metabolism ; *Fungal Proteins/genetics/metabolism ; Virulence ; *Curvularia ; }, abstract = {Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism of plant pathogens rapidly adapting to the dynamic host iron environments to assimilate iron for invasion and colonization remains largely unexplored. Here, we found that the GATA transcription factor SreC in Curvularia lunata is required for virulence and adaption to the host iron excess environment. SreC directly binds to the ATGWGATAW element in an iron-dependent manner to regulate the switch between different iron assimilation pathways, conferring adaption to host iron environments in different trophic stages of C. lunata. SreC also regulates the transition of trophic stages and developmental processes in C. lunata. SreC-dependent adaption to host iron environments is essential to the infectious growth and survival of C. lunata. We also demonstrate that CgSreA (a SreC orthologue) plays a similar role in Colletotrichum graminicola. We conclude that Sre mediates adaption to the host iron environment during infection, and the function is conserved in hemibiotrophic fungi.}, }
@article {pmid38480488, year = {2024}, author = {Munley, JA and Kelly, LS and Park, G and Drury, SK and Gillies, GS and Coldwell, PS and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Acute emergence of the intestinal pathobiome after postinjury pneumonia.}, journal = {The journal of trauma and acute care surgery}, volume = {97}, number = {1}, pages = {65-72}, pmid = {38480488}, issn = {2163-0763}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; T32 HL160491/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Rats, Sprague-Dawley ; Female ; Male ; Rats ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Sex Factors ; Disease Models, Animal ; Sepsis/microbiology ; Pneumonia/microbiology/etiology ; }, abstract = {BACKGROUND: Previous preclinical studies have demonstrated sex-specific alterations in the gut microbiome following traumatic injury or sepsis alone; however, the impact of host sex on dysbiosis in the setting of postinjury sepsis acutely is unknown. We hypothesized that multicompartmental injury with subsequent pneumonia would result in host sex-specific dysbiosis.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either multicompartmental trauma (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofracture), PT plus 2-hour daily restraint stress (PT/RS), PT with postinjury day 1 Pseudomonas aeruginosa pneumonia (PT-PNA), PT/RS with pneumonia (PT/RS-PNA), or naive controls. Fecal microbiome was measured on days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analyses. Microbial &#x3b1;-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. &#x3b2;-diversity was assessed using principal coordinate analysis. Significance was defined as p < 0.05.<br><br>RESULTS: All groups had drastic declines in the Chao1 (&#x3b1;-diversity) index compared with naive controls (p < 0.05). Groups PT-PNA and PT/RS-PNA resulted in different &#x3b2;-diversity arrays compared with uninfected counterparts (PT, PT/RS) (p = 0.001). Postinjury sepsis cohorts showed a loss of commensal bacteria along with emergence of pathogenic bacteria, with blooms of Proteus in PT-PNA and Escherichia-Shigella group in PT/RS-PNA compared with other cohorts. At day 2, PT-PNA resulted in &#x3b2;-diversity, which was unique between males and females (p = 0.004). Microbiome composition in PT-PNA males was dominated by Anaerostipes and Parasuterella , whereas females had increased Barnesiella and Oscillibacter . The PT/RS males had an abundance of Gastranaerophilales and Muribaculaceae .<br><br>CONCLUSION: Multicompartmental trauma complicated by sepsis significantly diminishes diversity and alters microbial composition toward a severely dysbiotic state early after injury, which varies between males and females. These findings highlight the role of sex in postinjury sepsis and the pathobiome, which may influence outcomes after severe trauma and sepsis.}, }
@article {pmid38477597, year = {2024}, author = {Miliotis, G and Sengupta, P and Hameed, A and Chuvochina, M and McDonagh, F and Simpson, AC and Parker, CW and Singh, NK and Rekha, PD and Morris, D and Raman, K and Kyrpides, NC and Hugenholtz, P and Venkateswaran, K}, title = {Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.}, journal = {mBio}, volume = {15}, number = {4}, pages = {e0018124}, pmid = {38477597}, issn = {2150-7511}, support = {FutureCare Seed Fund//University of Galway (NUI Galway)/ ; 2012 Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; DP220100900//Australian Research Council Discovery Project/ ; //U.S. Department of Energy Joint Genome Institute, DOE Office of Science User Facility, U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; }, mesh = {Humans ; *Fatty Acids/analysis ; *Ceftazidime ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Nucleic Acid Hybridization ; Spores/chemistry ; Nucleotides ; DNA ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {UNLABELLED: A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HS[T], exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HS[T] is most closely related to Virgibacillus halophilus 5B73C[T], sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HS[T] is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HS[T] = DSM 115946[T] = NRRL B-65666[T]), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73C[T] = DSM 21623[T] = JCM 21758[T] = KCTC 13935[T]). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6[T] = DSM 22952[T] = CCM 7714[T]). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins.<br><br>IMPORTANCE: The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.}, }
@article {pmid38476936, year = {2024}, author = {Dittoe, DK and Feye, KM and Ovall, C and Thompson, HA and Ricke, SC}, title = {Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1348159}, pmid = {38476936}, issn = {1664-302X}, abstract = {INTRODUCTION: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings.<br><br>METHODS: Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4&#xb0;C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P&#xa3;0.05).<br><br>RESULTS: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA.<br><br>DISCUSSION: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.}, }
@article {pmid38476935, year = {2024}, author = {Indong, RA and Park, JM and Hong, JK and Lyou, ES and Han, T and Hong, JK and Lee, TK and Lee, JI}, title = {A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1347797}, pmid = {38476935}, issn = {1664-302X}, abstract = {The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.}, }
@article {pmid38475926, year = {2024}, author = {Suarez, C and Rosenqvist, T and Dimitrova, I and Sedlacek, CJ and Modin, O and Paul, CJ and Hermansson, M and Persson, F}, title = {Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {51}, pmid = {38475926}, issn = {2049-2618}, support = {2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2020-01905//Svenska Forskningsr&#xe5;det Formas/ ; ZK74//Austrian Science Fund/ ; }, mesh = {*Ammonia ; *Anaerobic Ammonia Oxidation ; Phylogeny ; Sewage/microbiology ; Bacteria ; Bioreactors/microbiology ; Nitrogen ; Biofilms ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.<br><br>RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.<br><br>CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.}, }
@article {pmid38471203, year = {2024}, author = {Malinowski, N and Morgan, MJ and Wylie, J and Walsh, T and Domingos, S and Metcalfe, S and Kaksonen, AH and Barnhart, EP and Mueller, R and Peyton, BM and Puzon, GJ}, title = {Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri.}, journal = {Water research}, volume = {254}, number = {}, pages = {121426}, doi = {10.1016/j.watres.2024.121426}, pmid = {38471203}, issn = {1879-2448}, mesh = {*Naegleria fowleri ; Prospective Studies ; *Drinking Water ; Bacteria ; Biofilms ; }, abstract = {Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.}, }
@article {pmid38470030, year = {2024}, author = {Tittes, C and Nijland, J and Schoentag, AMC and Hackl, T and Di Cianni, N and Marchfelder, A and Quax, TEF}, title = {Development of a genetic system for Haloferax gibbonsii LR2-5, model host for haloarchaeal viruses.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0012924}, pmid = {38470030}, issn = {1098-5336}, support = {//Deutsche Forschungsgemeinschaft (DFG)/ ; //EC | European Research Council (ERC)/ ; }, mesh = {*Haloferax/genetics ; Gene Deletion ; *Haloferax volcanii/genetics/metabolism ; Promoter Regions, Genetic ; *Viruses/genetics ; *Archaeal Proteins/genetics ; }, abstract = {UNLABELLED: Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses.<br><br>IMPORTANCE: Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.}, }
@article {pmid38467467, year = {2024}, author = {Powell, ME and McCoy, SJ}, title = {Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.}, journal = {Journal of phycology}, volume = {60}, number = {2}, pages = {254-272}, doi = {10.1111/jpy.13443}, pmid = {38467467}, issn = {1529-8817}, support = {DGE-2040435//National Science Foundation/ ; OCE-2239425//National Science Foundation/ ; }, mesh = {*Ecosystem ; *Cyanobacteria/metabolism ; Sulfur/metabolism ; Carbon/metabolism ; }, abstract = {Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.}, }
@article {pmid38466433, year = {2024}, author = {Ważny, R and Jędrzejczyk, RJ and Rozpądek, P and Domka, A and Tokarz, KM and Janicka, M and Turnau, K}, title = {Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {50}, pmid = {38466433}, issn = {1432-184X}, mesh = {*Mycorrhizae/physiology ; *Rubus ; Spores, Fungal ; Plants/microbiology ; Bacteria ; Chlorophyll ; Water ; }, abstract = {Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.}, }
@article {pmid38465733, year = {2024}, author = {Javourez, U and Matassa, S and Vlaeminck, SE and Verstraete, W}, title = {Ruminations on sustainable and safe food: Championing for open symbiotic cultures ensuring resource efficiency, eco-sustainability and affordability.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14436}, pmid = {38465733}, issn = {1751-7915}, mesh = {Animals ; *Ruminants ; *Biotechnology ; Fermentation ; Animal Feed ; Costs and Cost Analysis ; }, abstract = {Microbes are powerful upgraders, able to convert simple substrates to nutritional metabolites at rates and yields surpassing those of higher organisms by a factor of 2 to 10. A summary table highlights the superior efficiencies of a whole array of microbes compared to conventionally farmed animals and insects, converting nitrogen and organics to food and feed. Aiming at the most resource-efficient class of microbial proteins, deploying the power of open microbial communities, coined here as 'symbiotic microbiomes' is promising. For instance, a production train of interest is to develop rumen-inspired technologies to upgrade fibre-rich substrates, increasingly available as residues from emerging bioeconomy initiatives. Such advancements offer promising perspectives, as currently only 5%-25% of the available cellulose is recovered by ruminant livestock systems. While safely producing food and feed with open cultures has a long-standing tradition, novel symbiotic fermentation routes are currently facing much higher market entrance barriers compared to axenic fermentation. Our global society is at a pivotal juncture, requiring a shift towards food production systems that not only embrace the environmental and economic sustainability but also uphold ethical standards. In this context, we propose to re-examine the place of spontaneous or natural microbial consortia for safe future food and feed biotech developments, and advocate for intelligent regulatory practices. We stress that reconsidering symbiotic microbiomes is key to achieve sustainable development goals and defend the need for microbial biotechnology literacy education.}, }
@article {pmid38465465, year = {2024}, author = {Van Goethem, MW and Marasco, R and Hong, PY and Daffonchio, D}, title = {The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14430}, pmid = {38465465}, issn = {1751-7915}, support = {//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Ecosystem ; Bacteria/genetics ; Drug Resistance, Microbial ; Agriculture ; }, abstract = {In the relentless battle for human health, the proliferation of antibiotic-resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening 'antibiotic discovery void'. With nearly 80% of our current antibiotics originating from natural or semi-synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so-called 'microbial oases of interactions'. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever-evolving microbial 'arms race' is constantly in place. Such a continuous cycle of adaptation and counter-adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a 'missing piece of the puzzle' in our fight against antibiotic resistance.}, }
@article {pmid38461750, year = {2024}, author = {Michielsen, S and Vercelli, GT and Cordero, OX and Bachmann, H}, title = {Spatially structured microbial consortia and their role in food fermentations.}, journal = {Current opinion in biotechnology}, volume = {87}, number = {}, pages = {103102}, doi = {10.1016/j.copbio.2024.103102}, pmid = {38461750}, issn = {1879-0429}, mesh = {*Fermentation ; *Microbial Consortia/physiology ; *Food Microbiology ; }, abstract = {Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.}, }
@article {pmid38458948, year = {2024}, author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q}, title = {Corrigendum to "Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment" [Sci. Total Environ. 820 (2022) 153286].}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171434}, doi = {10.1016/j.scitotenv.2024.171434}, pmid = {38458948}, issn = {1879-1026}, }
@article {pmid38457521, year = {2024}, author = {Colombi, E and Bertels, F and Doulcier, G and McConnell, E and Pichugina, T and Sohn, KH and Straub, C and McCann, HC and Rainey, PB}, title = {Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {11}, pages = {e2309263121}, pmid = {38457521}, issn = {1091-6490}, support = {MAU1709//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; SFB1182 Project C4//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Phylogeny ; *Conjugation, Genetic ; *Gene Transfer, Horizontal/genetics ; Biological Evolution ; DNA Transposable Elements/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.}, }
@article {pmid38453959, year = {2024}, author = {Guerrero-Egido, G and Pintado, A and Bretscher, KM and Arias-Giraldo, LM and Paulson, JN and Spaink, HP and Claessen, D and Ramos, C and Cazorla, FM and Medema, MH and Raaijmakers, JM and Carrión, VJ}, title = {bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2072}, pmid = {38453959}, issn = {2041-1723}, mesh = {*Genome, Bacterial/genetics ; *Pseudomonas syringae/genetics ; Workflow ; Genomics/methods ; }, abstract = {Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE (https://github.com/Carrion-lab/bacLIFE) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.}, }
@article {pmid38452350, year = {2024}, author = {Boutin, S and Lussier, E and Laforest-Lapointe, I}, title = {Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards.}, journal = {Canadian journal of microbiology}, volume = {70}, number = {6}, pages = {238-251}, doi = {10.1139/cjm-2023-0215}, pmid = {38452350}, issn = {1480-3275}, mesh = {*Malus/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Plant Leaves/microbiology ; Spatio-Temporal Analysis ; Biodiversity ; Mycobiome ; Flowers/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.}, }
@article {pmid38452018, year = {2024}, author = {Du, Z and Behrens, SF}, title = {Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299930}, pmid = {38452018}, issn = {1932-6203}, mesh = {Real-Time Polymerase Chain Reaction/methods ; Phylogeny ; Reproducibility of Results ; *Sulfates ; *Microbiota/genetics ; }, abstract = {Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.}, }
@article {pmid38450400, year = {2024}, author = {Duarte, RDC and Iannetta, PPM and Gomes, AM and Vasconcelos, MW}, title = {More than a meat- or synthetic nitrogen fertiliser-substitute: a review of legume phytochemicals as drivers of 'One Health' via their influence on the functional diversity of soil- and gut-microbes.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1337653}, pmid = {38450400}, issn = {1664-462X}, abstract = {Legumes are essential to healthy agroecosystems, with a rich phytochemical content that impacts overall human and animal well-being and environmental sustainability. While these phytochemicals can have both positive and negative effects, legumes have traditionally been bred to produce genotypes with lower levels of certain plant phytochemicals, specifically those commonly termed as 'antifeedants' including phenolic compounds, saponins, alkaloids, tannins, and raffinose family oligosaccharides (RFOs). However, when incorporated into a balanced diet, such legume phytochemicals can offer health benefits for both humans and animals. They can positively influence the human gut microbiome by promoting the growth of beneficial bacteria, contributing to gut health, and demonstrating anti-inflammatory and antioxidant properties. Beyond their nutritional value, legume phytochemicals also play a vital role in soil health. The phytochemical containing residues from their shoots and roots usually remain in-field to positively affect soil nutrient status and microbiome diversity, so enhancing soil functions and benefiting performance and yield of following crops. This review explores the role of legume phytochemicals from a 'one health' perspective, examining their on soil- and gut-microbial ecology, bridging the gap between human nutrition and agroecological science.}, }
@article {pmid38448699, year = {2024}, author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Reply to: Model uncertainty obscures major driver of soil carbon.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {E4-E6}, pmid = {38448699}, issn = {1476-4687}, mesh = {*Uncertainty ; }, }
@article {pmid38446847, year = {2024}, author = {Koslová, A and Hackl, T and Bade, F and Sanchez Kasikovic, A and Barenhoff, K and Schimm, F and Mersdorf, U and Fischer, MG}, title = {Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {11}, pages = {e2314606121}, pmid = {38446847}, issn = {1091-6490}, support = {5734//Gordon and Betty Moore Foundation (GBMF)/ ; ALTF 1150-2018//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Humans ; Virophages ; *Giant Viruses/genetics ; *Stramenopiles/genetics ; *Virus Diseases ; Antiviral Agents ; }, abstract = {Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.}, }
@article {pmid38441415, year = {2024}, author = {Lee, HJ and Hwang, JS and Lee, EK and Whang, KS}, title = {Erythrobacter oryzae sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {3}, pages = {}, doi = {10.1099/ijsem.0.006287}, pmid = {38441415}, issn = {1466-5034}, mesh = {*Sphingomonadaceae ; *Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Fatty Acids/chemistry ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; }, abstract = {Two novel bacterial strains, designated as COR-2[T] and CR-8, were isolated from paddy soil. These isolates were aerobic, Gram-stain-negative, non-spore-forming, non-motile, rod-shaped, and formed orange-coloured colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Erythrobacter. Strains COR-2[T] and CR-8 showed 99.9 % 16S rRNA gene sequence similarity. Both strains had the highest 16S rRNA gene similarity of 99.1-99.7 % to Erythrobacter colymbi TPW-24[T], Erythrobacter donghaensis SW-132[T] and Erythrobacter tepidarius DSM 10594[T], respectively. The genome of strain COR-2[T] comprised 3 559 918 bp and the genomic DNA G + C content was 67.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain COR-2[T] and its closely related species of the genus Erythrobacter were 79.3-85.5% and 24.1-29.1 %, respectively. The major respiratory quinone was Q-10, while the major fatty acids were C18 : 1 ω7c and C17 : 1 ω6c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and eight unidentified lipids. Based on phylogenetic and phenotypic considerations, the two strains [COR-2[T] (type strain; = KACC 22941[T]=JCM 35529[T]) and CR-8 (= KACC 22945=JCM 35530)] are considered to represent novel species of the genus Erythrobacter, for which the name Erythrobacter oryzae sp. nov. is proposed.}, }
@article {pmid38440286, year = {2024}, author = {Zeng, L and Noeparvar, P and Burne, RA and Glezer, BS}, title = {Genetic characterization of glyoxalase pathway in oral streptococci and its contribution to interbacterial competition.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2322241}, pmid = {38440286}, issn = {2000-2297}, support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; }, abstract = {OBJECTIVES: To analyze contributions to microbial ecology of Reactive Electrophile Species (RES), including methylglyoxal, generated during glycolysis.<br><br>METHODS: Genetic analyses were performed on the glyoxalase pathway in Streptococcus mutans (SM) and Streptococcus sanguinis (SS), followed by phenotypic assays and transcription analysis.<br><br>RESULTS: Deleting glyoxalase I (lguL) reduced RES tolerance to a far greater extent in SM than in SS, decreasing the competitiveness of SM against SS. Although SM displays a greater RES tolerance than SS, lguL-null mutants of either species showed similar tolerance; a finding consistent with the ability of methylglyoxal to induce the expression of lguL in SM, but not in SS. A novel paralogue of lguL (named gloA2) was identified in most streptococci. SM mutant &#x2206;gloA2SM showed little change in methylglyoxal tolerance yet a significant growth defect and increased autolysis on fructose, a phenotype reversed by the addition of glutathione, or by the deletion of a fructose: phosphotransferase system (PTS) that generates fructose-1-phosphate (F-1-P).<br><br>CONCLUSIONS: Fructose contributes to RES generation in a PTS-specific manner, and GloA2 may be required to degrade certain RES derived from F-1-P. This study reveals the critical roles of RES in fitness and interbacterial competition and the effects of PTS in modulating RES metabolism.}, }
@article {pmid38439944, year = {2024}, author = {Ma, H and Liu, J and Mo, L and Arias-Giraldo, LM and Xiang, M and Liu, X}, title = {Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad015}, pmid = {38439944}, issn = {2730-6151}, abstract = {Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.}, }
@article {pmid38436268, year = {2024}, author = {Wang, Q and Cole, JR}, title = {Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification.}, journal = {Microbiology resource announcements}, volume = {13}, number = {4}, pages = {e0106323}, pmid = {38436268}, issn = {2576-098X}, abstract = {The RDP Classifier is one of the most popular machine learning approaches for taxonomic classification due to its robustness and relatively high accuracy. Both the RDP taxonomy and RDP Classifier have been updated to incorporate newly described taxa and recent changes to prokaryotic nomenclature.}, }
@article {pmid38436256, year = {2024}, author = {Ling, J and Hryckowian, AJ}, title = {Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont.}, journal = {Infection and immunity}, volume = {92}, number = {9}, pages = {e0047823}, pmid = {38436256}, issn = {1098-5522}, support = {R35 GM150996/GM/NIGMS NIH HHS/United States ; R35GM150996//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DGE-2137424//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; 1U48DP006383//UW-Madison Prevention Research Center/ ; Gift//Judy L. and Sal A. Troia/ ; }, mesh = {*Streptococcus agalactiae ; Humans ; *Streptococcal Infections/microbiology ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Animals ; }, abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.}, }
@article {pmid38430754, year = {2024}, author = {Yan, X and Li, S and Abdullah Al, M and Mo, Y and Zuo, J and Grossart, HP and Zhang, H and Yang, Y and Jeppesen, E and Yang, J}, title = {Community stability of free-living and particle-attached bacteria in a subtropical reservoir with salinity fluctuations over 3 years.}, journal = {Water research}, volume = {254}, number = {}, pages = {121344}, doi = {10.1016/j.watres.2024.121344}, pmid = {38430754}, issn = {1879-2448}, mesh = {*Ecosystem ; Salinity ; Lakes/microbiology ; Bacteria/genetics ; *Microbiota/physiology ; Aquatic Organisms ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Changes in salinity have a profound influence on ecological services and functions of inland freshwater ecosystems, as well as on the shaping of microbial communities. Bacterioplankton, generally classified into free-living (FL) and particle-attached (PA) forms, are main components of freshwater ecosystems and play key functional roles for biogeochemical cycling and ecological stability. However, there is limited knowledge about the responses of community stability of both FL and PA bacteria to salinity fluctuations. Here, we systematically explored changes in community stability of both forms of bacteria based on high-frequency sampling in a shallow urban reservoir (Xinglinwan Reservoir) in subtropical China for 3 years. Our results indicated that (1) salinity was the strongest environmental factor determining FL and PA bacterial community compositions - rising salinity increased the compositional stability of both bacterial communities but decreased their α-diversity. (2) The community stability of PA bacteria was significantly higher than that of FL at high salinity level with low salinity variance scenarios, while the opposite was found for FL bacteria, i.e., their stability was higher than PA bacteria at low salinity level with high variance scenarios. (3) Both bacterial traits (e.g., bacterial genome size and interaction strength of rare taxa) and precipitation-induced factors (e.g., changes in salinity and particle) likely contributed collectively to differences in community stability of FL and PA bacteria under different salinity scenarios. Our study provides additional scientific basis for ecological management, protection and restoration of urban reservoirs under changing climatic and environmental conditions.}, }
@article {pmid38430049, year = {2024}, author = {Barnett, SE and Shade, A}, title = {Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance.}, journal = {Ecology letters}, volume = {27}, number = {3}, pages = {e14393}, doi = {10.1111/ele.14393}, pmid = {38430049}, issn = {1461-0248}, support = {1749544//National Science Foundation/ ; }, mesh = {Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Soil Microbiology ; Bacteria/genetics ; *Microbiota/physiology ; }, abstract = {Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.}, }
@article {pmid38427046, year = {2024}, author = {Alvarenga, DO and Priemé, A and Rousk, K}, title = {The Feather Moss Hylocomium splendens Affects the Transcriptional Profile of a Symbiotic Cyanobacterium in Relation to Acquisition and Turnover of Key Nutrients.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {49}, pmid = {38427046}, issn = {1432-184X}, support = {947719/ERC_/European Research Council/International ; }, mesh = {Symbiosis ; Nitrogen Fixation ; *Bryopsida/genetics/metabolism/microbiology ; *Bryophyta ; *Cyanobacteria/metabolism ; Amino Acids/metabolism ; }, abstract = {Moss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1 week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss-cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients.}, }
@article {pmid38426066, year = {2024}, author = {Yue, Y and Hao, H and Wang, Q and Xiao, T and Zhang, Y and Chen, Q and Chen, H and Zhang, J}, title = {Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1345231}, pmid = {38426066}, issn = {1664-302X}, abstract = {INTRODUCTION: The artificial cultivation of morels has been a global research focus owing to production variability. Understanding the microbial ecology in cultivated soil is essential to increase morel yield and alleviate pathogen harm.<br><br>METHODS: A total of nine Morchella cultivation experiments in four soil field types, forest, paddy, greenhouse, and orchard in Shanghai city were performed to determine the potential ecological relationship between Morchella growth and soil microbial ecology.<br><br>RESULTS: Generally, significant variation was observed in the soil microbial diversity and composition between the different experimental field types. The niche width analysis indicated that the bacterial habitat niche breadth was significantly greater than the fungal community width, which was further confirmed by a null model that revealed that homogeneous selection could explain 46.26 and 53.64% of the variance in the bacterial and fungal assemblies, respectively. Moreover, the neutral community model revealed that stochastic processes dominate the bacterial community in forests and paddies and both the bacterial and fungal communities in orchard crops, whereas deterministic processes mostly govern the fungal community in forests and paddies and both the bacterial and the fungal communities in greenhouses. Furthermore, co-occurrence patterns were constructed, and the results demonstrated that the dynamics of the soil microbial community are related to fluctuations in soil physicochemical characteristics, especially soil potassium. Importantly, structural equation modeling further demonstrated that the experimental soil type significantly affects the potassium content of the soil, which can directly or indirectly promote Morchella yield by inhibiting soil fungal richness.<br><br>DISCUSSION: This was the first study to predict morel yield through soil potassium fertilizer and soil fungal community richness, which provides new insights into deciphering the importance of microbial ecology in morel agroecosystems.}, }
@article {pmid38425054, year = {2024}, author = {Law, SR and Mathes, F and Paten, AM and Alexandre, PA and Regmi, R and Reid, C and Safarchi, A and Shaktivesh, S and Wang, Y and Wilson, A and Rice, SA and Gupta, VVSR}, title = {Life at the borderlands: microbiomes of interfaces critical to One Health.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {2}, pages = {}, pmid = {38425054}, issn = {1574-6976}, support = {//CSIRO/ ; }, mesh = {Animals ; Humans ; *One Health ; *Microbiota ; Biological Evolution ; Soil Microbiology ; Plants/microbiology ; }, abstract = {Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.}, }
@article {pmid38424049, year = {2024}, author = {Zhong, ZP and Du, J and Köstlbacher, S and Pjevac, P and Orlić, S and Sullivan, MB}, title = {Viral potential to modulate microbial methane metabolism varies by habitat.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1857}, pmid = {38424049}, issn = {2041-1723}, support = {3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 1759874//National Science Foundation (NSF)/ ; 1829831//National Science Foundation (NSF)/ ; NA//OSU | Byrd Polar and Climate Research Center, Ohio State University (Byrd Polar and Climate Research Center of The Ohio State University)/ ; }, mesh = {Animals ; Methane/metabolism ; Ecosystem ; *Viruses/genetics ; Metagenome ; *Euryarchaeota/genetics ; }, abstract = {Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.}, }
@article {pmid38423404, year = {2024}, author = {Das, S and Malik, M and Dastidar, DG and Roy, R and Paul, P and Sarkar, S and Chakraborty, P and Maity, A and Dasgupta, M and Gupta, AD and Chatterjee, S and Sarker, RK and Maiti, D and Tribedi, P}, title = {Piperine, a phytochemical prevents the biofilm city of methicillin-resistant Staphylococcus aureus: A biochemical approach to understand the underlying mechanism.}, journal = {Microbial pathogenesis}, volume = {189}, number = {}, pages = {106601}, doi = {10.1016/j.micpath.2024.106601}, pmid = {38423404}, issn = {1096-1208}, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Anti-Bacterial Agents/pharmacology/metabolism ; *Staphylococcal Infections ; Biofilms ; Phytochemicals/pharmacology ; DNA/metabolism ; Microbial Sensitivity Tests ; *Alkaloids ; *Piperidines ; *Benzodioxoles ; *Polyunsaturated Alkamides ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant human pathogen causes several nosocomial as well as community-acquired infections involving biofilm machinery. Hence, it has gained a wide interest within the scientific community to impede biofilm-induced MRSA-associated health complications. The current study focuses on the utilization of a natural bioactive compound called piperine to control the biofilm development of MRSA. Quantitative assessments like crystal violet, total protein recovery, and fluorescein-di-acetate (FDA) hydrolysis assays, demonstrated that piperine (8 and 16 μg/mL) could effectively compromise the biofilm formation of MRSA. Light and scanning electron microscopic image analysis confirmed the same. Further investigation revealed that piperine could reduce extracellular polysaccharide production by down-regulating the expression of icaA gene. Besides, piperine could reduce the cell-surface hydrophobicity of MRSA, a crucial factor of biofilm formation. Moreover, the introduction of piperine could interfere with microbial motility indicating the interaction of piperine with the quorum-sensing components. A molecular dynamics study showed a stable binding between piperine and AgrA protein (regulator of quorum sensing) suggesting the possible meddling of piperine in quorum-sensing of MRSA. Additionally, the exposure to piperine led to the accumulation of intracellular reactive oxygen species (ROS) and potentially heightened cell membrane permeability in inhibiting microbial biofilm formation. Besides, piperine could reduce the secretion of diverse virulence factors from MRSA. Further exploration revealed that piperine interacted with extracellular DNA (e-DNA), causing disintegration by weakening the biofilm architecture. Conclusively, this study suggests that piperine could be a potential antibiofilm molecule against MRSA-associated biofilm infections.}, }
@article {pmid38419638, year = {2024}, author = {Boase, K and Santini, T and Watkin, E}, title = {Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1308797}, pmid = {38419638}, issn = {1664-302X}, abstract = {Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9 M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further.}, }
@article {pmid38412470, year = {2024}, author = {Shi, TL and Jia, KH and Bao, YT and Nie, S and Tian, XC and Yan, XM and Chen, ZY and Li, ZC and Zhao, SW and Ma, HY and Zhao, Y and Li, X and Zhang, RG and Guo, J and Zhao, W and El-Kassaby, YA and Müller, N and Van de Peer, Y and Wang, XR and Street, NR and Porth, I and An, X and Mao, JF}, title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.}, journal = {Plant physiology}, volume = {195}, number = {1}, pages = {652-670}, pmid = {38412470}, issn = {1532-2548}, support = {2022YFD2200103//National Key R&amp;D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; }, mesh = {*Populus/genetics ; *Alleles ; *Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Haplotypes/genetics ; Hybridization, Genetic ; Machine Learning ; }, abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.}, }
@article {pmid38411098, year = {2024}, author = {Moreno, CM and Bernish, M and Meyer, MG and Li, Z and Waite, N and Cohen, NR and Schofield, O and Marchetti, A}, title = {Molecular physiology of Antarctic diatom natural assemblages and bloom event reveal insights into strategies contributing to their ecological success.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0130623}, pmid = {38411098}, issn = {2379-5077}, support = {PLR1440435//National Science Foundation (NSF)/ ; OPP1745036//National Science Foundation (NSF)/ ; }, mesh = {*Diatoms/genetics ; Antarctic Regions ; Phytoplankton/genetics ; Oceans and Seas ; Plankton/metabolism ; Iron/metabolism ; }, abstract = {UNLABELLED: The continental shelf of the Western Antarctic Peninsula (WAP) is a highly variable system characterized by strong cross-shelf gradients, rapid regional change, and large blooms of phytoplankton, notably diatoms. Rapid environmental changes coincide with shifts in plankton community composition and productivity, food web dynamics, and biogeochemistry. Despite the progress in identifying important environmental factors influencing plankton community composition in the WAP, the molecular basis for their survival in this oceanic region, as well as variations in species abundance, metabolism, and distribution, remains largely unresolved. Across a gradient of physicochemical parameters, we analyzed the metabolic profiles of phytoplankton as assessed through metatranscriptomic sequencing. Distinct phytoplankton communities and metabolisms closely mirrored the strong gradients in oceanographic parameters that existed from coastal to offshore regions. Diatoms were abundant in coastal, southern regions, where colder and fresher waters were conducive to a bloom of the centric diatom, Actinocyclus. Members of this genus invested heavily in growth and energy production; carbohydrate, amino acid, and nucleotide biosynthesis pathways; and coping with oxidative stress, resulting in uniquely expressed metabolic profiles compared to other diatoms. We observed strong molecular evidence for iron limitation in shelf and slope regions of the WAP, where diatoms in these regions employed iron-starvation induced proteins, a geranylgeranyl reductase, aquaporins, and urease, among other strategies, while limiting the use of iron-containing proteins. The metatranscriptomic survey performed here reveals functional differences in diatom communities and provides further insight into the environmental factors influencing the growth of diatoms and their predicted response to changes in ocean conditions.<br><br>IMPORTANCE: In the Southern Ocean, phytoplankton must cope with harsh environmental conditions such as low light and growth-limiting concentrations of the micronutrient iron. Using metratranscriptomics, we assessed the influence of oceanographic variables on the diversity of the phytoplankton community composition and on the metabolic strategies of diatoms along the Western Antarctic Peninsula, a region undergoing rapid climate change. We found that cross-shelf differences in oceanographic parameters such as temperature and variable nutrient concentrations account for most of the differences in phytoplankton community composition and metabolism. We opportunistically characterized the metabolic underpinnings of a large bloom of the centric diatom Actinocyclus in coastal waters of the WAP. Our results indicate that physicochemical differences from onshore to offshore are stronger than between southern and northern regions of the WAP; however, these trends could change in the future, resulting in poleward shifts in functional differences in diatom communities and phytoplankton blooms.}, }
@article {pmid38411061, year = {2024}, author = {Zhang, Y and Deng, Y and Wang, C and Li, S and Lau, FTK and Zhou, J and Zhang, T}, title = {Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0133323}, pmid = {38411061}, issn = {2379-5077}, support = {T21-604/19-R//Hong Kong Theme Based Research Scheme/ ; GRF17206120//Hong Kong General Research Fund/ ; DEMP-2017-03//Hong Kong DSD/ ; }, mesh = {Wastewater ; Sewage/microbiology ; Hong Kong/epidemiology ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants ; }, abstract = {UNLABELLED: Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies.<br><br>IMPORTANCE: Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.}, }
@article {pmid38410391, year = {2024}, author = {Duysburgh, C and Miclotte, L and Green, JB and Watts, KT and Sardi, MI and Chakrabarti, A and Khafipour, E and Marzorati, M}, title = {Saccharomyces cerevisiae derived postbiotic alters gut microbiome metabolism in the human distal colon resulting in immunomodulatory potential in vitro.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1358456}, pmid = {38410391}, issn = {1664-302X}, abstract = {The yeast-based postbiotic EpiCor is a well-studied formulation, consisting of a complex mixture of bioactive molecules. In clinical studies, EpiCor postbiotic has been shown to reduce intestinal symptoms in a constipated population and support mucosal defense in healthy subjects. Anti-inflammatory potential and butyrogenic properties have been reported in vitro, suggesting a possible link between EpiCor's gut modulatory activity and immunomodulation. The current study used a standardized in vitro gut model, the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), to obtain a deeper understanding on host-microbiome interactions and potential microbiome modulation following repeated EpiCor administration. It was observed that EpiCor induced a functional shift in carbohydrate fermentation patterns in the proximal colon environment. Epicor promoted an increased abundance of Bifidobacterium in both the proximal and distal colon, affecting overall microbial community structure. Co-occurrence network analysis at the phylum level provided additional evidence of changes in the functional properties of microbial community promoted by EpiCor, increasing positive associations between Actinobacteria with microbes belonging to the Firmicutes phylum. These results, together with a significant increase in butyrate production provide additional support of EpiCor benefits to gut health. Investigation of host-microbiome interactions confirmed the immunomodulatory potential of the applied test product. Specific microbial alterations were observed in the distal colon, with metabotyping indicating that specific metabolic pathways, such as bile acid and tryptophan metabolism, were affected following EpiCor supplementation. These results, especially considering many effects were seen distally, further strengthen the position of EpiCor as a postbiotic with health promoting functionality in the gut, which could be further assessed in vivo.}, }
@article {pmid38409540, year = {2024}, author = {Xu, T and Novotny, A and Zamora-Terol, S and Hambäck, PA and Winder, M}, title = {Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {48}, pmid = {38409540}, issn = {1432-184X}, support = {2016-04685//Swedish Research Council/ ; 2016-04685//Swedish Research Council/ ; }, mesh = {Animals ; Zooplankton/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; *Rotifera ; }, abstract = {In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.}, }
@article {pmid38408899, year = {2024}, author = {Banerjee, A and Ghosh, A and Saha, B and Bhadury, P and De, P}, title = {Surface Charge-Switchable Antifouling Block Copolymer with Bacteriostatic Properties.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {40}, number = {10}, pages = {5314-5325}, doi = {10.1021/acs.langmuir.3c03771}, pmid = {38408899}, issn = {1520-5827}, mesh = {*Biofouling/prevention &amp; control ; Proteins/metabolism ; Cations/chemistry ; Cell Membrane/metabolism ; Polymers/chemistry ; Surface Properties ; }, abstract = {Zwitterionic polymers are an emerging family of effective, low-fouling materials that can withstand unintended interactions with biological systems while exhibiting enhanced activity in bacterial matrix deterioration and biofilm eradication. Herein, we modularly synthesized an amphiphilic block copolymer, ZABCP, featuring potential bacteriostatic properties composed of a charge-switchable polyzwitterionic segment and a redox-sensitive pendant disulfide-labeled polymethacrylate block. The leucine-appended polyzwitterionic segment with alternatively positioned cationic amine and anionic carboxylate functionalities undergoes charge alterations (+ve → 0 → -ve) on pH variation. By introducing appropriate amphiphilicity, ZABCP forms distinct vesicles with redox-sensitive bilayer membranes and zwitterionic shielding coronas, enabling switching of surface charge. ZABCP vesicles exhibit 180 ± 20 nm hydrodynamic diameter, and its charge switching behavior in response to pH was confirmed by the change of zeta potential value from -23 to +36 mV. The binding interaction between ZABCP vesicles with lysozyme and pepsin proteins strengthens when the surface charge shifts from neutral (pH 7.4) to either anionic or cationic. This surface-charge-switchable phenomenon paves the way for implementing cationic ZABCP vesicles for bacterial cell growth inhibition, which is shown by the pronounced transition of cellular morphology, including clustering, aggregation, or elongation as well as membrane disruption for both Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative). Such enhanced bacteriostatic activity could be ascribed to a strong electrostatic interaction between cationic vesicles and negatively charged bacterial membranes, leading to cell membrane disruption. Overall, this study provides a tailor-made approach to adopt low-fouling properties and potential bacteriostatic activity using zwitterionic polymers through precise control of pH.}, }
@article {pmid38407642, year = {2024}, author = {Wang, Y and Xue, D and Chen, X and Qiu, Q and Chen, H}, title = {Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {47}, pmid = {38407642}, issn = {1432-184X}, support = {2022376//the Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//the Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; QNTS202201//the Youth Innovation Program of CIB/ ; 42001093//the National Natural Science Foundation of China/ ; 2019QZKK0304//the Second Tibetan Plateau Scientific Expedition/ ; }, mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Sphagnopsida ; Bacteria/genetics ; Carbon ; Nitrogen ; Nutrients ; }, abstract = {Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the [13]C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.}, }
@article {pmid38407587, year = {2024}, author = {Kempraj, V and Auth, J and Cha, DH and Mason, CJ}, title = {Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {46}, pmid = {38407587}, issn = {1432-184X}, support = {2040-22430-028-000-D//USDA ARS/ ; 2040-43000-018-000-D//USDA ARS/ ; 2040-22430-028-000-D//USDA ARS/ ; 60-2040-3-003//Animal and Plant Health Inspection Service/ ; }, mesh = {Humans ; Female ; Animals ; Larva ; RNA, Ribosomal, 16S/genetics ; *Fruit ; *Tephritidae ; }, abstract = {Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.}, }
@article {pmid38405409, year = {2024}, author = {Hoffbeck, C and Middleton, DMRL and Lamar, SK and Keall, SN and Nelson, NJ and Taylor, MW}, title = {Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11073}, pmid = {38405409}, issn = {2045-7758}, abstract = {Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.}, }
@article {pmid38403716, year = {2024}, author = {Nayman, EI and Schwartz, BA and Polmann, M and Gumabong, AC and Nieuwdorp, M and Cickovski, T and Mathee, K}, title = {Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4585}, pmid = {38403716}, issn = {2045-2322}, support = {09150182010020//ZONMW-VICI/ ; }, mesh = {Humans ; Female ; Ethnicity ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/epidemiology ; Adenosine Deaminase ; Minority Groups ; Intercellular Signaling Peptides and Proteins ; Fatty Acids, Volatile ; }, abstract = {Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.}, }
@article {pmid38402967, year = {2024}, author = {Zhou, P and Li, D and Zhang, C and Ping, Q and Wang, L and Li, Y}, title = {Comparison of different sewage sludge pretreatment technologies for improving sludge solubilization and anaerobic digestion efficiency: A comprehensive review.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171175}, doi = {10.1016/j.scitotenv.2024.171175}, pmid = {38402967}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Sewage/microbiology ; *Ultrasonics ; Methane/chemistry ; Hydrolysis ; Waste Disposal, Fluid ; Bioreactors ; }, abstract = {Anaerobic digestion (AD) of sewage sludge reduces organic solids and produces methane, but the complex nature of sludge, especially the difficulty in solubilization, limits AD efficiency. Pretreatments, by destroying sludge structure and promoting disintegration and hydrolysis, are valuable strategies to enhance AD performance. There is a plethora of reviews on sludge pretreatments, however, quantitative comparisons from multiple perspectives across different pretreatments remain scarce. This review categorized various pretreatments into three groups: Physical (ultrasonic, microwave, thermal hydrolysis, electric decomposition, and high pressure homogenization), chemical (acid, alkali, Fenton, calcium peroxide, and ozone), and biological (microaeration, exogenous bacteria, and exogenous hydrolase) pretreatments. The optimal conditions of various pretreatments and their impacts on enhancing AD efficiency were summarized; the effects of different pretreatments on microbial community in the AD system were comprehensively compared. The quantitative comparison based on dissolution degree of COD (DDCOD) indicted that the sludge solubilization performance is in the order of physical, chemical, and biological pretreatments, although with each below 40 % DDCOD. Biological pretreatment, particularly microaeration and exogenous bacteria, excel in AD enhancement. Pretreatments alter microbial ecology, favoring Firmicutes and Methanosaeta (acetotrophic methanogens) over Proteobacteria and Methanobacterium (hydrogenotrophic methanogens). Most pretreatments have unfavorable energy and economic outcomes, with electric decomposition and microaeration being exceptions. On the basis of the overview of the above pretreatments, a full energy and economy assessment for sewage sludge treatment was suggested. Finally, challenges associated with sludge pretreatments and AD were analyzed, and future research directions were proposed. This review may broaden comprehension of sludge pretreatments and AD, and provide an objective basis for the selection of sludge pretreatment technologies.}, }
@article {pmid38402751, year = {2024}, author = {Rosenqvist, T and Chan, S and Ahlinder, J and Salomonsson, EN and Suarez, C and Persson, KM and Rådström, P and Paul, CJ}, title = {Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production.}, journal = {Water research}, volume = {253}, number = {}, pages = {121203}, doi = {10.1016/j.watres.2024.121203}, pmid = {38402751}, issn = {1879-2448}, mesh = {*Drinking Water ; *Water Purification/methods ; Bacteria/genetics ; *Microbiota ; Firmicutes ; Filtration/methods ; Silicon Dioxide/chemistry ; }, abstract = {Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.}, }
@article {pmid38402201, year = {2024}, author = {Zhu, H and Li, M and Bi, D and Yang, H and Gao, Y and Song, F and Zheng, J and Xie, R and Zhang, Y and Liu, H and Yan, X and Kong, C and Zhu, Y and Xu, Q and Wei, Q and Qin, H}, title = {Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1688}, pmid = {38402201}, issn = {2041-1723}, support = {81972221//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81801564//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81902422//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 82072634//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; Humans ; Mice ; Carcinogenesis/genetics ; *Colorectal Neoplasms/pathology ; *Fusobacterium nucleatum/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA Helicases ; }, abstract = {Fusobacterium nucleatum (F. nucleatum) promotes intestinal tumor growth and its relative abundance varies greatly among patients with CRC, suggesting the presence of unknown, individual-specific effectors in F. nucleatum-dependent carcinogenesis. Here, we identify that F. nucleatum is enriched preferentially in KRAS p.G12D mutant CRC tumor tissues and contributes to colorectal tumorigenesis in Villin-Cre/Kras[G12D+/-] mice. Additionally, Parabacteroides distasonis (P. distasonis) competes with F. nucleatum in the G12D mouse model and human CRC tissues with the KRAS mutation. Orally gavaged P. distasonis in mice alleviates the F. nucleatum-dependent CRC progression. F. nucleatum invades intestinal epithelial cells and binds to DHX15, a protein of RNA helicase family expressed on CRC tumor cells, mechanistically involving ERK/STAT3 signaling. Knock out of Dhx15 in Villin-Cre/Kras[G12D+/-] mice attenuates the CRC phenotype. These findings reveal that the oncogenic effect of F. nucleatum depends on somatic genetics and gut microbial ecology and indicate that personalized modulation of the gut microbiota may provide a more targeted strategy for CRC treatment.}, }
@article {pmid38401719, year = {2024}, author = {Martin-Pozas, T and Cuezva, S and Fernandez-Cortes, A and Gonzalez-Pumariega, M and Elez, J and Duarte, E and de la Rasilla, M and Canaveras, JC and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain).}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171137}, doi = {10.1016/j.scitotenv.2024.171137}, pmid = {38401719}, issn = {1879-1026}, mesh = {Animals ; Cattle ; *Ecosystem ; Spain ; Floods ; Prokaryotic Cells ; *Microbiota ; Nitrogen ; Mammals ; }, abstract = {A flood event affecting Pindal Cave, a UNESCO World Heritage site, introduced a substantial amount of external sediments and waste into the cave. This event led to the burial of preexisting sediments, altering the biogeochemical characteristics of the cave ecosystem by introducing heightened levels of organic matter, nitrogen compounds, phosphorus, and heavy metals. The sediments included particulate matter and waste from a cattle farm located within the water catchment area of the cavity, along with diverse microorganisms, reshaping the cave microbial community. This study addresses the ongoing influence of a cattle farm on the cave ecosystem and aims to understand the adaptive responses of the underground microbial community to the sudden influx of waste allochthonous material. Here, we show that the flood event had an immediate and profound effect on the cave microbial community, marked by a significant increase in methanogenic archaea, denitrifying bacteria, and other microorganisms commonly associated with mammalian intestinal tracts. Furthermore, our findings reveal that one year after the flood, microorganisms related to the flood decreased, while the increase in inorganic forms of ammonium and nitrate suggests potential nitrification, aligning with increased abundances of corresponding functional genes involved in nitrogen cycling. The results reveal that the impact of pollution was neither recent nor isolated, and it was decisive in stopping livestock activity near the cave. The influence of the cattle farm has persisted since its establishment over the impluvium area, and this influence endures even a year after the flood. Our study emphasizes the dynamic interplay between natural events, anthropogenic activities, and microbial communities, offering insights into the resilience of cave ecosystems. Understanding microbial adaptation in response to environmental disturbances, as demonstrated in this cave ecosystem, has implications for broader ecological studies and underscores the importance of considering temporal dynamics in conservation efforts.}, }
@article {pmid38401169, year = {2024}, author = {Vieira, HH and Bulzu, PA and Kasalický, V and Haber, M and Znachor, P and Piwosz, K and Ghai, R}, title = {Isolation of a widespread giant virus implicated in cryptophyte bloom collapse.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38401169}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; GACR 23-06806S//Grant Agency of the Czech Republic/ ; 22-33245S//Czech Science Foundation/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {Humans ; *Giant Viruses ; Phytoplankton ; Cryptophyta/genetics ; Eukaryota ; *Viruses ; }, abstract = {Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.}, }
@article {pmid38400045, year = {2024}, author = {Johnson, ML and Zwart, MP}, title = {Robust Approaches to the Quantitative Analysis of Genome Formula Variation in Multipartite and Segmented Viruses.}, journal = {Viruses}, volume = {16}, number = {2}, pages = {}, pmid = {38400045}, issn = {1999-4915}, support = {016.Vidi.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Viruses/genetics ; Genome, Viral ; Biological Evolution ; }, abstract = {When viruses have segmented genomes, the set of frequencies describing the abundance of segments is called the genome formula. The genome formula is often unbalanced and highly variable for both segmented and multipartite viruses. A growing number of studies are quantifying the genome formula to measure its effects on infection and to consider its ecological and evolutionary implications. Different approaches have been reported for analyzing genome formula data, including qualitative description, applying standard statistical tests such as ANOVA, and customized analyses. However, these approaches have different shortcomings, and test assumptions are often unmet, potentially leading to erroneous conclusions. Here, we address these challenges, leading to a threefold contribution. First, we propose a simple metric for analyzing genome formula variation: the genome formula distance. We describe the properties of this metric and provide a framework for understanding metric values. Second, we explain how this metric can be applied for different purposes, including testing for genome-formula differences and comparing observations to a reference genome formula value. Third, we re-analyze published data to illustrate the applications and weigh the evidence for previous conclusions. Our re-analysis of published datasets confirms many previous results but also provides evidence that the genome formula can be carried over from the inoculum to the virus population in a host. The simple procedures we propose contribute to the robust and accessible analysis of genome-formula data.}, }
@article {pmid38399791, year = {2024}, author = {Stroeva, AR and Klyukina, AA and Vidishcheva, ON and Poludetkina, EN and Solovyeva, MA and Pyrkin, VO and Gavirova, LA and Birkeland, NK and Akhmanov, GG and Bonch-Osmolovskaya, EA and Merkel, AY}, title = {Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399791}, issn = {2076-2607}, support = {20-54-20001//Russian Foundation for Basic Research/ ; }, abstract = {The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.}, }
@article {pmid38395561, year = {2024}, author = {Aswathi, KN and Shirke, A and Praveen, A and Murthy, PS}, title = {Functioning of Saccharomyces cerevisiae in honey coffee (Coffea canephora) and their effect on metabolites, volatiles and flavor profiles.}, journal = {Food research international (Ottawa, Ont.)}, volume = {180}, number = {}, pages = {114092}, doi = {10.1016/j.foodres.2024.114092}, pmid = {38395561}, issn = {1873-7145}, mesh = {Saccharomyces cerevisiae/metabolism ; *Coffea/chemistry ; *Honey ; *Yeast, Dried ; Sugars/metabolism ; }, abstract = {Post-harvesting and microbial activity of coffee play a critical role in the metabolites and the sensory quality of the brew. The pulped natural/honey coffee process is an improvised semi-dry technique consisting of prolonged fermentation of depulped coffee beans excluding washing steps. The starter culture application in coffee industry plays an important role to enhance the cup quality. This work focuses on the fermentation of pulped natural/honey Robusta coffee with a starter culture (Saccharomyces cerevisiae MTCC 173) and the identification of fermentation patterns through [1]H NMR, microbial ecology, volatomics and organoleptics of brew. Fermentation was accelerated by yeast populace (10 cfu log/mL) for 192 h. Principal compound analysis performed on [1]H NMR led to the investigation of metabolites such as sugars, alkaloids, alcohols, organic acids and amino acids. Detection of some sugars and organic acids represented that the starter cultures imparted few metabolic changes during the process. A major activity of sugars in fermentation with 83.3 % variance in PC 1 and 16.7 % in PC 2 was observed. The chemical characteristics such as carbohydrates (41.88 ± 0.77 mg/g), polyphenols (34.16 ± 0.79 mg/g), proteins (58.54 ± 0.66 mg/g), caffeine (26.54 ± 0.06 mg/g), and CGA (21.83 ± 0.04 mg/g) were also evaluated. The heatmap-based visualization of GC-MS accorded characterization of additional 5 compounds in treated (T) coffee contributing to sweet, fruity and caramelly odor notes compared to untreated (UT). The sensory outlines 72.5 in T and 70.5 in UT scores. Preparation of honey coffee with Saccharomyces cerevisiae is the first report, which modulated the flavor and quality of coffee.}, }
@article {pmid38395158, year = {2024}, author = {Li, XM and Hu, HF and Chen, SC}, title = {Artificial light at night causes community instability of bacterial community in urban soils.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171129}, doi = {10.1016/j.scitotenv.2024.171129}, pmid = {38395158}, issn = {1879-1026}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Ecosystem ; *Soil ; Light Pollution ; Environment ; Bacteria ; Light ; }, abstract = {Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.}, }
@article {pmid38393401, year = {2024}, author = {Minahan, NT and Chen, CH and Chuang, YC and Tsai, KH and Shen, WC and Guo, YL}, title = {Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {45}, pmid = {38393401}, issn = {1432-184X}, mesh = {*Allergens ; Spores, Fungal/genetics ; *Fungi/genetics ; Air Microbiology ; Environmental Monitoring ; }, abstract = {Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.}, }
@article {pmid38391651, year = {2024}, author = {Hoffstadt, K and Nikolausz, M and Krafft, S and Bonatelli, ML and Kumar, V and Harms, H and Kuperjans, I}, title = {Optimization of the Ex Situ Biomethanation of Hydrogen and Carbon Dioxide in a Novel Meandering Plug Flow Reactor: Start-Up Phase and Flexible Operation.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {38391651}, issn = {2306-5354}, support = {KESW-1-2-032A-B//European Regional Development Fund (ERDF)/ ; }, abstract = {With the increasing use of renewable energy resources for the power grid, the need for long-term storage technologies, such as power-to-gas systems, is growing. Biomethanation provides the opportunity to store energy in the form of the natural gas-equivalent biomethane. This study investigates a novel plug flow reactor that employs a helical static mixer for the biological methanation of hydrogen and carbon dioxide. In tests, the reactor achieved an average methane production rate of 2.5 LCH4LR∗d (methane production [LCH4] per liter of reactor volume [LR] per day [d]) with a maximum methane content of 94%. It demonstrated good flexibilization properties, as repeated 12 h downtimes did not negatively impact the process. The genera Methanothermobacter and Methanobacterium were predominant during the initial phase, along with volatile organic acid-producing, hydrogenotrophic, and proteolytic bacteria. The average ratio of volatile organic acid to total inorganic carbon increased to 0.52 ± 0.04, while the pH remained stable at an average of pH 8.1 ± 0.25 from day 32 to 98, spanning stable and flexible operation modes. This study contributes to the development of efficient flexible biological methanation systems for sustainable energy storage and management.}, }
@article {pmid38388537, year = {2024}, author = {Faller, L and Leite, MFA and Kuramae, EE}, title = {Enhancing phosphate-solubilising microbial communities through artificial selection.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1649}, pmid = {38388537}, issn = {2041-1723}, mesh = {*Phosphates ; Ecosystem ; Soil Microbiology ; Agriculture ; Soil ; *Microbiota/genetics ; }, abstract = {Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.}, }
@article {pmid38385702, year = {2024}, author = {Zhao, Y and Ling, N and Liu, X and Li, C and Jing, X and Hu, J and Rui, J}, title = {Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {3}, pages = {e0007024}, pmid = {38385702}, issn = {1098-5336}, support = {41771293//MOST | National Natural Science Foundation of China (NSFC)/ ; 42277100//MOST | National Natural Science Foundation of China (NSFC)/ ; 20JR5RA308//Outstanding Youth Foundation of Gansu Province/ ; lzujbky-2019-ct01//Fundamental Research Funds for Central Universities of China/ ; lzujbky-2022-ct04//Fundamental Research Funds for Central Universities of China/ ; }, mesh = {*Bacteria/genetics ; *Soil/chemistry ; Ammonia ; Nitrification ; Oxidation-Reduction ; Soil Microbiology ; Archaea/genetics ; Phylogeny ; }, abstract = {Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.}, }
@article {pmid38380980, year = {2024}, author = {Van Gerrewey, T and Navarrete, O and Vandecruys, M and Perneel, M and Boon, N and Geelen, D}, title = {Bacterially enhanced plant-growing media for controlled environment agriculture.}, journal = {Microbial biotechnology}, volume = {17}, number = {2}, pages = {e14422}, pmid = {38380980}, issn = {1751-7915}, support = {HBC.2017.0209//Agentschap Innoveren en Ondernemen/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Agriculture ; *Bacteria/genetics ; Plants/genetics ; Soil/chemistry ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.}, }
@article {pmid38380088, year = {2024}, author = {Savaglia, V and Lambrechts, S and Tytgat, B and Vanhellemont, Q and Elster, J and Willems, A and Wilmotte, A and Verleyen, E and Vyverman, W}, title = {Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1316633}, pmid = {38380088}, issn = {1664-302X}, abstract = {Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.}, }
@article {pmid38378706, year = {2024}, author = {Papin, M and Philippot, L and Breuil, MC and Bru, D and Dreux-Zigha, A and Mounier, A and Le Roux, X and Rouard, N and Spor, A}, title = {Survival of a microbial inoculant in soil after recurrent inoculations.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4177}, pmid = {38378706}, issn = {2045-2322}, support = {ANR-20-CE02-0014//Agence Nationale de la Recherche/ ; }, mesh = {*Agricultural Inoculants ; Soil ; Nitrates ; Agriculture ; *Pseudomonas fluorescens ; Soil Microbiology ; }, abstract = {Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (10[6] and 10[8] cfu.g soil[-1]). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.}, }
@article {pmid38376218, year = {2024}, author = {Kridler, MR and Viney, IA and Custer, JM and Schlottman, B and Bartelme, R and Carini, P}, title = {Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona.}, journal = {Microbiology resource announcements}, volume = {13}, number = {3}, pages = {e0108923}, pmid = {38376218}, issn = {2576-098X}, support = {IOS-2141605//National Science Foundation (NSF)/ ; DGE-2137419//National Science Foundation (NSF)/ ; //Technology and Research Initiative Fund-WEES/ ; }, abstract = {Here, we present the genomes of two soil actinobacteria: Arthrobacter sp. strain AZCC_0090 and Mycobacterium sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.}, }
@article {pmid38376179, year = {2024}, author = {Bisesi, AT and Möbius, W and Nadell, CD and Hansen, EG and Bowden, SD and Harcombe, WR}, title = {Bacteriophage specificity is impacted by interactions between bacteria.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0117723}, pmid = {38376179}, issn = {2379-5077}, support = {IOS-2019304//National Science Foundation (NSF)/ ; IOS-2017879//National Science Foundation (NSF)/ ; BB/V011464/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Bacteriophages/physiology ; Bacteria ; Escherichia coli/physiology ; Bacterial Physiological Phenomena ; Symbiosis ; }, abstract = {UNLABELLED: Predators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest.<br><br>IMPORTANCE: There is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.}, }
@article {pmid38376167, year = {2024}, author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M}, title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0110523}, pmid = {38376167}, issn = {2379-5077}, support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; }, mesh = {Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; }, abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.<br><br>IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.}, }
@article {pmid38373802, year = {2024}, author = {O'Hara, E and Zaheer, R and Andrés-Lasheras, S and McAllister, TA and Gruninger, RJ}, title = {Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38373802}, issn = {1574-6941}, support = {//Agriculture and Agri-Food Canada/ ; //Genome Alberta/ ; ANH.02.19//Beef Cattle Research Council/ ; }, mesh = {Cattle ; Animals ; Tylosin/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Liver Abscess/veterinary/epidemiology/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Dietary Supplements/analysis ; *Microbiota ; Animal Feed/analysis ; }, abstract = {Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.}, }
@article {pmid38373396, year = {2025}, author = {Jaber, D and Younes, N and Khalil, E and Albsoul-Younes, A and Zawiah, M and Al-Bakri, AG}, title = {Studying Microbial Ecology of Diabetic Foot Infections: Significance of PCR Analysis for Prudent Antimicrobial Stewardship.}, journal = {The international journal of lower extremity wounds}, volume = {24}, number = {2}, pages = {497-505}, doi = {10.1177/15347346241230288}, pmid = {38373396}, issn = {1552-6941}, mesh = {*Diabetic Foot/microbiology/drug therapy/diagnosis ; Humans ; *Antimicrobial Stewardship/methods ; *Polymerase Chain Reaction/methods ; Male ; Female ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification ; }, abstract = {This study presents a comprehensive investigation into the microbial ecology of diabetic foot infections (DFIs), using molecular-polymerase chain reaction (PCR) analysis to accurately identify the causative agents. One hundred DFI patients were recruited and classified using the Depth Extent Phase and Associated Etiology (DEPA) score according to their severity. Results revealed polymicrobial infections in 75% of cases, predominantly featuring Staphylococcus epidermidis (83%) and Staphylococcus aureus (63%). Importantly, 20% of samples exhibited facultative anaerobes Bacteroides fragilis or Clostridium perfringens, exclusively in high DEPA score ulcers. Candida albicans coinfection was identified in 19.2% of cases, underscoring the need for mycological evaluation. Empirical antimicrobial therapy regimens were tailored to DEPA severity, yet our findings highlighted a potential gap in methicillin-resistant Staphylococcus aureus (MRSA) coverage. Despite an 88% prevalence of methicillin-resistant Staphylococci, vancomycin usage was suboptimal. This raises concerns about the underestimation of MRSA risk and the need for tailored antibiotic guidelines. Our study demonstrates the efficacy of molecular-PCR analysis in identifying diverse microbial communities in DFIs, influencing targeted antibiotic choices. The results advocate for refined antimicrobial guidelines, considering regional variations in microbial patterns and judiciously addressing multidrug-resistant strains. This research contributes crucial insights for optimizing DFIs management and helps the physicians to have a fast decision in selection the suitable antibiotic for each patient and to decrease the risk of bacterial resistance from the improper use of broad-spectrum empirical therapies.}, }
@article {pmid38370212, year = {2024}, author = {Taherkhani, H and KavianFar, A and Aminnezhad, S and Lanjanian, H and Ahmadi, A and Azimzadeh, S and Masoudi-Nejad, A}, title = {Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e24775}, pmid = {38370212}, issn = {2405-8440}, abstract = {In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.}, }
@article {pmid38367872, year = {2024}, author = {Tuts, L and Rasschaert, G and Heyndrickx, M and Boon, N and Eppinger, R and Becue, I}, title = {Detection of antibiotic residues in groundwater with a validated multiresidue UHPLC-MS/MS quantification method.}, journal = {Chemosphere}, volume = {352}, number = {}, pages = {141455}, doi = {10.1016/j.chemosphere.2024.141455}, pmid = {38367872}, issn = {1879-1298}, mesh = {Animals ; Humans ; Anti-Bacterial Agents/analysis ; Chromatography, High Pressure Liquid/methods ; Tandem Mass Spectrometry/methods ; Lactams, Macrocyclic/analysis ; Sulfanilamide/analysis ; Chloramphenicol/analysis ; Sulfonamides/analysis ; Lincosamides ; Pleuromutilins ; *Groundwater ; Macrolides/analysis ; *Drug Residues/analysis ; }, abstract = {The occurrence of antibiotic residues in the environment has received considerable attention because of their potential to select for bacterial resistance. The overuse of antibiotics in human medicine and animal production results in antibiotic residues entering the aquatic environment, but concentrations are currently not well determined. This study investigates the occurrence of antibiotics in groundwater in areas strongly related to agriculture and the antibiotic treatment of animals. A multiresidue method was validated according to EU Regulation 2021/808, to allow (semi-)quantitative analysis of 78 antibiotics from 10 different classes: β-lactams, sulfonamides, tetracyclines, lincosamides, amphenicols, (fluoro)quinolones, macrolides, pleuromutilins, ansamycins and diaminopyrimidines using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). This method was used to test different storage conditions of these water samples during a stability study over a period of 2 weeks. Sulfonamides, lincosamides and pleuromutilins were the most stable. Degradation was most pronounced for β-lactam antibiotics, macrolides and ansamycins. To maintain stability, storage of samples at -18 °C is preferred. With the validated method, antibiotic residues were detected in groundwater, sampled from regions associated with intensive livestock farming in Flanders (Belgium). Out of 50 samples, 14% contained at least one residue. Concentrations were low, ranging from < LOD to 0.03 μg/L. Chloramphenicol, oxolinic acid, tetracycline and sulfonamides (sulfadiazine, sulfadoxine, sulfamethazine and sulfisoxazole) were detected. This study presents a new method for the quantification of antibiotic residues, which was applied to investigate the presence of antibiotic residues in groundwater in Flanders.}, }
@article {pmid38367838, year = {2024}, author = {González-Feijoo, R and Santás-Miguel, V and Arenas-Lago, D and Álvarez-Rodríguez, E and Núñez-Delgado, A and Arias-Estévez, M and Pérez-Rodríguez, P}, title = {Effectiveness of cork and pine bark powders as biosorbents for potentially toxic elements present in aqueous solution.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118455}, doi = {10.1016/j.envres.2024.118455}, pmid = {38367838}, issn = {1096-0953}, mesh = {*Pinus/chemistry ; *Quercus/chemistry ; *Plant Bark/chemistry ; Adsorption ; *Water Pollutants, Chemical/analysis/chemistry ; Powders/chemistry ; Hydrogen-Ion Concentration ; Metals, Heavy/analysis/chemistry ; }, abstract = {Cork oak and pine bark, two of the most prolific byproducts of the European forestry sector, were assessed as biosorbents for eliminating potentially toxic elements (PTEs) from water-based solutions. Our research suggests that bioadsorption stands out as a viable and environmental eco-friendly technology, presenting a sustainable method for the extraction of PTEs from polluted water sources. This study aimed to evaluate and compare the efficiency of cork powder and pine bark powder as biosorbents. Specifically, the adsorption of Fe, Cu, Zn, Cd, Ni, Pb and Sn at equilibrium were studied through batch experiments by varying PTEs concentrations, pH, and ionic strength. Results from adsorption-desorption experiments demonstrate the remarkable capacity of both materials to retain the studied PTE. Cork powder and pine bark powder exhibited the maximum retention capacity for Fe and Cd, while they performed poorly for Pb and Sn, respectively. Nevertheless, pine bark showed a slightly lower retention capacity than cork. Increasing the pH resulted in cork showing the highest adsorption for Zn and the lowest for Sn, while for pine bark, Cd was the most adsorbed, and Sn was the least adsorbed, respectively. The highest adsorption of both materials occurred at pH 3.5-5, depending on the PTE tested. The ionic strength also influenced the adsorption of the various PTEs for both materials, with decreased adsorption as ionic strength increased. The findings suggest that both materials could be effective for capturing and eliminating the examined PTEs, albeit with different efficiencies. Remarkably, pine bark demonstrated superior adsorption capabilities, which were observed to vary based on the specific element and the experimental conditions. These findings contribute to elucidating the bio-adsorption potential of these natural materials, specifically their suitability in mitigating PTEs pollution, and favoring the recycling and revalorization of byproducts that might otherwise be considered residue.}, }
@article {pmid38367043, year = {2024}, author = {LeBlanc, NR and Harrigian, FC}, title = {Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {44}, pmid = {38367043}, issn = {1432-184X}, support = {2038-22430-003-000-D//Agricultural Research Service/ ; }, mesh = {Soil/chemistry ; Soil Microbiology ; *Composting ; *Fusarium ; Bacteria/genetics ; Sequence Analysis ; }, abstract = {The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.}, }
@article {pmid38366262, year = {2024}, author = {Wang, J and Zhu, YG and Tiedje, JM and Ge, Y}, title = {Global biogeography and ecological implications of cobamide-producing prokaryotes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366262}, issn = {1751-7370}, support = {42307162//National Natural Science Foundation of China/ ; 2019QZKK0308//Second Tibetan Plateau Scientific Expedition and Research Program/ ; DBI-1759892//US National Science Foundation/ ; //Institute for Cyber-Enabled Research at Michigan State University/ ; }, mesh = {*Cobamides ; Metagenome ; *Microbiota ; Soil ; }, abstract = {Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.}, }
@article {pmid38365962, year = {2024}, author = {Paes da Costa, D and das Graças Espíndola da Silva, T and Sérgio Ferreira Araujo, A and Prudêncio de Araujo Pereira, A and William Mendes, L and Dos Santos Borges, W and Felix da França, R and Alberto Fragoso de Souza, C and Alves da Silva, B and Oliveira Silva, R and Valente de Medeiros, E}, title = {Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3919}, pmid = {38365962}, issn = {2045-2322}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; Brazil ; Bacteria ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.}, }
@article {pmid38365802, year = {2024}, author = {Fenibo, EO and Nkuna, R and Matambo, T}, title = {Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3866}, pmid = {38365802}, issn = {2045-2322}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; Niger ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Microbiota/genetics ; *Petroleum/metabolism ; Hydrocarbons/metabolism ; Soil/chemistry ; DNA/metabolism ; }, abstract = {Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.}, }
@article {pmid38365260, year = {2024}, author = {Díez-Vives, C and Riesgo, A}, title = {High compositional and functional similarity in the microbiome of deep-sea sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365260}, issn = {1751-7370}, support = {100010434//'la Caixa' Foundation/ ; PID2019-105769GB-I00//Spanish Ministry of Science and Innovation/ ; 796011//Marie Sk&#x142;odowska-Curie Individual Fellowships Grant Agreement/ ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Microbiota ; Water/metabolism ; *Porifera ; }, abstract = {Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.}, }
@article {pmid38365254, year = {2024}, author = {Layoun, P and López-Pérez, M and Haro-Moreno, JM and Haber, M and Thrash, JC and Henson, MW and Kavagutti, VS and Ghai, R and Salcher, MM}, title = {Flexible genomic island conservation across freshwater and marine Methylophilaceae.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365254}, issn = {1751-7370}, support = {19-23469S//Czech Science Foundation/ ; KA131//University of South Bohemia, Faculty of Science, Department of Ecosystem Biology/ ; 116/2019/P//Grant Agency of the University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice/ ; }, mesh = {*Methylophilaceae ; Genome, Bacterial ; Genomic Islands ; Phylogeny ; Lakes ; }, abstract = {The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.}, }
@article {pmid38365250, year = {2024}, author = {Sher, AW and Aufrecht, JA and Herrera, D and Zimmerman, AE and Kim, YM and Munoz, N and Trejo, JB and Paurus, VL and Cliff, JB and Hu, D and Chrisler, WB and Tournay, RJ and Gomez-Rivas, E and Orr, G and Ahkami, AH and Doty, SL}, title = {Dynamic nitrogen fixation in an aerobic endophyte of Populus.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365250}, issn = {1751-7370}, support = {#50774//Environmental Molecular Sciences Laboratory/ ; //United States Department of Energy Office of Science/ ; DE-SC0021137//Office of Biological and Environmental Research/ ; }, mesh = {*Nitrogen Fixation/physiology ; *Populus/genetics/metabolism ; Endophytes/genetics ; Oxidoreductases/genetics ; In Situ Hybridization, Fluorescence ; Nitrogenase/genetics/metabolism ; Nitrogen ; }, abstract = {Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.}, }
@article {pmid38365248, year = {2024}, author = {Gottel, NR and Hill, MS and Neal, MJ and Allard, SM and Zengler, K and Gilbert, JA}, title = {Biocontrol in built environments to reduce pathogen exposure and infection risk.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365248}, issn = {1751-7370}, support = {UCSD 2223669//NSF ENG-EPSRC EFRI ELiS/ ; 80NSSC19K1604//NASA ROSBIO/ ; }, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; *Bacillus ; Anti-Bacterial Agents ; Built Environment ; }, abstract = {The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.}, }
@article {pmid38365244, year = {2024}, author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF}, title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365244}, issn = {1751-7370}, support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; }, mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; }, abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.}, }
@article {pmid38365240, year = {2024}, author = {Shen, L and Liu, Y and Chen, L and Lei, T and Ren, P and Ji, M and Song, W and Lin, H and Su, W and Wang, S and Rooman, M and Pucci, F}, title = {Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365240}, issn = {1751-7370}, support = {U21A20176//National Natural Science Foundation of China/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research/ ; 92251304//National Natural Science Foundation of China/ ; swzy202008//Open Project Fund of Anhui Provincial Key Laboratory of Protection and Utilization of Important Biological Resources/ ; 2022AH010012//Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics/ ; }, mesh = {*Exiguobacterium ; *Extremophiles ; Genomics ; Phylogeny ; Proteins ; }, abstract = {Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.}, }
@article {pmid38365232, year = {2024}, author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W}, title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365232}, issn = {1751-7370}, support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; }, mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.}, }
@article {pmid38363394, year = {2024}, author = {Duan, Y and Li, Y and Zhao, J and Zhang, J and Luo, C and Jia, R and Liu, X}, title = {Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {43}, pmid = {38363394}, issn = {1432-184X}, mesh = {Ecosystem ; Soil ; Sand ; Soil Microbiology ; *Lichens ; *Cyanobacteria ; *Microbiota ; Nitrogen ; Phosphorus ; China ; }, abstract = {Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.}, }
@article {pmid38362164, year = {2024}, author = {Pasciullo Boychuck, S and Brenner, LJ and Gagorik, CN and Schamel, JT and Baker, S and Tran, E and vonHoldt, BM and Koepfli, KP and Maldonado, JE and DeCandia, AL}, title = {The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11017}, pmid = {38362164}, issn = {2045-7758}, abstract = {California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.}, }
@article {pmid38361649, year = {2024}, author = {Parks, M and Lee, JS and Camua, K and Hollender, E}, title = {Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats.}, journal = {Access microbiology}, volume = {6}, number = {1}, pages = {}, pmid = {38361649}, issn = {2516-8290}, abstract = {Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.}, }
@article {pmid38357595, year = {2024}, author = {Fickling, NW and Abbott, CA and Brame, JE and Cando-Dumancela, C and Liddicoat, C and Robinson, JM and Breed, MF}, title = {Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11018}, pmid = {38357595}, issn = {2045-7758}, abstract = {Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.}, }
@article {pmid38356049, year = {2024}, author = {van Bergeijk, DA and Augustijn, HE and Elsayed, SS and Willemse, J and Carrión, VJ and Du, C and Urem, M and Grigoreva, LV and Cheprasov, MY and Grigoriev, S and Jansen, H and Wintermans, B and Budding, AE and Spaink, HP and Medema, MH and van Wezel, GP}, title = {Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16589}, doi = {10.1111/1462-2920.16589}, pmid = {38356049}, issn = {1462-2920}, support = {//Universiteit Leiden/ ; 101055020-COMMUNITY//European Research Council/International ; 948770-DECIPHER//European Research Council/International ; }, mesh = {Animals ; Phylogeny ; *Mammoths ; Genomics ; *Streptomyces/genetics ; *Actinomycetales ; Feces ; }, abstract = {Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.}, }
@article {pmid38356037, year = {2024}, author = {Xian, WD and Ding, J and Chen, J and Qu, W and Cao, P and Tang, C and Liu, X and Zhang, Y and Li, JL and Wang, P and Li, WJ and Wang, J}, title = {Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {42}, pmid = {38356037}, issn = {1432-184X}, mesh = {*Ecosystem ; *Rivers/microbiology ; Plankton/genetics ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water ; }, abstract = {The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.}, }
@article {pmid38354254, year = {2024}, author = {Doré, H and Eisenberg, AR and Junkins, EN and Leventhal, GE and Ganesh, A and Cordero, OX and Paul, BG and Valentine, DL and O'Malley, MA and Wilbanks, EG}, title = {Targeted hypermutation of putative antigen sensors in multicellular bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2316469121}, pmid = {38354254}, issn = {1091-6490}, support = {W911NF-19-2-0026//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; W911NF-19-D-0001//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; 508543//Joint Genome Institute (JGI)/ ; }, mesh = {*Bacteria/genetics ; Archaea/genetics ; Metagenome ; Retroelements ; *Bacteriophages/genetics ; }, abstract = {Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10[282] different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.}, }
@article {pmid38351424, year = {2024}, author = {Morelle, J and Bastos, A and Frankenbach, S and Frommlet, JC and Campbell, DA and Lavaud, J and Serôdio, J}, title = {The Photoprotective Behavior of a Motile Benthic Diatom as Elucidated from the Interplay Between Cell Motility and Physiological Responses to a Light Microgradient Using a Novel Experimental Setup.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {40}, pmid = {38351424}, issn = {1432-184X}, mesh = {*Diatoms/physiology ; Photosynthesis ; Chlorophyll ; Light ; Cell Movement ; }, abstract = {It has long been hypothesized that benthic motile pennate diatoms use phototaxis to optimize photosynthesis and minimize photoinhibitory damage by adjusting their position within vertical light gradients in coastal benthic sediments. However, experimental evidence to test this hypothesis remains inconclusive, mainly due to methodological difficulties in studying cell behavior and photosynthesis over realistic spatial microscale gradients of irradiance and cell position. In this study, a novel experimental approach was developed and used to test the hypothesis of photosynthesis optimization through motility, based on the combination of single-cell in vivo chlorophyll fluorometry and microfluidic chips. The approach allows the concurrent study of behavior and photosynthetic activity of individual cells of the epipelic diatom species Craspedostauros britannicus exposed to a light microgradient of realistic dimensions, simulating the irradiance and distance scales of light microgradients in benthic sediments. Following exposure to light, (i) cells explored their light environment before initiating light-directed motility; (ii) cells used motility to lower their light dose, when exposed to the highest light intensities; and (iii) motility was combined with reversible non-photochemical quenching, to allow cells to avoid photoinhibition. The results of this proof-of-concept study not only strongly support the photoprotective nature of photobehavior in the studied species but also revealed considerable variability in how individual cells reacted to a light microgradient. The experimental setup can be readily applied to study motility and photosynthetic light responses of other diatom species or natural assemblages, as well as other photoautotrophic motile microorganisms, broadening the toolset for experimental microbial ecology research.}, }
@article {pmid38351266, year = {2024}, author = {Arbulu, S and Kjos, M}, title = {Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {41}, pmid = {38351266}, issn = {1432-184X}, support = {101029099//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 296906//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Bacteriocins/pharmacology ; Biofilms ; Bacteria ; Peptides ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.}, }
@article {pmid38348184, year = {2024}, author = {Wang, W and Dong, Y and Guo, W and Zhang, X and Degen, AA and Bi, S and Ding, L and Chen, X and Long, R}, title = {Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1301258}, pmid = {38348184}, issn = {1664-302X}, abstract = {Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.}, }
@article {pmid38346660, year = {2024}, author = {Durán-Viseras, A and Lindner, BG and Hatt, JK and Lai, A and Wallace, R and Ginn, O and Brown, J and Konstantinidis, KT}, title = {Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities.}, journal = {The Science of the total environment}, volume = {920}, number = {}, pages = {170772}, doi = {10.1016/j.scitotenv.2024.170772}, pmid = {38346660}, issn = {1879-1026}, mesh = {Humans ; Animals ; Poultry ; Soil ; Metagenome ; Chickens ; Water ; *Microbiota ; *Anti-Infective Agents ; Anti-Bacterial Agents ; Metagenomics ; }, abstract = {In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.}, }
@article {pmid38345372, year = {2024}, author = {Campbell, BC and Greenfield, P and Barnhart, EP and Gong, S and Midgley, DJ and Paulsen, IT and George, SC}, title = {Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0173523}, pmid = {38345372}, issn = {2150-7511}, mesh = {*Coal/microbiology ; Carbon/metabolism ; Methane/metabolism ; *Deltaproteobacteria/metabolism ; }, abstract = {Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.}, }
@article {pmid38344937, year = {2024}, author = {Ugolini, GS and Wang, M and Secchi, E and Pioli, R and Ackermann, M and Stocker, R}, title = {Microfluidic approaches in microbial ecology.}, journal = {Lab on a chip}, volume = {24}, number = {5}, pages = {1394-1418}, pmid = {38344937}, issn = {1473-0189}, mesh = {Animals ; *Microfluidics/methods ; *Ecology ; }, abstract = {Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.}, }
@article {pmid38344169, year = {2024}, author = {Pertierra, LR and Varliero, G and Barbosa, A and Biersma, EM and Convey, P and Chown, SL and Cowan, D and De Los Rios, A and Escribano-Alvarez, P and Fontaneto, D and Fraser, C and Harris, M and Hughes, K and Griffiths, H and le Roux, P and Liu, XP and Lynch, H and Majewska, R and Martinez, PA and Molina-Montenegro, M and Olalla-Tarraga, MA and Peck, L and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, L and Terauds, A and Vianna, J and Wilmotte, A and Hortal, J and Greve, M}, title = {TerrANTALife 1.0 Biodiversity data checklist of known Antarctic terrestrial and freshwater life forms.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e106199}, pmid = {38344169}, issn = {1314-2828}, abstract = {BACKGROUND: Incomplete species inventories for Antarctica represent a key challenge for comprehensive ecological research and conservation in the region. Additionally, data required to understand population dynamics, rates of evolution, spatial ranges, functional traits, physiological tolerances and species interactions, all of which are fundamental to disentangle the different functional elements of Antarctic biodiversity, are mostly missing. However, much of the fauna, flora and microbiota in the emerged ice-free land of the continent have an uncertain presence and/or unresolved status, with entire biodiversity compendia of prokaryotic groups (e.g. bacteria) being missing. All the available biodiversity information requires consolidation, cross-validation, re-assessment and steady systematic inclusion in order to create a robust catalogue of biodiversity for the continent.<br><br>NEW INFORMATION: We compiled, completed and revised eukaryotic species inventories present in terrestrial and freshwater ecosystems in Antarctica in a new living database: terrANTALife (version 1.0). The database includes the first integration in a compendium for many groups of eukaryotic microorganisms. We also introduce a first catalogue of amplicon sequence variants (ASVs) of prokaryotic biodiversity. Available compendia and literature to date were searched for Antarctic terrestrial and freshwater species, integrated, taxonomically harmonised and curated by experts to create comprehensive checklists of Antarctic organisms. The final inventories comprises 470 animal species (including vertebrates, free-living invertebrates and parasites), 306 plants (including all Viridiplantae: embryophytes and green algae), 997 fungal species and 434 protists (sensu lato). We also provide a first account for many groups of microorganisms, including non-lichenised fungi and multiple groups of eukaryotic unicellular species (Stramenophila, Alveolata and Rhizaria (SAR), Chromists and Amoeba), jointly referred to as "protists". In addition, we identify 1753 bacterial (obtained from 348117 ASVs) and 34 archaeal genera (from 1848 ASVs), as well as, at least, 14 virus families. We formulate a basic tree of life in Antarctica with the main lineages listed in the region and their "known-accepted-species" numbers.}, }
@article {pmid38343862, year = {2024}, author = {Lin, H and Chen, Y and Abror, G and Price, M and Morris, A and Sun, J and Palella, F and Chew, KW and Brown, TT and Rinaldo, CR and Peddada, SD}, title = {The effect of sexual behavior on HIV-1 seroconversion is mediated by the gut microbiome and proinflammatory cytokines.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38343862}, issn = {2693-5015}, support = {U01 HL146208/HL/NHLBI NIH HHS/United States ; S10 OD023402/OD/NIH HHS/United States ; ZIA ES103390/ImNIH/Intramural NIH HHS/United States ; U01 HL146201/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146240/HL/NHLBI NIH HHS/United States ; }, abstract = {The association between HIV-1 seroconversion and gut dysbiosis is well documented, and its association with sexual activity is also widely recognized. However, it is not known whether the gut dysbiosis mediates the effects of high-risk sexual behavior on HIV-1 seroconversion. In this report we focused on men who engaged in high-risk sexual behavior where they had receptive anal intercourse with multiple men. We demonstrate that proinflammatory cytokines, sCD14 and sCD163, and gut microbiota mediate the effects of this high-risk sexual behavior on subsequent HIV seroconversion. We discovered changes in the gut microbial ecology, prior to seroconversion, both in terms of the composition as well as inter-relationships among the commensal species. Furthermore, these changes correlate with future HIV seroconversion. Specifically, as the number of sexual partners increased, we discovered in a "dose-response" manner, a decrease in the abundance of commensal and short-chain fatty acid-producing species, A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp, and an increase in proinflammatory species Dehalobacterium spp. and Methanobrevibacter spp. These changes were also observed among subsequent HIV seroconverters. Interestingly, we also discovered a reduction in correlations among these commensal and short-chain fatty acid producing bacteria in a "dose-response" manner with the number of sexual partners. Our mediation analysis not only provides a conceptual model for the disease process but also provides clues for future clinical interventions that will manipulate the gut microbiota to treat high-risk subjects to prevent HIV seroconversion.}, }
@article {pmid38338599, year = {2024}, author = {Bodie, AR and Wythe, LA and Dittoe, DK and Rothrock, MJ and O'Bryan, CA and Ricke, SC}, title = {Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38338599}, issn = {2304-8158}, abstract = {Food additives are employed in the food industry to enhance the color, smell, and taste of foods, increase nutritional value, boost processing efficiency, and extend shelf life. Consumers are beginning to prioritize food ingredients that they perceive as supporting a healthy lifestyle, emphasizing ingredients they deem acceptable as alternative or "clean-label" ingredients. Ready-to-eat (RTE) meat products can be contaminated with pathogens and spoilage microorganisms after the cooking step, contributing to food spoilage losses and increasing the risk to consumers for foodborne illnesses. More recently, consumers have advocated for no artificial additives or preservatives, which has led to a search for antimicrobials that meet these demands but do not lessen the safety or quality of RTE meats. Lactates and diacetates are used almost universally to extend the shelf life of RTE meats by reducing spoilage organisms and preventing the outgrowth of the foodborne pathogen Listeria monocytogenes. These antimicrobials applied to RTE meats tend to be broad-spectrum in their activities, thus affecting overall microbial ecology. It is to the food processing industry's advantage to target spoilage organisms and pathogens specifically.}, }
@article {pmid38337180, year = {2024}, author = {Finn, DR}, title = {A metagenomic alpha-diversity index for microbial functional biodiversity.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38337180}, issn = {1574-6941}, support = {522758166//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenome ; *Biodiversity ; RNA, Ribosomal ; Ecosystem ; }, abstract = {Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.}, }
@article {pmid38332550, year = {2024}, author = {Louw, NL and Wolfe, BE and Uricchio, LH}, title = {A phylogenomic perspective on interspecific competition.}, journal = {Ecology letters}, volume = {27}, number = {2}, pages = {e14359}, doi = {10.1111/ele.14359}, pmid = {38332550}, issn = {1461-0248}, support = {1942063//National Science Foundation/ ; 2021362//National Science Foundation/ ; }, mesh = {Phylogeny ; *Genome ; *Genomics ; Biological Evolution ; Phenotype ; }, abstract = {Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.}, }
@article {pmid38332365, year = {2024}, author = {Amaral, RR and Love, RM and Braga, T and Souza Côrtes, MI and Rachid, CTCC and Rôças, IN and Siqueira, JF}, title = {Impact of root canal preparation using two single-file systems on the intra-radicular microbiome of teeth with primary apical periodontitis.}, journal = {Clinical oral investigations}, volume = {28}, number = {2}, pages = {139}, pmid = {38332365}, issn = {1436-3771}, mesh = {Humans ; *Root Canal Preparation ; Dental Pulp Cavity/microbiology ; Root Canal Therapy ; *Periapical Periodontitis/microbiology ; Bacteria ; }, abstract = {OBJECTIVES: This study aimed to describe the effects of two single-file systems on the diversity of the endodontic microbiome of teeth with primary asymptomatic apical periodontitis.<br><br>MATERIALS AND METHODS: The root canals from single-rooted teeth with apical periodontitis were prepared using either the Reciproc Blue (RB) or the XP-endo Shaper (XPS) instrument system. The latter was followed by a supplementary step with the XP-endo Finisher (XPF) instrument. For irrigation, 5.25% sodium hypochlorite was used. Root canal samples were taken at the baseline (S1), after preparation (S2), and after the supplementary step (S3). DNA was extracted and subjected to high-throughput sequencing using the MiSeq Illumina platform.<br><br>RESULTS: Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems. The most dominant phyla in S2 were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria. The same phyla were found to dominate baseline samples and samples taken after using XPF, but with differences in the ranking of the most dominant ones. At the genus level, the most dominant genera identified after RB instrumentation were Bacteroidaceae [G-1], Fusobacterium, and Staphylococcus, while the most dominant genera after XPS instrumentation were Fusobacterium and Porphyromonas. These genera were also dominant in the initial samples.<br><br>CONCLUSIONS: Both treatment protocols had measurable effects on the root canal microbial diversity, with no significant differences between them. Most of the dominant taxa involved in the primary infection and probably in the aetiology of apical periodontitis were eliminated or substantially reduced.<br><br>CLINICAL RELEVANCE: The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus, and Bacteroidaceae [G-1].}, }
@article {pmid38332161, year = {2024}, author = {McDougall, FK and Speight, N and Funnell, O and Boardman, WSJ and Power, ML}, title = {Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {39}, pmid = {38332161}, issn = {1432-184X}, mesh = {Humans ; Animals ; *Chiroptera ; *Wildfires ; *Phascolarctidae ; Anti-Bacterial Agents/pharmacology ; Australia ; Drug Resistance, Bacterial/genetics ; Animals, Wild ; }, abstract = {In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.}, }
@article {pmid38331994, year = {2024}, author = {Tao, X and Yang, Z and Feng, J and Jian, S and Yang, Y and Bates, CT and Wang, G and Guo, X and Ning, D and Kempher, ML and Liu, XJA and Ouyang, Y and Han, S and Wu, L and Zeng, Y and Kuang, J and Zhang, Y and Zhou, X and Shi, Z and Qin, W and Wang, J and Firestone, MK and Tiedje, JM and Zhou, J}, title = {Experimental warming accelerates positive soil priming in a temperate grassland ecosystem.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1178}, pmid = {38331994}, issn = {2041-1723}, support = {DE-SC0004601//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020163//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0010570//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 41825016//National Natural Science Foundation of China (National Science Foundation of China)/ ; EF-2025558//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-2129235//NSF | BIO | Division of Environmental Biology (DEB)/ ; }, mesh = {*Ecosystem ; *Grassland ; Soil ; Carbon ; Climate Change ; }, abstract = {Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.}, }
@article {pmid38331428, year = {2024}, author = {Lee Díaz, AS and Minchev, Z and Raaijmakers, JM and Pozo, MJ and Garbeva, P}, title = {Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {2}, pages = {}, pmid = {38331428}, issn = {1574-6941}, support = {765290//European Union/ ; }, mesh = {*Agricultural Inoculants ; *Solanum lycopersicum ; Rhizosphere ; Herbivory ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; }, abstract = {Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.}, }
@article {pmid38329329, year = {2024}, author = {Amill, F and Gauthier, J and Rautio, M and Derome, N}, title = {Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0294323}, pmid = {38329329}, issn = {2165-0497}, support = {//UL | Sentinelle Nord, Universit&#xe9; Laval (Sentinel North)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Polar Knowledge Canada (PKC)/ ; }, mesh = {Animals ; Bays ; Canada ; Dysbiosis ; Gills ; *Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Trout/genetics/metabolism ; Water/metabolism ; }, abstract = {Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.}, }
@article {pmid38328439, year = {2024}, author = {Jaeger, JW and Brandt, A and Gui, W and Yergaliyev, T and Hernández-Arriaga, A and Muthu, MM and Edlund, K and Elashy, A and Molinaro, A and Möckel, D and Sarges, J and Halibasic, E and Trauner, M and Kahles, F and Rolle-Kampczyk, U and Hengstler, J and Schneider, CV and Lammers, T and Marschall, HU and von Bergen, M and Camarinha-Silva, A and Bergheim, I and Trautwein, C and Schneider, KM}, title = {Microbiota modulation by dietary oat beta-glucan prevents steatotic liver disease progression.}, journal = {JHEP reports : innovation in hepatology}, volume = {6}, number = {3}, pages = {100987}, pmid = {38328439}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Changes in gut microbiota in metabolic dysfunction-associated steatotic liver disease (MASLD) are important drivers of disease progression towards fibrosis. Therefore, reversing microbial alterations could ameliorate MASLD progression. Oat beta-glucan, a non-digestible polysaccharide, has shown promising therapeutic effects on hyperlipidemia associated with MASLD, but its impact on gut microbiota and most importantly MASLD-related fibrosis remains unknown.<br><br>METHODS: We performed detailed metabolic phenotyping, including assessments of body composition, glucose tolerance, and lipid metabolism, as well as comprehensive characterization of the gut-liver axis in a western-style diet (WSD)-induced model of MASLD and assessed the effect of a beta-glucan intervention on early and advanced liver disease. Gut microbiota were modulated using broad-spectrum antibiotic treatment.<br><br>RESULTS: Oat beta-glucan supplementation did not affect WSD-induced body weight gain or glucose intolerance and the metabolic phenotype remained largely unaffected. Interestingly, oat beta-glucan dampened MASLD-related inflammation, which was associated with significantly reduced monocyte-derived macrophage infiltration and fibroinflammatory gene expression, as well as strongly reduced fibrosis development. Mechanistically, this protective effect was not mediated by changes in bile acid composition or signaling, but was dependent on gut microbiota and was lost upon broad-spectrum antibiotic treatment. Specifically, oat beta-glucan partially reversed unfavorable changes in gut microbiota, resulting in an expansion of protective taxa, including Ruminococcus, and Lactobacillus followed by reduced translocation of Toll-like receptor ligands.<br><br>CONCLUSIONS: Our findings identify oat beta-glucan as a highly efficacious food supplement that dampens inflammation and fibrosis development in diet-induced MASLD. These results, along with its favorable dietary profile, suggest that it may be a cost-effective and well-tolerated approach to preventing MASLD progression and should be assessed in clinical studies.<br><br>IMPACT AND IMPLICATIONS: Herein, we investigated the effect of oat beta-glucan on the gut-liver axis and fibrosis development in a mouse model of metabolic dysfunction-associated steatotic liver disease (MASLD). Beta-glucan significantly reduced inflammation and fibrosis in the liver, which was associated with favorable shifts in gut microbiota that protected against bacterial translocation and activation of fibroinflammatory pathways. Together, oat beta-glucan may be a cost-effective and well-tolerated approach to prevent MASLD progression and should be assessed in clinical studies.}, }
@article {pmid38327124, year = {2024}, author = {Rudzki, EN and Antonson, ND and Jones, TM and Schelsky, WM and Trevelline, BK and Hauber, ME and Kohl, KD}, title = {Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?.}, journal = {Molecular ecology}, volume = {33}, number = {6}, pages = {e17289}, doi = {10.1111/mec.17289}, pmid = {38327124}, issn = {1365-294X}, support = {1953226//US National Science Foundation/ ; 2026836//US National Science Foundation/ ; 2139321//US National Science Foundation/ ; 2305848//US National Science Foundation/ ; }, mesh = {Animals ; *Parasites ; RNA, Ribosomal, 16S/genetics ; Nesting Behavior ; *Passeriformes ; }, abstract = {The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.}, }
@article {pmid38325783, year = {2024}, author = {Wang, B and Hu, K and Li, C and Zhang, Y and Hu, C and Liu, Z and Ding, J and Chen, L and Zhang, W and Fang, J and Zhang, H}, title = {Geographic distribution of bacterial communities of inland waters in China.}, journal = {Environmental research}, volume = {249}, number = {}, pages = {118337}, doi = {10.1016/j.envres.2024.118337}, pmid = {38325783}, issn = {1096-0953}, mesh = {China ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/analysis/genetics ; Biodiversity ; Water Microbiology ; Fresh Water/microbiology ; }, abstract = {Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.}, }
@article {pmid38325494, year = {2024}, author = {Forsmark, B and Bizjak, T and Nordin, A and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170741}, doi = {10.1016/j.scitotenv.2024.170741}, pmid = {38325494}, issn = {1879-1026}, mesh = {*Nitrogen/analysis ; Soil ; Carbon ; Forests ; *Microbiota ; Soil Microbiology ; }, abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha[-1] yr[-1]) and high (50 kg N ha[-1] yr[-1]) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.}, }
@article {pmid38325456, year = {2024}, author = {Redouane, EM and Núñez, A and Achouak, W and Barakat, M and Alex, A and Martins, JC and Tazart, Z and Mugani, R and Zerrifi, SEA and Haida, M and García, AM and Campos, A and Lahrouni, M and Oufdou, K and Vasconcelos, V and Oudra, B}, title = {Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170634}, doi = {10.1016/j.scitotenv.2024.170634}, pmid = {38325456}, issn = {1879-1026}, mesh = {*Vicia faba ; Soil ; Microcystins/toxicity ; Rhizosphere ; *Cyanobacteria ; *Microbiota ; Soil Microbiology ; Plant Roots/metabolism ; }, abstract = {Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L[-1] MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.}, }
@article {pmid38324120, year = {2024}, author = {Scaini, A and Mulligan, J and Berg, H and Brangarí, A and Bukachi, V and Carenzo, S and Chau Thi, D and Courtney-Mustaphi, C and Ekblom, A and Fjelde, H and Fridahl, M and Hansson, A and Hicks, L and Höjer, M and Juma, B and Kain, JH and Kariuki, RW and Kim, S and Lane, P and Leizeaga, A and Lindborg, R and Livsey, J and Lyon, SW and Marchant, R and McConville, JR and Munishi, L and Nilsson, D and Olang, L and Olin, S and Olsson, L and Rogers, PM and Rousk, J and Sandén, H and Sasaki, N and Shoemaker, A and Smith, B and Thai Huynh Phuong, L and Varela Varela, A and Venkatappa, M and Vico, G and Von Uexkull, N and Wamsler, C and Wondie, M and Zapata, P and Zapata Campos, MJ and Manzoni, S and Tompsett, A}, title = {Pathways from research to sustainable development: Insights from ten research projects in sustainability and resilience.}, journal = {Ambio}, volume = {53}, number = {4}, pages = {517-533}, pmid = {38324120}, issn = {1654-7209}, support = {2016-06359//Vetenskapsr&#xe5;det/ ; 2016-06355//Vetenskapsr&#xe5;det/ ; 2016-06297//Vetenskapsr&#xe5;det/ ; 2016-06300//Vetenskapsr&#xe5;det/ ; 2016-06327//Vetenskapsr&#xe5;det/ ; 2016-06329//Vetenskapsr&#xe5;det/ ; 2016-06334//Vetenskapsr&#xe5;det/ ; 2016-06289//Vetenskapsr&#xe5;det/ ; 2016-06313//Vetenskapsr&#xe5;det/ ; 2016-06389//Vetenskapsr&#xe5;det/ ; }, mesh = {Humans ; *Resilience, Psychological ; }, abstract = {Drawing on collective experience from ten collaborative research projects focused on the Global South, we identify three major challenges that impede the translation of research on sustainability and resilience into better-informed choices by individuals and policy-makers that in turn can support transformation to a sustainable future. The three challenges comprise: (i) converting knowledge produced during research projects into successful knowledge application; (ii) scaling up knowledge in time when research projects are short-term and potential impacts are long-term; and (iii) scaling up knowledge across space, from local research sites to larger-scale or even global impact. Some potential pathways for funding agencies to overcome these challenges include providing targeted prolonged funding for dissemination and outreach, and facilitating collaboration and coordination across different sites, research teams, and partner organizations. By systematically documenting these challenges, we hope to pave the way for further innovations in the research cycle.}, }
@article {pmid38322759, year = {2023}, author = {Yang, X and Narvaez-Bravo, C and Zhang, P}, title = {Driving forces shaping the microbial ecology in meat packing plants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1333696}, pmid = {38322759}, issn = {1664-302X}, abstract = {Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.}, }
@article {pmid38319112, year = {2024}, author = {Guo, J and Ning, H and Li, Y and Xu, Q and Shen, Q and Ling, N and Guo, S}, title = {Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0273323}, pmid = {38319112}, issn = {2150-7511}, support = {32372808//National Natural Science Foundation of China (NSFC)/ ; 41977080//National Natural Science Foundation of China (NSFC)/ ; U2003210//National Natural Science Foundation of China (NSFC)/ ; 202206193000001, 20220816113416001//Shenzhen Science and Technology Program/ ; JCYJ20230807111217035//Shenzhen Science and Technology Program/ ; 2019QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; }, mesh = {*Oryza ; *Microbiota ; Bacteria ; Fungi ; Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; Soil/chemistry ; }, abstract = {UNLABELLED: The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.<br><br>IMPORTANCE: The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.}, }
@article {pmid38317822, year = {2024}, author = {Kop, LFM and Koch, H and Jetten, MSM and Daims, H and Lücker, S}, title = {Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad017}, pmid = {38317822}, issn = {2730-6151}, abstract = {The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.}, }
@article {pmid38317643, year = {2024}, author = {Vlasselaer, L and Crauwels, S and Lievens, B and De Coninck, B}, title = {Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38317643}, issn = {1574-6941}, support = {HBC.2020.3181//VLAIO/ ; }, mesh = {Lactuca ; *Phytophthora/genetics ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Microbiota/genetics ; Rhizosphere ; Flavobacterium/genetics ; Soil Microbiology ; }, abstract = {Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.}, }
@article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0360223}, pmid = {38315121}, issn = {2165-0497}, support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; }, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, }
@article {pmid38313259, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38313259}, issn = {2692-8205}, abstract = {Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.}, }
@article {pmid38312729, year = {2024}, author = {Wang, Y and Long, C and Yin, L and Liu, R and Liao, Y and He, G and Liu, Z}, title = {Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers.}, journal = {RSC advances}, volume = {14}, number = {7}, pages = {4482-4491}, pmid = {38312729}, issn = {2046-2069}, abstract = {Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2[-]-N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.}, }
@article {pmid38311160, year = {2024}, author = {Guo, M and Shang, X and Ma, Y and Zhang, K and Zhang, L and Zhou, Y and Gong, Z and Miao, R}, title = {Biochars assisted phytoremediation of polycyclic aromatic hydrocarbons contaminated agricultural soil: Dynamic responses of functional genes and microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {345}, number = {}, pages = {123476}, doi = {10.1016/j.envpol.2024.123476}, pmid = {38311160}, issn = {1873-6424}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/analysis ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; *Charcoal ; }, abstract = {A biochar-intensified phytoremediation experiment was designed to investigate the dynamic effects of different biochars on polycyclic aromatic hydrocarbon (PAH) removal in ryegrass rhizosphere contaminated soil. Maize and wheat straw biochar pyrolyzed at 300 °C and 500 °C were amended into PAH-contaminated soil, and then ryegrass (Lolium multiflorum L.) was planted for 90 days. Spearman's correlations among PAH removal, enzyme activity, abundance of PAH-ring hydroxylating dioxygenase (PAH-RHDα), and fungal and bacterial community structure were analyzed to elucidate the microbial degradation mechanisms during the combined remediation process. The results showed that 500 °C wheat straw biochar had higher surface area and more nutrients, and significantly accelerated the phytoremediation of PAHs (62.5 %), especially for high molecular weight PAH in contaminated soil. The activities of urease and dehydrogenase and the abundance of total and PAH-degrading bacteria, which improved with time by biochar and ryegrass, had a positive correlation with the removal rate of PAHs. Biochar enhanced the abundance of gram-negative (GN) PAH-RHDα genes. The GN PAH-degraders, Sphingomonas, bacteriap25, Haliangium, and Dongia may play vital roles in PAH degradation in biochar-amended rhizosphere soils. Principal coordinate analysis indicated that biochar led to significant differences in fungal community structures before 30 days, while the diversity of the bacterial community composition depended on planting ryegrass after 60 days. These findings imply that the structural reshaping of microbial communities results from incubation time and the selection of biochar and ryegrass in PAH-contaminated soils. Applying 500 °C wheat straw biochar could enhance the rhizoremediation of PAH-contaminated soil and benefit the soil microbial ecology.}, }
@article {pmid38307852, year = {2024}, author = {Jimonet, P and Druart, C and Blanquet-Diot, S and Boucinha, L and Kourula, S and Le Vacon, F and Maubant, S and Rabot, S and Van de Wiele, T and Schuren, F and Thomas, V and Walther, B and Zimmermann, M and , }, title = {Gut Microbiome Integration in Drug Discovery and Development of Small Molecules.}, journal = {Drug metabolism and disposition: the biological fate of chemicals}, volume = {52}, number = {4}, pages = {274-287}, doi = {10.1124/dmd.123.001605}, pmid = {38307852}, issn = {1521-009X}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Drug Discovery ; Drug Interactions ; }, abstract = {Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.}, }
@article {pmid38305149, year = {2024}, author = {Mukhia, S and Kumar, A and Kumar, R}, title = {Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38305149}, issn = {1574-6941}, support = {45/17/2020-/BIO/BMS//Indian Council of Medical Research/ ; DBT/JRF/BET-17/I/2017/AL/367//Department of Biotechnology/ ; DST/INSPIRE/04/2014/001280//Department of Science and Technology/ ; SRG/2019/001071//Science and Engineering Research Board/ ; }, mesh = {*Ecosystem ; Ice Cover ; Metagenomics ; Bacteria ; Metagenome ; *Microbiota ; Proteobacteria/genetics ; Sulfur/metabolism ; }, abstract = {Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.}, }
@article {pmid38305133, year = {2024}, author = {Ramakodi, MP}, title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae009}, pmid = {38305133}, issn = {1574-6968}, mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.}, }
@article {pmid38303015, year = {2024}, author = {Mejías-Molina, C and Pico-Tomàs, A and Martínez-Puchol, S and Itarte, M and Torrell, H and Canela, N and Borrego, CM and Corominas, L and Rusiñol, M and Bofill-Mas, S}, title = {Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {10}, pmid = {38303015}, issn = {1479-7364}, support = {202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; }, mesh = {Humans ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; Virome/genetics ; *Viruses/genetics ; *Virus Diseases ; }, abstract = {BACKGROUND: Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome.<br><br>RESULTS: The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression.<br><br>CONCLUSIONS: This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.}, }
@article {pmid38302681, year = {2024}, author = {Wdowiak-Wróbel, S and Kalita, M and Palusińska-Szysz, M and Marek-Kozaczuk, M and Sokołowski, W and Coutinho, TA}, title = {Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2698}, pmid = {38302681}, issn = {2045-2322}, support = {PL-RPA2/07/TRIFOMIKRO/2019//Narodowe Centrum Bada&#x144; i Rozwoju/ ; POL180702349288//National Research Foundation/ ; }, mesh = {Sequence Analysis, DNA ; *Pantoea/genetics ; *Trifolium/genetics ; RNA, Ribosomal, 16S/genetics ; DNA ; Phylogeny ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; }, abstract = {A novel bacterium, designated strain MMK2[T], was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2[T] and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2[T] strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2[T] and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2[T] (= DSM 115063[T] = LMG 33049[T]).}, }
@article {pmid38302544, year = {2024}, author = {Prasoodanan P K, V and Kumar, S and Dhakan, DB and Waiker, P and Saxena, R and Sharma, VK}, title = {Metagenomic exploration of Andaman region of the Indian Ocean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2717}, pmid = {38302544}, issn = {2045-2322}, mesh = {Indian Ocean ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota/genetics ; Water ; Seawater ; }, abstract = {Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.}, }
@article {pmid38299778, year = {2024}, author = {León-Sobrino, C and Ramond, JB and Coclet, C and Kapitango, RM and Maggs-Kölling, G and Cowan, DA}, title = {Temporal dynamics of microbial transcription in wetted hyperarid desert soils.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38299778}, issn = {1574-6941}, support = {113308//University of Pretoria/ ; }, mesh = {*Ecosystem ; Soil ; Desert Climate ; Soil Microbiology ; *Microbiota/genetics ; Water ; RNA, Messenger ; }, abstract = {Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.}, }
@article {pmid38297006, year = {2024}, author = {Maza-Márquez, P and Lee, MD and Bebout, BM}, title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2561}, pmid = {38297006}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; }, abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.}, }
@article {pmid38296863, year = {2024}, author = {Bååth, E and Kritzberg, ES}, title = {Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {38}, pmid = {38296863}, issn = {1432-184X}, mesh = {Temperature ; *Cold Temperature ; *Lakes ; Bacteria/metabolism ; Seasons ; }, abstract = {Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.}, }
@article {pmid38294246, year = {2024}, author = {Kashani, M and Engle, MA and Kent, DB and Gregston, T and Cozzarelli, IM and Mumford, AC and Varonka, MS and Harris, CR and Akob, DM}, title = {Illegal dumping of oil and gas wastewater alters arid soil microbial communities.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0149023}, pmid = {38294246}, issn = {1098-5336}, support = {//DOI | U.S. Geological Survey (USGS)/ ; }, mesh = {*Wastewater ; Soil Microbiology ; Soil/chemistry ; Phylogeny ; Desert Climate ; *Microbiota ; Hydrocarbons ; }, abstract = {The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.}, }
@article {pmid38293374, year = {2024}, author = {Choi, YJ and Lim, JY and Kang, MJ and Choi, JY and Yang, JH and Chung, YB and Park, SH and Min, SG and Lee, MA}, title = {Changes in bacterial composition and metabolite profiles during kimchi fermentation with different garlic varieties.}, journal = {Heliyon}, volume = {10}, number = {2}, pages = {e24283}, pmid = {38293374}, issn = {2405-8440}, abstract = {Garlic, a key ingredient in kimchi, is an indispensable source of lactic acid bacteria, which are essential for fermentation. This study explored the effects of various garlic varieties on kimchi fermentation, focusing on changes in microbial communities and metabolite profiles. We observed that the type of garlic used did not significantly alter the microbial community. However, the presence of garlic itself made a significant difference. Specifically, kimchi with garlic showed higher abundance of Leuconostoc and Weissella, which are bacteria primarily responsible for kimchi fermentation. Additionally, kimchi containing garlic had increased levels of mannitol and fructose, which significantly influence taste; however, lactic acid and putrescine levels were decreased. Therefore, the addition of garlic directly contributes to the flavor profile of kimchi. Sixty-two metabolites were identified using gas chromatography and mass spectrometry. The variety of garlic added influenced the metabolite profiles of kimchi, particularly in the later stages of fermentation. These profiles were categorized based on the garlic's origin, whether from southern or northern ecotypes (R[2]X = 0.933, R[2]Y = 0.986, Q[2] = 0.878). These findings confirm that both the presence and the variety of garlic significantly impact the microbial ecology and metabolites during kimchi fermentation, underscoring its essential role in the process.}, }
@article {pmid38293109, year = {2024}, author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.16.575907}, pmid = {38293109}, issn = {2692-8205}, abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.}, }
@article {pmid38289133, year = {2024}, author = {Op De Beeck, M and Troein, C and Peterson, C and Tunlid, A and Persson, P}, title = {Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0148923}, pmid = {38289133}, issn = {1098-5336}, support = {2020-04293//Vetenskapsr&#xe5;det (VR)/ ; 2021-05188//Vetenskapsr&#xe5;det (VR)/ ; }, mesh = {*Basidiomycota ; *Mycorrhizae ; Hyphae ; Cellulose ; Spectrophotometry, Infrared/methods ; }, abstract = {In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.IMPORTANCEInfrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus Paxillus involutus at the interface between individual fungal hyphae and cellulose substrates.}, }
@article {pmid38289092, year = {2024}, author = {Bontemps, Z and Moënne-Loccoz, Y and Hugoni, M}, title = {Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0123323}, pmid = {38289092}, issn = {2379-5077}, support = {//DRAC Nouvelle Aquitaine/ ; }, mesh = {*Coloring Agents ; *Microbiota ; Caves ; }, abstract = {Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.}, }
@article {pmid38286834, year = {2024}, author = {Wang, X and Liu, Y and Qing, C and Zeng, J and Dong, J and Xia, P}, title = {Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {37}, pmid = {38286834}, issn = {1432-184X}, mesh = {*Ecosystem ; Lakes ; Metagenome ; Bacteria/genetics/metabolism ; *Potamogetonaceae/genetics/microbiology ; Nitrogen/metabolism ; }, abstract = {Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.}, }
@article {pmid38286067, year = {2024}, author = {Lamprea-Pineda, PA and Demeestere, K and González-Cortés, JJ and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C}, title = {Addition of (bio)surfactants in the biofiltration of hydrophobic volatile organic compounds in air.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120132}, doi = {10.1016/j.jenvman.2024.120132}, pmid = {38286067}, issn = {1095-8630}, mesh = {Humans ; Surface-Active Agents/chemistry ; *Volatile Organic Compounds ; Hexanes ; Polysorbates ; Cyclohexanes ; *Saponins ; Filtration/methods ; }, abstract = {The removal of volatile organic compounds (VOCs) in air is of utmost importance to safeguard both environmental quality and human well-being. However, the low aqueous solubility of hydrophobic VOCs results in poor removal in waste gas biofilters (BFs). In this study, we evaluated the addition of (bio)surfactants in three BFs (BF1 and BF2 mixture of compost and wood chips (C + WC), and BF3 filled with expanded perlite) to enhance the removal of cyclohexane and hexane from a polluted gas stream. Experiments were carried out to select two (bio)surfactants (i.e., Tween 80 and saponin) out of five (sodium dodecyl sulfate (SDS), Tween 80, surfactin, rhamnolipid and saponin) from a physical-chemical (i.e., decreasing VOC gas-liquid partitioning) and biological (i.e., the ability of the microbial consortium to grow on the (bio)surfactants) point of view. The results show that adding Tween 80 at 1 critical micelle concentration (CMC) had a slight positive effect on the removal of both VOCs, in BF1 (e.g., 7.0 ± 0.6 g cyclohexane m[-3] h[-1], 85 ± 2% at 163 s; compared to 6.7 ± 0.4 g cyclohexane m[-3] h[-1], 76 ± 2% at 163 s and 0 CMC) and BF2 (e.g., 4.3 ± 0.4 g hexane m[-3] h[-1], 27 ± 2% at 82 s; compared to 3.1 ± 0.7 g hexane m[-3] h[-1], 16 ± 4% at 82 s and 0 CMC), but a negative effect in BF3 at either 1, 3 and 9 CMC (e.g., 2.4 ± 0.4 g hexane m[-3] h[-1], 30 ± 4% at 163 s and 1 CMC; compared to 4.6 ± 1.0 g hexane m[-3] h[-1], 43 ± 8% at 163 s and 0 CMC). In contrast, the performance of all BFs improved with the addition of saponin, particularly at 3 CMC. Notably, in BF3, the elimination capacity (EC) and removal efficiency (RE) doubled for both VOCs (i.e., 9.1 ± 0.6 g cyclohexane m[-3] h[-1], 49 ± 3%; 4.3 ± 0.3 g hexane m[-3] h[-1], 25 ± 3%) compared to no biosurfactant addition (i.e., 4.5 ± 0.4 g cyclohexane m[-3] h[-1], 23 ± 3%; hexane 2.2 ± 0.5 g m[-3] h[-1], 10 ± 2%) at 82 s. Moreover, the addition of the (bio)surfactants led to a shift in the microbial consortia, with a different response in BF1-BF2 compared to BF3. This study evaluates for the first time the use of saponin in BFs, it demonstrates that cyclohexane and hexane RE can be improved by (bio)surfactant addition, and it provides recommendations for future studies in this field.}, }
@article {pmid38282644, year = {2024}, author = {Schauberger, C and Thamdrup, B and Lemonnier, C and Trouche, B and Poulain, J and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L}, title = {Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad005}, pmid = {38282644}, issn = {2730-6151}, abstract = {Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.}, }
@article {pmid38281398, year = {2024}, author = {Van Peteghem, L and Sakarika, M and Matassa, S and Pikaar, I and Ganigué, R and Rabaey, K}, title = {Corrigendum to "Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production" [Bioresour. Technol. 349 (2022) 126853].}, journal = {Bioresource technology}, volume = {395}, number = {}, pages = {130362}, doi = {10.1016/j.biortech.2024.130362}, pmid = {38281398}, issn = {1873-2976}, }
@article {pmid38280409, year = {2024}, author = {Yao, S and Swanson, CS and Cheng, Z and He, Q and Yuan, H}, title = {Alternating polarity as a novel strategy for building synthetic microbial communities capable of robust Electro-Methanogenesis.}, journal = {Bioresource technology}, volume = {395}, number = {}, pages = {130374}, doi = {10.1016/j.biortech.2024.130374}, pmid = {38280409}, issn = {1873-2976}, mesh = {RNA, Ribosomal, 16S/genetics ; Biofuels ; Charcoal ; Bayes Theorem ; *Microbiota ; *Euryarchaeota/genetics ; Methane ; }, abstract = {Electro-methanogenic microbial communities can produce biogas with high efficiency and have attracted extensive research interest. In this study an alternating polarity strategy was developed to build electro-methanogenic communities. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4th enrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities assembled under alternating polarity were electroactive and structurally different from those assembled under other conditions. One Methanobacterium population and two Geobacter populations were consistently abundant and active in the communities. Their 16S rRNA was up-regulated by electrode potentials. Bayesian networks inferred close associations between these populations. Overall, electro-methanogenic communities have been successfully assembled with alternating polarity.}, }
@article {pmid38279257, year = {2024}, author = {Córdova-Espinoza, MG and González-Vázquez, R and Barron-Fattel, RR and Gónzalez-Vázquez, R and Vargas-Hernández, MA and Albores-Méndez, EM and Esquivel-Campos, AL and Mendoza-Pérez, F and Mayorga-Reyes, L and Gutiérrez-Nava, MA and Medina-Quero, K and Escamilla-Gutiérrez, A}, title = {Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38279257}, issn = {1422-0067}, mesh = {Humans ; *Aptamers, Nucleotide ; SELEX Aptamer Technique ; Gram-Negative Bacteria/genetics ; Bacteria ; *Communicable Diseases ; }, abstract = {Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.}, }
@article {pmid38278954, year = {2024}, author = {Ma, X and Vanneste, S and Chang, J and Ambrosino, L and Barry, K and Bayer, T and Bobrov, AA and Boston, L and Campbell, JE and Chen, H and Chiusano, ML and Dattolo, E and Grimwood, J and He, G and Jenkins, J and Khachaturyan, M and Marín-Guirao, L and Mesterházy, A and Muhd, DD and Pazzaglia, J and Plott, C and Rajasekar, S and Rombauts, S and Ruocco, M and Scott, A and Tan, MP and Van de Velde, J and Vanholme, B and Webber, J and Wong, LL and Yan, M and Sung, YY and Novikova, P and Schmutz, J and Reusch, TBH and Procaccini, G and Olsen, JL and Van de Peer, Y}, title = {Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.}, journal = {Nature plants}, volume = {10}, number = {2}, pages = {240-255}, pmid = {38278954}, issn = {2055-0278}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Alismatales/genetics ; *Zosteraceae/genetics ; Ecosystem ; }, abstract = {We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.}, }
@article {pmid38278226, year = {2024}, author = {Sabrekov, AF and Semenov, MV and Terentieva, IE and Krasnov, GS and Kharitonov, SL and Glagolev, MV and Litti, YV}, title = {Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170213}, doi = {10.1016/j.scitotenv.2024.170213}, pmid = {38278226}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; Anaerobiosis ; Methane/metabolism ; Soil ; RNA, Ribosomal, 16S ; Acetates ; *Microbiota ; Isotopes ; }, abstract = {Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ[13]C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO4[2-] and NO3[-] as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.}, }
@article {pmid38276724, year = {2024}, author = {Hassan, Z and Westerhoff, HV}, title = {Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes.}, journal = {Toxics}, volume = {12}, number = {1}, pages = {}, pmid = {38276724}, issn = {2305-6304}, abstract = {At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.}, }
@article {pmid38275746, year = {2023}, author = {Seppi, M and Pasqualini, J and Facchin, S and Savarino, EV and Suweis, S}, title = {Emergent Functional Organization of Gut Microbiomes in Health and Diseases.}, journal = {Biomolecules}, volume = {14}, number = {1}, pages = {}, pmid = {38275746}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Microbiota ; Metagenome ; Metagenomics ; }, abstract = {Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.}, }
@article {pmid38274012, year = {2023}, author = {Ulčar, B and Regueira, A and Podojsteršek, M and Boon, N and Ganigué, R}, title = {Why do lactic acid bacteria thrive in chain elongation microbiomes?.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1291007}, pmid = {38274012}, issn = {2296-4185}, abstract = {Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h[-1]) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h[-1]), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.}, }
@article {pmid38273535, year = {2024}, author = {Lewis, ASL and Lau, MP and Jane, SF and Rose, KC and Be'eri-Shlevin, Y and Burnet, SH and Clayer, F and Feuchtmayr, H and Grossart, HP and Howard, DW and Mariash, H and Delgado Martin, J and North, RL and Oleksy, I and Pilla, RM and Smagula, AP and Sommaruga, R and Steiner, SE and Verburg, P and Wain, D and Weyhenmeyer, GA and Carey, CC}, title = {Anoxia begets anoxia: A positive feedback to the deoxygenation of temperate lakes.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17046}, doi = {10.1111/gcb.17046}, pmid = {38273535}, issn = {1365-2486}, support = {//College of Science Roundtable at Virginia Tech/ ; //Cornell Atkinson Center for Sustainability, Cornell University/ ; GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; //EMALCSA Chair/ ; //Institute for Critical Technology and Applied Science/ ; //Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; //LTSER Platform Tyrolean Alps (LTER-Austria)/ ; C01X2205//Ministry of Business, Innovation and Employment/ ; //Missouri Department of Natural Resources/ ; 1737424//National Science Foundation/ ; 1753639//National Science Foundation/ ; 1754265//National Science Foundation/ ; 1840995//National Science Foundation/ ; 1933016//National Science Foundation/ ; 2019528//National Science Foundation/ ; 2048031//National Science Foundation/ ; NE/R016429/1//Natural Environment Research Council/ ; //Oak Ridge National Laboratory/ ; 2020-01091//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03222//Vetenskapsr&#xe5;det/ ; //Water Power Technologies Office/ ; }, mesh = {Humans ; *Lakes ; Chlorophyll A/analysis ; *Environmental Monitoring/methods ; Feedback ; Hypoxia ; Phosphorus/analysis ; Oxygen ; Eutrophication ; }, abstract = {Declining oxygen concentrations in the deep waters of lakes worldwide pose a pressing environmental and societal challenge. Existing theory suggests that low deep-water dissolved oxygen (DO) concentrations could trigger a positive feedback through which anoxia (i.e., very low DO) during a given summer begets increasingly severe occurrences of anoxia in following summers. Specifically, anoxic conditions can promote nutrient release from sediments, thereby stimulating phytoplankton growth, and subsequent phytoplankton decomposition can fuel heterotrophic respiration, resulting in increased spatial extent and duration of anoxia. However, while the individual relationships in this feedback are well established, to our knowledge, there has not been a systematic analysis within or across lakes that simultaneously demonstrates all of the mechanisms necessary to produce a positive feedback that reinforces anoxia. Here, we compiled data from 656 widespread temperate lakes and reservoirs to analyze the proposed anoxia begets anoxia feedback. Lakes in the dataset span a broad range of surface area (1-126,909 ha), maximum depth (6-370 m), and morphometry, with a median time-series duration of 30 years at each lake. Using linear mixed models, we found support for each of the positive feedback relationships between anoxia, phosphorus concentrations, chlorophyll a concentrations, and oxygen demand across the 656-lake dataset. Likewise, we found further support for these relationships by analyzing time-series data from individual lakes. Our results indicate that the strength of these feedback relationships may vary with lake-specific characteristics: For example, we found that surface phosphorus concentrations were more positively associated with chlorophyll a in high-phosphorus lakes, and oxygen demand had a stronger influence on the extent of anoxia in deep lakes. Taken together, these results support the existence of a positive feedback that could magnify the effects of climate change and other anthropogenic pressures driving the development of anoxia in lakes around the world.}, }
@article {pmid38273527, year = {2024}, author = {Fontaine, S and Abbadie, L and Aubert, M and Barot, S and Bloor, JMG and Derrien, D and Duchene, O and Gross, N and Henneron, L and Le Roux, X and Loeuille, N and Michel, J and Recous, S and Wipf, D and Alvarez, G}, title = {Plant-soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17034}, doi = {10.1111/gcb.17034}, pmid = {38273527}, issn = {1365-2486}, support = {ANR-20-PCA-0006//ANR/ ; //European Union/ ; //INRAE-CNRS/ ; //ISITE Clermont-Ferrand/ ; }, mesh = {Humans ; *Soil ; *Ecosystem ; Agriculture ; Plants ; Carbon ; }, abstract = {Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant-soil and plant-plant interactions, eco-physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2 O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature-based practices allowing for site-specific modifications. This new synthetized knowledge should help practitioners to improve the long-term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.}, }
@article {pmid38273522, year = {2024}, author = {Lí, JT and Hicks, LC and Brangarí, AC and Tájmel, D and Cruz-Paredes, C and Rousk, J}, title = {Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17040}, doi = {10.1111/gcb.17040}, pmid = {38273522}, issn = {1365-2486}, support = {202006100130//Distinguished International Students Scholarship/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2022-01478//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; }, mesh = {*Soil Microbiology ; Seasons ; Soil/chemistry ; Carbon ; *Resilience, Psychological ; Climate Change ; }, abstract = {Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.}, }
@article {pmid38272989, year = {2024}, author = {Laanbroek, HJ and Rains, MC and Verhoeven, JTA and Whigham, DF}, title = {The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2165}, pmid = {38272989}, issn = {2045-2322}, mesh = {*Wetlands ; *Avicennia ; Ecosystem ; Mosquito Control ; Nitrogen/analysis ; Plant Breeding ; Forests ; Soil/chemistry ; }, abstract = {Coastal wetlands such as mangrove forests are breeding grounds for nuisance-causing insects. Rotational Impoundment Management (RIM) for mosquito control involves annual summer inundation of impounded mangrove forests with estuarine water during the summer half year. However, in addition to controlling mosquitos, RIM may change biogeochemical pathways. This study set out to investigate how RIM quantitatively affects physicochemical soil characteristics and potential nitrifying and denitrifying activities (PNA and PDA), which are key in the global nitrogen cycle. Before and after the implementation of RIM, soil samples were collected annually in habitats differing in size and abundance of black mangroves (Avicennia germinans) in an impoundment with RIM and in an adjacent impoundment with a more open connection to the lagoon. Compared to the non-managed impoundment, soil moisture content, total nitrogen and PDA increased, while salinity decreased after the start of annual summer flooding, but only in the dwarf habitat. In the sparse and dense habitats, total nitrogen and PDA increased independently of summer flooding, whereas soil moisture content and salinity were not affected by RIM. Labile organic nitrogen increased only in the RIM impoundment, irrespective of the habitat type. PNA was generally not affected with time, except in the dwarf habitat in the absence of intentional summer flooding where it increased. Changes in the non-managed impoundment adjacent to the RIM impoundment demonstrate the importance of groundwater exchange in linked ecosystems. The consequences of interventions in the management of mangrove impoundments and adjacent forests for the nitrogen budget are discussed.}, }
@article {pmid38271645, year = {2024}, author = {De Bondt, Y and Verdonck, C and Brandt, MJ and De Vuyst, L and Gänzle, MG and Gobbetti, M and Zannini, E and Courtin, CM}, title = {Wheat Sourdough Breadmaking: A Scoping Review.}, journal = {Annual review of food science and technology}, volume = {15}, number = {1}, pages = {265-282}, doi = {10.1146/annurev-food-110923-034834}, pmid = {38271645}, issn = {1941-1421}, mesh = {*Bread/microbiology ; *Fermentation ; *Triticum ; Food Handling ; Humans ; Food Microbiology ; Taste ; Nutritive Value ; }, abstract = {Using sourdough in breadmaking can enhance bread's shelf-life and flavor compared to exclusive baker's yeast use and is believed to increase its nutritional quality and healthiness. Previous research established insight into the microbial ecology of sourdough, but the link between leavening agent use, processing, and bread quality remains elusive. However, such knowledge is key for standardization, research on the health benefits, and the definition of sourdough bread. In this systematic scoping review, we analyzed 253 studies and identified large variations in the type and amount of leavening agent, fermentation conditions, and bread quality (specific loaf volume and acidification). The interrelation between these elements and their effect on the extent of fermentation is discussed, together with issues preventing proper comparison of breadmaking procedures. With this review, we want to contribute to the dialogue concerning the definition of sourdough-type bread products and the research into the health benefits attributed to them.}, }
@article {pmid38267517, year = {2024}, author = {Acuña, JJ and Rilling, JI and Inostroza, NG and Zhang, Q and Wick, LY and Sessitsch, A and Jorquera, MA}, title = {Variovorax sp. strain P1R9 applied individually or as part of bacterial consortia enhances wheat germination under salt stress conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2070}, pmid = {38267517}, issn = {2045-2322}, support = {1221228//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1201386//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Triticum ; Salt Stress ; Plant Development ; Salt Tolerance ; *Comamonadaceae ; *Magnesium ; *Radioisotopes ; }, abstract = {Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized as both halotolerant auxin producers (2-51 mg L[-1]) and 1-aminocyclopropane-1-carboxylate (ACC)-degrading bacteria (15-28 µmol αKB mg protein[-1] h[-1]). The most efficient isolates were tested as single strains, in dual and triple consortia, or in combination with previously reported PGP rhizobacteria (Klebsiella sp. 27IJA and 8LJA) for their impact on the germination of salt-exposed (0.15 M and 0.25 M NaCl) wheat seeds. Interestingly, strain P1R9, identified as Variovorax sp., enhanced wheat germination under salt stress conditions when applied individually or as part of bacterial consortia. Under salt stress, plants inoculated with dual consortia containing the strain Variovorax sp. P1R9 showed higher biomass (41%) and reduced lipid peroxidation (33-56%) than uninoculated plants. Although the underlying mechanisms remain elusive, our data suggest that the application of Variovorax sp. P1R9, alone or as a member of PGP consortia, may improve the salt stress tolerance of wheat plants.}, }
@article {pmid38265481, year = {2024}, author = {He, B and Li, Q and Zou, S and Bai, X and Li, W and Chen, Y}, title = {Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {36}, pmid = {38265481}, issn = {1432-184X}, support = {Qiankehe Jichu-ZK [2021] 231//the Project of Guizhou Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bkhzdzx [2021]1//Bijie Science and Technology Major Project/ ; Bikelianhezi Guigongcheng [2021] 8//the Opening Fund for Guizhou Province Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands/ ; [2022]096//the Technology Top Talent Project in Department of Education of Guizhou Province/ ; Qianjiaohe KY [2022]120 and 123//the Support Plan for Young Science and Technology talents of Guizhou Province Education Department/ ; }, mesh = {*Microbiota ; *Mycobiome ; China ; *Pinus ; Soil ; }, abstract = {Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the "space instead of time" approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.}, }
@article {pmid38261090, year = {2024}, author = {Deschamps, C and Denis, S and Humbert, D and Priymenko, N and Chalancon, S and De Bodt, J and Van de Wiele, T and Ipharraguerre, I and Alvarez-Acero, I and Achard, C and Apper, E and Blanquet-Diot, S}, title = {Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {166}, pmid = {38261090}, issn = {1432-0614}, mesh = {Dogs ; Animals ; *Ecosystem ; Colon ; *Actinobacteria ; Ammonia ; Anaerobiosis ; }, abstract = {Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.}, }
@article {pmid38261068, year = {2024}, author = {Pei, P and Aslam, M and Wang, H and Ye, P and Li, T and Liang, H and Lin, Q and Chen, W and Du, H}, title = {Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {35}, pmid = {38261068}, issn = {1432-184X}, support = {2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 41976125//the National Natural Science Foundation of China/ ; 42206116//the Natural Science Foundation of China grants/ ; 2022KCXTD008//the Program for University Innovation Team of Guangdong Province/ ; 2018KCXTD012//the Team Project of Department of Education of Guangdong Province/ ; }, mesh = {*Urease ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Seaweed ; Nitrogen ; Urea ; }, abstract = {Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ[15]N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ[15]N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ[15]N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.}, }
@article {pmid38261023, year = {2024}, author = {Herren, P and Dunn, AM and Meyling, NV and Savio, C and Hesketh, H}, title = {Effect of CO2 Concentrations on Entomopathogen Fitness and Insect-Pathogen Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {34}, pmid = {38261023}, issn = {1432-184X}, support = {859850//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; *Carbon Dioxide ; Insecta ; Larva ; *Bacillus thuringiensis ; Biological Control Agents ; }, abstract = {Numerous insect species and their associated microbial pathogens are exposed to elevated CO2 concentrations in both artificial and natural environments. However, the impacts of elevated CO2 on the fitness of these pathogens and the susceptibility of insects to pathogen infections are not well understood. The yellow mealworm, Tenebrio molitor, is commonly produced for food and feed purposes in mass-rearing systems, which increases risk of pathogen infections. Additionally, entomopathogens are used to control T. molitor, which is also a pest of stored grains. It is therefore important to understand how elevated CO2 may affect both the pathogen directly and impact on host-pathogen interactions. We demonstrate that elevated CO2 concentrations reduced the viability and persistence of the spores of the bacterial pathogen Bacillus thuringiensis. In contrast, conidia of the fungal pathogen Metarhizium brunneum germinated faster under elevated CO2. Pre-exposure of the two pathogens to elevated CO2 prior to host infection did not affect the survival probability of T. molitor larvae. However, larvae reared at elevated CO2 concentrations were less susceptible to both pathogens compared to larvae reared at ambient CO2 concentrations. Our findings indicate that whilst elevated CO2 concentrations may be beneficial in reducing host susceptibility in mass-rearing systems, they may potentially reduce the efficacy of the tested entomopathogens when used as biological control agents of T. molitor larvae. We conclude that CO2 concentrations should be carefully selected and monitored as an additional environmental factor in laboratory experiments investigating insect-pathogen interactions.}, }
@article {pmid38260895, year = {2023}, author = {Tan, H and Du, XH and Bonito, G and Masaphy, S}, title = {Editorial: Morels: physiology, genetics, and interactions with the environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1352719}, pmid = {38260895}, issn = {1664-302X}, }
@article {pmid38260330, year = {2024}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {A toxic environment selects for specialist microbiome in poison frogs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38260330}, issn = {2692-8205}, support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; }, abstract = {Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.}, }
@article {pmid38259105, year = {2024}, author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR}, title = {Disturbance-diversity relationships of microbial communities change based on growth substrate.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0088723}, pmid = {38259105}, issn = {2379-5077}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria ; Cellulose ; Glucose ; }, abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95-7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity-disturbance relationships observed in microbial systems.IMPORTANCEA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community's response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.}, }
@article {pmid38259093, year = {2024}, author = {Fadum, JM and Borton, MA and Daly, RA and Wrighton, KC and Hall, EK}, title = {Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0105923}, pmid = {38259093}, issn = {2379-5077}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Ecosystem ; Nitrates/analysis ; Lakes/chemistry ; Organic Chemicals ; *Ammonium Compounds ; Water ; Nitrogen ; }, abstract = {Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.}, }
@article {pmid38256774, year = {2024}, author = {Reyes-Ardila, WL and Rugeles-Silva, PA and Duque-Zapata, JD and Vélez-Martínez, GA and Tarazona Pulido, L and Cardona Tobar, KM and Díaz Gallo, SA and Muñoz Flórez, JE and Díaz-Ariza, LA and López-Alvarez, D}, title = {Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38256774}, issn = {2223-7747}, support = {FP44842-221-2018//Pontificia Universidad Javeriana/ ; FP44842-221-2018//Ministry of Science, Technology, and Innovation, the Ministry of National Education/ ; FP44842-221-2018//Ministry of Industry, Commerce and Tourism/ ; FP44842-221-2018//ICETEX/ ; FP44842-221-2018//Ministry of National Education/ ; }, abstract = {Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.}, }
@article {pmid38254227, year = {2024}, author = {Gul, F and Herrema, H and Davids, M and Keating, C and Nasir, A and Ijaz, UZ and Javed, S}, title = {Gut microbial ecology and exposome of a healthy Pakistani cohort.}, journal = {Gut pathogens}, volume = {16}, number = {1}, pages = {5}, pmid = {38254227}, issn = {1757-4749}, support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC).<br><br>METHODS: 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment.<br><br>RESULTS: A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history.<br><br>CONCLUSIONS: This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.}, }
@article {pmid38253620, year = {2024}, author = {Zeng, J and Xie, C and Huang, Z and Cho, CH and Chan, H and Li, Q and Ashktorab, H and Smoot, DT and Wong, SH and Yu, J and Gong, W and Liang, C and Xu, H and Chen, H and Liu, X and Wu, JCY and Ip, M and Gin, T and Zhang, L and Chan, MTV and Hu, W and Wu, WKK}, title = {LOX-1 acts as an N[6]-methyladenosine-regulated receptor for Helicobacter pylori by binding to the bacterial catalase.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {669}, pmid = {38253620}, issn = {2041-1723}, mesh = {Animals ; Humans ; Mice ; *Adenosine/analogs &amp; derivatives ; Catalase/metabolism ; *Helicobacter Infections/metabolism ; *Helicobacter pylori/metabolism ; RNA, Messenger/genetics ; *Scavenger Receptors, Class E/genetics ; }, abstract = {The role of N[6]-methyladenosine (m[6]A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulates host m[6]A methylases and increases m[6]A levels in gastric epithelial cells. Reducing m[6]A methylase activity via hemizygotic deletion of methylase-encoding gene Mettl3 in mice, or via small interfering RNAs targeting m[6]A methylases, enhances H. pylori colonization. We identify LOX-1 mRNA as a key m[6]A-regulated target during H. pylori infection. m[6]A modification destabilizes LOX-1 mRNA and reduces LOX-1 protein levels. LOX-1 acts as a membrane receptor for H. pylori catalase and contributes to bacterial adhesion. Pharmacological inhibition of LOX-1, or genetic ablation of Lox-1, reduces H. pylori colonization. Moreover, deletion of the bacterial catalase gene decreases adhesion of H. pylori to human gastric sections. Our results indicate that m[6]A modification of host LOX-1 mRNA contributes to protection against H. pylori infection by downregulating LOX-1 and thus reducing H. pylori adhesion.}, }
@article {pmid38251984, year = {2024}, author = {Shoemaker, WR and Grilli, J}, title = {Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38251984}, issn = {2050-084X}, support = {2010885//National Science Foundation/ ; }, mesh = {Logistic Models ; Phylogeny ; *Biological Evolution ; Biodiversity ; *Microbiota ; }, abstract = {The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.}, }
@article {pmid38251877, year = {2024}, author = {Schloss, PD}, title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.}, journal = {mSphere}, volume = {9}, number = {2}, pages = {e0035423}, pmid = {38251877}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.<br><br>IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.}, }
@article {pmid38248928, year = {2023}, author = {Masigol, H and Retter, A and Pourmoghaddam, MJ and Amini, H and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Kimiaei, M and Grossart, HP}, title = {Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {38248928}, issn = {2309-608X}, support = {DFG GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.}, }
@article {pmid38248338, year = {2024}, author = {Kirby, TO and Sapp, PA and Townsend, JR and Govaert, M and Duysburgh, C and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®] Induces a Favorable Impact on Gut Microbial Structure and Functionality in the Simulator of Human Intestinal Microbial Ecosystem[®] Model.}, journal = {Current issues in molecular biology}, volume = {46}, number = {1}, pages = {557-569}, pmid = {38248338}, issn = {1467-3045}, support = {N/A//Athletic Greens International/ ; }, abstract = {Modulation of the human gut microbiome has become an area of interest in the nutraceutical space. We explored the effect of the novel foundational nutrition supplement AG1[®] on the composition of human microbiota in an in vitro experimental design. Employing the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]) model, AG1[®] underwent digestion, absorption, and subsequent colonic microenvironment simulation under physiologically relevant conditions in healthy human fecal inocula. Following 48 h of colonic simulation, the gut microbiota were described using shallow shotgun, whole genome sequencing. Metagenomic data were used to describe changes in community structure (alpha diversity, beta diversity, and changes in specific taxa) and community function (functional heterogeneity and changes in specific bacterial metabolic pathways). Results showed no significant change in alpha diversity, but a significant effect of treatment and donor and an interaction between the treatment and donor effect on structural heterogeneity likely stemming from the differential enrichment of eight bacterial taxa. Similar findings were observed for community functional heterogeneity likely stemming from the enrichment of 20 metabolic pathways characterized in the gene ontology term database. It is logical to conclude that an acute dose of AG1 has significant effects on gut microbial composition that may translate into favorable effects in humans.}, }
@article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; }, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, }
@article {pmid38244618, year = {2024}, author = {Yalçın, G and Yıldız, D and Calderó-Pascual, M and Yetim, S and Şahin, Y and Parakatselaki, ME and Avcı, F and Karakaya, N and Ladoukakis, ED and Berger, SA and Ger, KA and Jeppesen, E and Beklioğlu, M}, title = {Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170140}, doi = {10.1016/j.scitotenv.2024.170140}, pmid = {38244618}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; *Lakes/microbiology ; Dissolved Organic Matter ; Bacteria ; Biomass ; Plankton ; }, abstract = {Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.}, }
@article {pmid38244196, year = {2024}, author = {Truter, M and Koopman, JE and Jordaan, K and Tsamkxao, LO and Cowan, DA and Underdown, SJ and Ramond, JB and Rifkin, RF}, title = {Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome.}, journal = {Cell reports}, volume = {43}, number = {2}, pages = {113690}, doi = {10.1016/j.celrep.2024.113690}, pmid = {38244196}, issn = {2211-1247}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Prevotella ; *Saccharomycetales ; }, abstract = {We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.}, }
@article {pmid38244160, year = {2024}, author = {Wang, N and Wang, Q and Song, S and Sun, Z and Zhao, A and Ali, A and Xu, G and Zhong, X and Wang, F and Xu, H}, title = {Microplastics drive community dynamics of periphytic protozoan fauna in marine environments.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {9}, pages = {13327-13334}, pmid = {38244160}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//the Youth Project of the Natural Science Foundation of Shandong Province, China/ ; }, mesh = {Ecosystem ; Biodiversity ; Environmental Monitoring ; Microplastics ; Plastics ; *Ciliophora/physiology ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The pollution of microplastics (MPs) to the marine environment has become a widespread focus of attention. To assess MP-induced ecotoxicity on marine ecosystems, periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1]. Protozoan samples were collected using microscope slides from coastal waters of the Yellow Sea, northern China. A total of 13 protozoan species were identified and represented different tolerance to MP-induced ecotoxicity. Inhibition effects of MPs on the test protozoan communities were clearly shown in terms of both the species richness and individual abundance and followed linear relationships to MP concentrations. The community patterns were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. Our findings demonstrated that MPs may induce the community-level ecotoxic response of periphytic protozoan fauna and followed significant community dynamics. Thus, it is suggested that periphytic protozoan fauna may be used as useful community-based test model organisms for evaluating MP-induced ecotoxicity in marine environments.}, }
@article {pmid38243487, year = {2023}, author = {Saintillan, D}, title = {Dispersion of run-and-tumble microswimmers through disordered media.}, journal = {Physical review. E}, volume = {108}, number = {6-1}, pages = {064608}, doi = {10.1103/PhysRevE.108.064608}, pmid = {38243487}, issn = {2470-0053}, abstract = {Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.}, }
@article {pmid38241807, year = {2024}, author = {Wang, D and Han, I and McCullough, K and Klaus, S and Lee, J and Srinivasan, V and Li, G and Wang, ZL and Bott, CB and McQuarrie, J and Stinson, BM and deBarbadillo, C and Dombrowski, P and Barnard, J and Gu, AZ}, title = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) enables effective phosphorus removal in a pilot-scale A-B stage shortcut nitrogen removal system for mainstream municipal wastewater treatment.}, journal = {Water research}, volume = {251}, number = {}, pages = {121050}, doi = {10.1016/j.watres.2023.121050}, pmid = {38241807}, issn = {1879-2448}, mesh = {*Sewage ; Denitrification ; Phosphorus/metabolism ; Rivers ; Nitrogen ; RNA, Ribosomal, 16S ; Phylogeny ; Nitrites ; Pilot Projects ; Bioreactors ; *Water Purification/methods ; Polyphosphates/metabolism ; Carbon ; }, abstract = {While the adsorption/bio-oxidation (A/B) process has been widely studied for carbon capture and shortcut nitrogen (N) removal, its integration with enhanced biological phosphorus (P) removal (EBPR) has been considered challenging and thus unexplored. Here, full-scale pilot testing with an integrated system combining A-stage high-rate activated sludge with B-stage partial (de)nitrification/anammox and side-stream EBPR (HRAS-P(D)N/A-S2EBPR) was conducted treating real municipal wastewater. The results demonstrated that, despite the relatively low influent carbon load, the B-stage P(D)N-S2EBPR system could achieve effective P removal performance, with the carbon supplement and redirection of the A-stage sludge fermentate to the S2EBPR. The novel process configuration design enabled a system shift in carbon flux and distribution for efficient EBPR, and provided unique selective factors for ecological niche partitioning among different key functionally relevant microorganisms including polyphosphate accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). The combined nitrite from B-stage to S2EBPR and aerobic-anoxic conditions in our HRAS-P(D)N/A-S2EBPR system promoted DPAOs for simultaneous internal carbon-driven denitrification via nitrite and P removal. 16S rRNA gene-based oligotyping analysis revealed high phylogenetic microdiversity within the Accumulibacter population and discovered coexistence of certain oligotypes of Accumulibacter and Competibacter correlated with efficient P removal. Single-cell Raman micro-spectroscopy-based phenotypic profiling showed high phenotypic microdiversity in the active PAO community and the involvement of unidentified PAOs and internal carbon-accumulating organisms that potentially played an important role in system performance. This is the first pilot study to demonstrate that the P(D)N-S2EBPR system could achieve shortcut N removal and influent carbon-independent EBPR simultaneously, and the results provided insights into the effects of incorporating S2EBPR into A/B process on metabolic activities, microbial ecology, and resulted system performance.}, }
@article {pmid38236289, year = {2024}, author = {Bergman, I and Lindström, ES and Sassenhagen, I}, title = {Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {33}, pmid = {38236289}, issn = {1432-184X}, support = {146-300-188//Olle Engkvists Stiftelse/ ; 146-300-188//Olle Engkvists Stiftelse/ ; }, mesh = {Ecosystem ; *Microalgae ; Semen ; Carbon ; *Ciliophora ; Lakes ; }, abstract = {The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.}, }
@article {pmid38236100, year = {2023}, author = {Singh, A and Sharma, P and Singh, A and Agarwal, C and Patel M, G and Ganapathy, K}, title = {RELEVANCE FOR DIAGNOSIS, THERAPY, AND STRATEGIES OF GUT MICROBES DYSBIOSIS IN CHRONIC KIDNEY DISEASE: A SYSTEMATIC REVIEW.}, journal = {Georgian medical news}, volume = {}, number = {344}, pages = {57-63}, pmid = {38236100}, issn = {1512-0112}, mesh = {Humans ; Animals ; Rats ; Dysbiosis/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Inflammation ; *Renal Insufficiency, Chronic/complications/diagnosis/therapy ; }, abstract = {Dysbiosis and weakened gastrointestinal barrier function have been identified as potential regulators of Chronic Kidney Disease (CKD). The complex connection among gut micro biota and CKD is provided in this study, with particular attention to how inflammation contributes to the CKD path physiology. It establishes the inverse association between CKD and gut microbial dysbiosis by exploring the collision of CKD about the organization and capabilities of the gut micro biota. The possibility of new diagnostic tools in measuring the dynamic changes within the gut microbial ecology illustrates the importance of accurately diagnosing gut micro biota abnormalities in CKD. Additionally, the study explores the targeted medicines that focus on gut micro biota in CKD. Using data from both human clinical trials and rat models, the study demonstrates the variety of therapeutic approaches and their ability to limit the rate of development of CKD and its accompanying problems. The study we performed was based on the Preferred Reporting Items for Systematic reviews and Meta Analyses (PRISMA) approach. The findings show the significance of investigating the relationship between gut micro biota and CKD, paving up the possibility for new therapeutic strategies to improve the patient outcomes and quality of life. The present understanding of CKD-induced modifications to the gut micro biota and the ensuing effects on gastrointestinal health, emphasizing studies, will be highlighted in this review.}, }
@article {pmid38236032, year = {2024}, author = {Hozalski, RM and Zhao, X and Kim, T and LaPara, TM}, title = {On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0165823}, pmid = {38236032}, issn = {1098-5336}, support = {M.L. 2018 Chp. 214 Art. 4 Sec. 02 Subd. 04f//Minnesota Environment and Natural Resources Trust Fund (ENRTF)/ ; }, mesh = {*Drinking Water/microbiology ; *Legionella pneumophila ; Propidium/*analogs &amp; derivatives ; *Mycobacterium/genetics ; Water Microbiology ; Water Supply ; *Legionella/genetics ; *Azides ; }, abstract = {In this study, we compared conventional vacuum filtration of small volumes through disc membranes (effective sample volumes for potable water: 0.3-1.0 L) with filtration of high volumes using ultrafiltration (UF) modules (effective sample volumes for potable water: 10.6-84.5 L) for collecting bacterial biomass from raw, finished, and tap water at seven drinking water systems. Total bacteria, Legionella spp., Legionella pneumophila, Mycobacterium spp., and Mycobacterium avium complex in these samples were enumerated using both conventional quantitative PCR (qPCR) and viability qPCR (using propidium monoazide). In addition, PCR-amplified gene fragments were sequenced for microbial community analysis. The frequency of detection (FOD) of Legionella spp. in finished and tap water samples was much greater using UF modules (83% and 77%, respectively) than disc filters (24% and 33%, respectively). The FODs for Mycobacterium spp. in raw, finished, and tap water samples were also consistently greater using UF modules than disc filters. Furthermore, the number of observed operational taxonomic units and diversity index values for finished and tap water samples were often substantially greater when using UF modules as compared to disc filters. Conventional and viability qPCR yielded similar results, suggesting that membrane-compromised cells represented a minor fraction of total bacterial biomass. In conclusion, our research demonstrates that large-volume filtration using UF modules improved the detection of opportunistic pathogens at the low concentrations typically found in public drinking water systems and that the majority of bacteria in these systems appear to be viable in spite of disinfection with free chlorine and/or chloramine.IMPORTANCEOpportunistic pathogens, such as Legionella pneumophila, are a growing public health concern. In this study, we compared sample collection and enumeration methods on raw, finished, and tap water at seven water systems throughout the State of Minnesota, USA. The results showed that on-site filtration of large water volumes (i.e., 500-1,000 L) using ultrafiltration membrane modules improved the frequency of detection of relatively rare organisms, including opportunistic pathogens, compared to the common approach of filtering about 1 L using disc membranes. Furthermore, results from viability quantitative PCR (qPCR) with propidium monoazide were similar to conventional qPCR, suggesting that membrane-compromised cells represent an insignificant fraction of microorganisms. Results from these ultrafiltration membrane modules should lead to a better understanding of the microbial ecology of drinking water distribution systems and their potential to inoculate premise plumbing systems with opportunistic pathogens where conditions are more favorable for their growth.}, }
@article {pmid38235197, year = {2023}, author = {Meesters, C and Weldegergis, BT and Dicke, M and Jacquemyn, H and Lievens, B}, title = {Limited effects of plant-beneficial fungi on plant volatile composition and host-choice behavior of Nesidiocoris tenuis.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1322719}, pmid = {38235197}, issn = {1664-462X}, abstract = {Biological control using plant-beneficial fungi has gained considerable interest as a sustainable method for pest management, by priming the plant for enhanced defense against pathogens and insect herbivores. However, despite promising outcomes, little is known about how different fungal strains mediate these beneficial effects. In this study, we evaluated whether inoculation of tomato seeds with the plant-beneficial fungi Beauveria bassiana ARSEF 3097, Metarhizium brunneum ARSEF 1095 and Trichoderma harzianum T22 affected the plant's volatile organic compound (VOC) profile and the host-choice behavior of Nesidiocoris tenuis, an emerging pest species in NW-European tomato cultivation, and the related zoophytophagous biocontrol agent Macrolophus pygmaeus. Results indicated that fungal inoculation did not significantly alter the VOC composition of tomato plants. However, in a two-choice cage assay where female insects were given the option to select between control plants and fungus-inoculated plants, N. tenuis preferred control plants over M. brunneum-inoculated plants. Nearly 72% of all N. tenuis individuals tested chose the control treatment. In all other combinations tested, no significant differences were found for none of the insects. We conclude that inoculation of tomato with plant-beneficial fungi had limited effects on plant volatile composition and host-choice behavior of insects. However, the observation that N. tenuis was deterred from the crop when inoculated with M. brunneum and attracted to non-inoculated plants may provide new opportunities for future biocontrol based on a push-pull strategy.}, }
@article {pmid38234383, year = {2022}, author = {Tan, YP and Bishop-Hurley, SL and Shivas, RG and Cowan, DA and Maggs-Kölling, G and Maharachchikumbura, SSN and Pinruan, U and Bransgrove, KL and De la Peña-Lastra, S and Larsson, E and Lebel, T and Mahadevakumar, S and Mateos, A and Osieck, ER and Rigueiro-Rodríguez, A and Sommai, S and Ajithkumar, K and Akulov, A and Anderson, FE and Arenas, F and Balashov, S and Bañares, &#xc1; and Berger, DK and Bianchinotti, MV and Bien, S and Bilański, P and Boxshall, AG and Bradshaw, M and Broadbridge, J and Calaça, FJS and Campos-Quiroz, C and Carrasco-Fernández, J and Castro, JF and Chaimongkol, S and Chandranayaka, S and Chen, Y and Comben, D and Dearnaley, JDW and Ferreira-Sá, AS and Dhileepan, K and Díaz, ML and Divakar, PK and Xavier-Santos, S and Fernández-Bravo, A and Gené, J and Guard, FE and Guerra, M and Gunaseelan, S and Houbraken, J and Janik-Superson, K and Jankowiak, R and Jeppson, M and Jurjević, &#x17d; and Kaliyaperumal, M and Kelly, LA and Kezo, K and Khalid, AN and Khamsuntorn, P and Kidanemariam, D and Kiran, M and Lacey, E and Langer, GJ and López-Llorca, LV and Luangsa-Ard, JJ and Lueangjaroenkit, P and Lumbsch, HT and Maciá-Vicente, JG and Mamatha Bhanu, LS and Marney, TS and Marqués-Gálvez, JE and Morte, A and Naseer, A and Navarro-Ródenas, A and Oyedele, O and Peters, S and Piskorski, S and Quijada, L and Ramírez, GH and Raja, K and Razzaq, A and Rico, VJ and Rodríguez, A and Ruszkiewicz-Michalska, M and Sánchez, RM and Santelices, C and Savitha, AS and Serrano, M and Leonardo-Silva, L and Solheim, H and Somrithipol, S and Sreenivasa, MY and Stępniewska, H and Strapagiel, D and Taylor, T and Torres-Garcia, D and Vauras, J and Villarreal, M and Visagie, CM and Wołkowycki, M and Yingkunchao, W and Zapora, E and Groenewald, JZ and Crous, PW}, title = {Fungal Planet description sheets: 1436-1477.}, journal = {Persoonia}, volume = {49}, number = {}, pages = {261-350}, pmid = {38234383}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilaxglyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareus soils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes. Citation: Tan YP, Bishop-Hurley SL, Shivas RG, et al. 2022. Fungal Planet description sheets: 1436-1477. Persoonia 49: 261-350. https://doi.org/10.3767/persoonia.2022.49.08.}, }
@article {pmid38232435, year = {2024}, author = {Cagri Ozturk, R and Feyzioglu, AM and Capkin, E and Yildiz, I and Altinok, I}, title = {Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea.}, journal = {Marine environmental research}, volume = {195}, number = {}, pages = {106344}, doi = {10.1016/j.marenvres.2024.106344}, pmid = {38232435}, issn = {1879-0291}, mesh = {*Seawater/chemistry ; RNA, Ribosomal, 16S/genetics ; Black Sea ; Bacteria/genetics ; *Microbiota ; Water ; }, abstract = {The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.}, }
@article {pmid38229613, year = {2023}, author = {Pavan, S and Gorthi, SP and Prabhu, AN and Das, B and Mutreja, A and Vasudevan, K and Shetty, V and Ramamurthy, T and Ballal, M}, title = {Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India.}, journal = {Annals of Indian Academy of Neurology}, volume = {26}, number = {6}, pages = {908-916}, pmid = {38229613}, issn = {0972-2327}, abstract = {OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson's disease (PD). We sequenced microbial DNA using fecal samples collected from PD cases and healthy controls (HCs) to evaluate the role of gut microbiota.<br><br>METHODS: Full-length bacterial 16S rRNA gene sequencing of fecal samples was performed using amplified polymerase chain reaction (PCR) products on the GridION Nanopore sequencer. Sequenced data were analyzed using web-based tools BugSeq and MicrobiomeAnalyst.<br><br>RESULTS: We found that certain bacterial families like Clostridia UCG 014, Cristensenellaceae, and Oscillospiraceae are higher in abundance, and Lachinospiracea, Coriobacteriaceae and genera associated with short-chain fatty acid production, Faecalibacterium, Fusicatenibacter, Roseburia and Blautia, are lower in abundance among PD cases when compared with the HC. Genus Akkermansia, Dialister, Bacteroides, and Lachnospiraceae NK4A136 group positively correlated with constipation in PD.<br><br>CONCLUSION: Observations from this study support the other global research on the PD gut microbiome background and provide fresh insight into the gut microbial composition of PD patients from a south Indian population. We report a higher abundance of Clostridia UCG 014 group, previously not linked to PD.}, }
@article {pmid38228918, year = {2024}, author = {Alonso, A and Boyero, L and Solla, A and Ferreira, V}, title = {Dieback and Replacement of Riparian Trees May Impact Stream Ecosystem Functioning.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {32}, pmid = {38228918}, issn = {1432-184X}, mesh = {*Ecosystem ; Trees ; Rivers/microbiology ; Biomass ; Nitrogen ; Plant Leaves/microbiology ; *Alnus/microbiology ; }, abstract = {Alders are nitrogen (N)-fixing riparian trees that promote leaf litter decomposition in streams through their high-nutrient leaf litter inputs. While alders are widespread across Europe, their populations are at risk due to infection by the oomycete Phytophthora ×alni, which causes alder dieback. Moreover, alder death opens a space for the establishment of an aggressive N-fixing invasive species, the black locust (Robinia pseudoacacia). Shifts from riparian vegetation containing healthy to infected alder and, eventually, alder loss and replacement with black locust may alter the key process of leaf litter decomposition and associated microbial decomposer assemblages. We examined this question in a microcosm experiment comparing three types of leaf litter mixtures: one representing an original riparian forest composed of healthy alder (Alnus lusitanica), ash (Fraxinus angustifolia), and poplar (Populus nigra); one with the same species composition where alder had been infected by P. ×alni; and one where alder had been replaced with black locust. The experiment lasted six weeks, and every two weeks, microbially driven decomposition, fungal biomass, reproduction, and assemblage structure were measured. Decomposition was highest in mixtures with infected alder and lowest in mixtures with black locust, reflecting differences in leaf nutrient concentrations. Mixtures with alder showed distinct fungal assemblages and higher sporulation rates than mixtures with black locust. Our results indicate that alder loss and its replacement with black locust may alter key stream ecosystem processes and assemblages, with important changes already occurring during alder infection. This highlights the importance of maintaining heathy riparian forests to preserve proper stream ecosystem functioning.}, }
@article {pmid38228915, year = {2024}, author = {Iqbal, Z and Ahmad, M and Raza, MA and Hilger, T and Rasche, F}, title = {Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {31}, pmid = {38228915}, issn = {1432-184X}, mesh = {*Phosphates ; Triticum/microbiology ; *Bacillus ; Soil ; Phosphorus ; Bacillus subtilis ; Soil Microbiology ; }, abstract = {Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya's broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL[-1] solubilization in vitro. All strains produced organic acids in Pikovskaya's broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g[-1] dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g[-1] dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.}, }
@article {pmid38225668, year = {2024}, author = {Terzin, M and Laffy, PW and Robbins, S and Yeoh, YK and Frade, PR and Glasl, B and Webster, NS and Bourne, DG}, title = {The road forward to incorporate seawater microbes in predictive reef monitoring.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {5}, pmid = {38225668}, issn = {2524-6372}, abstract = {Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g. elevated temperature, nutrient loads and macroalgae cover). Through positive feedback mechanisms, disturbance-triggered heterotrophic activity of seawater microbes is hypothesised to drive keystone benthic organisms towards the limit of their resilience and translate into shifts in biogeochemical cycles which influence marine food webs, ultimately affecting entire reef ecosystems. However, despite nearly two decades of work in this space, a major limitation to using seawater microbes in reef monitoring is a lack of a unified and focused approach that would move beyond the indicator discovery phase and towards the development of rapid microbial indicator assays for (near) real-time reef management and decision-making. By reviewing the current state of knowledge, we provide a comprehensive framework (defined as five phases of research and innovation) to catalyse a shift from fundamental to applied research, allowing us to move from descriptive to predictive reef monitoring, and from reactive to proactive reef management.}, }
@article {pmid38224372, year = {2024}, author = {Syiemiong, D and Rabha, J}, title = {Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds.}, journal = {Archives of microbiology}, volume = {206}, number = {2}, pages = {64}, pmid = {38224372}, issn = {1432-072X}, mesh = {*Actinobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Actinomycetales ; *Nocardia ; }, abstract = {Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.}, }
@article {pmid38223759, year = {2024}, author = {Liu, B and Lee, CW and Bong, CW and Wang, AJ}, title = {Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16556}, pmid = {38223759}, issn = {2167-8359}, mesh = {*Escherichia coli ; *Lakes/microbiology ; Water Microbiology ; Water Quality ; Ecosystem ; }, abstract = {BACKGROUND: Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.<br><br>METHODS: This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.<br><br>RESULTS: The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g[-1], and was about one order higher than in the water column (1 to 2,300 cfu mL[-1]). The habitat transition rates ranged from 0.03 to 0.41 h[-1]. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h[-1]. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.<br><br>DISCUSSION: Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.}, }
@article {pmid38218325, year = {2024}, author = {Eberhardt, N and Santamarina, BG and Enghardt, ML and Rohland, O and Hussain, I and Tannert, A and Thieme, L and Rubio, I and Jürgen Rödel,  and Bettina Löffler,  and Arndt, HD and Bauer, M and Busch, A}, title = {The effects of photoactivated ciprofloxacin and bile acids on biofilms on bile duct catheters.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {4}, pages = {107086}, doi = {10.1016/j.ijantimicag.2024.107086}, pmid = {38218325}, issn = {1872-7913}, mesh = {Humans ; *Ciprofloxacin/pharmacology ; *Bile Acids and Salts/pharmacology ; Pilot Projects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms ; Bile Ducts ; Catheters ; Escherichia coli ; }, abstract = {OBJECTIVES: This study examined the potential of a novel photoactivatable ciprofloxacin to act against bacterial infections and microbiomes related to biliary diseases. It also evaluated treatment by combining the impact of bile acids and antibiotics on biofilms. Innovative strategies were evaluated to address the elusive bile duct microbiome resulting in biofilm-related infections linked to biliary catheters. The healthy biliary system is considered sterile, but bile microbiomes can occur in disease, and these correlate with hepatobiliary diseases. Causes include biofilms that form on internal-external biliary drainage catheters. These biliary catheters were used to noninvasively study the otherwise elusive bile microbiome for a pilot study.<br><br>METHODS: A new photoactivatable antibiotic was tested for efficacy against human-derived pathogenic bacterial isolates - Salmonella enterica and Escherichia coli - and catheter-derived bile duct microbiomes. In addition, the effect of bile acids on the antibiotic treatment of biofilms was quantified using crystal violet staining, confocal laser scanning microscopy, and biofilm image analysis. Two novel approaches for targeting biliary biofilms were tested.<br><br>RESULTS: A photoactivated antibiotic based on ciprofloxacin showed efficacy in preventing biofilm formation and reducing bacterial viability without harming eukaryotic cells. Furthermore, combination treatment of antibiotics with bile acids, such as ursodesoxycholic acid, mildly influenced biofilm biomass but reduced bacterial survival within biofilms.<br><br>CONCLUSION: Bile acids, in addition to their endocrine and paracrine functions, may enhance antibiotic killing of bacterial biofilms compared with antibiotics alone. These approaches hold promise for treating biliary infections such as cholangitis.}, }
@article {pmid38217646, year = {2024}, author = {Blache, A and Achouak, W}, title = {Extraction and Purification of Outer Membrane Vesicles and Their Associated RNAs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2741}, number = {}, pages = {11-24}, pmid = {38217646}, issn = {1940-6029}, mesh = {*Gram-Negative Bacteria/genetics ; Escherichia coli/genetics ; RNA, Bacterial/genetics/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; *Extracellular Vesicles/metabolism ; }, abstract = {Outer membrane vesicles (OMVs), produced by Gram negative-bacteria and sRNAs, are key players in cell-to-cell communication and interactions of bacteria with the environment. OMVs act as information carriers and encapsulate various molecules such as proteins, lipids, metabolites, and RNAs. OMVs and sRNAs play a broad range of functions from pathogenesis to stress resistance, to biofilm formation and both mediate interkingdom signaling. Various studies indicate that there is a mechanism of intercellular communication mediated by OMV-derived bacterial RNAs that is conserved among certain bacterial species. Here we describe methods for the extraction and purification of vesicles produced by Gram-negative bacteria, such as Pseudomonas brassicacearum and Escherichia coli, and address methods for the extraction of OMVs-derived sRNA and techniques for the analysis of sRNAs.}, }
@article {pmid38217094, year = {2024}, author = {Garuglieri, E and Marasco, R and Odobel, C and Chandra, V and Teillet, T and Areias, C and Sánchez-Román, M and Vahrenkamp, V and Daffonchio, D}, title = {Searching for microbial contribution to micritization of shallow marine sediments.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16573}, doi = {10.1111/1462-2920.16573}, pmid = {38217094}, issn = {1462-2920}, support = {OSR#4097//King Abdullah University of Science and Technology/ ; }, mesh = {*Geologic Sediments/chemistry ; Carbonates ; Calcium Carbonate ; *Microbiota ; }, abstract = {Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.}, }
@article {pmid38216372, year = {2024}, author = {Pogoreutz, C and Ziegler, M}, title = {Frenemies on the reef? Resolving the coral-Endozoicomonas association.}, journal = {Trends in microbiology}, volume = {32}, number = {5}, pages = {422-434}, doi = {10.1016/j.tim.2023.11.006}, pmid = {38216372}, issn = {1878-4380}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.}, }
@article {pmid38214516, year = {2024}, author = {Weller, DL and Murphy, CM and Love, TMT and Danyluk, MD and Strawn, LK}, title = {Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0183523}, pmid = {38214516}, issn = {1098-5336}, support = {P30 ES001247/ES/NIEHS NIH HHS/United States ; 2019-51181-30016//U.S. Department of Agriculture (USDA)/ ; //VT | Virginia Agricultural Experiment Station, Virginia Polytechnic Institute and State University (VAES)/ ; }, mesh = {*Escherichia coli ; Environmental Microbiology ; Salmonella ; *Listeria ; Food ; Food Microbiology ; Food Safety ; }, abstract = {Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.}, }
@article {pmid38212738, year = {2024}, author = {Varliero, G and Lebre, PH and Adams, B and Chown, SL and Convey, P and Dennis, PG and Fan, D and Ferrari, B and Frey, B and Hogg, ID and Hopkins, DW and Kong, W and Makhalanyane, T and Matcher, G and Newsham, KK and Stevens, MI and Weigh, KV and Cowan, DA}, title = {Biogeographic survey of soil bacterial communities across Antarctica.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {9}, pmid = {38212738}, issn = {2049-2618}, support = {310030_215119/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Humans ; Antarctic Regions ; Phylogeny ; *Soil ; *Cyanobacteria ; Biodiversity ; Soil Microbiology ; }, abstract = {BACKGROUND: Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.<br><br>RESULTS: Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.<br><br>CONCLUSIONS: Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.}, }
@article {pmid38212192, year = {2024}, author = {Ayeni, KI and Berry, D and Ezekiel, CN and Warth, B}, title = {Enhancing microbiome research in sub-Saharan Africa.}, journal = {Trends in microbiology}, volume = {32}, number = {2}, pages = {111-115}, doi = {10.1016/j.tim.2023.11.003}, pmid = {38212192}, issn = {1878-4380}, mesh = {Humans ; Africa South of the Sahara ; *Microbiota ; }, abstract = {While there are lighthouse examples of microbiome research in sub-Saharan Africa (SSA), a significant proportion of local researchers face several challenges. Here, we highlight prevailing issues limiting microbiome research in SSA and suggest potential technological, societal, and research-based solutions. We emphasize the need for considerable investment in infrastructures, training, and appropriate funding to democratize modern technologies with a view to providing useful data to improve human health.}, }
@article {pmid38211751, year = {2024}, author = {Busch, A and Roy, S and Helbing, DL and Colic, L and Opel, N and Besteher, B and Walter, M and Bauer, M and Refisch, A}, title = {Gut microbiome in atypical depression.}, journal = {Journal of affective disorders}, volume = {349}, number = {}, pages = {277-285}, doi = {10.1016/j.jad.2024.01.060}, pmid = {38211751}, issn = {1573-2517}, mesh = {Humans ; Depression ; *Depressive Disorder, Major/diagnosis ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Recent studies showed that immunometabolic dysregulation is related to unipolar major depressive disorder (MDD) and that it more consistently maps to MDD patients endorsing an atypical symptom profile, characterized by energy-related symptoms including increased appetite, weight gain, and hypersomnia. Despite the documented influence of the microbiome on immune regulation and energy homeostasis, studies have not yet investigated microbiome differences among clinical groups in individuals with MDD.<br><br>METHODS: Fifteen MDD patients with atypical features according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5)-5, forty-four MDD patients not fulfilling the DSM-5 criteria for the atypical subtype, and nineteen healthy controls were included in the study. Participants completed detailed clinical assessment and stool samples were collected. Samples were sequenced for the prokaryotic 16S rRNA gene, in the V3-V4 variable regions. Only samples with no antibiotic exposure in the previous 12&#xa0;months and a minimum of >2000 quality-filtered reads were included in the analyses.<br><br>RESULTS: There were no statistically significant differences in alpha- and beta-diversity between the MDD groups and healthy controls. However, within the atypical MDD group, there was an increase in the Verrucomicrobiota phylum, with Akkermansia as the predominant bacterial genus.<br><br>LIMITATIONS: Cross-sectional data, modest sample size, and significantly increased body mass index in the atypical MDD group.<br><br>CONCLUSIONS: There were no overall differences among the investigated groups. However, differences were found at several taxonomic levels. Studies in larger longitudinal samples with relevant confounders are needed to advance the understanding of the microbial influences on the clinical heterogeneity of depression.}, }
@article {pmid38206365, year = {2024}, author = {Reyes-Reyes, EM and Brown, J and Trial, MD and Chinnasamy, D and Wiegand, JP and Bradford, D and Brinton, RD and Rodgers, KE}, title = {Vivaria housing conditions expose sex differences in brain oxidation, microglial activation, and immune system states in aged hAPOE4 mice.}, journal = {Experimental brain research}, volume = {242}, number = {3}, pages = {543-557}, pmid = {38206365}, issn = {1432-1106}, support = {P01 AG026572/AG/NIA NIH HHS/United States ; P30 AG072980/AG/NIA NIH HHS/United States ; R01 AG057931/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; Female ; Male ; Aged ; Infant ; *Apolipoprotein E4/genetics/metabolism ; Microglia/pathology ; *Alzheimer Disease/genetics ; Housing Quality ; Sex Characteristics ; CD8-Positive T-Lymphocytes/metabolism/pathology ; Brain/metabolism ; Immune System/metabolism/pathology ; Mice, Transgenic ; }, abstract = {Apolipoprotein E ε4 allele (APOE4) is the predominant genetic risk factor for late-onset Alzheimer's disease (AD). APOE4 mouse models have provided advances in the understanding of disease pathogenesis, but unaccounted variables like rodent housing status may hinder translational outcomes. Non-sterile aspects like food and bedding can be major sources of changes in rodent microflora. Alterations in intestinal microbial ecology can cause mucosal barrier impairment and increase pro-inflammatory signals. The present study examined the role of sterile and non-sterile food and housing on redox indicators and the immune status of humanized-APOE4 knock-in mice (hAPOe4). hAPOE4 mice were housed under sterile conditions until 22 months of age, followed by the transfer of a cohort of mice to non-sterile housing for 2 months. At 24 months of age, the redox/immunologic status was evaluated by flow cytometry/ELISA. hAPOE4 females housed under non-sterile conditions exhibited: (1) higher neuronal and microglial oxygen radical production and (2) lower CD68[+] microglia (brain) and CD8[+] T cells (periphery) compared to sterile-housed mice. In contrast, hAPOE4 males in non-sterile housing exhibited: (1) higher MHCII[+] microglia and CD11b[+]CD4[+] T cells (brain) and (2) higher CD11b[+]CD4[+] T cells and levels of lipopolysaccharide-binding protein and inflammatory cytokines in the periphery relative to sterile-housed mice. This study demonstrated that sterile vs. non-sterile housing conditions are associated with the activation of redox and immune responses in the brain and periphery in a sex-dependent manner. Therefore, housing status may contribute to variable outcomes in both the brain and periphery.}, }
@article {pmid38202384, year = {2023}, author = {Wang, B and Sun, M and Wang, Y and Yan, T and Li, Y and Wu, X and Wang, Y and Zhuang, W}, title = {Cadmium-Tolerant Bacterium Strain Cdb8-1 Contributed to the Remediation of Cadmium Pollution through Increasing the Growth and Cadmium Uptake of Chinese Milk Vetch (Astragalus sinicus L.) in Cadmium-Polluted Soils.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {38202384}, issn = {2223-7747}, support = {32271916//National Natural Science Foundation of China/ ; JSPKLB202211//Independent Scientific Research Project of Institute of Botany, Jiangsu Province, and Chinese Academy of Sciences/ ; }, abstract = {Cadmium (Cd) pollution has attracted global attention because it not only jeopardizes soil microbial ecology and crop production, but also threatens human health. As of now, microbe-assisted phytoremediation has proven to be a promising approach for the revegetation of Cd-contaminated soil. Therefore, it is important to find such tolerant microorganisms. In the present study, we inoculated a bacteria strain tolerant to Cd, Cdb8-1, to Cd-contaminated soils and then explored the effects of Cdb8-1 inoculation on the performance of the Chinese milk vetch. The results showed plant height, root length, and fresh and dry weight of Chinese milk vetch grown in Cdb8-1-inoculated soils increased compared to the non-inoculated control group. The inoculation of Cd-contaminated soils with Cdb8-1 also enhanced their antioxidant defense system and decreased the H2O2 and malondialdehyde (MDA) contents, which alleviated the phytotoxicity of Cd. The inoculation of Cdb8-1 in Cd-contaminated soils attenuated the contents of total and available Cd in the soil and augmented the BCF and TF of Chinese milk vetch, indicating that the combined application of Cd-tolerant bacteria Cdb8-1 and Chinese milk vetch is a potential solution to Cd-contaminated soils.}, }
@article {pmid38200027, year = {2024}, author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Aarts, R and Tabury, K and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F}, title = {Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity.}, journal = {NPJ microgravity}, volume = {10}, number = {1}, pages = {3}, pmid = {38200027}, issn = {2373-8065}, support = {4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; }, abstract = {Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLife[TM] PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.}, }
@article {pmid38199186, year = {2024}, author = {Truong, D and Changey, F and Rondags, E and Framboisier, X and Etienne, M and Guedon, E}, title = {Evaluation of short-circuited electrodes in combination with dark fermentation for promoting biohydrogen production process.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {157}, number = {}, pages = {108631}, doi = {10.1016/j.bioelechem.2023.108631}, pmid = {38199186}, issn = {1878-562X}, mesh = {Fermentation ; *Manure ; *Bioreactors ; Hydrogen ; Electrodes ; }, abstract = {Short-circuited electrodes, in combination with dark fermentation, were evaluated in a biohydrogen production process. The system is based on an innovative design of a non-compartmented electromicrobial bioreactor with a conductive tubular membrane as cathode and a graphite felt as anode. In particular, the electrode specialization occurred when the bioreactor was inoculated with manure as the whole medium and when a vacuum was applied in the tubular membrane, for allowing continuous extraction of gaseous species (H2, CH4, CO2) from the bioreactor. This specialization of the electrodes as anode and cathode was further confirmed by microbial ecology analysis of biofilms and by cyclic voltammetry measurements. In these experimental conditions, the potential of the electrochemical system (short-circuited electrodes) reached values as low as -320 mV vs. SHE, associated with a significant bioH2 production. Moreover, a higher bioH2 production occurred and a potential of the electrochemical system as low as -429 mV vs SHE was temporarily observed, when additional heat treatments of the whole manure were applied in order to remove methanogen microorganisms (i.e., hydrogen consumers). In the bioreactor, the higher production of bioH2 would be promoted by electrofermentation from the current flow observed between short-circuited anode and cathode.}, }
@article {pmid38193259, year = {2024}, author = {De Paepe, E and Plekhova, V and Vangeenderhuysen, P and Baeck, N and Bullens, D and Claeys, T and De Graeve, M and Kamoen, K and Notebaert, A and Van de Wiele, T and Van Den Broeck, W and Vanlede, K and Van Winckel, M and Vereecke, L and Elliott, C and Cox, E and Vanhaecke, L}, title = {Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow's milk allergy.}, journal = {Allergy}, volume = {79}, number = {4}, pages = {949-963}, doi = {10.1111/all.16005}, pmid = {38193259}, issn = {1398-9995}, support = {//Fonds Wetenschappelijk Onderzoek/ ; //Bijzonder Onderzoeksfonds UGent/ ; }, mesh = {Humans ; Child ; Child, Preschool ; Cattle ; Female ; Mice ; Animals ; *Milk Hypersensitivity ; Dysbiosis ; RNA, Ribosomal, 16S ; *Microbiota ; Inflammation ; Allergens ; Lactoglobulins ; Immunoglobulin E ; Metabolome ; }, abstract = {BACKGROUND: IgE-mediated cow's milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies.<br><br>METHODS: We report a longitudinal in&#xa0;vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n&#x2009;=&#x2009;6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-&#x3b3;) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome-metabolome data from our population of IgE-CMA (n&#x2009;=&#x2009;22) and healthy (n&#x2009;=&#x2009;23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In&#xa0;vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes.<br><br>RESULTS: During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in&#xa0;vitro digestions and multi-omics, which was accompanied by metabolic signatures of low-grade inflammation.<br><br>CONCLUSION: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.}, }
@article {pmid38191744, year = {2024}, author = {Nawata, K and Kadoya, A and Suzuki, S}, title = {Persistence of Marine Bacterial Plasmid in the House Fly (Musca domestica): Marine-Derived Antimicrobial Resistance Genes Have a Chance of Invading the Human Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {30}, pmid = {38191744}, issn = {1432-184X}, support = {KAKENHI 20H00633//Japanese Society of Promotion of Science/ ; Endowed Chair Program//The Sumitomo Electric Industries Group Corporate Social Responsibility Foundation/ ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Houseflies ; Angiotensin Receptor Antagonists ; Escherichia coli/genetics ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Enterobacteriaceae/genetics ; *Anti-Infective Agents ; }, abstract = {The house fly is known to be a vector of antibiotic-resistant bacteria (ARB) in animal farms. It is also possible that the house fly contributes to the spread of ARB and antibiotic resistance genes (ARGs) among various environments. We hypothesized that ARB and ARGs present in marine fish and fishery food may gain access to humans via the house fly. We show herein that pAQU1, a marine bacterial ARG-bearing plasmid, persists in the house fly intestine for 5 days after fly ingestion of marine bacteria. In the case of Escherichia coli bearing the same plasmid, the persistence period exceeded 7 days. This interval is sufficient for transmission to human environments, meaning that the house fly is capable of serving as a vector of marine-derived ARGs. Time course monitoring of the house fly intestinal microflora showed that the initial microflora was occupied abundantly with Enterobacteriaceae. Experimentally ingested bacteria dominated the intestinal environment immediately following ingestion; however, after 72 h, the intestinal microflora recovered to resemble that observed at baseline, when diverse genera of Enterobacteriaceae were seen. Given that pAQU1 in marine bacteria and E. coli were detected in fly excrement (defined here as any combination of feces and regurgitated material) at 7 days post-bacterial ingestion, we hypothesize that the house fly may serve as a vector for transmission of ARGs from marine items and fish to humans via contamination with fly excrement.}, }
@article {pmid38191681, year = {2024}, author = {de Pontes, JS and Oehl, F and Pereira, CD and de Toledo Machado, CT and Coyne, D and da Silva, DKA and Maia, LC}, title = {Heterogeneity in Arbuscular Mycorrhizal Fungi and Plant Communities of the Brazilian Cerrado, Transitional Areas toward the Caatinga, and the Atlantic Forest.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {29}, pmid = {38191681}, issn = {1432-184X}, mesh = {*Mycorrhizae/genetics ; Brazil ; Forests ; Rainforest ; *Microbiota ; Soil ; }, abstract = {The Cerrado is the most diverse tropical savanna worldwide and the second-largest biome in South America. The objective of this study was to understand the heterogeneity and dynamics of arbuscular mycorrhizal fungi (AMF) in different types of natural Cerrado vegetation and areas that are transitioning to dryer savannas or tropical rainforests and to elucidate the driving factors responsible for the differences between these ecosystems. Twenty-one natural sites were investigated, including typical Cerrado forest, typical Caatinga, Atlantic Rainforest, transitions between Cerrado and Caatinga, Cerrado areas near Caatinga or rainforest, and Carrasco sites. Spores were extracted from the soils, counted, and morphologically analyzed. In total, 82 AMF species were detected. AMF species richness varied between 36 and 51, with the highest richness found in the area transitioning between Cerrado and Caatinga, followed by areas of Cerrado close to Caatinga and typical Cerrado forest. The types of Cerrado vegetation and the areas transitioning to the Caatinga shared the highest numbers of AMF species (32-38). Vegetation, along with chemical and physical soil parameters, affected the AMF communities, which may also result from seasonal rainfall patterns. The Cerrado has a great AMF diversity and is, consequently, a natural refuge for AMF. The plant and microbial communities as well as the diversity of habitats require urgent protection within the Cerrado, as it represents a key AMF hotspot.}, }
@article {pmid38190944, year = {2024}, author = {Kim, G and Yang, H and Lee, J and Cho, KS}, title = {Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources.}, journal = {Chemosphere}, volume = {350}, number = {}, pages = {141144}, doi = {10.1016/j.chemosphere.2024.141144}, pmid = {38190944}, issn = {1879-1298}, mesh = {Fermentation ; *Food ; *Refuse Disposal ; Bacteria ; Hydrogen ; Bioreactors ; }, abstract = {This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L[-1] and 117 mL·L[-1]·h[-1]), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L[-1] and 127 mL·L[-1]·h[-1]). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.}, }
@article {pmid38190786, year = {2024}, author = {Zhao, A and Wang, Q and Xu, H and Xu, G}, title = {Effects of continuous warming on homogeneity of periphytic protozoan fauna in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {199}, number = {}, pages = {116017}, doi = {10.1016/j.marpolbul.2023.116017}, pmid = {38190786}, issn = {1879-3363}, mesh = {*Ecosystem ; *Environmental Biomarkers ; Temperature ; }, abstract = {As a powerful biological indicator, multivariate dispersion in a community is widely used to evaluate the biological evaluation of environmental heterogeneity. To investigate the effects of persistent warming on microbial fauna in marine environments, the periphytic protozoan communities were used as test organisms and incubated in five temperature-controlled circulation system at 22 (control), 25, 28, 31 and 34 °C, respectively. The results showed that (1) there was a clear variation in species occurrence, and the α-/γ-diversity measures decreased with the increase of temperatures; (2) the compositional pattern was significantly driven by the persistent warming compared to community pattern from species-abundance data; and (3) both traditional β-diversity and multivariate dispersion measures on species compositional matrix were significantly correlative with changes in the temperature. Therefore, it is suggested that continuous temperature fluctuations have a greater impact on homogeneity of species composition of protozoan communities than that of their community structure.}, }
@article {pmid38187389, year = {2023}, author = {Roland, MM and Peacock, TE and Hall, N and Mohammed, AD and Ball, R and Jolly, A and Alexeev, S and Dopkins, N and Nagarkatti, M and Nagarkatti, P and Kubinak, JL}, title = {B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1253674}, pmid = {38187389}, issn = {1664-3224}, support = {P20 GM103641/GM/NIGMS NIH HHS/United States ; R01 AI155887/AI/NIAID NIH HHS/United States ; R56 AI162986/AI/NIAID NIH HHS/United States ; S10 OD032271/OD/NIH HHS/United States ; }, mesh = {Animals ; Mice ; Antilymphocyte Serum ; B-Lymphocytes ; Homeodomain Proteins/genetics ; *Immunoglobulin A ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Genes, MHC Class II ; }, abstract = {BACKGROUND: The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown.<br><br>METHODS: Here, we developed a novel Rag1 [-/-] adoptive co-transfer model to answer this question. In this model, Rag1 [-/-] mice were reconstituted with na&#xef;ve CD4[+] T cells and either MhcII-sufficient or MhcII-deficient na&#xef;ve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities.<br><br>RESULTS: Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 [-/-] mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities.<br><br>CONCLUSION: Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.}, }
@article {pmid38185942, year = {2024}, author = {Zayed, N and Munjaković, H and Aktan, MK and Simoens, K and Bernaerts, K and Boon, N and Braem, A and Pamuk, F and Saghi, M and Van Holm, W and Fidler, A and Gašperšič, R and Teughels, W}, title = {Electrolyzed Saline Targets Biofilm Periodontal Pathogens In Vitro.}, journal = {Journal of dental research}, volume = {103}, number = {3}, pages = {243-252}, doi = {10.1177/00220345231216660}, pmid = {38185942}, issn = {1544-0591}, mesh = {Humans ; *Interleukin-8 ; Dysbiosis ; Biofilms ; *Anti-Infective Agents ; Inflammation ; }, abstract = {Preventing the development and recurrence of periodontal diseases often includes antimicrobial mouthrinses to control the growth of the periodontal pathogens. Most antimicrobials are nonselective, targeting the symbiotic oral species as well as the dysbiosis-inducing ones. This affects the overall microbial composition and metabolic activity and consequently the host-microbe interactions, which can be detrimental (associated with inflammation) or beneficial (health-associated). Consequently, guiding the antimicrobial effect for modulating the microbial composition to a health-associated one should be considered. For such an approach, this study investigated electrolyzed saline as a novel rinse. Electrolyzed saline was prepared from sterile saline using a portable electrolysis device. Multispecies oral homeostatic and dysbiotic biofilms were grown on hydroxyapatite discs and rinsed daily with electrolyzed saline (EOS). Corresponding positive (NaOCl) and negative (phosphate-buffered saline) controls were included. After 3 rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis (high-performance liquid chromatography) through measuring organic acid content. In addition, human oral keratinocytes (HOKs) were exposed to EOS to test biocompatibility (cytotoxicity and inflammation induction) and also to rinsed biofilms to assess their immunogenicity after rinsing. Rinsing the dysbiotic biofilms with EOS could reduce the counts of the pathobionts (>3 log10 Geq/mm[2] reduction) and avert biofilm dysbiosis (≤1% pathobiont abundance), leading to the dominance of commensal species (≥99%), which altered both biofilm metabolism and interleukin 8 (IL-8) induction in HOKs. EOS had no harmful effects on homeostatic biofilms. The scanning electron micrographs confirmed the same. In addition, tested concentrations of EOS did not have any cytotoxic effects and did not induce IL-8 production in HOKs. EOS showed promising results for diverting dysbiosis in in vitro rinsed biofilms and controlling key periopathogens, with no toxic effects on commensal species or human cells. This novel rinsing should be considered for clinical applications.}, }
@article {pmid38185393, year = {2024}, author = {Wang, L and Zheng, M and Liu, J and Jin, Z and Wang, C and Gao, M and Zhang, H and Zhang, X and Xia, X}, title = {LDLa containing C-type lectin mediates phagocytosis of V.anguillarum and regulates immune effector genes in shrimp.}, journal = {Fish &amp; shellfish immunology}, volume = {145}, number = {}, pages = {109361}, doi = {10.1016/j.fsi.2024.109361}, pmid = {38185393}, issn = {1095-9947}, mesh = {Animals ; Lectins, C-Type/genetics ; Phagocytosis ; *Bacterial Infections ; Receptors, Pattern Recognition/genetics ; Bacteria/metabolism ; Crustacea/metabolism ; *Penaeidae ; Immunity, Innate/genetics ; Hemocytes ; Arthropod Proteins/genetics ; }, abstract = {C-type lectins (CTLs) function as pattern recognition receptors (PRRs) by recognizing invading microorganisms, thereby triggering downstream immune events against infected pathogens. In this study, a novel CTL containing a low-density lipoprotein receptor class A (LDLa) domain was obtained from Litopenaeus vannamei, designed as LvLDLalec. Stimulation by the bacterial pathogen Vibrio anguillarum (V. anguillarum) resulted in remarkable up-regulation of LvLDLalec, as well as release of LvLDLalec into hemolymph. The rLvLDLalec protein possessed broad-spectrum bacterial binding and agglutinating activities, as well as hemocyte attachment ability. Importantly, LvLDLalec facilitated the bacterial clearance in shrimp hemolymph and protected shrimp from bacterial infection. Further studies revealed that LvLDLalec promoted hemocytes phagocytosis against V. anguillarum and lysosomes were involved in the process. Meanwhile, LvLDLalec participated in humoral immunity through activating and inducing nuclear translocation of Dorsal to regulate phagocytosis-related genes and antimicrobial peptides (AMPs) genes, thereby accelerated the removal of invading pathogens in vivo and improved the survival rate of L. vannamei. These results unveil that LvLDLalec serves as a PRR participate in cellular and humoral immunity exerting opsonin activity to play vital roles in the immune regulatory system of L. vannamei.}, }
@article {pmid38182675, year = {2024}, author = {Zhou, Y and Meng, F and Ochieng, B and Xu, J and Zhang, L and Kimirei, IA and Feng, M and Zhu, L and Wang, J}, title = {Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {28}, pmid = {38182675}, issn = {1432-184X}, mesh = {*Rivers ; Tanzania ; Bacteria/genetics ; Biofilms ; *Microbiota ; }, abstract = {High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.}, }
@article {pmid38181473, year = {2024}, author = {Zhao, A and Zhong, X and Xu, H and Xu, G}, title = {Continuous warming shifts the community pattern of periphytic protozoan fauna in marine environments.}, journal = {Marine pollution bulletin}, volume = {199}, number = {}, pages = {116016}, doi = {10.1016/j.marpolbul.2023.116016}, pmid = {38181473}, issn = {1879-3363}, mesh = {*Ecosystem ; Environmental Monitoring/methods ; *Ciliophora ; Food Chain ; Environmental Biomarkers ; Biodiversity ; }, abstract = {Protozoan fauna is playing an important role in the functioning of microbial food webs by transferring the flux of material and energy from low to high tropic levels in marine ecosystems. To assess effects of elevated temperature on the marine ecosystem, periphytic protozoan communities were used as the test microbial fauna, and were incubated in a temperature-controlled circulation system in a successive temperature gradient of 22 (control), 25, 28, 31 and 34 °C. The results showed that: (1) the test microbial fauna was shifted in both species composition and community structure; (2) the average taxonomic distinctness represented a clear decreasing trend, (3) while the variation in taxonomic distinctness significantly increased with increase of water temperature; and (4) the community pattern was significantly departed from an expectation when temperature increased by 12 °C. These results suggested that Protozoa may be used as a useful bioindicator of global warming in marine ecosystems.}, }
@article {pmid38179971, year = {2024}, author = {Price, CE and Valls, RA and Ramsey, AR and Loeven, NA and Jones, JT and Barrack, KE and Schwartzman, JD and Royce, DB and Cramer, RA and Madan, JC and Ross, BD and Bliska, J and O'Toole, GA}, title = {Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0314423}, pmid = {38179971}, issn = {2150-7511}, support = {R01 ES033988/ES/NIEHS NIH HHS/United States ; P30 DK117469/DK/NIDDK NIH HHS/United States ; R35 GM142685/GM/NIGMS NIH HHS/United States ; T32 HL134598/HL/NHLBI NIH HHS/United States ; T32 AI007363/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Infant ; Humans ; Mice ; Animals ; *Cystic Fibrosis/complications ; Cystic Fibrosis Transmembrane Conductance Regulator ; Propionates ; Bacteroides/genetics ; Caco-2 Cells ; Inflammation/complications ; Disease Models, Animal ; Dysbiosis/complications ; Escherichia coli ; }, abstract = {Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. We demonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR-/-) Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1β-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroides-supplemented stool from infants with cystic fibrosis into the gut of Cftr[F508del] mice results in higher propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serum compared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Taken together, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airway inflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate it produces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic and airway inflammation for persons with CF.IMPORTANCEThe composition of the gut microbiome in persons with CF is correlated with lung health outcomes, a phenomenon referred to as the gut-lung axis. Here, we demonstrate that the intestinal microbe Bacteroides decreases inflammation through the production of the short-chain fatty acid propionate. Supplementing the levels of Bacteroides in an animal model of CF is associated with reduced systemic inflammation and reduction in the relative abundance of the opportunistically pathogenic group Escherichia/Shigella in the gut. Taken together, these data demonstrate a key role for Bacteroides and microbially produced propionate in modulating inflammation, gut microbial ecology, and the gut-lung axis in cystic fibrosis. These data support the role of Bacteroides as a potential probiotic in CF.}, }
@article {pmid38179905, year = {2024}, author = {Huffines, JT and Boone, RL and Kiedrowski, MR}, title = {Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0058923}, pmid = {38179905}, issn = {2379-5042}, support = {P30 DK072482/DK/NIDDK NIH HHS/United States ; T32 GM008111/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Temperature ; Coculture Techniques ; *Staphylococcus aureus ; Dysbiosis ; *Sinusitis/microbiology ; Epithelial Cells/microbiology ; Inflammation ; Chronic Disease ; }, abstract = {Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.}, }
@article {pmid38179459, year = {2023}, author = {Parsons, RJ and Liu, S and Longnecker, K and Yongblah, K and Johnson, C and Bolaños, LM and Comstock, J and Opalk, K and Kido Soule, MC and Garley, R and Carlson, CA and Temperton, B and Bates, NR}, title = {Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287477}, pmid = {38179459}, issn = {1664-302X}, abstract = {Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L[-1] of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.}, }
@article {pmid38175304, year = {2024}, author = {Marčiulynas, A and Menkis, A}, title = {Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {27}, pmid = {38175304}, issn = {1432-184X}, mesh = {*Mycobiome ; *Quercus ; High-Throughput Nucleotide Sequencing ; Trees ; Wood ; }, abstract = {We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.}, }
@article {pmid38175217, year = {2024}, author = {Grandhay, C and Prétot, E and Klaba, V and Celle, H and Normand, AC and Bertrand, X and Grenouillet, F}, title = {Yeast Biodiversity of Karst Waters: Interest of Four Culture Media and an Improved MALDI-TOF MS Database.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {26}, pmid = {38175217}, issn = {1432-184X}, mesh = {Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Culture Media ; *Drinking Water ; Biodiversity ; }, abstract = {Karst aquifers are a significant source of drinking water and highly vulnerable to pollution and microbial contamination. Microbiological regulations for the quality of drinking water mostly focus on bacterial levels and lack guidance concerning fungal contamination. Moreover, there is no standardised microbial analysis methodology for identifying fungi in water. Our main objective was to establish the most effective culture and identification methodology to examine yeast diversity in karst waters. We assessed the comparative efficacy of four culture media (CHROMagar Candida, dichloran glycerol 18% [DG18], dichloran rose Bengal chloramphenicol [DRBC], and SYMPHONY agar) for yeast isolation from karst water samples. Furthermore, we investigated the comprehensiveness of databases used in MALDI-TOF mass spectrometry (MALDI-TOF MS) for identifying environmental yeast species. In total, we analysed 162 water samples, allowing the identification of 2479 yeast isolates. We demonstrate that a combination of four culture media, each with distinct specifications, more efficiently covers a wide range of yeast species in karst water than a combination of only two or three. Supplementation of a MALDI-TOF MS database is also critical for analysing environmental microbial samples and improved the identification of yeast biodiversity. This study is an initial step towards standardising the analysis of fungal biodiversity in karst waters, enabling a better understanding of the significance of this environmental reservoir in relation to public health.}, }
@article {pmid38172411, year = {2024}, author = {Kankonkar, HT and Khandeparker, RS}, title = {Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {53}, pmid = {38172411}, issn = {1432-0991}, mesh = {*Polyhydroxyalkanoates ; Phylogeny ; *Micrococcaceae/metabolism ; Bacteria/genetics/metabolism ; Acyltransferases/metabolism ; }, abstract = {Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.}, }
@article {pmid38171425, year = {2024}, author = {Gao, T and Tian, H and Xiang, L and Wang, Z and Fu, Y and Shi, J and Wen, X and Jiang, X and He, W and Hashsham, SA and Wang, F}, title = {Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {343}, number = {}, pages = {123286}, doi = {10.1016/j.envpol.2023.123286}, pmid = {38171425}, issn = {1873-6424}, mesh = {*Atrazine/analysis ; Soil ; Soil Microbiology ; *Herbicides/analysis ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Biomarkers/metabolism ; Biodegradation, Environmental ; }, abstract = {The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg[-1]) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg[-1]), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg[-1]). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.}, }
@article {pmid38171124, year = {2024}, author = {Soni, K and Kothamasi, D and Chandra, R}, title = {Municipal wastewater treatment plant showing a potential reservoir for clinically relevant MDR bacterial strains co-occurrence of ESBL genes and integron-integrase genes.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119938}, doi = {10.1016/j.jenvman.2023.119938}, pmid = {38171124}, issn = {1095-8630}, mesh = {Humans ; beta-Lactamases/genetics ; Integrons/genetics ; Integrases ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Wastewater ; *Bacillus ; *Water Purification ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Municipal wastewater treatment plants (MWWTPs) are a milieu for co-occurrence of multiple antibiotic resistance genes (ARGs). This facilitates mixing and genetic exchange; and promotes dissemination of multidrug resistance (MDR) to wastewater bacterial communities which is hazardous for the effluent receiving environment. This study investigated the co-occurrence of extended-spectrum beta-lactamase (ESBL) genes (blaTEM, blaCTX-M, blaSHV, blaOXA), and integron-integrase genes (intI1, intI2, intI3) in MDR bacteria isolated from the Bharwara MWWTP in Lucknow, India. Thirty-one MDR bacterial colonies resistant to three or more antibiotics were isolated from three treatment stages of this MWWTP. Six of these: Staphylococcus aureus, Serratia marcescens, Salmonella enterica, Shigella sonnei, Escherichia coli, and Bacillus sp. Had co-occurrence of ESBL and integron-integrase genes. These six isolates were examined for the occurrence of MDR efflux genes (qacA, acrB) and ARGs (aac(3)-1, qnrA1, tetA, vanA) and tested for resistance against 12 different antibiotics. The highest resistance was against penicillin-G (100%) and lowest for chloramphenicol (16.66%). Bacillus sp. Isolate BWKRC6 had the highest co-occurrence of antibiotic resistance-determining genes and was resistant to all the 12 antibiotics tested. The co-occurrence of ESBL, integron-integrase, antibiotic resistance-determining and MDR efflux genes in bacteria isolated from the Bharwara MWWTP indicates that the wastewaters of this treatment plant may have become a hotspot for MDR bacteria and may present human and environmental health hazards. Therefore, there is need for a rapid action to limit the spread of this threat. Public regulatory authorities must urgently implement measures to prevent MWWTPs becoming reservoirs for evolution of antibiotic resistance genes and development of antibiotic resistance.}, }
@article {pmid38169617, year = {2023}, author = {Song, W and Wu, F and Yan, Y and Li, Y and Wang, Q and Hu, X and Li, Y}, title = {Gut microbiota landscape and potential biomarker identification in female patients with systemic lupus erythematosus using machine learning.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1289124}, pmid = {38169617}, issn = {2235-2988}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Lupus Erythematosus, Systemic/diagnosis ; Biomarkers ; Machine Learning ; }, abstract = {OBJECTIVES: Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease that disproportionately affects women. Early diagnosis and prevention are crucial for women's health, and the gut microbiota has been found to be strongly associated with SLE. This study aimed to identify potential biomarkers for SLE by characterizing the gut microbiota landscape using feature selection and exploring the use of machine learning (ML) algorithms with significantly dysregulated microbiotas (SDMs) for early identification of SLE patients. Additionally, we used the SHapley Additive exPlanations (SHAP) interpretability framework to visualize the impact of SDMs on the risk of developing SLE in females.<br><br>METHODS: Stool samples were collected from 54 SLE patients and 55 Negative Controls (NC) for microbiota analysis using 16S rRNA sequencing. Feature selection was performed using Elastic Net and Boruta on species-level taxonomy. Subsequently, four ML algorithms, namely logistic regression (LR), Adaptive Boosting (AdaBoost), Random Forest (RF), and eXtreme gradient boosting (XGBoost), were used to achieve early identification of SLE with SDMs. Finally, the best-performing algorithm was combined with SHAP to explore how SDMs affect the risk of developing SLE in females.<br><br>RESULTS: Both alpha and beta diversity were found to be different in SLE group. Following feature selection, 68 and 21 microbiota were retained in Elastic Net and Boruta, respectively, with 16 microbiota overlapping between the two, i.e., SDMs for SLE. The four ML algorithms with SDMs could effectively identify SLE patients, with XGBoost performing the best, achieving Accuracy, Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, and AUC values of 0.844, 0.750, 0.938, 0.923, 0.790, and 0.930, respectively. The SHAP interpretability framework showed a complex non-linear relationship between the relative abundance of SDMs and the risk of SLE, with Escherichia_fergusonii having the largest SHAP value.<br><br>CONCLUSIONS: This study revealed dysbiosis in the gut microbiota of female SLE patients. ML classifiers combined with SDMs can facilitate early identification of female patients with SLE, particularly XGBoost. The SHAP interpretability framework provides insight into the impact of SDMs on the risk of SLE and may inform future scientific treatment for SLE.}, }
@article {pmid38169416, year = {2024}, author = {Kim, K and Jinno, C and Li, X and Bravo, D and Cox, E and Ji, P and Liu, Y}, title = {Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {1}, pmid = {38169416}, issn = {1674-9782}, support = {W4002 and NC1202//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.<br><br>RESULTS: Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q&#x2009;<&#x2009;0.2 and fold change&#x2009;>&#x2009;2.0). In addition, pigs in antibiotic had a reduced (P&#x2009;<&#x2009;0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P&#x2009;<&#x2009;0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.<br><br>CONCLUSIONS: The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.}, }
@article {pmid38167150, year = {2024}, author = {Alahmad, A and Harir, M and Fochesato, S and Tulumello, J and Walker, A and Barakat, M and Ndour, PMS and Schmitt-Kopplin, P and Cournac, L and Laplaze, L and Heulin, T and Achouak, W}, title = {Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {1}, pmid = {38167150}, issn = {2049-2618}, support = {ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; }, mesh = {*Pennisetum/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Plant Roots/microbiology ; *Microbiota ; Soil/chemistry ; Plants/microbiology ; Exudates and Transudates ; Soil Microbiology ; Rhizosphere ; }, abstract = {BACKGROUND: The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities.<br><br>RESULTS: Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The &#xdf;-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines.<br><br>CONCLUSIONS: This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.}, }
@article {pmid38166159, year = {2024}, author = {Chen, X and He, C and Zhang, Q and Bayakmetov, S and Wang, X}, title = {Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies.}, journal = {ACS synthetic biology}, volume = {13}, number = {1}, pages = {183-194}, pmid = {38166159}, issn = {2161-5063}, support = {R01 EB031893/EB/NIBIB NIH HHS/United States ; R01 GM131405/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbial Consortia/genetics ; *Bacteria/genetics ; }, abstract = {Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.}, }
@article {pmid38165515, year = {2024}, author = {Fowler, AE and McFrederick, QS and Adler, LS}, title = {Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {25}, doi = {10.1007/s00248-023-02323-6}, pmid = {38165515}, issn = {1432-184X}, support = {GNE19-200-33243//Northeast SARE/ ; AFRI-2018-08591//U.S. Department of Agriculture/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; Medicago sativa ; Pollen ; }, abstract = {Pollinators face many stressors, including reduced floral diversity. A low-diversity diet can impair organisms' ability to cope with additional stressors, such as pathogens, by altering the gut microbiome and/or immune function, but these effects are understudied for most pollinators. We investigated the impact of pollen diet diversity on two ecologically and economically important generalist pollinators, the social bumble bee (Bombus impatiens) and the solitary alfalfa leafcutter bee (Megachile rotundata). We experimentally tested the effect of one-, two-, or three-species pollen diets on gut bacterial communities in both species, and the melanization immune response in B. impatiens. Pollen diets included dandelion (Taraxacum officinale), staghorn sumac (Rhus typhina), and hawthorn (Crataegus sp.) alone, each pair-wise combination, or a mix of all three species. We fed bees their diet for 7 days and then dissected out guts and sequenced 16S rRNA gene amplicons to characterize gut bacterial communities. To assess melanization in B. impatiens, we inserted microfilament implants into the bee abdomen and measured melanin deposition on the implant. We found that pollen diet did not influence gut bacterial communities in M. rotundata. In B. impatiens, pollen diet composition, but not diversity, affected gut bacterial richness in older, but not newly-emerged bees. Pollen diet did not affect the melanization response in B. impatiens. Our results suggest that even a monofloral, low-quality pollen diet such as dandelion can support diverse gut bacterial communities in captive-reared adults of these bee species. These findings shed light on the effects of reduced diet diversity on bee health.}, }
@article {pmid38165150, year = {2024}, author = {Kanchongkittiphon, W and Nopnipa, S and Mathuranyanon, R and Nonthabenjawan, N and Sritournok, S and Manuyakorn, W and Wanapaisan, P}, title = {Characterization of gut microbiome profile in children with confirmed wheat allergy.}, journal = {Asian Pacific journal of allergy and immunology}, volume = {}, number = {}, pages = {}, doi = {10.12932/AP-080623-1626}, pmid = {38165150}, issn = {0125-877X}, abstract = {BACKGROUND: Food allergies pose serious health risks, including life-threatening anaphylactic reactions, increased morbidity, and reduced quality of life. Wheat allergy is a common concern in Asia. There is growing interest in understanding the potential association between dysregulation of the gut microbiome and the development of food allergies.<br><br>OBJECTIVE: This study aimed to explore the gut microbiome of Thai children with wheat allergy and its potential association with allergic responses.<br><br>METHODS: Microbial abundance was assessed using Quantitative Insights into Microbial Ecology 2 (QIIME2) microbiome analysis based on 16S rDNA data. The correlation between microbial richness and relevant parameters was evaluated using the Spearman correlation analysis. Additionally, the microbial community functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2).<br><br>RESULTS: The gut microbiome analysis revealed significant differences between the two groups at the phylum and genus levels. Firmicutes (p = 0.012) and Verrucomicrobia (p < 0.001) were enriched in wheat-allergic children, whereas specific gut microbes such as Megamonas (p = 0.04), Romboutsia (p < 0.001), Fusobacterium (p < 0.001), Clostridium senso stricto1 (p < 0.001), and Turicibacter (p < 0.001) were more abundant in healthy children. Anaerostripes (p = 0.011), Erysipelatoclostridium (p < 0.001), Prevotella 2 (p < 0.001), Ruminiclostridium 5 (p < 0.001), and Clostridium innnocuum (p < 0.001) were enriched in children with a confirmed wheat allergy. Functional analysis indicated disparities in the pathways related to arginine and polyamine biosynthesis.<br><br>CONCLUSION: These findings offer valuable insights into the gut microbiome of children with wheat allergy and its potential impact on symptom severity, laying the groundwork for further research and interventions aimed at addressing this health concern.}, }
@article {pmid38163403, year = {2024}, author = {Dufour, OK and Hoffman, E and Sleith, RS and Katz, LA and Weiner, AKM and Sehein, TR}, title = {Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing.}, journal = {European journal of protistology}, volume = {92}, number = {}, pages = {126049}, pmid = {38163403}, issn = {1618-0429}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {*Amoeba/genetics ; Ecosystem ; Wetlands ; Phylogeny ; *Amoebozoa ; *Lobosea ; New England ; }, abstract = {Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.}, }
@article {pmid38162520, year = {2023}, author = {Capeding, MRZ and Phee, LCM and Ming, C and Noti, M and Vidal, K and Le Carrou, G and Frézal, A and Moll, JM and Vogt, JK and Myers, PN and Nielsen, BH and Boulangé, CL and Samuel, TM and Berger, B and Cercamondi, CI}, title = {Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1319873}, pmid = {38162520}, issn = {2296-861X}, abstract = {INTRODUCTION: Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation.<br><br>METHODS: This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21&#x2009;days old) randomized for 8&#x2009;weeks to a control group (CG; n&#x2009;=&#x2009;77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*10[8] CFU/day; n&#x2009;=&#x2009;75) or high dose (Hi-EG; 1.8*10[10] CFU/day; n&#x2009;=&#x2009;76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids.<br><br>RESULTS: Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups.<br><br>DISCUSSION: B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.}, }
@article {pmid38162026, year = {2023}, author = {Modolon, F and Schultz, J and Duarte, G and Vilela, CLS and Thomas, T and Peixoto, RS}, title = {In situ devices can culture the microbial dark matter of corals.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108374}, pmid = {38162026}, issn = {2589-0042}, abstract = {Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.}, }
@article {pmid38159169, year = {2023}, author = {Wang, G and Wang, X and Yang, Z and Wang, S and Li, W and Shang, S and Luo, Y and Wang, L}, title = {Effects of Fusarium solani on the Growth and Development of Anoplophora glabripennis Larvae.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {23}, pmid = {38159169}, issn = {1432-184X}, mesh = {Animals ; Larva/microbiology ; *Coleoptera/microbiology ; *Fusarium ; }, abstract = {Anoplophora glabripennis (Asian longhorned beetle) is a wood-boring pest that can inhabit a wide range of healthy deciduous host trees in native and non-native habitats. Lignocellulose degradation plays a major role in the acquisition of nutrients during the growth and development of A. glabripennis larvae. In this study, the lignocellulose degradation capacity of Fusarium solani, a fungal symbiont of A. glabripennis, was investigated in fermentation culture and in four host tree species. The impact of F. solani on larval growth and survival parameters was assessed. Fermentation culture demonstrated continuous and stable production of lignocellulolytic enzymes over the cultivation period. Furthermore, F. solani was able to degrade host tree lignocellulose, as shown by decreased soluble sugar and cellulose contents and an increase in protein content. No significant differences in larval survival were observed in larvae fed with or without F. solani. However, weight and head capsule width were higher in larvae fed on F. solani, and gut lignocellulose activities were elevated in fed larvae. Our results indicate a role for F. solani in the predigestion of lignocellulose during the colonization and parasitic stages of A. glabripennis larval development, and also the F. solani an important symbiotic partner to A. glabripennis, lowering barriers to colonization and development in a range of habitats.}, }
@article {pmid38159125, year = {2023}, author = {Hao, Z and Wang, Q and Wang, J and Deng, Y and Yan, Z and Tian, L and Jiang, H}, title = {Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {24}, pmid = {38159125}, issn = {1432-184X}, support = {51839011//National Natural Science Foundation of China/ ; }, mesh = {*Water ; Nitrates ; *Microbiota/genetics ; Metagenome ; Nitrogen/metabolism ; }, abstract = {Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.}, }
@article {pmid38157893, year = {2024}, author = {Guarin, TC and Li, L and Haak, L and Teel, L and Pagilla, KR}, title = {Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169637}, doi = {10.1016/j.scitotenv.2023.169637}, pmid = {38157893}, issn = {1879-1026}, mesh = {Charcoal/chemistry ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/chemistry ; *Water Purification/methods ; Filtration/methods ; *Ozone/chemistry ; *Drinking Water ; }, abstract = {This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.}, }
@article {pmid38157796, year = {2024}, author = {Wang, L and Nabi, F and Yi, W and Wang, D and Zhu, Y and Jiang, X}, title = {Low-dose thiram exposure elicits dysregulation of the gut microbial ecology in broiler chickens.}, journal = {Ecotoxicology and environmental safety}, volume = {270}, number = {}, pages = {115879}, doi = {10.1016/j.ecoenv.2023.115879}, pmid = {38157796}, issn = {1090-2414}, mesh = {Animals ; Thiram/toxicity ; Chickens/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Fungicides, Industrial/toxicity ; Bacteria/genetics ; }, abstract = {Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also primarily attributed to long-term accumulation. However, there is a paucity of information regarding the impact of prolonged utilization of thiram at low doses on the gut microbiota, particularly with respect to gut fungi. Our objective is to explore the effect of thiram on broilers from the perspective of gut microbiota, which includes both bacteria and fungi. We developed a long-term low-dose thiram model to simulate thiram residue and employed 16 S rRNA and ITS gene sequencing to investigate the diversity and profile of gut microbiota between group CC (normal diet) and TC (normal diet supplemented with 5 mg/kg thiram). The results revealed that low doses of thiram had a detrimental effect on broiler's growth performance, resulting in an approximate reduction of 669.33 g in their final body weight at day 45. Our findings indicated that low-dose thiram had a negative impact on the gut bacterial composition, leading to a notable reduction in the abundance of Merdibacter, Paenibacillus, Macrococcus, Fournierella, and Anaeroplasma (p < 0.05) compared to the CC group. Conversely, the relative level of Myroides was significantly increased (p < 0.05) in response to thiram exposure. In gut fungi, thiram significantly enhanced the diversity and richness of gut fungal populations (p < 0.05), as evidenced by the notable increase in alpha indices, i.e. ACE (CC: 346.49 ± 117.27 vs TC: 787.27 ± 379.14, p < 0.05), Chao 1 (CC: 317.63 ± 69.13 vs TC: 504.85 ± 104.50, p < 0.05), Shannon (CC: 1.28 ± 1.19 vs TC: 5.39 ± 2.66, p < 0.05), Simpson (CC: 0.21 ± 0.21 vs TC: 0.78 ± 0.34, p < 0.05). Furthermore, the abundance of Ascomycota, Kickxellomycota, and Glomeromycota were significantly increased (p < 0.05) by exposure to thiram, conversely, the level of Basidiomycota was decreased (p < 0.05) in the TC group compared to the CC group. Overall, this study demonstrated that low doses of thiram induced significant changes in the composition and abundance of gut microbiota in broilers, with more pronounced changes observed in the gut fungal community as compared to the gut bacterial community. Importantly, our findings further emphasize the potential risks associated with low dose thiram exposure and have revealed a novel discovery indicating that significant alterations in gut fungi may serve as the crucial factor contributing to the detrimental effects exerted by thiram residues.}, }
@article {pmid38157058, year = {2023}, author = {Chowaniec, K and Styburski, J and Kozioł, S and Pisańska, Z and Skubała, K}, title = {Dune Blowouts as Microbial Hotspots and the Changes of Overall Microbial Activity and Photosynthetic Biomass Along with Succession of Biological Soil Crusts.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {22}, pmid = {38157058}, issn = {1432-184X}, support = {U1U/W18/NO/28.34//Faculty of Biology, Jagiellonian University/ ; }, mesh = {Biomass ; *Ecosystem ; *Soil ; Soil Microbiology ; Desert Climate ; }, abstract = {Biological soil crust (BSC) constitutes a consortium of cyanobacteria, algae, lichen, mosses, and heterotrophic microorganisms, forming a miniature ecosystem within the uppermost soil layer. The biomass of different organisms forming BSC and their activity changes along with succession. Previous studies focused primarily on BSC in hyper-arid/arid regions, whereas the ecophysiology of BSC in temperate climates is still not well recognized. In order to determine changes in overall microbial activity and photosynthetic biomass in BSC at different stages of the succession of inland sandy grasslands, we analyzed dehydrogenase activity and determined the content of photosynthetic pigments. We also compared these parameters between BSC developed on the dune ridges and aeolian blowouts in the initial stage of succession. Our study revealed a significant increase in both photosynthetic biomass and overall microbial activity in BSC as the succession of inland shifting sands progresses. We found that chl a concentration in BSC could be considered a useful quantitative indicator of both the presence of photoautotrophs and the degree of soil crust development in warm-summer humid continental climates. The photosynthetic biomass was closely related to increased microbial activity in BSC, which suggests that photoautotrophs constitute a major BSC component. Dune blowouts constitute environmental niches facilitating the development of BSC, compared to dune ridges. High biomass of microorganisms in the dune blowouts may be associated with a high amount of organic material and more favorable moisture conditions. We conclude that deflation fields are key places for keeping a mosaic of habitats in the area of shifting sands and can be a reservoir of microorganisms supporting further settlement of dune slopes by BSC.}, }
@article {pmid38156301, year = {2023}, author = {Wani, AK and Ahmad, S and Américo-Pinheiro, JHP and Tizro, N and Singh, R}, title = {Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study.}, journal = {Iranian journal of microbiology}, volume = {15}, number = {6}, pages = {723-733}, pmid = {38156301}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.<br><br>MATERIALS AND METHODS: In the present study, physiochemical parameters including temperature (65-75&#xb0;C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.<br><br>RESULTS: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).<br><br>CONCLUSION: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.}, }
@article {pmid38153618, year = {2023}, author = {Xiong, L and Li, Y and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Revealing viral diversity in the Napahai plateau wetland based on metagenomics.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {3}, pmid = {38153618}, issn = {1572-9699}, support = {32160294, 42267059//National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Ecosystem ; Phylogeny ; China ; *Bacteriophages ; }, abstract = {We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.}, }
@article {pmid38153543, year = {2023}, author = {Ciric, M and Šaraba, V and Budin, C and de Boer, T and Nikodinovic-Runic, J}, title = {Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {21}, pmid = {38153543}, issn = {1432-184X}, support = {870292//EU Horizon 2020 Research and Innovation Programme - BioICEP/ ; 451-03-47/2023-01/200042//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; }, mesh = {Humans ; Polyurethanes ; *Comamonadaceae ; DNA, Ribosomal ; *Groundwater ; Pseudomonas ; Suppuration ; }, abstract = {Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6-7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 - Na + K, Cl - Na + K and OH, Cl - Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.}, }
@article {pmid38151633, year = {2024}, author = {Paulino, PG and Abuin-Denis, L and Maitre, A and Piloto-Sardiñas, E and Obregon, D and Santos, HA and Cabezas-Cruz, A}, title = {Dissecting the impact of Anaplasma phagocytophilum infection on functional networks and community stability of the tick microbiome.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {1205-1218}, pmid = {38151633}, issn = {1618-1905}, support = {E-26/211.312/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 313753/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; SGCE - RAPPORT No 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; }, mesh = {*Anaplasma phagocytophilum/physiology/genetics ; Animals ; *Ixodes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ehrlichiosis/microbiology ; Nymph/microbiology ; Gastrointestinal Microbiome/physiology ; }, abstract = {CONTEXT: Pathogens can manipulate microbial interactions to ensure survival, potentially altering the functional patterns and microbiome assembly. The present study investigates how Anaplasma phagocytophilum infection affects the functional diversity, composition, and assembly of the Ixodes scapularis microbiome, with a focus on high central pathways-those characterized by elevated values in centrality metrics such as eigenvector, betweenness, and degree measures, in the microbial community.<br><br>METHODS: Using previously published data from nymphs' gut V4 region's amplicons of bacterial 16S rRNA, we predicted the functional diversity and composition in control and A. phagocytophilum-infected ticks and inferred co-occurrence networks of taxa and ubiquitous pathways in each condition to associate the high central pathways to the microbial community assembly.<br><br>RESULTS: Although no differences were observed concerning pathways richness and diversity, there was a significant impact on taxa and functional assembly when ubiquitous pathways in each condition were filtered. Moreover, a notable shift was observed in the microbiome's high central functions. Specifically, pathways related to the degradation of nucleosides and nucleotides emerged as the most central functions in response to A. phagocytophilum infection. This finding suggests a reconfiguration of functional relationships within the microbial community, potentially influenced by the pathogen's limited metabolic capacity. This limitation implies that the tick microbiome may provide additional metabolic resources to support the pathogen's functional needs.<br><br>CONCLUSIONS: Understanding the metabolic interactions within the tick microbiome can enhance our knowledge of pathogen colonization mechanisms and uncover new disease control and prevention strategies. For example, certain pathways that were more abundant or highly central during infection may represent potential targets for microbiota-based vaccines.}, }
@article {pmid38148858, year = {2023}, author = {Khan, A and Singh, AV and Gautam, SS and Agarwal, A and Punetha, A and Upadhayay, VK and Kukreti, B and Bundela, V and Jugran, AK and Goel, R}, title = {Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1270039}, pmid = {38148858}, issn = {1664-462X}, abstract = {Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.}, }
@article {pmid38148389, year = {2023}, author = {Petrović, M and Janakiev, T and Grbić, ML and Unković, N and Stević, T and Vukićević, S and Dimkić, I}, title = {Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {19}, pmid = {38148389}, issn = {1432-184X}, mesh = {Bacillus subtilis ; Bacillus ; Plant Development ; Endophytes ; Plant Roots/microbiology ; Phosphates ; *Beta vulgaris ; }, abstract = {Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth-promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth-promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet-associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.}, }
@article {pmid38148362, year = {2023}, author = {Ofek, T and Trabelcy, B and Izhaki, I and Halpern, M}, title = {Vibrio cholerae O1 Inhabit Intestines and Spleens of Fish in Aquaculture Ponds.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {20}, pmid = {38148362}, issn = {1432-184X}, support = {2728/17//the India-Israel Joint UGC-ISF/ ; 2015103//the United States-Israel Binational Science Foundation, BSF/ ; }, mesh = {Animals ; *Vibrio cholerae O1 ; Cholera Toxin ; Ponds ; Spleen ; *Cholera/epidemiology ; Intestines ; Fishes ; }, abstract = {Vibrio cholerae is the causative agent of cholera, an acute diarrheal disease that spreads locally and globally in epidemics and pandemics. Although it was discovered that fish harbor V. cholerae strains in their intestines, most investigations revealed non-toxic V. cholerae serogroups in fish. Due to the rarity of toxigenic V. cholerae serogroups, it is difficult to cultivate these strains from environmental samples. Hence, here we aimed to uncover evidence of the occurrence of toxigenic V. cholerae in the intestines and spleens of various fish species. By using molecular detection tools, we show that V. cholerae O1 and strains positive for the cholera toxin inhabit both healthy and diseased fish intestines and spleens, suggesting that fish may serve as intermediate vectors of toxigenic V. cholerae. No significant differences were found between the abundance of toxigenic V. cholerae (either O1 or cholera toxin positive strains) in the healthy and the diseased fish intestines or spleens. In conclusion, a variety of fish species may serve as potential vectors and reservoirs of toxigenic V. cholerae as they form a link between the other reservoirs of V. cholerae (chironomids, copepods, and waterbirds). Similarly, they may aid in the spread of this bacterium between water bodies.}, }
@article {pmid38147140, year = {2023}, author = {Lee, H and Chaudhary, DK and Lim, OB and Kim, DU}, title = {Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {42}, pmid = {38147140}, issn = {1432-072X}, support = {NIBR202203112//National Institute of Biological Resources/ ; }, mesh = {Phylogeny ; *Cardiolipins ; Forests ; *Paenibacillus/genetics ; DNA ; }, abstract = {During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38[T] and TW40[T]. Both strains were catalase positive and oxidase negative. Strains TW38[T] and TW40[T] demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38[T] and TW40[T] affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17[T] (98.6%) and Paenibacillus arachidis E3[T] (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38[T], TW40[T], and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38[T] and TW40[T] was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38[T] and TW40[T] from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38[T] and TW40[T] represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38[T] (= KCTC 43468[T] = NBRC 116015[T]) and type strain of Paenibacillus humicola is TW40[T] (= KCTC 43469[T] = NBRC 116016[T]).}, }
@article {pmid38146666, year = {2024}, author = {Sveen, TR and Viketoft, M and Bengtsson, J and Bahram, M}, title = {Core taxa underpin soil microbial community turnover during secondary succession.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16561}, doi = {10.1111/1462-2920.16561}, pmid = {38146666}, issn = {1462-2920}, support = {2021-03724//The Swedish Research Council/ ; //The Swedish University of Agricultural Sciences (early career grant)/ ; 2020-00807//The Swedish Research Council Formas/ ; }, mesh = {*Soil ; Phylogeny ; Soil Microbiology ; Forests ; *Microbiota/genetics ; Bacteria/genetics ; Grassland ; }, abstract = {Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.}, }
@article {pmid38146049, year = {2024}, author = {Santos, LRC and Barros, PSDR and Monteiro, DA and Tabosa, JN and de Melo, AF and de Lyra, MDCCP and Oliveira, JRS and Fernandes Júnior, PI and de Freitas, ADS and Rachid, CTCDC}, title = {Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {1}, pages = {789-797}, pmid = {38146049}, issn = {1678-4405}, mesh = {*Zea mays/microbiology ; Brazil ; Endophytes/genetics ; Bacteria/genetics ; *Actinomycetales ; Genotype ; Plant Roots/microbiology ; }, abstract = {Endophytic bacteria play a crucial role in plant development and adaptation, and the knowledge of how endophytic bacteria assemblage is influenced by cultivation site and plant genotype is an important step to achieve microbiome manipulation. This work aimed to study the roots and stems of endophytic bacteriome of four maize genotypes cultivated in two regions of the semi-arid region of Pernambuco - Brazil. Our hypothesis is that the endophytic community assemblage will be influenced by plant genotypes and cultivation region. Metabarcoding sequencing data revealed significant differences in alfa diversity in function of both factors, genotypes, and maize organs. Beta diversity analysis showed that the bacterial communities differ mainly in function of the plant organ. The most abundant genera found in the samples were Leifsonia, Bacillus, Klebsiella, Streptomyces, and Bradyrhizobium. To understand ecological interactions within each compartment, we constructed co-occurrence network for each organ. This analysis revealed important differences in network structure and complexity and suggested that Leifsonia (the main genera found) had distinct ecological roles depending on the plant organ. Our data showed that root endophytic maize bacteria would be influenced by cultivation site, but not by genotype. We believe that, collectively, our data not only characterize the bacteriome associated with this plant and how different factors shape it, but also increase the knowledge to select potential bacteria for bioinoculant production.}, }
@article {pmid38143001, year = {2024}, author = {Shi, B and Cheng, X and Jiang, S and Pan, J and Zhu, D and Lu, Z and Jiang, Y and Liu, C and Guo, H and Xie, J}, title = {Unveiling the power of COD/N on constructed wetlands in a short-term experiment: Exploring microbiota co-occurrence patterns and assembly dynamics.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169568}, doi = {10.1016/j.scitotenv.2023.169568}, pmid = {38143001}, issn = {1879-1026}, mesh = {*Denitrification ; Wetlands ; Biological Oxygen Demand Analysis ; Nitrification ; *Microbiota ; Nitrogen/chemistry ; Water ; Waste Disposal, Fluid/methods ; }, abstract = {Constructed wetlands (CWs) are a cost-effective and environmentally friendly wastewater treatment technology. The influent chemical oxygen demand (COD)/nitrogen (N) ratio (CNR) plays a crucial role in microbial activity and purification performance. However, the effects of CNR changes on microbial diversity, interactions, and assembly processes in CWs are not well understood. In this study, we conducted comprehensive mechanistic experiments to investigate the response of CWs to changes in influent CNR, focusing on the effluent, rhizosphere, and substrate microbiota. Our goal is to provide new insights into CW management by integrating microbial ecology and environmental engineering perspectives. We constructed two groups of horizontal subsurface flow constructed wetlands (HFCWs) and set up three influent CNRs to analyse the microbial responses and nutrient removal. The results indicated that increasing influent CNR led to a decrease in microbial α-diversity and niche width. Genera involved in nitrogen removal and denitrification, such as Rhodobacter, Desulfovibrio, and Zoogloea, were enriched under medium/high CNR conditions, resulting in higher nitrate (NO3[-]-N) removal (up to 99 %) than that under lower CNR conditions (<60 %). Environmental factors, including water temperature (WT), pH, and phosphorus (P), along with CNR-induced COD and NO3[-]-N play important roles in microbial succession in HFCWs. The genus Nitrospira, which is involved in nitrification, exhibited a significant negative correlation (p < 0.05) with WT, COD, and P. Co-occurrence network analysis revealed that increasing influent CNR reduced the complexity of the network structure and increased microbial competition. Analysis using null models demonstrated that the microbial community assembly in HFCWs was primarily driven by stochastic processes under increasing influent CNR conditions. Furthermore, HFCWs with more stochastic microbial communities exhibited better denitrification performance (NO3[-]-N removal). Overall, this study enhances our understanding of nutrient removal, microbial co-occurrence, and assembly mechanisms in CWs under varying influent CNRs.}, }
@article {pmid38140550, year = {2023}, author = {Vickos, U and Camasta, M and Grandi, N and Scognamiglio, S and Schindler, T and Belizaire, MRD and Lango-Yaya, E and Koyaweda, GW and Senzongo, O and Pounguinza, S and Estimé, KKJF and N'yetobouko, S and Gadia, CLB and Feiganazoui, DA and Le Faou, A and Orsini, M and Perno, CF and Zinzula, L and Rafaï, CD}, title = {COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome.}, journal = {Viruses}, volume = {15}, number = {12}, pages = {}, pmid = {38140550}, issn = {1999-4915}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; Proteome ; *COVID-19/epidemiology ; Central African Republic/epidemiology ; Phylogeny ; Genomics ; Antiviral Agents ; }, abstract = {Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.}, }
@article {pmid38139130, year = {2023}, author = {Popov, IV and Popov, IV and Krikunova, AA and Lipilkina, TA and Derezina, TN and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139130}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; Agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; //K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics ; }, abstract = {Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.}, }
@article {pmid38138049, year = {2023}, author = {Lourenço, KS and Cantarella, H and Kuramae, EE}, title = {Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138049}, issn = {2076-2607}, abstract = {Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.}, }
@article {pmid38137974, year = {2023}, author = {Pérez, G and Krause, SMB and Bodelier, PLE and Meima-Franke, M and Pitombo, L and Irisarri, P}, title = {Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38137974}, issn = {2076-2607}, support = {CSIC-4562//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; POS_EXT_2016_1_133774//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; 32050410288//National Science Foundation of China 568 (NSFC), International (Regional) Cooperation and Exchange Program/ ; }, abstract = {Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.}, }
@article {pmid38136731, year = {2023}, author = {Balcha, ES and Gómez, F and Gemeda, MT and Bekele, FB and Abera, S and Cavalazzi, B and Woldesemayat, AA}, title = {Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136731}, issn = {2079-6382}, abstract = {The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.}, }
@article {pmid38133854, year = {2024}, author = {Chatterjee, S and Paul, P and Chakraborty, P and Das, S and Das Gupta, A and Roy, R and Malik, M and Sarkar, S and Sarker, RK and Tribedi, P}, title = {Combinatorial application of cuminaldehyde and gentamicin shows enhanced antimicrobial and antibiofilm action on Pseudomonas aeruginosa.}, journal = {Folia microbiologica}, volume = {69}, number = {4}, pages = {823-834}, pmid = {38133854}, issn = {1874-9356}, mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Gentamicins/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; Cymenes/pharmacology ; Virulence Factors ; Drug Synergism ; Humans ; }, abstract = {The emergence of biofilm-induced drug tolerance poses a critical challenge to public healthcare management. Pseudomonas aeruginosa, a gram-negative opportunistic bacterium, is involved in various biofilm-associated infections in human hosts. Towards this direction, in the present study, a combinatorial approach has been explored as it is a demonstrably effective strategy for managing microbial infections. Thus, P. aeruginosa has been treated with cuminaldehyde (a naturally occurring phytochemical) and gentamicin (an aminoglycoside antibiotic) in connection to the effective management of the biofilm challenges. It was also observed that the test molecules could show increased antimicrobial activity against P. aeruginosa. A fractional inhibitory concentration index (FICI) of 0.65 suggested an additive interaction between cuminaldehyde and gentamicin. Besides, a series of experiments such as crystal violet assay, estimation of extracellular polymeric substance (EPS), and microscopic images indicated that an enhanced antibiofilm activity was obtained when the selected compounds were applied together on P. aeruginosa. Furthermore, the combination of the selected compounds was found to reduce the secretion of virulence factors from P. aeruginosa. Taken together, this study suggested that the combinatorial application of cuminaldehyde and gentamicin could be considered an effective approach towards the control of biofilm-linked infections caused by P. aeruginosa.}, }
@article {pmid38133759, year = {2024}, author = {Hidalgo, J and Artetxe, U and Becerril, JM and Gómez-Sagasti, MT and Epelde, L and Vilela, J and Garbisu, C}, title = {Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {4}, pages = {6010-6024}, pmid = {38133759}, issn = {1614-7499}, support = {Project Phy2SUDOE - SOE4/P5/E1021//Interreg/ ; AGL 2015-64481-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76592-R//Ministerio de Econom&#xed;a y Competitividad/ ; UPV/EHU-GV IT-1648-22//Eusko Jaurlaritza/ ; }, mesh = {Sewage ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil ; *Polychlorinated Biphenyls ; Soil Microbiology ; }, abstract = {The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.}, }
@article {pmid38127978, year = {2023}, author = {Liuu, S and Nepelska, M and Pfister, H and Gamelas Magalhaes, J and Chevalier, G and Strozzi, F and Billerey, C and Maresca, M and Nicoletti, C and Di Pasquale, E and Pechard, C and Bardouillet, L and Girardin, SE and Boneca, IG and Doré, J and Blottière, HM and Bonny, C and Chene, L and Cultrone, A}, title = {Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {52}, pages = {e2306863120}, pmid = {38127978}, issn = {1091-6490}, support = {FP7/2007-2013//European community's Seventh Framework Programme/ ; FP7/2007-2013//European community's Seventh framework Programme/ ; }, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Peptidoglycan/metabolism ; Intestines/pathology ; Inflammation/metabolism ; Membrane Transport Proteins/metabolism ; Anti-Inflammatory Agents/metabolism ; Dextran Sulfate ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism ; Mice, Inbred C57BL ; }, abstract = {The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.}, }
@article {pmid38126787, year = {2024}, author = {Walsh, C and Stallard-Olivera, E and Fierer, N}, title = {Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0205023}, pmid = {38126787}, issn = {2150-7511}, support = {Graduate Research Assistantship//Cooperative Institute for Research in Environmental Sciences (CIRES)/ ; }, mesh = {*Machine Learning ; Algorithms ; *Microbiota ; }, abstract = {Due to the complex nature of microbiome data, the field of microbial ecology has many current and potential uses for machine learning (ML) modeling. With the increased use of predictive ML models across many disciplines, including microbial ecology, there is extensive published information on the specific ML algorithms available and how those algorithms have been applied. Thus, our goal is not to summarize the breadth of ML models available or compare their performances. Rather, our goal is to provide more concrete and actionable information to guide microbial ecologists in how to select, run, and interpret ML algorithms to predict the taxa or genes associated with particular sample categories or environmental gradients of interest. Such microbial data often have unique characteristics that require careful consideration of how to apply ML models and how to interpret the associated results. This review is intended for practicing microbial ecologists who may be unfamiliar with some of the intricacies of ML models. We provide examples and discuss common opportunities and pitfalls specific to applying ML models to the types of data sets most frequently collected by microbial ecologists.}, }
@article {pmid38125540, year = {2023}, author = {Dhivahar, J and Parthasarathy, A and Krishnan, K and Kovi, BS and Pandian, GN}, title = {Bat-associated microbes: Opportunities and perils, an overview.}, journal = {Heliyon}, volume = {9}, number = {12}, pages = {e22351}, pmid = {38125540}, issn = {2405-8440}, abstract = {The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.}, }
@article {pmid38115223, year = {2024}, author = {Euler, S and Jeffrey, LC and Maher, DT and Johnston, SG and Sugimoto, R and Tait, DR}, title = {Microbiome mediating methane and nitrogen transformations in a subterranean estuary.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16558}, doi = {10.1111/1462-2920.16558}, pmid = {38115223}, issn = {1462-2920}, support = {DE180100535//Australian Research Council/ ; }, mesh = {*Greenhouse Gases ; Estuaries ; Methane ; Dissolved Organic Matter ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Ammonium Compounds ; }, abstract = {Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 μM, 273.31 ± 6.05 μM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.}, }
@article {pmid38114339, year = {2024}, author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butchart, SHM and Butterworth, HM and Clarke, SJ and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, AC and James, J and Kaartokallio, H and Le Roux, X and Lickorish, FA and Newport, S and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Primack, RB and Primack, WE and Schloss, IR and Spalding, MD and Ten Brink, D and Tew, E and Timoshyna, A and Tubbs, N and Watson, JEM and Wentworth, J and Wilson, JD and Thornton, A}, title = {A horizon scan of global biological conservation issues for 2024.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {1}, pages = {89-100}, doi = {10.1016/j.tree.2023.11.001}, pmid = {38114339}, issn = {1872-8383}, mesh = {*Ecosystem ; *Biodiversity ; Conservation of Natural Resources ; Forecasting ; Food ; }, abstract = {We present the results of our 15th horizon scan of novel issues that could influence biological conservation in the future. From an initial list of 96 issues, our international panel of scientists and practitioners identified 15 that we consider important for societies worldwide to track and potentially respond to. Issues are novel within conservation or represent a substantial positive or negative step-change with global or regional extents. For example, new sources of hydrogen fuel and changes in deep-sea currents may have profound impacts on marine and terrestrial ecosystems. Technological advances that may be positive include benchtop DNA printers and the industrialisation of approaches that can create high-protein food from air, potentially reducing the pressure on land for food production.}, }
@article {pmid38112791, year = {2023}, author = {Yue, Y and Yang, Z and Wang, F and Chen, X and Huang, Y and Ma, J and Cai, L and Yang, M}, title = {Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {18}, pmid = {38112791}, issn = {1432-184X}, mesh = {*Ecosystem ; Biodiversity ; Fresh Water ; Rivers/microbiology ; *Microbiota ; Bacteria/genetics ; China ; Nitrogen ; }, abstract = {Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.}, }
@article {pmid38112441, year = {2024}, author = {Foxall, RL and Means, J and Marcinkiewicz, AL and Schillaci, C and DeRosia-Banick, K and Xu, F and Hall, JA and Jones, SH and Cooper, VS and Whistler, CA}, title = {Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0285123}, pmid = {38112441}, issn = {2150-7511}, support = {R/SFA-4//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R-HCE-3//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R/SFA-13//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; NH00698//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00625//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00658//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; }, mesh = {Prophages ; *Vibrio parahaemolyticus/genetics ; Inoviridae ; Ecosystem ; Bacteria ; *Bacteriophages/genetics ; }, abstract = {An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.}, }
@article {pmid38111463, year = {2024}, author = {Li, C and Gillings, MR and Zhang, C and Chen, Q and Zhu, D and Wang, J and Zhao, K and Xu, Q and Leung, PH and Li, X and Liu, J and Jin, L}, title = {Ecology and risks of the global plastisphere as a newly expanding microbial habitat.}, journal = {Innovation (Cambridge (Mass.))}, volume = {5}, number = {1}, pages = {100543}, pmid = {38111463}, issn = {2666-6758}, abstract = {Plastic offers a new niche for microorganisms, the plastisphere. The ever-increasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects. Here, we present a global fingerprint of the plastisphere, analyzing samples collected from freshwater, seawater, and terrestrial ecosystems. The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats. New coexistence patterns-loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats-are seen in the plastisphere. Plastisphere microbiomes generally have a great potential to metabolize organic compounds, which could accelerate carbon turnover. Microorganisms involved in the nitrogen cycle are also altered in the plastisphere, especially in freshwater plastispheres, where a high abundance of denitrifiers may increase the release of nitrite (aquatic toxicant) and nitrous oxide (greenhouse gas). Enrichment of animal, plant, and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms. Our findings highlight that if the trajectory of plastic emissions is not reversed, the expanding plastisphere could pose critical planetary health challenges.}, }
@article {pmid38110747, year = {2023}, author = {Steinberger, Y and Doniger, T and Applebaum, I and Sherman, C and Rotbart, N}, title = {Effects of Vineyard Agro-management Practices on Soil Bacterial Community Composition, and Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {17}, pmid = {38110747}, issn = {1432-184X}, mesh = {Humans ; *Soil/chemistry ; Farms ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; *Microbiota ; }, abstract = {Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.}, }
@article {pmid38110491, year = {2023}, author = {Elsayed, SS and van der Heul, HU and Xiao, X and Nuutila, A and Baars, LR and Wu, C and Metsä-Ketelä, M and van Wezel, GP}, title = {Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis.}, journal = {Communications chemistry}, volume = {6}, number = {1}, pages = {281}, pmid = {38110491}, issn = {2399-3669}, support = {16439//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.}, }
@article {pmid38108886, year = {2023}, author = {Morrill, A and Forbes, MR and Vesterinen, EJ and Tamminen, M and Sääksjärvi, IE and Kaunisto, KM}, title = {Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {16}, pmid = {38108886}, issn = {1432-184X}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Ecology ; Feces ; Host Specificity ; *Odonata ; }, abstract = {Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species. Using metabarcoding based on the 16S rRNA gene, we identified 1513 sequence variants, representing distinct bacterial 'taxa'. Intriguingly, the damselfly species showed somewhat different magnitudes of richness of ZOTUs, ranging from 480 to 914 ZOTUs. In total, 921 (or 60.8% of the 1513) distinct ZOTUs were non-shared, each found only in one species, and then most often in only a single individual. There was a surfeit of these non-shared incidental ZOTUs in the Enallagma species accounting for it showing the highest bacterial richness and accounting for a sample-wide pattern of more single-species ZOTUs than expected, based on comparisons to the null model. Future studies should address the extent to which faecal bacteria represent non-incidental gut bacteria and whether abundant and shared taxa are true gut symbionts. Pictures of odonates adopted from Norske Art databank under Creative Commons License (CC BY 4.0).}, }
@article {pmid38107863, year = {2023}, author = {Vandeweyer, D and Bruno, D and Bonelli, M and IJdema, F and Lievens, B and Crauwels, S and Casartelli, M and Tettamanti, G and De Smet, J}, title = {Bacterial biota composition in gut regions of black soldier fly larvae reared on industrial residual streams: revealing community dynamics along its intestinal tract.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276187}, pmid = {38107863}, issn = {1664-302X}, abstract = {Some insect species have gained attention as efficient bioconverters of low-value organic substrates (i.e., residual streams) into high-value biomass. Black soldier fly (BSF) (Hermetia illucens) larvae are particularly interesting for bioconversion due to their ability to grow on a wide range of substrates, including low-value industrial residual streams. This is in part due to the plasticity of the gut microbiota of polyphagous insects, like BSF. Gut microbiota composition varies depending on rearing substrates, via a mechanism that might support the recruitment of microorganisms that facilitate digestion of a specific substrate. At the same time, specific microbial genera do persist on different substrates via unknown mechanisms. This study aimed to offer insights on this microbial plasticity by investigating how the composition of the bacterial community present in the gut of BSF larvae responds to two industrial residual streams: swill (a mixture of catering and supermarket leftovers) and distiller's dried grains with solubles. The bacterial biota composition of substrates, whole larvae at the beginning of the rearing period and at harvest, rearing residues, and larval gut regions were investigated through 16S rRNA gene sequencing. It was observed that both substrate and insect development influenced the bacterial composition of the whole larvae. Zooming in on the gut regions, there was a clear shift in community composition from a higher to a lower diversity between the anterior/middle midgut and the posterior midgut/hindgut, indicating a selective pressure occurring in the middle midgut region. Additionally, the abundance of the bacterial biota was always high in the hindgut, while its diversity was relatively low. Even more, the bacterial community in the hindgut was found to be relatively more conserved over the different substrates, harboring members of the BSF core microbiota. We postulate a potential role of the hindgut as a reservoir for insect-associated microbes. This warrants further research on that underexplored region of the intestinal tract. Overall, these findings contribute to our understanding of the bacterial biota structure and dynamics along the intestinal tract, which can aid microbiome engineering efforts to enhance larval performance on (industrial) residual streams.}, }
@article {pmid38105519, year = {2024}, author = {Pinto, S and Benincà, E and Galazzo, G and Jonkers, D and Penders, J and Bogaards, JA}, title = {Heterogeneous associations of gut microbiota with Crohn's disease activity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2292239}, pmid = {38105519}, issn = {1949-0984}, mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Inflammation ; Bacteria/genetics ; Bacteroidetes ; }, abstract = {The multi-factorial involvement of gut microbiota with Crohn's disease (CD) necessitates robust analysis to uncover possible associations with particular microbes. CD has been linked to specific bacteria, but reported associations vary widely across studies. This inconsistency may result from heterogeneous associations across individual patients, resulting in no apparent or only weak relationships with the means of bacterial abundances. We investigated the relationship between bacterial relative abundances and disease activity in a longitudinal cohort of CD patients (n = 57) and healthy controls (n = 15). We applied quantile regression, a statistical technique that allows investigation of possible relationships outside the mean response. We found several significant and mostly negative associations with CD, especially in lower quantiles of relative abundance on family or genus level. Associations found by quantile regression deviated from the mean response in relative abundances of Coriobacteriaceae, Pasteurellaceae, Peptostreptococcaceae, Prevotellaceae, and Ruminococcaceae. For the family Streptococcaceae we found a significant elevation in relative abundance for patients experiencing an exacerbation relative to those who remained without self-reported symptoms or measurable inflammation. Our analysis suggests that specific bacterial families are related to CD and exacerbation, but associations vary between patients due to heterogeneity in disease course, medication history, therapy response, gut microbiota composition and historical contingency. Our study underscores that microbial diversity is reduced in the gut of CD patients, but suggests that the process of diversity loss is rather irregular with respect to specific taxonomic groups. This novel insight may advance our ecological understanding of this complex disease.}, }
@article {pmid38103698, year = {2024}, author = {Yuan, J and Yang, L and Yu, P and Tang, N and Liu, L and Wang, W and Wang, P and Yang, Q and Guo, S and Li, J}, title = {Comparison and development of scanning electron microscope techniques for delicate plant tissues.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {340}, number = {}, pages = {111963}, doi = {10.1016/j.plantsci.2023.111963}, pmid = {38103698}, issn = {1873-2259}, mesh = {Microscopy, Electron, Scanning ; *Plants ; Temperature ; *Water ; }, abstract = {Cell deformation often occurs during sample preparation and imaging with scanning electron microscope (SEM), especially with delicate samples, which influences the accuracy of the results. Here we investigate the influence of several preparation methods on cell deformation, using water content and tissue hardness as indicators to classify "delicate" samples of plant species. The degree of deformation in samples resulting from five preparation methods was measured at the tissue and single-cell levels, revealing that a cryo- and methanol-fixation produced lower degrees of tissue dimension deformation and better preservation of cell shape for delicate samples, while for harder tissues, other preparation methods for a dehydrated specimen are also suitable. Stability and image quality of delicate samples could be improved with the application of a cryo-protectant combined with a lower cryo-stage temperature, e.g. - 30 °C. We show that the sample stability under the beam was improved by combining larger sample size and cryo-stage application. Furthermore, the influence of adaxial and abaxial tissue surfaces, the accelerating voltage, and sputter coating time on sample stability and image quality was evaluated. Our study is valuable for artifact reduction and easy application of SEM.}, }
@article {pmid38102317, year = {2023}, author = {Modra, H and Ulmann, V and Gersl, M and Babak, V and Konecny, O and Hubelova, D and Caha, J and Kudelka, J and Falkinham, JO and Pavlik, I}, title = {River Sediments Downstream of Villages in a Karstic Watershed Exhibited Increased Numbers and Higher Diversity of Nontuberculous Mycobacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {15}, pmid = {38102317}, issn = {1432-184X}, mesh = {*Nontuberculous Mycobacteria ; *Rivers ; Prevalence ; Water Quality ; Phosphorus ; }, abstract = {The impact of residential villages on the nontuberculous mycobacteria (NTM) in streams flowing through them has not been studied in detail. Water and sediments of streams are highly susceptible to anthropogenic inputs such as surface water flows. This study investigated the impact of seven residential villages in a karst watershed on the prevalence and species spectrum of NTM in water and sediments. Higher NTM species diversity (i.e., 19 out of 28 detected) was recorded downstream of the villages and wastewater treatment plants (WWTPs) compared to sampling sites upstream (i.e., 5). Significantly, higher Zn and lower silicon concentrations were detected in sediments inside the village and downstream of the WWTP's effluents. Higher phosphorus concentration in sediment was downstream of WWTPs compared to other sampling sites. The effluent from the WWTPs had a substantial impact on water quality parameters with significant increases in total phosphorus, anions (Cl[-]and N-NH3[-]), and cations (Na[+] and K[+]). The results provide insights into NTM numbers and species diversity distribution in a karst watershed and the impact of urban areas. Although in this report the focus is on the NTM, it is likely that other water and sediment microbes will be influenced as well.}, }
@article {pmid38098978, year = {2023}, author = {Gonzalez, OA and Kirakodu, SS and Ebersole, JL}, title = {DAMPs and alarmin gene expression patterns in aging healthy and diseased mucosal tissues.}, journal = {Frontiers in oral health}, volume = {4}, number = {}, pages = {1320083}, pmid = {38098978}, issn = {2673-4842}, support = {P20 GM103538/GM/NIGMS NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; }, abstract = {INTRODUCTION: Periodontitis is delineated by a dysbiotic microbiome at sites of lesions accompanied by a dysregulated persistent inflammatory response that undermines the integrity of the periodontium. The interplay of the altered microbial ecology and warning signals from host cells would be a critical feature for maintaining or re-establishing homeostasis in these tissues.<br><br>METHODS: This study used a nonhuman primate model (Macaca mulatta) with naturally-occurring periodontitis (n&#x2009;=&#x2009;34) and experimental ligature-induced periodontitis (n&#x2009;=&#x2009;36) to describe the features of gene expression for an array of damage-associate molecular patterns (DAMPs) or alarmins within the gingival tissues. The animals were age stratified into: &#x2264;3 years (Young), 7-12 years (Adolescent), 12-15 years (Adult) and 17-23 years (Aged). Gingival tissue biopsies were examined via microarray. The analysis focused on 51 genes representative of the DAMPs/alarmins family of host cell warning factors and 18 genes associated with tissue destructive processed in the gingival tissues. Bacterial plaque samples were collected by curette sampling and 16S rRNA gene sequences used to describe the oral microbiome.<br><br>RESULTS: A subset of DAMPs/alarmins were expressed in healthy and naturally-occurring periodontitis tissues in the animals and suggested local effects on gingival tissues leading to altered levels of DAMPs/alarmins related to age and disease. Significant differences from adult healthy levels were most frequently observed in the young and adolescent animals with few representatives in this gene array altered in the healthy aged gingival tissues. Of the 51 target genes, only approximately &#x2153; were altered by &#x2265;1.5-fold in any of the age groups of animals during disease, with those increases observed during disease initiation. Distinctive positive and negative correlations were noted with the DAMP/alarmin gene levels and comparative expression changes of tissue destructive molecules during disease across the age groups. Finally, specific correlations of DAMP/alarmin genes and relative abundance of particular microbes were observed in health and resolution samples in younger animals, while increased correlations during disease in the older groups were noted.<br><br>CONCLUSIONS: Thus, using this human-like preclinical model of induced periodontitis, we demonstrated the dynamics of the activation of the DAMP/alarmin warning system in the gingival tissues that showed some specific differences based on age.}, }
@article {pmid38098078, year = {2023}, author = {Huete-Stauffer, TM and Logares, R and Ansari, MI and Røstad, A and Calleja, ML and Morán, XAG}, title = {Increased prokaryotic diversity in the Red Sea deep scattering layer.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {87}, pmid = {38098078}, issn = {2524-6372}, support = {CCF-2017/2018//King Abdullah University of Science and Technology/ ; RYC-2013-12554//Ministerio de Econom&#xed;a y Competitividad/ ; }, abstract = {BACKGROUND: The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m.<br><br>RESULTS: Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer.<br><br>CONCLUSIONS: We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200&#xa0;m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.}, }
@article {pmid38097563, year = {2023}, author = {Riva, A and Rasoulimehrabani, H and Cruz-Rubio, JM and Schnorr, SL and von Baeckmann, C and Inan, D and Nikolov, G and Herbold, CW and Hausmann, B and Pjevac, P and Schintlmeister, A and Spittler, A and Palatinszky, M and Kadunic, A and Hieger, N and Del Favero, G and von Bergen, M and Jehmlich, N and Watzka, M and Lee, KS and Wiesenbauer, J and Khadem, S and Viernstein, H and Stocker, R and Wagner, M and Kaiser, C and Richter, A and Kleitz, F and Berry, D}, title = {Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8210}, pmid = {38097563}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; P27831-B28//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 741623//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Inulin/metabolism ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; Prebiotics ; }, abstract = {Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.}, }
@article {pmid38096695, year = {2024}, author = {Wang, Q and Sun, Z and Song, S and Ali, A and Xu, H}, title = {Can salinity variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.}, journal = {Marine pollution bulletin}, volume = {198}, number = {}, pages = {115882}, doi = {10.1016/j.marpolbul.2023.115882}, pmid = {38096695}, issn = {1879-3363}, mesh = {*Biodiversity ; Environmental Monitoring ; Salinity ; *Ciliophora ; Logistic Models ; Ecosystem ; }, abstract = {To investigate effects of salinity variability on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems (TCCSs). Periphytic protozoan communities were incubated using glass slides as artificial substrata in five TCCS aquaria with a large-scale salinity gradient of 9, 19, 29 (control), 39, and 49 PSU, respectively. The colonization dynamics were observed on days 3, 5, 7, 10, 14, and 21. The colonization dynamics were well fitted to the MacArthur-Wilson and logistic model equations in colonization and growth curves in all five treatments, respectively. However, the maximum species richness and abundance were reduced, and the colonization patterns were significantly shifted in four treatments with salinity changed by 20 PSU compared to the control (29 PSU). Thus, it is suggested that the large-scale salinity variability may reduce the species richness significantly and affect colonization dynamics of periphytic protozoan fauna in marine environments.}, }
@article {pmid38095470, year = {2024}, author = {Guo, Q and Gong, L}, title = {Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0264223}, pmid = {38095470}, issn = {2165-0497}, support = {2021XJKK0900//the third comprehensive scientific investigtion project in xinjiang/ ; }, mesh = {*Soil Microbiology ; Forests ; Trees ; *Microbiota ; Soil/chemistry ; }, abstract = {The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.}, }
@article {pmid38095319, year = {2024}, author = {Forman-Ankjaer, B and Hvid-Jensen, F and Kobel, CM and Greve, T}, title = {Short communication: first case of bacteraemia caused by Dielma fastidiosa in a patient hospitalized with diverticulitis.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {132}, number = {2}, pages = {130-133}, doi = {10.1111/apm.13367}, pmid = {38095319}, issn = {1600-0463}, mesh = {Phylogeny ; Firmicutes ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Humans ; *Bacteremia/diagnosis ; Likelihood Functions ; *Diverticulitis ; }, abstract = {Dielma fastidiosa is a gram-negative, anaerobic rod belonging to the family Erysipelotrichaceae. D. fastidiosa has previously been isolated in human stool samples as part of the commensal flora; however, prior to this case, it has never been identified as a human pathogen. We present the first case of bacteraemia with D. fastidiosa. Bacterial growth in the blood culture bottle was detected by the automated blood culture system BacT/ALERT 3D. Culturing was performed, and bacterial colonies were identified as D. fastidiosa using MALDI-TOF MS. A subsequent whole-genome sequencing using Illumina NovaSeq was performed, and a phylogenetic tree depicting all available sequences of D. fastidiosa was generated. The reference MALDI-TOF spectrum and species identification was compared with the previously published spectrum. Whole-genome sequencing confirmed the tentative MALDI-TOF species identification. Notably, the maximum-likelihood-based phylogenetic analysis placed the D. fastidiosa isolate from this clinical case within the known variation of the eight publicly available sequences of this species. We identified D. fastidiosa by whole-genome sequencing followed by maximum-likelihood analysis as a possible pathogen in this case of bacteraemia in a patient hospitalized with diverticulitis.}, }
@article {pmid38094622, year = {2023}, author = {Ollison, GA and Hu, SK and Hopper, JV and Stewart, BP and Beatty, JL and Caron, DA}, title = {Physiology governing diatom vs. dinoflagellate bloom and decline in coastal Santa Monica Bay.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287326}, pmid = {38094622}, issn = {1664-302X}, abstract = {Algal blooms on the Southern California coast are typically dominated by diatom and dinoflagellate taxa, and are governed by their physiological responses to environmental cues; however, we lack a predictive understanding of the environmental controls underlying the establishment and persistence of these distinct bloom events. In this study, we examined gene expression among the numerically dominant diatom and dinoflagellate taxa during spring upwelling bloom events to compare the physiological underpinnings of diatom vs. dinoflagellate bloom dynamics. Diatoms, which bloomed following upwelling events, expressed genes related to dissolved inorganic nitrogen utilization, and genes related to the catabolism of chitin that may have prolonged their bloom duration following nitrogen depletion. Conversely, dinoflagellates bloomed under depleted inorganic nitrogen conditions, exhibited less variation in transcriptional activity, and expressed few genes associated with dissolved inorganic nutrients during their bloom. Dinoflagellate profiles exhibited evidence of proteolysis and heterotrophy that may have enabled them to bloom to high abundances under depleted inorganic nutrients. Taken together, diatom and dinoflagellate transcriptional profiles illustrated guild-specific physiologies that are tuned to respond to and thrive under distinct environmental "windows of opportunity."}, }
@article {pmid38091083, year = {2023}, author = {Perez-Bou, L and Muñoz-Palazon, B and Gonzalez-Lopez, J and Gonzalez-Martinez, A and Correa-Galeote, D}, title = {Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {14}, pmid = {38091083}, issn = {1432-184X}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Waste Disposal, Fluid ; Genes, Bacterial/genetics ; Ecosystem ; Drug Resistance, Microbial/genetics ; Sewage/microbiology ; }, abstract = {Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.}, }
@article {pmid38088973, year = {2023}, author = {Liu, ZS and Wang, KH and Cai, M and Yang, ML and Wang, XK and Ma, HL and Yuan, YH and Wu, LH and Li, DF and Liu, SJ}, title = {Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1289110}, pmid = {38088973}, issn = {1664-302X}, abstract = {There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research was carried out on five bacterial strains which were isolated and cultivated from polycyclic aromatic hydrocarbons, and heavy metals polluted soil of an abandoned coking plant. Phylogenetical analysis showed that they belonged to the phyla Proteobacteria and Actinobacteria, and their 16S rRNA gene sequence identities were lower than 98.5% to any known and validly nominated bacterial species, suggesting that they were potentially representing new species. Using polyphasic taxonomic approaches, the five strains were classified as new species of the families Microbacteriaceae and Sphingomonadaceae. Genome sizes of the five strains ranged from 3.07 to 6.60 Mb, with overall DNA G+C contents of 63.57-71.22 mol%. The five strains had average nucleotide identity of 72.38-87.38% and digital DNA-DNA hybridization of 14.0-34.2% comparing with their closely related type strains, which were all below the thresholds for species delineation, supporting these five strains as novel species. Based on the phylogenetic, phylogenomic, and phenotypic characterizations, the five novel species are proposed as Agromyces chromiiresistens (type strain H3Y2-19a[T] = CGMCC 1.61332[T]), Salinibacterium metalliresistens (type strain H3M29-4[T] = CGMCC 1.61335T), Novosphingobium album (type strain H3SJ31-1[T] = CGMCC 1.61329[T]), Sphingomonas pollutisoli (type strain H39-1-10[T] = CGMCC 1.61325[T]), and Sphingobium arseniciresistens (type strain H39-3-25[T] = CGMCC 1.61326[T]). Comparative genome analysis revealed that the species of the family Sphingomonadaceae represented by H39-1-10[T], H39-3-25[T], and H3SJ31-1[T] possessed more functional protein-coding genes for the degradation of aromatic pollutants than the species of the family Microbacteriaceae represented by H3Y2-19a[T] and H3M29-4[T]. Furthermore, their capacities of resisting heavy metals and metabolizing aromatic compounds were investigated. The results indicated that strains H3Y2-19a[T] and H39-3-25[T] were robustly resistant to chromate (VI) and/or arsenite (III). Strains H39-1-10[T] and H39-3-25[T] grew on aromatic compounds, including naphthalene, as carbon sources even in the presence of chromate (VI) and arsenite (III). These features reflected their adaptation to the polluted soil environment.}, }
@article {pmid38088573, year = {2024}, author = {Lücking, G and Albrecht, K and Märtlbauer, E and Schauer, K}, title = {Draft genome sequences of two thermophilic, spore-forming Aeribacillus pallidus strains isolated from dairy products.}, journal = {Microbiology resource announcements}, volume = {13}, number = {1}, pages = {e0089623}, pmid = {38088573}, issn = {2576-098X}, abstract = {The presence of thermophilic spore-forming bacteria is challenging in industrial food processing. The presented genome sequences of Aeribacillus pallidus, isolated from raw milk and cocoa powder, provide insights into how to prevent damage to minimally processed foods and products with extended shelf life, such as milk products.}, }
@article {pmid38087672, year = {2024}, author = {Effenberger, M and Grander, C and Hausmann, B and Enrich, B and Pjevac, P and Zoller, H and Tilg, H}, title = {Apelin and the gut microbiome: Potential interaction in human MASLD.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {56}, number = {6}, pages = {932-940}, doi = {10.1016/j.dld.2023.11.023}, pmid = {38087672}, issn = {1878-3562}, mesh = {Humans ; *Apelin/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; Aged ; *Carcinoma, Hepatocellular/microbiology/blood ; *Liver Cirrhosis/microbiology/blood ; Liver Neoplasms/microbiology ; Apelin Receptors/metabolism ; Cytokines/blood ; Feces/microbiology/chemistry ; Adult ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease with increasing numbers worldwide. Adipokines like apelin (APLN) can act as key players in the complex pathophysiology of MASLD.<br><br>AIMS: Investigating the role of APLN in MASLD.<br><br>METHODS: Fecal and blood samples were collected in a MASLD cohort and healthy controls (HC). MASLD patients with liver fibrosis and MASLD-associated hepatocellular carcinoma (HCC) were included into the study. Systemic concentration of Apelin, Apelin receptor (APLNR) and circulating cytokines were measured in serum samples.<br><br>RESULTS: Apelin concentration correlated with the Fib-4 score and was elevated in MASLD patients (mild fibrosis, mF (Fib-4 <3.25) and severe fibrosis, sF (Fib-4 >3.25)) as well as in MASLD-associated HCC patients compared to HC. In accordance APLNR and circulating cytokines were also elevated in mF and sF. In contrast apelin levels were negatively associated with liver survival at three and five years. Changes in taxa composition at phylum level showed an increase of Enterobactericae, Prevotellaceae and Lactobacillaceae in patients with sF compared to mF. We could also observe an association between apelin concentrations and bacterial lineages (phyla).<br><br>CONCLUSIONS: Circulating apelin is associated with liver fibrosis and HCC. In addition, there might exist an interaction between systemic apelin and the gut microbiome.}, }
@article {pmid38087002, year = {2023}, author = {Montaño-Salazar, S and Quintanilla, E and Sánchez, JA}, title = {Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22049}, pmid = {38087002}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology ; El Nino-Southern Oscillation ; Biodiversity ; Acclimatization ; Cold Temperature ; Bacteria ; Coral Reefs ; }, abstract = {The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.}, }
@article {pmid38086476, year = {2024}, author = {Zhang, M and Zhao, B and Yan, Y and Cheng, Z and Li, Z and Han, L and Sun, Y and Zheng, Y and Xia, Y}, title = {Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169203}, doi = {10.1016/j.scitotenv.2023.169203}, pmid = {38086476}, issn = {1879-1026}, mesh = {Metagenome ; *Arsenic/analysis ; Carbon/metabolism ; *Microbiota ; Bacteria/metabolism ; Geologic Sediments/chemistry ; }, abstract = {The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d[-1] and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.}, }
@article {pmid38085721, year = {2023}, author = {Coleman, ME and Oscar, TP and Negley, TL and Stephenson, MM}, title = {Suppression of pathogens in properly refrigerated raw milk.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0289249}, pmid = {38085721}, issn = {1932-6203}, mesh = {Humans ; Animals ; Milk ; Food Microbiology ; Pilot Projects ; Colony Count, Microbial ; Salmonella ; *Escherichia coli O157 ; *Listeria monocytogenes ; }, abstract = {Conflicting claims exist regarding pathogen growth in raw milk. A small pilot study was designed to provide definitive data on trends for pathogen growth and decline in raw bovine milk hygienically produced for direct human consumption. An independent laboratory conducted the study, monitoring growth and decline of pathogens inoculated into raw milk. Raw milk samples were inoculated with foodborne pathogens (Campylobacter, E. coli O157:H7, Listeria monocytogenes, or Salmonella) at lower (<162 colony forming units (CFU) per mL) and higher levels (<8,300 CFU/mL). Samples were stored at 4.4°C and quantified over time after inoculation (days 0, 3, 6, 9, 12, and 14) by standard culture-based methods. Statistical analysis of trends using the Mann-Kendall Trend Test and Analysis of Variance were conducted for 48 time series observations. Evidence of pathogen growth was documented for L. monocytogenes in 8 of 12 replicates (P = 0.001 to P = 0.028). Analysis of variance confirmed significant increases for L. monocytogenes at both initial levels in week 2. No evidence of growth was documented over 14 days for the three pathogens predominantly associated with raw milk outbreaks in the US (Campylobacter, E. coli O157:H7, and Salmonella). Further research is needed to characterize parameters for pathogen growth and decline to support re-assessment of risks that were based on incorrect assumptions about interactions of pathogens with the raw milk microbiota.}, }
@article {pmid38082204, year = {2024}, author = {Li, X and Yu, S and Cheng, Z and Chang, X and Yun, Y and Jiang, M and Chen, X and Wen, X and Li, H and Zhu, W and Xu, S and Xu, Y and Wang, X and Zhang, C and Wu, Q and Hu, J and Lin, Z and Aury, JM and Van de Peer, Y and Wang, Z and Zhou, X and Wang, J and Lü, P and Zhang, L}, title = {Origin and evolution of the triploid cultivated banana genome.}, journal = {Nature genetics}, volume = {56}, number = {1}, pages = {136-142}, pmid = {38082204}, issn = {1546-1718}, support = {833522//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Musa/genetics ; *Fusarium/genetics ; Triploidy ; Plant Breeding ; Transcription Factors/genetics ; Plant Diseases/genetics ; }, abstract = {Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.}, }
@article {pmid38082143, year = {2023}, author = {Botero Rute, LM and Caro-Quintero, A and Acosta-González, A}, title = {Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {13}, pmid = {38082143}, issn = {1432-184X}, mesh = {Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Rumen/microbiology ; Bacteria ; *Microbiota ; }, abstract = {The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10[-2], 10[-6], 10[-12]), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10[-2] and 10[-6] dilutions clustered closely while the 10[-12] dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.}, }
@article {pmid38078767, year = {2024}, author = {Smith, AB and Specker, JT and Hewlett, KK and Scoggins, TR and Knight, M and Lustig, AM and Li, Y and Evans, KM and Guo, Y and She, Q and Christopher, MW and Garrett, TJ and Moustafa, AM and Van Tyne, D and Prentice, BM and Zackular, JP}, title = {Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0165623}, pmid = {38078767}, issn = {2150-7511}, support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R21 AI164018/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; R03 AI168491/AI/NIAID NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile ; Enterococcus faecalis ; *Clostridium Infections/microbiology ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.}, }
@article {pmid38078555, year = {2024}, author = {Zhang, X and Dai, H and Huang, Y and Liu, K and Li, X and Zhang, S and Fu, S and Jiao, S and Chen, C and Dong, B and Yang, Z and Cui, Y and Li, H and Liu, S}, title = {Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and β-diversity during forest secondary succession.}, journal = {Molecular ecology}, volume = {33}, number = {4}, pages = {e17241}, doi = {10.1111/mec.17241}, pmid = {38078555}, issn = {1365-294X}, support = {31700383//Natural Science Foundation of China/ ; 31800375//Natural Science Foundation of China/ ; 31930078//Natural Science Foundation of China/ ; 32071556//Natural Science Foundation of China/ ; U1904204//Natural Science Foundation of China/ ; 222300420036//Natural Science Foundation of Henan Province/ ; //the Fundamental Research Funds of Northwest A&amp;F University/ ; QCYRCXM-2022-347//the high-level innovation and entrepreneurship talent project of Qinchuangyuan/ ; }, mesh = {*Biodiversity ; Forests ; Ecology ; *Microbiota ; Bacteria/genetics ; Soil ; Ecosystem ; }, abstract = {Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on β-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in β-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but β-diversity is constrained by environmental selection.}, }
@article {pmid38076468, year = {2024}, author = {Nikita, R and Ghosh, A and Yash,  and Kumar, C and Mandal, A and Saini, N and Dubey, SK and Gogoi, K and Rajts, F and Belton, B and Bhadury, P}, title = {Dataset of biological community structure in Deepor Beel using eDNA approach-A RAMSAR wetland of Assam, India.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109786}, pmid = {38076468}, issn = {2352-3409}, abstract = {Deepor Beel, located in the state of Assam in India, is a Wetland of International Importance with a Wildlife Sanctuary and is the only RAMSAR site in the state. Though of invaluable ecological significance, the wetland is facing anthropogenic stressors, leading to rapid degradation of ecological health. In December 2022, surface water was collected from six stations of Deepor Beel to elucidate biological communities using the eDNA approach. At the time of sampling, in-situ environmental parameters were measured in triplicates. The dissolved nutrients and concentrations of metals and metalloids were estimated using UV-Vis Spectrophotometry and ICP-MS approaches respectively. The study revealed a high concentration of dissolved nitrate in the surface water. High-throughput sequencing using Nanopore sequencing chemistry in a MinION platform indicated the overwhelming abundance of Moraxellaceae (Prokaryotes) and Eumetazoa (Eukaryotes). The abundance of Cyprinidae were also encountered in the studied wetland reflecting the biodiversity of fish populations. High nitrate along with elucidated microbial signals are crucial to designate ecological health status of Deeper Beel. This study is aimed at generating baseline information to aid long-term monitoring and restoration of the Deepor Beel as well as the first comprehensive assessment of a RAMSAR Site located in northeast of India.}, }
@article {pmid38075488, year = {2024}, author = {Wang, X and Guo, K and Rabaey, K and Prévoteau, A}, title = {(Bio)electrochemistry for the environment, ready for ignition?.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100336}, pmid = {38075488}, issn = {2666-4984}, }
@article {pmid38073168, year = {2023}, author = {Kumar, G and Bhadury, P}, title = {Exploring the influences of geographical variation on sequence signatures in the human gut microbiome.}, journal = {Journal of genetics}, volume = {102}, number = {}, pages = {}, pmid = {38073168}, issn = {0973-7731}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Firmicutes/genetics ; Bacteroidetes/genetics ; Geography ; }, abstract = {Geography shapes the structure and function of human gut microbiomes. In this study, we have explored the available human gut microbiome 16S rRNA sequence datasets of cohorts representing large geographical gradients. The 16S rRNA sequences representing V3-V4 as well as V4 regions generated using Illumina sequencing chemistry in the MiSeq platform encompassing the United States of America, Chile, South Africa, Kuwait, and Malaysia were subjected to in-depth computational biology analyses. Firmicutes and Bacteroidetes were the most dominant phyla present in all studied cohorts but Actinobacteria was exclusively present in high abundance in cohorts from Malaysia (15.99%). The relative abundance of five families, namely Bacteroidaceae, Ruminococcaceae, Prevotellaceae, Clostridiaceae, and Eubacteriaceae were highest representing the studied cohorts. The permutational multivariate analysis of variance (PERMANOVA) showed that the dissimilarity in the gut microbiome structure of cohorts representing studied countries was significant (R[2] = 0.28, P<0.001). The calculated Firmicutes to Bacteroidetes (F : B) ratio was found to be lowest in cohorts from South Africa (1.11) and Chile (0.95). The cohorts from South Africa exhibited the highest alpha diversity based on Hill numbers at q=0, whereas at q=1 and 2, cohorts from Malaysia had the highest alpha diversity. The beta diversity analysis revealed that cohorts from Chile formed a distinct cluster among all the studied geographical locations. For the first time, the study also showed that cohorts from Malaysia representing short geographical distances exhibited distinct intrapopulation differences in the gut microbiome and may not be influenced by cultural and genetic factors.}, }
@article {pmid38072930, year = {2023}, author = {Sakarika, M and Kerckhof, FM and Van Peteghem, L and Pereira, A and Van Den Bossche, T and Bouwmeester, R and Gabriels, R and Van Haver, D and Ulčar, B and Martens, L and Impens, F and Boon, N and Ganigué, R and Rabaey, K}, title = {The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {254}, pmid = {38072930}, issn = {1475-2859}, support = {CO2PERATE//Agentschap Innoveren en Ondernemen/ ; HBC.2019.2601//Agentschap Innoveren en Ondernemen/ ; HBC.2018.0188//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2205//Agentschap Innoveren en Ondernemen/ ; 1286824N//Fonds Wetenschappelijk Onderzoek/ ; 1S27821N//Fonds Wetenschappelijk Onderzoek/ ; BOF19/STA/044//Universiteit Gent/ ; }, mesh = {Biomass ; *Amino Acids ; *Proteome ; Cysteine ; Cell Size ; }, abstract = {BACKGROUND: It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value. Apart from the properties and nutritional quality of the produced microbial food (ingredient), this can also impact its sustainability. To qualitatively assess these aspects, here, we investigated the link between substrate availability, growth rate, cell composition and size of Cupriavidus necator and Komagataella phaffii.<br><br>RESULTS: Biomass with decreased nucleic acid and increased protein content was produced at low growth rates. Conversely, high rates resulted in larger cells, which could enable more efficient biomass harvesting. The proteome allocation varied across the different growth rates, with more ribosomal proteins at higher rates, which could potentially affect the techno-functional properties of the biomass. Considering the distinct amino acid profiles established for the different cellular components, variations in their abundance impacts the product quality leading to higher cysteine and phenylalanine content at low growth rates. Therefore, we hint that costly external amino acid supplementations that are often required to meet the nutritional needs could be avoided by carefully applying conditions that enable targeted growth rates.<br><br>CONCLUSION: In summary, we demonstrate tradeoffs between nutritional quality and production rate, and we discuss the microbial biomass properties that vary according to the growth conditions.}, }
@article {pmid38072911, year = {2023}, author = {Arnolds, KL and Higgins, RC and Crandall, J and Li, G and Linger, JG and Guarnieri, MT}, title = {Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {12}, pmid = {38072911}, issn = {1432-184X}, support = {DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; }, mesh = {*Ecosystem ; Saccharomyces cerevisiae/genetics ; Soil Microbiology ; *Microbiota ; Soil ; Risk Assessment ; }, abstract = {Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.}, }
@article {pmid38072409, year = {2023}, author = {Ide, H and Ishii, K and Takahashi, Y and Fujitani, H and Tsuneda, S}, title = {Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga.}, journal = {Microbes and environments}, volume = {38}, number = {4}, pages = {}, pmid = {38072409}, issn = {1347-4405}, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Gallionellaceae/metabolism ; Nitrogen/metabolism ; }, abstract = {Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.}, }
@article {pmid38070605, year = {2024}, author = {Suman, J and Sredlova, K and Fraraccio, S and Jerabkova, M and Strejcek, M and Kabickova, H and Cajthaml, T and Uhlik, O}, title = {Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140909}, doi = {10.1016/j.chemosphere.2023.140909}, pmid = {38070605}, issn = {1879-1298}, mesh = {Animals ; *Polychlorinated Biphenyls/metabolism ; Hydroxylation ; Mixed Function Oxygenases/metabolism ; Bacteria/metabolism ; }, abstract = {Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.}, }
@article {pmid38070053, year = {2024}, author = {Deng, W and Bai, NE and Qi, FL and Yang, XY and She, R and Xiao, W}, title = {Temporal dynamics of the microbial heterogeneity-diversity relationship in microcosmic systems.}, journal = {Oecologia}, volume = {204}, number = {1}, pages = {35-46}, pmid = {38070053}, issn = {1432-1939}, support = {32371557//National Natural Science Foundation of China/ ; 2019QZKK2002//Second Tibetan Plateau Scientifc Expedition and Research Program/ ; }, mesh = {Animals ; *Biodiversity ; *Plants ; Ecosystem ; }, abstract = {Spatial heterogeneity significantly enhances biodiversity, representing one of the ecology's most enduring paradigms. However, many studies have found decreasing, humped, and neutral correlations between spatial heterogeneity and biodiversity (heterogeneity-diversity relationships, HDR). These findings have pushed this widely accepted theory back into controversy. Microbial HDR research has lagged compared to that of plants and animals. Nevertheless, microbes have features that add a temporal-scale perspective to HDR research that is critical to understanding patterns of HDR. In this study, 157 microcosms with different types spatial heterogeneity were set up to map the HDR of microorganisms and their temporal dynamics using high-throughput sequencing techniques. The results show that the following: 1. Spatial heterogeneity can significantly alter microbial diversity in microcosmic systems. Changes in microbial diversity, in turn, lead to changes in environmental conditions. These changes caused microorganisms to exhibit increasing, decreasing, humped, U-shaped, and neutral HDR patterns. 2. The emergence of HDR patterns is characterized by temporal dynamics. Additionally, the HDR patterns generated by spatial structural and compositional heterogeneity exhibit inconsistent emergence times. These results suggest that the temporal dynamics of HDR may be one of the reasons for the coexistence of multiple patterns in previous studies. The feedback regulation between spatial heterogeneity-biodiversity-environmental conditions is an essential reason for the temporally dynamics of HDR patterns. All future ecological studies should pay attention to the temporal dynamic patterns of ecological factors.}, }
@article {pmid38067489, year = {2023}, author = {Singh, SK and Shrivastava, S and Mishra, AK and Kumar, D and Pandey, VK and Srivastava, P and Pradhan, B and Behera, BC and Bahuguna, A and Baek, KH}, title = {Friedelin: Structure, Biosynthesis, Extraction, and Its Potential Health Impact.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {23}, pages = {}, pmid = {38067489}, issn = {1420-3049}, mesh = {Humans ; *Triterpenes/chemistry ; Anti-Inflammatory Agents ; Antioxidants/pharmacology ; Phytochemicals ; }, abstract = {Pharmaceutical companies are investigating more source matrices for natural bioactive chemicals. Friedelin (friedelan-3-one) is a pentacyclic triterpene isolated from various plant species from different families as well as mosses and lichen. The fundamental compounds of these friedelane triterpenoids are abundantly found in cork tissues and leaf materials of diverse plant genera such as Celastraceae, Asteraceae, Fabaceae, and Myrtaceae. They possess many pharmacological effects, including anti-inflammatory, antioxidant, anticancer, and antimicrobial activities. Friedelin also has an anti-insect effect and the ability to alter the soil microbial ecology, making it vital to agriculture. Ultrasound, microwave, supercritical fluid, ionic liquid, and acid hydrolysis extract friedelin with reduced environmental impact. Recently, the high demand for friedelin has led to the development of CRISPR/Cas9 technology and gene overexpression plasmids to produce friedelin using genetically engineered yeast. Friedelin with low cytotoxicity to normal cells can be the best phytochemical for the drug of choice. The review summarizes the structural interpretation, biosynthesis, physicochemical properties, quantification, and various forms of pharmacological significance.}, }
@article {pmid38067008, year = {2023}, author = {Popov, IV and Berezinskaia, IS and Popov, IV and Martiusheva, IB and Tkacheva, EV and Gorobets, VE and Tikhmeneva, IA and Aleshukina, AV and Tverdokhlebova, TI and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {23}, pages = {}, pmid = {38067008}, issn = {2076-2615}, support = {23-14-00316//Russian Science Foundation/ ; agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo.//Centre for Healthy Eating &amp; Food Innovation (HEFI)/ ; }, abstract = {The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.}, }
@article {pmid38066493, year = {2023}, author = {Shuanglian, Y and Huiling, Z and Xunting, L and Yifang, D and Yufen, L and Shanshan, X and Lijuan, S and Yunpeng, L}, title = {Establishment and validation of early prediction model for hypertriglyceridemic severe acute pancreatitis.}, journal = {Lipids in health and disease}, volume = {22}, number = {1}, pages = {218}, pmid = {38066493}, issn = {1476-511X}, support = {3502Z20204007//Xiamen Key Programs of Medicine and Health/ ; 3502Z20199172//Xiamen Priority Programs of Medicine and Health/ ; 2023zsyyhlky-010//Nursing research Programs of Zhongshan Hospital Xiamen University/ ; }, mesh = {Humans ; *Pancreatitis/diagnosis ; Severity of Illness Index ; Acute Disease ; Ascites ; Retrospective Studies ; Prognosis ; Biomarkers ; C-Reactive Protein ; *Hypertriglyceridemia ; }, abstract = {BACKGROUND: The prevalence of hypertriglyceridaemia-induced acute pancreatitis (HTG-AP) is increasing due to improvements in living standards and dietary changes. However, currently, there is no clinical multifactor scoring system specific to HTG-AP. This study aimed to screen the predictors of HTG-SAP and combine several indicators to establish and validate a visual model for the early prediction of HTG-SAP.<br><br>METHODS: The clinical data of 266 patients with HTG-SAP were analysed. Patients were classified into severe (N&#x2009;=&#x2009;42) and non-severe (N&#x2009;=&#x2009;224) groups according to the Atlanta classification criteria. Several statistical analyses, including one-way analysis, least absolute shrinkage with selection operator (LASSO) regression model, and binary logistic regression analysis, were used to evaluate the data.<br><br>RESULTS: The univariate analysis showed that several factors showed no statistically significant differences, including the number of episodes of pancreatitis, abdominal pain score, and several blood diagnostic markers, such as lactate dehydrogenase (LDH), serum calcium (Ca[2+]), C-reactive protein (CRP), and the incidence of pleural effusion, between the two groups (P&#x2009;<&#x2009;0.000). LASSO regression analysis identified six candidate predictors: CRP, LDH, Ca[2+], procalcitonin (PCT), ascites, and Balthazar computed tomography grade. Binary logistic regression multivariate analysis showed that CRP, LDH, Ca[2+], and ascites were independent predictors of HTG-SAP, and the area under the curve (AUC) values were 0.886, 0.893, 0.872, and 0.850, respectively. The AUC of the newly established HTG-SAP model was 0.960 (95% confidence interval: 0.936-0.983), which was higher than that of the bedside index for severity in acute pancreatitis (BISAP) score, modified CT severity index, Ranson score, and Japanese severity score (JSS) CT grade (AUC: 0.794, 0.796, 0.894 and 0.764, respectively). The differences were significant (P&#x2009;<&#x2009;0.01), except for the JSS prognostic indicators (P&#x2009;=&#x2009;0.130). The Hosmer-Lemeshow test showed that the predictive results of the model were highly consistent with the actual situation (P&#x2009;>&#x2009;0.05). The decision curve analysis plot suggested that clinical intervention can benefit patients when the model predicts that they are at risk for developing HTG-SAP.<br><br>CONCLUSIONS: CRP, LDH, Ca[2+], and ascites are independent predictors of HTG-SAP. The prediction model constructed based on these indicators has a high accuracy, sensitivity, consistency, and practicability in predicting HTG-SAP.}, }
@article {pmid38065941, year = {2023}, author = {Zhou, Y and Yang, Z and Liu, J and Li, X and Wang, X and Dai, C and Zhang, T and Carrión, VJ and Wei, Z and Cao, F and Delgado-Baquerizo, M and Li, X}, title = {Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8126}, pmid = {38065941}, issn = {2041-1723}, mesh = {Soil ; *Microbiota ; *Fabaceae ; Arachis ; Rhizosphere ; Crop Production ; Soil Microbiology ; Plant Roots ; }, abstract = {It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.}, }
@article {pmid38063370, year = {2024}, author = {Tamames, J and Jiménez-Lalana, D and Redondo, &#xc1; and Martínez-García, S and de Los Rios, A}, title = {In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13909}, doi = {10.1111/1755-0998.13909}, pmid = {38063370}, issn = {1755-0998}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Spain ; }, abstract = {We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.}, }
@article {pmid38060022, year = {2023}, author = {Abu Bakar, N and Lau, BYC and González-Aravena, M and Smykla, J and Krzewicka, B and Karsani, SA and Alias, SA}, title = {Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {11}, pmid = {38060022}, issn = {1432-184X}, support = {Postgraduate sponsorship//Majlis Amanah Rakyat/ ; HICoE grant (IOES-2014G)//Ministry of Higher Education, Malaysia/ ; UMRP (RP026A-18SUS)//Universiti Malaya/ ; }, mesh = {*Cold-Shock Response ; Proteomics ; *Ascomycota ; Soil Microbiology ; Soil ; Antarctic Regions ; Cold Temperature ; }, abstract = {In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.}, }
@article {pmid38059790, year = {2023}, author = {Martinez-Gutierrez, CA and Uyeda, JC and Aylward, FO}, title = {A timeline of bacterial and archaeal diversification in the ocean.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38059790}, issn = {2050-084X}, support = {IIBR-2141862//National Science Foundation/ ; Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; }, mesh = {*Archaea/genetics ; Phylogeny ; *Cyanobacteria ; Oxygen ; Oceans and Seas ; Seawater/microbiology ; }, abstract = {Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.}, }
@article {pmid38057381, year = {2023}, author = {Oliveira, FR and Lansac-Tôha, FM and Meira, BR and Progênio, M and Velho, LFM}, title = {Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {10}, pmid = {38057381}, issn = {1432-184X}, mesh = {*Ecosystem ; Plankton ; Phylogeny ; Fresh Water ; Biodiversity ; *Ciliophora ; Water ; }, abstract = {Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.}, }
@article {pmid38055943, year = {2023}, author = {Rodríguez, MA and Fernández, LA and Daisley, BA and Reynaldi, FJ and Allen-Vercoe, E and Thompson, GJ}, title = {Probiotics and in-hive fermentation as a source of beneficial microbes to support the gut microbial health of honey bees.}, journal = {Journal of insect science (Online)}, volume = {23}, number = {6}, pages = {}, pmid = {38055943}, issn = {1536-2442}, support = {//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas Buenos Aires/ ; //Global Affairs Canada Emerging Leaders/ ; //Americas Scholarship Program/ ; //Mar&#xed;a Agustina Rodr&#xed;guez/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Anti-Bacterial Agents/immunology/pharmacology/therapeutic use ; *Beekeeping/methods ; *Bees/drug effects/immunology/microbiology ; *Fermentation/immunology ; *Gastrointestinal Microbiome/immunology ; *Probiotics/pharmacology/therapeutic use ; }, abstract = {Managed populations of honey bees (Apis mellifera Linnaeus; Hymenoptera: Apidae) are regularly exposed to infectious diseases. Good hive management including the occasional application of antibiotics can help mitigate infectious outbreaks, but new beekeeping tools and techniques that bolster immunity and help control disease transmission are welcome. In this review, we focus on the applications of beneficial microbes for disease management as well as to support hive health and sustainability within the apicultural industry. We draw attention to the latest advances in probiotic approaches as well as the integration of fermented foods (such as water kefir) with disease-fighting properties that might ultimately be delivered to hives as an alternative or partial antidote to antibiotics. There is substantial evidence from in vitro laboratory studies that suggest beneficial microbes could be an effective method for improving disease resistance in honey bees. However, colony level evidence is lacking and there is urgent need for further validation via controlled field trials experimentally designed to test defined microbial compositions against specific diseases of interest.}, }
@article {pmid38054947, year = {2024}, author = {Knight, T and Sureka, S}, title = {A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT).}, journal = {Health security}, volume = {22}, number = {1}, pages = {31-38}, pmid = {38054947}, issn = {2326-5108}, mesh = {Humans ; *Intelligence ; }, }
@article {pmid38054712, year = {2024}, author = {Schloss, PD}, title = {Waste not, want not: revisiting the analysis that called into question the practice of rarefaction.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0035523}, pmid = {38054712}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computer Simulation ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {In 2014, McMurdie and Holmes published the provocatively titled "Waste not, want not: why rarefying microbiome data is inadmissible." The claims of their study have significantly altered how microbiome researchers control for the unavoidable uneven sequencing depths that are inherent in modern 16S rRNA gene sequencing. Confusion over the distinction between the definitions of rarefying and rarefaction continues to cloud the interpretation of their results. More importantly, the authors made a variety of problematic choices when designing and analyzing their simulations. I identified 11 factors that could have compromised the results of the original study. I reproduced the original simulation results and assessed the impact of those factors on the underlying conclusion that rarefying data is inadmissible. Throughout, the design of the original study made choices that caused rarefying and rarefaction to appear to perform worse than they truly did. Most important were the approaches used to assess ecological distances, the removal of samples with low sequencing depth, and not accounting for conditions where sequencing effort is confounded with treatment group. Although the original study criticized rarefying for the arbitrary removal of valid data, repeatedly rarefying data many times (i.e., rarefaction) incorporates all the data. In contrast, it is the removal of rare taxa that would appear to remove valid data. Overall, I show that rarefaction is the most robust approach to control for uneven sequencing effort when considered across a variety of alpha and beta diversity metrics.IMPORTANCEOver the past 10 years, the best method for normalizing the sequencing depth of samples characterized by 16S rRNA gene sequencing has been contentious. An often cited article by McMurdie and Holmes forcefully argued that rarefying the number of sequence counts was "inadmissible" and should not be employed. However, I identified a number of problems with the design of their simulations and analysis that compromised their results. In fact, when I reproduced and expanded upon their analysis, it was clear that rarefaction was actually the most robust approach for controlling for uneven sequencing effort across samples. Rarefaction limits the rate of falsely detecting and rejecting differences between treatment groups. Far from being "inadmissible", rarefaction is a valuable tool for analyzing microbiome sequence data.}, }
@article {pmid38054526, year = {2023}, author = {Altaisaikhan, A and Yoshihara, K and Hata, T and Miyata, N and Asano, Y and Suematsu, T and Kadota, Y and Sudo, N}, title = {Dietary supplementation with 1-kestose induces altered locomotor activity and increased striatal dopamine levels with a change in gut microbiota in male mice.}, journal = {Physiological reports}, volume = {11}, number = {23}, pages = {e15882}, pmid = {38054526}, issn = {2051-817X}, support = {JP20H04106//KAKENHI/ ; JP23K18276//KAKENHI/ ; 2020-192//Smoking Research Foundation (SRF)/ ; }, mesh = {Mice ; Animals ; Male ; *Dopamine ; *Gastrointestinal Microbiome ; Trisaccharides ; Prebiotics ; }, abstract = {1-Kestose (KES), a dietary fiber and prebiotic carbohydrate, benefits various physiological functions. This study aimed to examine whether diets supplemented with KES over three consecutive generations could significantly affect some host physiological aspects, including behavioral phenotypes and gut microbial ecology. Mice that received KES-supplemented diets for three generations demonstrated increased activity compared with those fed diets lacking KES. Furthermore, the KES group showed increased striatal dopamine (DA) and serotonin (5-HT) levels. The observed increase in DA levels within the striatum was positively correlated with locomotor activity in the KES group but not in the control (CON) group. The α-diversities were significantly lower in the KES group compared to the CON group. The three-dimensional principal coordinate analysis revealed a substantial distinction between the KES and CON groups across each generation. At the genus level, most gut microbiota genera exhibited lower abundances in the KES group than in the CON group, except for Bifidobacteria and Akkermansia. Spearman's rank-order analysis indicated significant negative correlations between the striatal DA levels and α-diversity values. These findings suggest that prolonged supplementation with KES may stimulate increased locomotor activity along with elevated striatal DA levels, which are potentially associated with KES-induced alterations in the gut microbiota.}, }
@article {pmid38053549, year = {2023}, author = {Song, W and Li, H and Zhou, Y and Liu, X and Li, Y and Wang, M and Li, DD and Tu, Q}, title = {Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291242}, pmid = {38053549}, issn = {1664-302X}, abstract = {A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.}, }
@article {pmid38053159, year = {2023}, author = {Costa, LSAS and de Faria, MR and Chiaramonte, JB and Mendes, LW and Sepo, E and de Hollander, M and Fernandes, JMC and Carrión, VJ and Bettiol, W and Mauchline, TH and Raaijmakers, JM and Mendes, R}, title = {Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {85}, pmid = {38053159}, issn = {2524-6372}, support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X010953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.<br><br>RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.<br><br>CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.}, }
@article {pmid38049781, year = {2023}, author = {Thapa, S and Zhou, S and O'Hair, J and Al Nasr, K and Ropelewski, A and Li, H}, title = {Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach.}, journal = {BMC biotechnology}, volume = {23}, number = {1}, pages = {51}, pmid = {38049781}, issn = {1472-6750}, support = {2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; OCI 1053575//NSF/ ; }, mesh = {Animals ; *Cellulase/metabolism ; Metagenome ; Goats/genetics/metabolism/microbiology ; Rumen/metabolism/microbiology ; Escherichia coli/genetics ; Bacteria ; *Cellulases/genetics ; Cellulose ; }, abstract = {BACKGROUND: Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.<br><br>RESULTS: Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.<br><br>CONCLUSIONS: In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.}, }
@article {pmid38047964, year = {2023}, author = {Guo, D and Ge, J and Tang, Z and Tian, B and Li, W and Li, C and Xu, L and Luo, J}, title = {Dynamic Gut Microbiota of Apolygus lucorum Across Different Life Stages Reveals Potential Pathogenic Bacteria for Facilitating the Pest Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {9}, pmid = {38047964}, issn = {1432-184X}, mesh = {Adult ; Animals ; Humans ; *Gastrointestinal Microbiome ; Firmicutes ; Proteobacteria ; China ; Nymph ; Serratia/genetics ; }, abstract = {Insect's gut microbiota has diverse effects on their fitness, and a comprehensive understanding of gut microbiota functions requires analyzing its diversity. Apolygus lucorum is a highly destructive pest that threatens many economically important crops in China. This study investigated the gut microbiota of A. lucorum across its life cycle using both culture-dependent and culture-independent methods. A total of 87 gut bacterial isolates were identified, belonging to 4 phyla, 27 families, and 45 genera, while Miseq sequencing detected 91 amplicon sequence variants (ASVs) assigned to 5 phyla, 28 families, and 39 genera. Proteobacteria and Firmicutes were the predominant phyla, with Staphylococcus and Serratia as the major genera. There were significant differences in the relative abundance of these genera between the nymph and adult stages. Staphylococcus was significantly more abundant in nymphs than it in adults, while Serratia was significantly more abundant in sexually mature adults than in other developmental stages. Notably, Serratia is a common opportunistic pathogen in many insects. Injecting the gut-dominant isolate Serratia marcescens verified its high pathogenicity. Additionally, immune indicators of the bug at different developmental stages supported the hypothesis that Serratia is a pathogen of A. lucorum. This study provides a foundation for understanding the role of gut bacteria in the life history of A. lucorum and developing new pest control strategies based on microbes.}, }
@article {pmid38047636, year = {2023}, author = {Hill, MS and Gilbert, JA}, title = {Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {4}, pages = {e0012121}, pmid = {38047636}, issn = {1098-5557}, mesh = {Animals ; Humans ; *Built Environment ; *Environmental Microbiology ; }, abstract = {SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.}, }
@article {pmid38047236, year = {2023}, author = {Lupatelli, CA and Attard, A and Kuhn, ML and Cohen, C and Thomen, P and Noblin, X and Galiana, E}, title = {Automated high-content image-based characterization of microorganism behavioral diversity and distribution.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5640-5649}, pmid = {38047236}, issn = {2001-0370}, abstract = {Microorganisms have evolved complex systems to respond to environmental signals. Gradients of particular molecules and elemental ions alter the behavior of microbes and their distribution within their environment. Microdevices coupled with automated image-based methods are now employed to analyze the instantaneous distribution and motion behaviors of microbial species in controlled environments at small temporal scales, mimicking, to some extent, macro conditions. Such technologies have so far been adopted for investigations mainly on individual species. Similar versatile approaches must now be developed for the characterization of multiple and complex interactions between a microbial community and its environment. Here, we provide a comprehensive step-by-step method for the characterization of species-specific behavior in a synthetic mixed microbial suspension in response to an environmental driver. By coupling accessible microfluidic devices with automated image analysis approaches, we evaluated the behavioral response of three morphologically different telluric species (Phytophthora parasitica, Vorticella microstoma, Enterobacter aerogenes) to a potassium gradient driver. Using the TrackMate plug-in algorithm, we performed morphometric and then motion analyses to characterize the response of each microbial species to the driver. Such an approach enabled to confirm the different morphological features of the three species and simultaneously characterize their specific motion in reaction to the driver and their co-interaction dynamics. By increasing the complexity of suspensions, this approach could be integrated in a framework for phenotypic analysis in microbial ecology research, helping to characterize how key drivers influence microbiota assembly at microbiota host-environment interfaces.}, }
@article {pmid38042956, year = {2023}, author = {Alfonso, S and Mente, E and Fiocchi, E and Manfrin, A and Dimitroglou, A and Papaharisis, L and Barkas, D and Toomey, L and Boscarato, M and Losasso, C and Peruzzo, A and Stefani, A and Zupa, W and Spedicato, MT and Nengas, I and Lembo, G and Carbonara, P}, title = {Growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax) fed an environmentally and economically sustainable low marine protein diet in sea cages.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21269}, pmid = {38042956}, issn = {2045-2322}, support = {Grant no. 817737//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {Animals ; *Bass/metabolism ; *Gastrointestinal Microbiome ; Diet ; Fish Oils/metabolism ; Fatty Acids/metabolism ; Diet, Protein-Restricted ; Animal Feed/analysis ; }, abstract = {The large use of fish meal/fish oil in carnivorous fish feeds is the main concern regarding environmental sustainability of aquaculture. Here, we evaluated the effects of an innovative diet, designed to be (1) environmentally sustainable by lowering the marine protein content while being (2) cost effective by using sustainable alternative raw materials with acceptable cost and produced on an industrial scale, on growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax), a key species of the Mediterranean marine aquaculture, reared in sea cages. Results show that the specific growth rate of fish fed the low marine protein diet was significantly lower than those fed conventional diet (0.67% vs 0.69%). Fatty acid profile of fillets from fish fed a low marine protein diet presented significant lower n-6 and higher n-3 content when compared to conventional ones. Then, a significant increase in the abundance of Vibrio and reduction of Photobacterium were found in the gut of fish fed with the low marine protein diet but effects on sea bass health needs further investigation. Finally, no major health and welfare alterations for fish fed the low marine protein diet were observed, combined with a potential slight benefit related to humoral immunity. Overall, these results suggest that despite the low marine protein diet moderately affects growth performance, it nevertheless may enhance environmental and economic sustainability of the sea bass aquaculture.}, }
@article {pmid38040657, year = {2023}, author = {Baril, X and Constant, P}, title = {Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, pmid = {38040657}, issn = {1574-6941}, support = {RGPIN-2018-05262//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Carbon/metabolism ; *Hydrogenase/genetics/metabolism ; Oxidation-Reduction ; Soil ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrogen/metabolism ; Bacteria ; *Microbiota ; Cellulose/metabolism ; Sucrose/metabolism ; }, abstract = {High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.}, }
@article {pmid38038797, year = {2024}, author = {Mustaq, S and Moin, A and Pandit, B and Tiwary, BK and Alam, M}, title = {Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications.}, journal = {Folia microbiologica}, volume = {69}, number = {1}, pages = {17-32}, pmid = {38038797}, issn = {1874-9356}, mesh = {Humans ; *Phyllobacteriaceae/genetics ; Phylogeny ; Bacteria/genetics ; *Fabaceae/microbiology ; Nitrogen/metabolism ; DNA, Bacterial/metabolism ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.}, }
@article {pmid38036921, year = {2023}, author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A}, title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {8}, pmid = {38036921}, issn = {1432-184X}, support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {Humans ; *Antimicrobial Cationic Peptides/genetics/pharmacology ; Antimicrobial Peptides ; Bacteria/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.}, }
@article {pmid38036897, year = {2023}, author = {Hernández-Pelegrín, L and Ros, VID and Herrero, S and Crava, CM}, title = {Non-retroviral Endogenous Viral Elements in Tephritid Fruit Flies Reveal Former Viral Infections Not Related to Known Circulating Viruses.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {7}, pmid = {38036897}, issn = {1432-184X}, mesh = {Animals ; RNA, Small Interfering/genetics/metabolism ; *Viruses/genetics ; *RNA Viruses/genetics ; *Virus Diseases ; *Diptera ; }, abstract = {A wide variety of insect-specific non-retroviral RNA viruses specifically infect insects. During viral infection, fragments of viral sequences can integrate into the host genomes creating non-retroviral endogenous viral elements (nrEVEs). Although the exact function of nrEVEs is so far unknown, some studies suggest that nrEVEs may interfere with virus replication by producing PIWI-interacting RNAs (piRNAs) that recognize and degrade viral RNAs through sequence complementarity. In this article, we identified the nrEVEs repertoire of ten species within the dipteran family Tephritidae (true fruit flies), which are considered a major threat to agriculture worldwide. Our results suggest that each of these species contains nrEVEs, although in limited numbers, and that nrEVE integration may have occurred both before and after speciation. Furthermore, the majority of nrEVEs originated from viruses with negative single-stranded RNA genomes and represent structural viral functions. Notably, these nrEVEs exhibit low similarity to currently known circulating viruses. To explore the potential role of nrEVEs, we investigated their transcription pattern and the production of piRNAs in different tissues of Ceratitis capitata. We successfully identified piRNAs that are complementary to the sequence of one nrEVE in C. capitata, thereby highlighting a potential link between nrEVEs and the piRNA pathway. Overall, our results provide valuable insights into the comparative landscape of nrEVEs in true fruit flies, contributing to the understanding of the intimate relation between fruit flies and their past and present viral pathogens.}, }
@article {pmid38033596, year = {2023}, author = {Zhang, M and Kong, Z and Fu, H and Shu, X and Xue, Q and Lai, H and Guo, Q}, title = {Rhizosphere microbial ecological characteristics of strawberry root rot.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286740}, pmid = {38033596}, issn = {1664-302X}, abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.<br><br>METHODS: In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.<br><br>RESULTS: According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.<br><br>DISCUSSION: In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.}, }
@article {pmid38033562, year = {2023}, author = {Farmer, M and Rajasabhai, R and Tarpeh, W and Tyo, K and Wells, G}, title = {Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287491}, pmid = {38033562}, issn = {1664-302X}, abstract = {Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.}, }
@article {pmid38030916, year = {2023}, author = {Mlewski, EC and Saona, LA and Boidi, FJ and Chiappero, MF and Vaieretti, MV and Soria, M and Farías, ME and Izquierdo, AE}, title = {Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {6}, pmid = {38030916}, issn = {1432-184X}, support = {PICT 2018-4129//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; }, mesh = {Humans ; *Ecosystem ; Wetlands ; Soil/chemistry ; Altitude ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; }, abstract = {High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.}, }
@article {pmid38030815, year = {2023}, author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W}, title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {5}, pmid = {38030815}, issn = {1432-184X}, mesh = {Humans ; Bifidobacterium/genetics ; Klebsiella/genetics ; RNA, Ribosomal, 16S/genetics ; Bile ; *Gastrointestinal Microbiome ; *Microbiota ; Firmicutes/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; }, abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.}, }
@article {pmid38029116, year = {2023}, author = {Ouamba, AJK and Gagnon, M and Varin, T and Chouinard, PY and LaPointe, G and Roy, D}, title = {Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175663}, pmid = {38029116}, issn = {1664-302X}, abstract = {INTRODUCTION: The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.<br><br>METHODS: We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.<br><br>RESULTS AND DISCUSSION: Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.}, }
@article {pmid38029109, year = {2023}, author = {Crosby, KC and Rojas, M and Sharma, P and Johnson, MA and Mazloom, R and Kvitko, BH and Smits, THM and Venter, SN and Coutinho, TA and Heath, LS and Palmer, M and Vinatzer, BA}, title = {Genomic delineation and description of species and within-species lineages in the genus Pantoea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1254999}, pmid = {38029109}, issn = {1664-302X}, support = {R25 GM072767/GM/NIGMS NIH HHS/United States ; }, abstract = {As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.}, }
@article {pmid38029094, year = {2023}, author = {Semenov, M and Li, H and Luo, Y and Deng, Y and Kuzyakov, Y}, title = {Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1295624}, pmid = {38029094}, issn = {1664-302X}, }
@article {pmid38029079, year = {2023}, author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK}, title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1245818}, pmid = {38029079}, issn = {1664-302X}, abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.}, }
@article {pmid38026034, year = {2023}, author = {Gjini, E and Madec, S}, title = {Towards a mathematical understanding of invasion resistance in multispecies communities.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {231034}, pmid = {38026034}, issn = {2054-5703}, abstract = {Multispecies community composition and dynamics are key to health and disease across biological systems, a prominent example being microbial ecosystems. Explaining the forces that govern diversity and resilience in the microbial consortia making up our body's defences remains a challenge. In this, theoretical models are crucial, to bridge the gap between species dynamics and underlying mechanisms and to develop analytic insight. Here we propose a replicator equation framework to model multispecies dynamics where an explicit notion of invasion resistance of a system emerges and can be studied explicitly. For illustration, we derive the conceptual link between such replicator equation and N microbial species' growth and interaction traits, stemming from micro-scale environmental modification. Within this replicator framework, mean invasion fitness arises, evolves dynamically, and may undergo critical predictable shifts with global environmental changes. This mathematical approach clarifies the key role of this resident system trait for invader success, and highlights interaction principles among N species that optimize their collective resistance to invasion. We propose this model based on the replicator equation as a powerful new avenue to study, test and validate mechanisms of invasion resistance and colonization in multispecies microbial ecosystems and beyond.}, }
@article {pmid38026022, year = {2023}, author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE}, title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {230963}, pmid = {38026022}, issn = {2054-5703}, abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.}, }
@article {pmid38023904, year = {2023}, author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H}, title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1252821}, pmid = {38023904}, issn = {1664-462X}, abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.}, }
@article {pmid38016221, year = {2024}, author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L}, title = {Microbiome-functionality in anaerobic digesters: A critical review.}, journal = {Water research}, volume = {249}, number = {}, pages = {120891}, doi = {10.1016/j.watres.2023.120891}, pmid = {38016221}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Microbiota ; Methane/metabolism ; Metabolic Networks and Pathways ; }, abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.}, }
@article {pmid38015286, year = {2023}, author = {Liu, D and Wei, L}, title = {Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {4}, pmid = {38015286}, issn = {1432-184X}, mesh = {*Carbon Dioxide ; Epigenesis, Genetic ; Histones/genetics ; *Microalgae/genetics ; Adaptation, Physiological ; Carbon ; }, abstract = {Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.}, }
@article {pmid38008827, year = {2023}, author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W}, title = {The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {2}, pmid = {38008827}, issn = {1432-184X}, support = {32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Ecosystem ; Rhizosphere ; Bacteria/genetics ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Plants ; Nitrogen ; Soil Microbiology ; }, abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.}, }
@article {pmid38008821, year = {2023}, author = {Fuster, M and Ruiz, T and Lamarque, A and Coulon, M and Legrand, B and Sabart, M and Latour, D and Mallet, C}, title = {Cyanosphere Dynamic During Dolichospermum Bloom: Potential Roles in Cyanobacterial Proliferation.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {3}, pmid = {38008821}, issn = {1432-184X}, mesh = {*Cyanobacteria/genetics ; *Microcystis ; *Microbiota ; Cell Proliferation ; Lakes ; Eutrophication ; }, abstract = {Under the effect of global change, management of cyanobacterial proliferation becomes increasingly pressing. Given the importance of interactions within microbial communities in aquatic ecosystems, a handful of studies explored the potential relations between cyanobacteria and their associated bacterial community (i.e., cyanosphere). Yet, most of them specifically focused on the ubiquitous cyanobacteria Microcystis, overlooking other genera. Here, based on 16s rDNA metabarcoding analysis, we confirmed the presence of cyanosphere representing up to 30% of the total bacterial community diversity, during bloom episode of another preponderant cyanobacterial genus, Dolichospermum. Moreover, we highlighted a temporal dynamic of this cyanosphere. A sPLS-DA model permits to discriminate three important dates and 220 OTUs. With their affiliations, we were able to show how these variations potentially imply a turnover in ecological functions depending on bloom phases. Although more studies are necessary to quantify the impacts of these variations, we argue that cyanosphere can have an important, yet underestimated, role in the modulation of cyanobacterial blooms.}, }
@article {pmid38006200, year = {2023}, author = {Houldcroft, CJ and Underdown, S}, title = {Infectious disease in the Pleistocene: Old friends or old foes?.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {513-531}, doi = {10.1002/ajpa.24737}, pmid = {38006200}, issn = {2692-7691}, support = {//Oxford Brookes University/ ; }, mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; }, abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.}, }
@article {pmid38004650, year = {2023}, author = {Aponte, H and Sulbaran-Bracho, Y and Mondaca, P and Vidal, C and Pérez, R and Meier, S and Cornejo, P and Rojas, C}, title = {Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004650}, issn = {2076-2607}, support = {3210752//FONDECYT/ ; InES19-FRO19101//MINEDUC/ ; }, abstract = {The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroResp[TM] system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.}, }
@article {pmid38001901, year = {2023}, author = {Macedo-Viñas, M and Lucas, A}, title = {Evolution of Microbial Flora Colonizing Burn Wounds during Hospitalization in Uruguay.}, journal = {Biomedicines}, volume = {11}, number = {11}, pages = {}, pmid = {38001901}, issn = {2227-9059}, abstract = {(1) Background: Infections are a main cause of morbidity and mortality among burn patients. The spectrum of microorganisms depends on the epidemiological context and treatment practices. We aimed to describe the evolution of microbial flora colonizing burn wounds among patients hospitalized during 15 or more days at the National Burn Center in 2015. (2) Methods: Demographic data, length of stay, total body surface area burn, and status at discharge were collected from electronic records and culture results from the laboratory database. (3) Results: Among 98 included patients, 87 were colonized. The mean length of stay was 39 days overall and 16 days in the ICU. Acinetobacter spp., Enterococcus spp., and Staphylococcus aureus predominated. Fifty-six patients harbored multidrug-resistant bacteria and had a significantly greater TBSA. The mean time to colonization was 6 days overall and 14 days for multidrug-resistant bacteria; it was significantly longer for methicillin-resistant S. aureus than for methicillin-susceptible S. aureus. (4) Conclusions: This is the first report describing the dynamics of microbial colonization of burn wounds in Uruguay. Similarities were found with reports elsewhere, but early colonization with yeasts and the absence of Streptococcus pyogenes were unique. Each burn center needs to monitor its microbial ecology to tailor their antimicrobial strategies effectively.}, }
@article {pmid38000643, year = {2024}, author = {Jiang, M and Khunjar, W and Li, A and Chandran, K}, title = {Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130069}, doi = {10.1016/j.biortech.2023.130069}, pmid = {38000643}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Food Loss and Waste ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Bioreactors ; Fatty Acids, Volatile/metabolism ; Methane ; }, abstract = {In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.}, }
@article {pmid38000642, year = {2024}, author = {Wu, K and Leliveld, T and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Impact of mixed microalgal and bacterial species on organic micropollutants removal in photobioreactors under natural light.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130083}, doi = {10.1016/j.biortech.2023.130083}, pmid = {38000642}, issn = {1873-2976}, mesh = {Photobioreactors/microbiology ; *Microalgae ; *Chlorella ; Sewage ; Bacteria ; Biomass ; }, abstract = {Single microalgae species are effective at the removal of various organic micropollutants (OMPs), however increased species diversity might enhance this removal. Sixteen OMPs were added to 2 continuous photobioreactors, one inoculated with Chlorella sorokiniana and the other with a microalgal-bacterial community, for 112 d under natural light. Three media were sequentially used in 3 Periods: I) synthetic sewage (d 0-28), II) 10x diluted anaerobically digested black water (AnBW) (d 28-94) and III) 5x diluted AnBW (d 94-112). Twelve OMPs were removed > 30 %, while 4 were < 10 % removed. Removal efficiencies were similar for 9 OMPs, yet the mixed community showed a 2-3 times higher removal capacity (µg OMP/g dry weight) than C. sorokiniana during Period II pseudo steady state. The removal decreased drastically in Period III due to overgrowth of filamentous green algae. This study shows for the first time how microbial community composition and abundance are key for OMPs removal.}, }
@article {pmid37999395, year = {2023}, author = {Hernanz-Torrijos, M and Ortega, MJ and Úbeda, B and Bartual, A}, title = {Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999395}, issn = {1660-3397}, support = {RTI2018-101272-B-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Plan Propio UCA 2022-2023//University of C&#xe1;diz/ ; }, mesh = {*Diatoms/chemistry ; Aldehydes/pharmacology/chemistry ; Oceans and Seas ; Bacteria ; Marine Biology ; }, abstract = {Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.}, }
@article {pmid37997641, year = {2024}, author = {Tájmel, D and Cruz-Paredes, C and Rousk, J}, title = {Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17032}, doi = {10.1111/gcb.17032}, pmid = {37997641}, issn = {1365-2486}, support = {9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; }, mesh = {*Ecosystem ; *Hot Temperature ; Soil Microbiology ; Climate Change ; Temperature ; Soil/chemistry ; Carbon ; }, abstract = {Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.}, }
@article {pmid37994377, year = {2024}, author = {Lyche Solheim, A and Gundersen, H and Mischke, U and Skjelbred, B and Nejstgaard, JC and Guislain, ALN and Sperfeld, E and Giling, DP and Haande, S and Ballot, A and Moe, SJ and Stephan, S and Walles, TJW and Jechow, A and Minguez, L and Ganzert, L and Hornick, T and Hansson, TH and Stratmann, CN and Järvinen, M and Drakare, S and Carvalho, L and Grossart, HP and Gessner, MO and Berger, SA}, title = {Lake browning counteracts cyanobacteria responses to nutrients: Evidence from phytoplankton dynamics in large enclosure experiments and comprehensive observational data.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17013}, doi = {10.1111/gcb.17013}, pmid = {37994377}, issn = {1365-2486}, support = {603378, 226273//European Union FP7/ ; 731065//European Union H2020/ ; 01LC1501, 033L041B//German Federal Ministry of Education and Research/ ; GE 1775/2-1//German Research Foundation/ ; K45/2017, SAW-2015-IGB-1//Leibniz Association/ ; //Morsa River Basin authority, Norway/ ; }, mesh = {*Phytoplankton ; Lakes/microbiology ; Humic Substances ; Eutrophication ; *Cyanobacteria ; Nutrients ; Phosphorus/analysis ; China ; }, abstract = {Lakes worldwide are affected by multiple stressors, including climate change. This includes massive loading of both nutrients and humic substances to lakes during extreme weather events, which also may disrupt thermal stratification. Since multi-stressor effects vary widely in space and time, their combined ecological impacts remain difficult to predict. Therefore, we combined two consecutive large enclosure experiments with a comprehensive time-series and a broad-scale field survey to unravel the combined effects of storm-induced lake browning, nutrient enrichment and deep mixing on phytoplankton communities, focusing particularly on potentially toxic cyanobacterial blooms. The experimental results revealed that browning counteracted the stimulating effect of nutrients on phytoplankton and caused a shift from phototrophic cyanobacteria and chlorophytes to mixotrophic cryptophytes. Light limitation by browning was identified as the likely mechanism underlying this response. Deep-mixing increased microcystin concentrations in clear nutrient-enriched enclosures, caused by upwelling of a metalimnetic Planktothrix rubescens population. Monitoring data from a 25-year time-series of a eutrophic lake and from 588 northern European lakes corroborate the experimental results: Browning suppresses cyanobacteria in terms of both biovolume and proportion of the total phytoplankton biovolume. Both the experimental and observational results indicated a lower total phosphorus threshold for cyanobacterial bloom development in clearwater lakes (10-20 μg P L[-1]) than in humic lakes (20-30 μg P L[-1]). This finding provides management guidance for lakes receiving more nutrients and humic substances due to more frequent extreme weather events.}, }
@article {pmid37991947, year = {2023}, author = {Arya, S and George, AB and O'Dwyer, JP}, title = {Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {48}, pages = {e2307313120}, pmid = {37991947}, issn = {1091-6490}, support = {376199//Simons Foundation (SF)/ ; }, mesh = {*Microbiota ; *Machine Learning ; }, abstract = {Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.}, }
@article {pmid37991578, year = {2023}, author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL}, title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {1}, pmid = {37991578}, issn = {1432-184X}, support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; }, abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.}, }
@article {pmid37989722, year = {2024}, author = {Yuan, M and Na, M and Hicks, LC and Rousk, J}, title = {Limiting resources for soil microbial growth in climate change simulation treatments in the subarctic.}, journal = {Ecology}, volume = {105}, number = {1}, pages = {e4210}, doi = {10.1002/ecy.4210}, pmid = {37989722}, issn = {1939-9170}, support = {KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-03858//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 2020-04083//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Swedish Research Council's/ ; }, mesh = {*Ecosystem ; *Climate Change ; Soil ; Soil Microbiology ; Tundra ; Arctic Regions ; Plants ; Carbon ; Nitrogen ; Bacteria ; }, abstract = {The microbial use of resources to sustain life and reproduce influences for example, decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N), or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples in which changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3), and P (as KH2 PO4 /K2 HPO4) additions ("limiting factor assays," LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and, combined with a systematic tendency for growth increases by C, this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N fertilization. The microbial growth response to the LFA-C and LFA-P addition was strongest in the field-treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that, under a climate change scenario, increased C availability resulting from Arctic greening, treeline advance, and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem.}, }
@article {pmid37987191, year = {2023}, author = {Garbisu, C and Alkorta, I}, title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {12}, pages = {e2300153}, doi = {10.1002/bies.202300153}, pmid = {37987191}, issn = {1521-1878}, support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; }, mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.}, }
@article {pmid37986012, year = {2023}, author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV}, title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {59}, pmid = {37986012}, issn = {2524-4671}, abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.<br><br>RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The &#x3b1; diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted&#x2009;<&#x2009;0.01) in the diversity of genera between CT and MET samples (R2&#x2009;=&#x2009;0.112, P&#x2009;=&#x2009;0.003) and a non-significant difference between MET and PUS samples (R2&#x2009;=&#x2009;0.036, P&#x2009;=&#x2009;0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.<br><br>CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased &#x3b1;-diversity but decreased &#x3b2;-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.}, }
@article {pmid37984648, year = {2024}, author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R}, title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140743}, doi = {10.1016/j.chemosphere.2023.140743}, pmid = {37984648}, issn = {1879-1298}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Methane/metabolism ; Bacteria/metabolism ; Sewage ; }, abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.}, }
@article {pmid37982643, year = {2023}, author = {Lo, H-Y and Wink, K and Nitz, H and Kästner, M and Belder, D and Müller, JA and Kaster, A-K}, title = {scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0099823}, pmid = {37982643}, issn = {2379-5077}, mesh = {Workflow ; *Genomics/methods ; *Microfluidics/methods ; }, abstract = {A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.}, }
@article {pmid37981701, year = {2023}, author = {Sadeghi, J and Chaganti, SR and Johnson, TB and Heath, DD}, title = {Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {258}, pmid = {37981701}, issn = {2049-2618}, mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; Fishes ; *Gastrointestinal Microbiome/genetics ; Water ; }, abstract = {BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.<br><br>RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.<br><br>CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.}, }
@article {pmid37980777, year = {2023}, author = {Acosta, DJ and Alper, HS}, title = {Advances in enzymatic and organismal technologies for the recycling and upcycling of petroleum-derived plastic waste.}, journal = {Current opinion in biotechnology}, volume = {84}, number = {}, pages = {103021}, doi = {10.1016/j.copbio.2023.103021}, pmid = {37980777}, issn = {1879-0429}, mesh = {Mutation ; *Petroleum ; Polymers ; Recycling ; Plastics ; }, abstract = {Biological catalysts are emerging with the capability to depolymerize a wide variety of plastics. Improving and discovering these catalysts has leveraged a range of tools, including microbial ecology studies, high-throughput selections, and computationally guided mutational studies. In this review, we discuss the prospects for biological solutions to plastic recycling and upcycling with a focus on major advances in polyethylene terephthalate depolymerization, expanding the range of polymers with known biological catalysts, and the utilization of derived products. We highlight several recent improvements in enzymes and reaction properties, the discovery of a wide variety of novel plastic-depolymerizing biocatalysts, and how depolymerization products can be utilized in recycling and upcycling.}, }
@article {pmid37979870, year = {2024}, author = {Xiao, Z and Lu, C and Wu, Z and Li, X and Ding, K and Zhu, Z and Han, R and Zhao, J and Ge, T and Li, G and Zhu, YG}, title = {Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {168558}, doi = {10.1016/j.scitotenv.2023.168558}, pmid = {37979870}, issn = {1879-1026}, mesh = {*Solanum lycopersicum ; *Solanum melongena ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; Soil/chemistry ; Rhizosphere ; }, abstract = {Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.}, }
@article {pmid37977011, year = {2023}, author = {Scaria, SS and Balasubramanian, B and Dandin, VS and Meyyazhagan, A and Pappuswamy, M and Sattanathan, G and Liu, WC and Kadanthottu Sebastian, J and Park, S}, title = {Review on impacts of micro- and nano-plastic on aquatic ecosystems and mitigation strategies.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {265}, number = {}, pages = {106759}, doi = {10.1016/j.aquatox.2023.106759}, pmid = {37977011}, issn = {1879-1514}, mesh = {Animals ; Humans ; *Ecosystem ; Microplastics/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Food Chain ; }, abstract = {The rapid proliferation of microplastics (MPs) and nanoplastics (NPs) in our environment presents a formidable hazard to both biotic and abiotic components. These pollutants originate from various sources, including commercial production and the breakdown of larger plastic particles. Widespread contamination of the human body, agroecosystems, and animals occurs through ingestion, entry into the food chain, and inhalation. Consequently, the imperative to devise innovative methods for MPs and NPs remediation has become increasingly apparent. This review explores the current landscape of strategies proposed to mitigate the escalating threats associated with plastic waste. Among the array of methods in use, microbial remediation emerges as a promising avenue for the decomposition and reclamation of MPs and NPs. In response to the growing concern, numerous nations have already implemented or are in the process of adopting regulations to curtail MPs and NPs in aquatic habitats. This paper aims to address this gap by delving into the environmental fate, behaviour, transport, ecotoxicity, and management of MPs and NPs particles within the context of nanoscience, microbial ecology, and remediation technologies. Key findings of this review encompass the intricate interdependencies between MPs and NPs and their ecosystems. The ecological impact, from fate to ecotoxicity, is scrutinized in light of the burgeoning environmental imperative. As a result, this review not only provides an encompassing understanding of the ecological ramifications of MPs and NPs but also highlights the pressing need for further research, innovation, and informed interventions.}, }
@article {pmid37976624, year = {2023}, author = {Liu, S and Lin, Y and Liu, T and Xu, X and Wang, J and Chen, Q and Sun, W and Dang, C and Ni, J}, title = {Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River.}, journal = {Water research}, volume = {247}, number = {}, pages = {120829}, doi = {10.1016/j.watres.2023.120829}, pmid = {37976624}, issn = {1879-2448}, mesh = {Humans ; *Archaea/genetics ; *Plankton ; Geologic Sediments/microbiology ; Rivers/microbiology ; Water ; Carbon ; RNA, Ribosomal, 16S ; Phylogeny ; DNA, Archaeal ; }, abstract = {Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.}, }
@article {pmid37975506, year = {2023}, author = {Lequime, S}, title = {The sociality continuum of viruses: a commentary on Leeks et al. 2023.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {11}, pages = {1568-1570}, doi = {10.1111/jeb.14247}, pmid = {37975506}, issn = {1420-9101}, mesh = {*Onions ; *Viruses/genetics ; Evolution, Molecular ; }, }
@article {pmid37974054, year = {2023}, author = {Minnebo, Y and De Paepe, K and Raes, J and Van de Wiele, T}, title = {Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad149}, pmid = {37974054}, issn = {1574-6941}, support = {30770923//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Feeding Behavior ; Colon/microbiology ; Feces/microbiology ; }, abstract = {Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardized for a dynamic gut model (feeding at 09, 17, and 01 h), a typical Western (breakfast, lunch, and dinner at 09, 13, and 19 h, respectively), and a time-restricted pattern (single meal at 09 h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every 4 h revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured the growth of slower-growing species, such as Akkermansia, Dialister, and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.}, }
@article {pmid37973932, year = {2023}, author = {Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20073}, pmid = {37973932}, issn = {2045-2322}, support = {PCI2019-111932-2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021 FISDU00132//Generalitat de Catalunya/ ; UdG-AG-575//Universitat de Girona/ ; }, mesh = {*Clostridium acetobutylicum/genetics ; *Clostridium cellulovorans/genetics ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Clostridium/genetics ; Butanols ; 1-Butanol ; Fermentation ; }, abstract = {Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.}, }
@article {pmid37971428, year = {2023}, author = {Silcocks, M and Chang, X and Thuong Thuong, NT and Qin, Y and Minh Ha, DT and Khac Thai, PV and Vijay, S and Anh Thu, DD and Ngoc Ha, VT and Ngoc Nhung, H and Huu Lan, N and Quynh Nhu, NT and Edwards, D and Nath, A and Pham, K and Duc Bang, N and Hong Chau, TT and Thwaites, G and Heemskerk, AD and Chuen Khor, C and Teo, YY and Inouye, M and Ong, RT-H and Caws, M and Holt, KE and Dunstan, SJ}, title = {Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0256223}, pmid = {37971428}, issn = {2165-0497}, support = {/WT_/Wellcome Trust/United Kingdom ; U19 AI162583/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology/therapeutic use ; Beijing ; Vietnam/epidemiology ; Genotype ; *Tuberculosis, Multidrug-Resistant/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; }, abstract = {Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.}, }
@article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0062923}, pmid = {37971255}, issn = {1098-5336}, support = {113308//National Research Foundation (NRF)/ ; }, mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; }, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, }
@article {pmid37970641, year = {2023}, author = {Spencer-Williams, I and Meyer, M and DePas, W and Elliott, E and Haig, SJ}, title = {Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {48}, pages = {20360-20369}, pmid = {37970641}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; RNA, Ribosomal, 16S/genetics ; Corrosion ; Nontuberculous Mycobacteria/genetics ; Phosphates ; Water Microbiology ; }, abstract = {Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.}, }
@article {pmid37970497, year = {2023}, author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB}, title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.}, journal = {Journal of animal science and technology}, volume = {65}, number = {4}, pages = {856-864}, pmid = {37970497}, issn = {2055-0391}, abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.}, }
@article {pmid37968548, year = {2024}, author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A}, title = {Characterization of the soil resistome and mobilome in Namib Desert soils.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {967-975}, pmid = {37968548}, issn = {1618-1905}, mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Desert Climate ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Gene Transfer, Horizontal ; Soil/chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; }, abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.}, }
@article {pmid37968339, year = {2023}, author = {Sadiq, FA and De Reu, K and Steenackers, H and Van de Walle, A and Burmølle, M and Heyndrickx, M}, title = {Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {118}, pmid = {37968339}, issn = {2730-6151}, support = {101025683//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 35906//Villum Fonden (Villum Foundation)/ ; }, abstract = {Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.}, }
@article {pmid37966591, year = {2024}, author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J}, title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {31-71}, pmid = {37966591}, issn = {1940-6029}, mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; }, abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.}, }
@article {pmid37966223, year = {2023}, author = {Liu, S and Greenhut, IV and Heist, EP and Heist, MR and Moe, LA}, title = {Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0162423}, pmid = {37966223}, issn = {2165-0497}, mesh = {*Saccharomyces cerevisiae ; Fermentation ; *Ethanol ; Bacteria/genetics ; Sugars ; }, abstract = {Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as "contaminants" meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.}, }
@article {pmid37966203, year = {2023}, author = {Miliotis, G and McDonagh, F and Singh, NK and O'Connor, L and Tuohy, A and Morris, D and Venkateswaran, K}, title = {Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0189723}, pmid = {37966203}, issn = {2165-0497}, support = {2021_ECRAward//University of Galway (NUI Galway)/ ; Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {Humans ; *Space Flight ; Bacteria/genetics ; Klebsiella/genetics ; Plasmids ; Genomics ; Klebsiella pneumoniae/genetics ; }, abstract = {The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.}, }
@article {pmid37965618, year = {2023}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109726}, pmid = {37965618}, issn = {2352-3409}, abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.}, }
@article {pmid37964521, year = {2023}, author = {Brunetti, AE and Lyra, ML and Monteiro, JPC and Zurano, JP and Baldo, D and Haddad, CFB and Moeller, AH}, title = {Convergence of gut microbiota in myrmecophagous amphibians.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2011}, pages = {20232223}, pmid = {37964521}, issn = {1471-2954}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Biological Evolution ; *Microbiota ; Mammals/microbiology ; Anura ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.}, }
@article {pmid37961388, year = {2023}, author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR}, title = {Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961388}, issn = {2692-8205}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, abstract = {The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.}, }
@article {pmid37959068, year = {2023}, author = {Bettera, L and Levante, A and Bancalari, E and Bottari, B and Cirlini, M and Neviani, E and Gatti, M}, title = {Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {21}, pages = {}, pmid = {37959068}, issn = {2304-8158}, support = {FIL-Quota Incentivante//University of Parma/ ; }, abstract = {The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.}, }
@article {pmid37957741, year = {2023}, author = {Moldovan, OT and Carrell, AA and Bulzu, PA and Levei, E and Bucur, R and Sitar, C and Faur, L and Mirea, IC and Șenilă, M and Cadar, O and Podar, M}, title = {The gut microbiome mediates adaptation to scarce food in Coleoptera.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {80}, pmid = {37957741}, issn = {2524-6372}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; R01DE024463/NH/NIH HHS/United States ; }, abstract = {Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.}, }
@article {pmid37956766, year = {2024}, author = {Dong, CD and Huang, CP and Chen, CW and Hung, CM}, title = {The remediation of marine sediments containing polycyclic aromatic hydrocarbons by peroxymonosulfate activated with Sphagnum moss-derived biochar and its benthic microbial ecology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {341}, number = {}, pages = {122912}, doi = {10.1016/j.envpol.2023.122912}, pmid = {37956766}, issn = {1873-6424}, mesh = {*Sphagnopsida ; *Polycyclic Aromatic Hydrocarbons ; Peroxides ; Carbon ; Geologic Sediments/chemistry ; }, abstract = {This research was to study the efficiency of Sphagnum moss-derived biochar (SMBC) in removing polycyclic aromatic hydrocarbons (PAHs) from marine sediment using a peroxymonosulfate (PMS)-based carbon-advanced oxidation process (PMS-CAOPs). Sphagnum moss-derived biochar (SMBC) was generated via a simple thermochemical process for PMS activation toward enhancing decontamination of sediments. At pH 6, the SMBC/PMS system achieved a PAH removal efficiency exceeding 78% in 12 h reaction time. Moreover, PAHs of 6-, 5-, 4-, 3-, and 2-ring structures exhibited 98%, 74%, 68%, 85%, and 91%, of removal, respectively. The SMBC activation of PMS generated both radicals (SO4[•-] and HO•) and nonradical ([1]O2), species responsible for PAHs degradation, attributed primarily to inherent iron and carbon moieties. The significant PAHs degradation efficiency showcased by the SMBC/PMS process holds promise for augmenting the performance of indigenous benthic microbial activity in sediment treatment contexts. The response of sediment microbial communities to PAH-induced stress was particularly associated with the Proteobacteria phylum, specifically the Sulfurovum genus. The findings of the present study highlight the efficacy of environmentally benign reactive radical/nonradical-based PMS-CAOP using pristine carbon materials, offering a sustainable strategy for sediment treatment.}, }
@article {pmid37956735, year = {2024}, author = {Cohen, E and Azriel, S and Auster, O and Gal, A and Mikhlin, S and Crauwels, S and Rahav, G and Gal-Mor, O}, title = {A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile.}, journal = {Microbes and infection}, volume = {26}, number = {3}, pages = {105249}, doi = {10.1016/j.micinf.2023.105249}, pmid = {37956735}, issn = {1769-714X}, mesh = {Animals ; Mice ; *Salmonella enterica/genetics ; Salmonella typhimurium/genetics ; Serogroup ; *Salmonella Infections, Animal/microbiology ; *Sparrows ; Virulence/genetics ; *Arsenic ; }, abstract = {Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.}, }
@article {pmid37956179, year = {2023}, author = {Sauters, TJC and Roth, C and Murray, D and Sun, S and Floyd Averette, A and Onyishi, CU and May, RC and Heitman, J and Magwene, PM}, title = {Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.}, journal = {PLoS pathogens}, volume = {19}, number = {11}, pages = {e1011763}, pmid = {37956179}, issn = {1553-7374}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Amoeba/microbiology ; Metagenomics ; Predatory Behavior ; *Cryptococcus neoformans/genetics ; *Cryptococcosis/genetics/microbiology ; }, abstract = {The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.}, }
@article {pmid37954239, year = {2023}, author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D}, title = {Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258775}, pmid = {37954239}, issn = {1664-302X}, abstract = {Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.}, }
@article {pmid37951257, year = {2024}, author = {Ye, J and Li, J and Li, L and Zhang, S and Chen, J and Zhu, D and Zhang, C and Xie, B and Zhang, B and Hou, K}, title = {Trends in global ambient fine particulate matter pollution and diabetes mortality rates attributable to it in the 1990-2019: 30 years systematic analysis of global burden of disease.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168358}, doi = {10.1016/j.scitotenv.2023.168358}, pmid = {37951257}, issn = {1879-1026}, mesh = {Humans ; Particulate Matter ; Global Burden of Disease ; *Diabetes Mellitus/epidemiology ; Environmental Pollution ; Environmental Exposure ; *Air Pollution ; Quality-Adjusted Life Years ; }, abstract = {AIM: To analyze the trends in ambient fine particulate matter pollution (PM2.5) and the age-standardized mortality rate (ASMR) of diabetes attributable to it from 1990 to 2019 by region, country, and socio-economic development status.<br><br>METHODS: The main data, including the summary exposure value (SEV) of ambient PM2.5 and the ASMR of diabetes due to ambient PM2.5, was collected from the Global Burden of Disease 2019 database. The socio-demographic index (SDI) was employed for assessing a particular region or country's degree of socio-economic development. Joinpoint regression analysis was used to assess the changes of ambient PM2.5 and ASMR of diabetes attributable to it.<br><br>RESULTS: Globally, the SEV of ambient PM2.5 increased from 15.65&#xa0;&#x3bc;g/m[3] in 1990 to 26.22&#xa0;&#x3bc;g/m[3] in 2019, with an annual average percent change (AAPC) of 1.788 (95&#xa0;% CI 1.687-1.889) &#x3bc;g/m[3]. The ASMR of diabetes attributable to ambient PM2.5 increased from 1.57 per 100,000 population in 1990 to 2.47 per 100.000 population in 2019 (AAPC&#xa0;=&#xa0;1.569 [95&#xa0;% CI 1.42-1.718]). Most regions and countries had an increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to ambient PM2.5. The largest increase of SEV of ambient PM2.5 was observed in South Asia (AAPC&#xa0;=&#xa0;3.556 [95&#xa0;% CI 3.329-3.875]), while the largest increase of ASMR of diabetes was in Central Asia (AAPC&#xa0;=&#xa0;5.170 [95%CI 4.696-5.647]). Moreover, the increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to it were positively associated with SDI in low SDI countries (SDI&#xa0;<&#xa0;0.46), whereas the opposite result was observed when SDI&#xa0;&#x2265;&#xa0;0.46.<br><br>CONCLUSION: From 1990 to 2019, the population's exposure to ambient PM2.5 and ASMR of diabetes attributable to it increased generally, especially in low-middle SDI regions. Ambient PM2.5 remains a threat to global health. Greater investment in ambient PM2.5 and the mortality attributable to it are needed.}, }
@article {pmid37950563, year = {2023}, author = {White, A and Giannetto, M and Mulla, L and Del Rosario, A and Lim, T and Culver, E and Timmer, M and Bushell, J and Lambert, MR and Hernández-Gómez, O}, title = {Bacterial communities of the threatened Western Pond Turtle may be impacted by land use.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad143}, pmid = {37950563}, issn = {1574-6941}, support = {//David H. Smith Postdoctoral Fellowship/ ; //Association of Zoos and Aquariums Saving Animals From Extinction Western Pond Turtle Range-wide Conservation Coalition Grant/ ; //Northern California Herpetological Society/ ; }, mesh = {Animals ; *Turtles/microbiology ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Fresh Water ; }, abstract = {As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.}, }
@article {pmid37942081, year = {2023}, author = {Han, X and Beck, K and Bürgmann, H and Frey, B and Stierli, B and Frossard, A}, title = {Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1279041}, pmid = {37942081}, issn = {1664-302X}, abstract = {Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.}, }
@article {pmid37941937, year = {2023}, author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y}, title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16257}, pmid = {37941937}, issn = {2167-8359}, mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; }, abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.}, }
@article {pmid37941395, year = {2022}, author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B}, title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37941395}, issn = {2047-217X}, mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.<br><br>RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.<br><br>CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.}, }
@article {pmid37938301, year = {2022}, author = {McDaniel, EA and van Steenbrugge, JJM and Noguera, DR and McMahon, KD and Raaijmakers, JM and Medema, MH and Oyserman, BO}, title = {TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {111}, pmid = {37938301}, issn = {2730-6151}, support = {MCB-1518130//National Science Foundation (NSF)/ ; MCB-1518130//National Science Foundation (NSF)/ ; }, abstract = {A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.}, }
@article {pmid37934729, year = {2023}, author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA}, title = {CGG toolkit: Software components for computational genomics.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011498}, pmid = {37934729}, issn = {1553-7358}, mesh = {Reproducibility of Results ; *Genomics/methods ; *Software ; Computational Biology/methods ; Genome ; }, abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.}, }
@article {pmid37934609, year = {2023}, author = {Qiao, N and Gaur, G and Modesto, M and Chinnici, F and Scarafile, D and Borruso, L and Marin, AC and Spiezio, C and Valente, D and Sandri, C and Gänzle, MG and Mattarelli, P}, title = {Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.}, journal = {Journal of applied microbiology}, volume = {134}, number = {11}, pages = {}, doi = {10.1093/jambio/lxad255}, pmid = {37934609}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Canada Research Chairs/ ; //China Scholarship Council/ ; }, mesh = {Animals ; *Indriidae/metabolism ; Madagascar ; Coumaric Acids/metabolism ; *Lactobacillus plantarum/genetics/metabolism ; Genomics ; *Anti-Infective Agents/metabolism ; }, abstract = {AIMS: Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris.<br><br>METHODS AND RESULTS: Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.<br><br>CONCLUSIONS: Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.}, }
@article {pmid37933257, year = {2023}, author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Moreno, L and Moraga, CA and Gaete, K and Eguiarte, LE and Souza, V}, title = {Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16290}, pmid = {37933257}, issn = {2167-8359}, mesh = {Animals ; *Spheniscidae ; RNA, Ribosomal, 16S ; *Microbiota ; Soil ; }, abstract = {Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.}, }
@article {pmid37932283, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19207}, pmid = {37932283}, issn = {2045-2322}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Prevalence ; Phenotype ; *Paenibacillus/genetics ; Fatty Acids/analysis ; DNA ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (= NRRL B-65660[T] = DSM 115933[T]), Leifsonia virtsii F6_8S_P_1A[T] (= NRRL B-65661[T] = DSM 115931[T]), Leifsonia williamsii F6_8S_P_1B[T] (= NRRL B-65662[T] = DSM 115932[T]), Paenibacillus vandeheii F6_3S_P_1C[T] (= NRRL B-65663[T] = DSM 115940[T]), and Sporosarcina highlanderae F6_3S_P_2[T] (= NRRL B-65664[T] = DSM 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, }
@article {pmid37931689, year = {2024}, author = {Álvarez-Pérez, S and Lievens, B and de Vega, C}, title = {Floral nectar and honeydew microbial diversity and their role in biocontrol of insect pests and pollination.}, journal = {Current opinion in insect science}, volume = {61}, number = {}, pages = {101138}, doi = {10.1016/j.cois.2023.101138}, pmid = {37931689}, issn = {2214-5753}, mesh = {Animals ; *Plant Nectar ; *Pollination ; Insecta ; Carbohydrates ; Ecosystem ; }, abstract = {Sugar-rich plant-related secretions, such as floral nectar and honeydew, that are commonly used as nutrient sources by insects and other animals, are also the ecological niche for diverse microbial communities. Recent research has highlighted the great potential of nectar and honeydew microbiomes in biological pest control and improved pollination, but the exploitation of these microbiomes requires a deep understanding of their community dynamics and plant-microbe-insect interactions. Additionally, the successful application of microbes in crop fields is conditioned by diverse ecological, legal, and ethical challenges that should be taken into account. In this article, we provide an overview of the nectar and honeydew microbiomes and discuss their potential applications in sustainable agricultural practices.}, }
@article {pmid37931135, year = {2023}, author = {Naik, AT and Kamensky, KM and Hellum, AM and Moisander, PH}, title = {Disturbance frequency directs microbial community succession in marine biofilms exposed to shear.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0024823}, pmid = {37931135}, issn = {2379-5042}, support = {N00014220-1-2170//DOD | USN | Office of Naval Research (ONR)/ ; Multi-Institutional Collaborative Seed Funding//University of Massachusetts Dartmouth (UMD)/ ; N00014-16-1-3051//Michigan State University (MSU)/ ; }, mesh = {*Biofilms ; *Microbiota ; Prokaryotic Cells ; }, abstract = {Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.}, }
@article {pmid37926855, year = {2023}, author = {Minnebo, Y and Delbaere, K and Goethals, V and Raes, J and Van de Wiele, T and De Paepe, K}, title = {Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {240}, pmid = {37926855}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Butyrates/metabolism ; Nutrients ; Fermentation ; Carbohydrates ; Feces/microbiology ; }, abstract = {BACKGROUND: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.<br><br>RESULTS: Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time.<br><br>CONCLUSION: Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.}, }
@article {pmid37925991, year = {2023}, author = {Chen, C and Li, P and Yin, M and Wang, J and Sun, Y and Ju, W and Liu, L and Li, ZH}, title = {Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes.}, journal = {Marine pollution bulletin}, volume = {197}, number = {}, pages = {115739}, doi = {10.1016/j.marpolbul.2023.115739}, pmid = {37925991}, issn = {1879-3363}, mesh = {Seasons ; *Microbiota ; Temperature ; Microbial Consortia ; Bacteria ; }, abstract = {Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.}, }
@article {pmid37925029, year = {2024}, author = {Ghosh, A and Yash,  and Kumar, C and Bhadury, P}, title = {Cascading effects of trace metals enrichment on phytoplankton communities of the River Ganga in South Asia.}, journal = {Chemosphere}, volume = {347}, number = {}, pages = {140607}, doi = {10.1016/j.chemosphere.2023.140607}, pmid = {37925029}, issn = {1879-1298}, mesh = {Phytoplankton ; Rivers ; Ecosystem ; Asia, Southern ; *Arsenic/toxicity ; *Diatoms ; *Trace Elements/pharmacology ; Iron/pharmacology ; }, abstract = {Globally freshwater ecosystems and associated biota including phytoplankton communities are at extreme risk from trace metal pollution originating from geogenic as well as from anthropogenic sources such as release of untreated industrial effluents. In the present study influence of iron- and arsenic-enrichments on structure and metabolism of phytoplankton communities of River Ganga, one of the largest rivers of South Asia, was assessed under laboratory-based microcosm experiments. Surface water samples were collected and subsequently enriched with higher than recommended concentrations of iron (10 mg/L) and arsenic (10 μg/L). The set-up comprised of nine containers of 25 L volume with three containers each for iron- and arsenic-enrichment and was maintained for 30 days. Trace metal enrichment rapidly changed the phytoplankton community structure and chemistry of nutrients uptake. Iron-enrichment prompted diatom blooms comprising of Thalassiosira, succeeded by green algae Coelastrum. Arsenic-enrichment maintained cyanobacteria for longer time-spans compared to the control and iron-enriched containers but significantly lesser abundance of diatoms. Variations in community composition was also reflected in nutrient uptake rates with silicate release in the arsenic-enriched containers at the end of the experiment. Changes in macronutrient dynamics also altered genus growth rates wherein both iron- and arsenic appeared to lower the death rate of Thalassosira but stimulated growth of other genera including Skeletonema and Pandorina. Iron appeared to influence lesser number of genera compared to arsenic which altered growth rates of both diatoms and green algae. This consequently influenced the gross primary productivity values which lowered both in the iron- and arsenic-enriched containers compared to the control owing to decrease in phytoplankton diversity. Iron appeared to drive phytoplankton communities toward a less general and more specialized composition with high abundance of selective species comprising of small diatoms such as Thalassiosira, whereas arsenic appears to select for green algal enrichment in freshwater ecosystems.}, }
@article {pmid37920817, year = {2023}, author = {Talavera-Marcos, S and Parras-Moltó, M and Aguirre de Cárcer, D}, title = {Leveraging phylogenetic signal to unravel microbiome function and assembly rules.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5165-5173}, pmid = {37920817}, issn = {2001-0370}, abstract = {Clarifying the general rules behind microbial community assembly will foster the development of microbiome-based technological solutions. Here, we study microbial community assembly through a computational analysis of phylogenetic core groups (PCGs): discrete portions of the bacterial phylogeny with high prevalence in the ecosystem under study. We first show that the existence of PCGs was a predominant feature of the varied set of microbial ecosystems studied. Then, we re-analyzed an in vitro experimental dataset using a PCG-based approach, drawing only from its community composition data and from publicly available genomic databases. Using mainly genome scale metabolic models and population dynamics modeling, we obtained ecological insights on metabolic niche structure and population dynamics comparable to those gained after canonical experimentation. Thus, leveraging phylogenetic signal to help unravel microbiome function and assembly rules offers a potential avenue to gain further insight on Earth's microbial ecosystems.}, }
@article {pmid37920261, year = {2023}, author = {Poirier, S and Coeuret, G and Champomier-Vergès, MC and Desmonts, MH and Werner, D and Feurer, C and Frémaux, B and Guillou, S and Luong, NM and Rué, O and Loux, V and Zagorec, M and Chaillou, S and , }, title = {Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286661}, pmid = {37920261}, issn = {1664-302X}, abstract = {BACKGROUND: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.<br><br>METHODS: Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.<br><br>RESULTS: Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.<br><br>CONCLUSION: We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.}, }
@article {pmid37920009, year = {2023}, author = {Yuan, X and Song, W and Li, Y and Wang, Q and Qing, J and Zhi, W and Han, H and Qin, Z and Gong, H and Hou, G and Li, Y}, title = {Using Bayesian networks with tabu algorithm to explore factors related to chronic kidney disease with mental illness: A cross-sectional study.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {20}, number = {9}, pages = {16194-16211}, doi = {10.3934/mbe.2023723}, pmid = {37920009}, issn = {1551-0018}, mesh = {Humans ; Cross-Sectional Studies ; Bayes Theorem ; Algorithms ; *Renal Insufficiency, Chronic/epidemiology ; *Mental Disorders/epidemiology ; }, abstract = {While Bayesian networks (BNs) offer a promising approach to discussing factors related to many diseases, little attention has been poured into chronic kidney disease with mental illness (KDMI) using BNs. This study aimed to explore the complex network relationships between KDMI and its related factors and to apply Bayesian reasoning for KDMI, providing a scientific reference for its prevention and treatment. Data was downloaded from the online open database of CHARLS 2018, a population-based longitudinal survey. Missing values were first imputed using Random Forest, followed by propensity score matching (PSM) for class balancing regarding KDMI. Elastic Net was then employed for variable selection from 18 variables. Afterwards, the remaining variables were included in BNs model construction. Structural learning of BNs was achieved using tabu algorithm and the parameter learning was conducted using maximum likelihood estimation. After PSM, 427 non-KDMI cases and 427 KDMI cases were included in this study. Elastic Net identified 11 variables significantly associated with KDMI. The BNs model comprised 12 nodes and 24 directed edges. The results suggested that diabetes, physical activity, education levels, sleep duration, social activity, self-report on health and asset were directly related factors for KDMI, whereas sex, age, residence and Internet access represented indirect factors for KDMI. BN model not only allows for the exploration of complex network relationships between related factors and KDMI, but also could enable KDMI risk prediction through Bayesian reasoning. This study suggests that BNs model holds great prospects in risk factor detection for KDMI.}, }
@article {pmid37919394, year = {2023}, author = {Dougherty, PE and Nielsen, TK and Riber, L and Lading, HH and Forero-Junco, LM and Kot, W and Raaijmakers, JM and Hansen, LH}, title = {Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2415-2425}, pmid = {37919394}, issn = {1751-7370}, support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 801199//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Prophages/genetics ; *Triticum ; Bacteria/genetics ; }, abstract = {Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 10[8] virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.}, }
@article {pmid37914532, year = {2023}, author = {Ray, AE and Tribbia, DZ and Cowan, DA and Ferrari, BC}, title = {Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {4}, pages = {e0004823}, pmid = {37914532}, issn = {1098-5557}, support = {FT170100341, DP220103430//Department of Education and Training | Australian Research Council (ARC)/ ; 4406//Department of the Environment and Energy | Australian Antarctic Division (AAD)/ ; }, mesh = {*Carbon Monoxide/metabolism ; *Gases ; Hydrogen/metabolism ; Soil ; Methane/metabolism ; Water ; }, abstract = {Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.}, }
@article {pmid37914126, year = {2024}, author = {Abkar, L and Moghaddam, HS and Fowler, SJ}, title = {Microbial ecology of drinking water from source to tap.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168077}, doi = {10.1016/j.scitotenv.2023.168077}, pmid = {37914126}, issn = {1879-1026}, mesh = {*Drinking Water/analysis ; Water Supply ; *Water Purification/methods ; Sanitary Engineering ; Public Health ; Water Microbiology ; }, abstract = {As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.}, }
@article {pmid37909775, year = {2023}, author = {Mason, G and Footer, MJ and Rojas, ER}, title = {Mechanosensation induces persistent bacterial growth during bacteriophage predation.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0276622}, pmid = {37909775}, issn = {2150-7511}, support = {R35 GM143057/GM/NIGMS NIH HHS/United States ; 5R35GM143057-02//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Escherichia coli/virology/growth &amp; development ; *Bacteriophages/physiology/growth &amp; development ; }, abstract = {Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.}, }
@article {pmid37909659, year = {2024}, author = {Quiroga, MV and Stegen, JC and Mataloni, G and Cowan, D and Lebre, PH and Valverde, A}, title = {Microdiverse bacterial clades prevail across Antarctic wetlands.}, journal = {Molecular ecology}, volume = {33}, number = {1}, pages = {e17189}, doi = {10.1111/mec.17189}, pmid = {37909659}, issn = {1365-294X}, support = {PICT 2016-2517//ANPCyT - Argentina/ ; PICT 2020-3113//ANPCyT - Argentina/ ; //European Union/ ; //Instituto Ant&#xe1;rtico Argentino - Direcci&#xf3;n Nacional del Ant&#xe1;rtico/ ; CLU-2019-05 IRNASA/CSIC//Junta de Castilla y Le&#xf3;n/ ; //NRF - South Africa/ ; Contract DE-AC05-76RL01830 -JCS//U.S. Department of Energy-BER program/ ; }, mesh = {Phylogeny ; Antarctic Regions ; *Wetlands ; Bacteria/genetics ; *Microbiota ; }, abstract = {Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.}, }
@article {pmid37903921, year = {2023}, author = {Jansson, JK and McClure, R and Egbert, RG}, title = {Soil microbiome engineering for sustainability in a changing environment.}, journal = {Nature biotechnology}, volume = {41}, number = {12}, pages = {1716-1728}, pmid = {37903921}, issn = {1546-1696}, mesh = {*Soil ; *Microbiota/genetics ; Soil Microbiology ; Synthetic Biology ; Biotechnology ; }, abstract = {Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.}, }
@article {pmid37902333, year = {2023}, author = {van der Meij, A and Elsayed, SS and Du, C and Willemse, J and Wood, TM and Martin, NI and Raaijmakers, JM and van Wezel, GP}, title = {The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0123923}, pmid = {37902333}, issn = {1098-5336}, support = {14221//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {*Plant Growth Regulators ; *Amino Acids ; Anti-Bacterial Agents ; Hormones ; }, abstract = {Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.}, }
@article {pmid37901816, year = {2023}, author = {Li, Y and Hou, Y and Hou, Q and Long, M and Wang, Z and Rillig, MC and Liao, Y and Yong, T}, title = {Soil microbial community parameters affected by microplastics and other plastic residues.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258606}, pmid = {37901816}, issn = {1664-302X}, abstract = {INTRODUCTION: The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors.<br><br>METHODS: We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities.<br><br>RESULTS AND DISCUSSION: This study indicated that plastics accelerated soil organic carbon loss (effect size&#x2009;=&#x2009;-0.05, p&#x2009;=&#x2009;0.004) and increased microbial functionality (effect size&#x2009;=&#x2009;0.04, p&#x2009;=&#x2009;0.003), but also reduced microbial biomass (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) while polypropylene significantly increased it (effect size&#x2009;=&#x2009;0.17, p&#x2009;<&#x2009;0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40&#x2009;g/kg. Approximately 3564.78&#x2009;&#x3bc;m was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R[2]&#x2009;=&#x2009;0.04-0.73, p&#x2009;<&#x2009;0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.}, }
@article {pmid37897125, year = {2023}, author = {Seppey, CVW and Cabrol, L and Thalasso, F and Gandois, L and Lavergne, C and Martinez-Cruz, K and Sepulveda-Jauregui, A and Aguilar-Muñoz, P and Astorga-España, MS and Chamy, R and Dellagnezze, BM and Etchebehere, C and Fochesatto, GJ and Gerardo-Nieto, O and Mansilla, A and Murray, A and Sweetlove, M and Tananaev, N and Teisserenc, R and Tveit, AT and Van de Putte, A and Svenning, MM and Barret, M}, title = {Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3364-3386}, doi = {10.1111/1462-2920.16526}, pmid = {37897125}, issn = {1462-2920}, support = {Project MATCH C16B03//ECOS sud CONICYT/ ; grant no. 256132/H30//ECOS sud CONICYT/ ; project METHANOBASE (ELAC2014_DCC-0092)//ERANet-LAC program/ ; //French Ministries of Foreign Affairs and International Development (MAEDI)/ ; //German Federal Ministry of Education and Research, WISNA program/ ; grant no. 277238//Mexican National Council for Science and Technology (CONACYT)/ ; //National Education, Superior Education and Research (MENESR)/ ; MillenniumScienceInitiativeProgram-ICN2021_002//Chilean National Agency of Research and Development (ANID)/ ; }, mesh = {*Microbiota/genetics ; *Euryarchaeota/genetics ; Wetlands ; Soil/chemistry ; Methane ; }, abstract = {Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.}, }
@article {pmid37895286, year = {2023}, author = {Aboushaala, K and Wong, AYL and Barajas, JN and Lim, P and Al-Harthi, L and Chee, A and Forsyth, CB and Oh, CD and Toro, SJ and Williams, FMK and An, HS and Samartzis, D}, title = {The Human Microbiome and Its Role in Musculoskeletal Disorders.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895286}, issn = {2073-4425}, support = {R21 AR079679/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Bacteria ; *Musculoskeletal Diseases ; Oxygen ; }, abstract = {Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.}, }
@article {pmid37894228, year = {2023}, author = {Jech, SD and Day, N and Barger, NN and Antoninka, A and Bowker, MA and Reed, S and Tucker, C}, title = {Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894228}, issn = {2076-2607}, support = {RC18-1322//Department of Defense Strategic Environmental Research and Development Program/ ; NA//Canyonlands Research Center/ ; NA//Wildlife Conservation Society Climate Adaptation Fund/ ; }, abstract = {Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.}, }
@article {pmid37883861, year = {2024}, author = {Zhang, X and Luther, AK and Rabaey, K and Prévoteau, A}, title = {Periodic polarization duty cycle tunes performance and adhesion of anodic electroactive biofilms.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {155}, number = {}, pages = {108581}, doi = {10.1016/j.bioelechem.2023.108581}, pmid = {37883861}, issn = {1878-562X}, mesh = {*Geobacter ; Biofilms ; Electrodes ; Carbon ; *Bioelectric Energy Sources ; }, abstract = {Periodic polarization can improve the performance of anodic electroactive biofilms (EABs). The impact of the half-period duration was previously investigated at constant duty cycle (50%), i.e., the proportion of a period during which the electrode is polarized. Here, we cultured eight EABs on glassy carbon electrodes at four different duty cycles (50%, 67%, 80% and 91%) by varying the time interval under open circuit conditions, while keeping the polarization duration at 10 s. The shorter duty cycles slightly slowed initial growth but produced EABs generating higher faradaic currents. The total charge recovery over 38 days increased with decreasing duty cycles from 0.53 kC.cm[-2] (duty cycle of 91%) to 1.65 kC.cm[-2] (50%). EABs with the shortest duty cycle fully detached twice from the electrode surface, but detachments were quickly followed by the formation of more efficient EABs. We then carried out controlled removal of some aged and low current-producing EABs by applying a 30 s cathodic current (H2 evolution at -15 mA.cm[-2]) and observed the subsequent rapid development of fresh EABs displaying better electrochemical performance. Our results illustrate that well-chosen dynamic controls of electrode potentials can substantially improve the average current production of EABs, or allow a simple replacement of underperforming EABs.}, }
@article {pmid37878053, year = {2023}, author = {Maisnam, P and Jeffries, TC and Szejgis, J and Bristol, D and Singh, BK and Eldridge, DJ and Horn, S and Chieppa, J and Nielsen, UN}, title = {Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3097-3110}, pmid = {37878053}, issn = {1432-184X}, support = {DP150104199; DP190101968//Australian Research Council/ ; }, mesh = {Humans ; Ecosystem ; Droughts ; Soil Microbiology ; Australia ; Soil/chemistry ; Bacteria/genetics ; *Chytridiomycota ; *Microbiota ; }, abstract = {Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.}, }
@article {pmid37878052, year = {2023}, author = {Chen, M and Su, S and Zhang, C and Zhu, J and Feng, W and Chen, H and Jiang, J and Lu, Z and Liu, W and Gan, J}, title = {The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3111-3127}, pmid = {37878052}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Astacoidea/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fatty Acids ; }, abstract = {Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.}, }
@article {pmid37877729, year = {2023}, author = {Eng, AY and Narayanan, A and Alster, CJ and DeAngelis, KM}, title = {Thermal adaptation of soil microbial growth traits in response to chronic warming.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0082523}, pmid = {37877729}, issn = {1098-5336}, support = {DEB-1749206, DEB-1832110//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Soil ; *Global Warming ; Soil Microbiology ; Climate Change ; Biomass ; }, abstract = {Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.}, }
@article {pmid37877306, year = {2023}, author = {Zhu, B and Gu, H and He, J and Li, F and Yu, J and Liu, W and Chen, Q and Lai, Y and Yu, S}, title = {The impact of smash-ridge tillage on agronomic traits of tobacco plants, soil enzymatic activity, microbial community structure, and functional diversity.}, journal = {Plant signaling &amp; behavior}, volume = {18}, number = {1}, pages = {2260640}, pmid = {37877306}, issn = {1559-2324}, mesh = {*Soil/chemistry ; Nicotiana/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Agriculture/methods ; *Microbiota ; }, abstract = {Smash-ridge tillage is a novel cultivation technique that significantly influences the quality of arable land and crop yield. In this study, we employed high-throughput 16S rRNA sequencing and Biolog-ECO methods to systematically investigate the impact of smash-ridge tillage on soil microbial community structure and functional diversity. The results demonstrate that both ST30 and ST50 treatments significantly enhance the average plant height, average plant diameter, average fresh root weight, stem fresh weight, and leaf area of tobacco plants, with the ST50 treatment exhibiting superior performance. Furthermore, both ST30 and ST50 treatments exhibit significantly higher soil enzyme activity and microbial community diversity compared to the CK treatment. They also improve the soil microbial utilization of carbon sources. Additionally, the ST50-treated soil samples demonstrate 15 microbial functional pathways that exceed those of the CK and ST30 treatments. In conclusion, the Smash-ridge tillage treatment at a depth of 50 cm yields more favorable results. This study provides a theoretical foundation for enhancing soil quality in Smash-ridge tillage by elucidating the mechanisms through which it impacts soil microbial ecology.}, }
@article {pmid37875737, year = {2023}, author = {Dahl, SA and Seifert, J and Camarinha-Silva, A and Cheng, YC and Hernández-Arriaga, A and Hudler, M and Windisch, W and König, A}, title = {Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3082-3096}, pmid = {37875737}, issn = {1432-184X}, mesh = {Animals ; Rumen/microbiology ; *Deer ; Forests ; Bacteria ; Nutrients ; *Microbiota ; }, abstract = {Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.}, }
@article {pmid37875201, year = {2024}, author = {Chen, S and Kuramae, EE and Jia, Z and Liu, B}, title = {Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167968}, doi = {10.1016/j.scitotenv.2023.167968}, pmid = {37875201}, issn = {1879-1026}, mesh = {*Soil ; *Nitrates/analysis ; Agriculture ; DNA ; Isotopes ; Denitrification ; Soil Microbiology ; }, abstract = {Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from [13]C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0-0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5-9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.}, }
@article {pmid37874854, year = {2023}, author = {George, AB and O'Dwyer, J}, title = {Universal abundance fluctuations across microbial communities, tropical forests, and urban populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {44}, pages = {e2215832120}, pmid = {37874854}, issn = {1091-6490}, support = {376199//Simons Foundation (SF)/ ; 220020439//James S. McDonnell Foundation (JSMF)/ ; }, mesh = {Humans ; Urban Population ; *Forests ; Population Dynamics ; *Microbiota ; Cities ; }, abstract = {The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to understand each individual system, a unified analysis of different complex populations is lacking; such an analysis could deepen our understanding of each system and facilitate cross-pollination of tools and insights across fields. Here, we use a shared framework to analyze time-series data of the human gut microbiome, tropical forest, and urban employment. We demonstrate that a single, three-parameter model of stochastic population dynamics can reproduce the empirical distributions of population abundances and fluctuations in all three datasets. The three parameters characterizing a species measure its mean abundance, deterministic stability, and stochasticity. Our analysis reveals that, despite the vast differences in scale, all three systems occupy a similar region of parameter space when time is measured in generations. In other words, although the fluctuations observed in these systems may appear different, this difference is primarily due to the different physical timescales associated with each system. Further, we show that the distribution of temporal abundance fluctuations is described by just two parameters and derive a two-parameter functional form for abundance fluctuations to improve risk estimation and forecasting.}, }
@article {pmid37871765, year = {2024}, author = {Brandt, A and Csarmann, K and Hernández-Arriaga, A and Baumann, A and Staltner, R and Halilbasic, E and Trauner, M and Camarinha-Silva, A and Bergheim, I}, title = {Antibiotics attenuate diet-induced nonalcoholic fatty liver disease without altering intestinal barrier dysfunction.}, journal = {The Journal of nutritional biochemistry}, volume = {123}, number = {}, pages = {109495}, doi = {10.1016/j.jnutbio.2023.109495}, pmid = {37871765}, issn = {1873-4847}, mesh = {Male ; Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; Liver/metabolism ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Diet/adverse effects ; Inflammation/metabolism ; *Gastrointestinal Diseases ; Fructose/metabolism ; Diet, High-Fat ; }, abstract = {To date the role of the alterations of intestinal microbiota in the development of intestinal barrier dysfunction in settings of nonalcoholic fatty liver disease (NAFLD) has not been fully understood. Here, we assessed the effect of antibiotics on development of NAFLD and their impact on intestinal barrier dysfunction. Male C57BL/6J mice were either pair-fed a liquid control diet (C) or fat- and fructose-rich diet (FFr) +/- antibiotics (AB, ampicillin/vancomycin/metronidazole/gentamycin) for 7 weeks. Fasting blood glucose was determined and markers of liver damage, inflammation, intestinal barrier function, and microbiota composition were assessed. The development of hepatic steatosis with early signs of inflammation found in FFr-fed mice was significantly abolished in FFr+AB-fed mice. Also, while prevalence of bacteria in feces was not detectable and TLR4 ligand levels in portal plasma were at the level of controls in FFr+AB-fed mice, impairments of intestinal barrier function like an increased permeation of xylose and iNOS protein levels persisted to a similar extent in both FFr-fed groups irrespective of AB use. Exposure of everted small intestinal tissue sacs of naïve mice to fructose resulted in a significant increase in tissue permeability and loss of tight junction proteins, being not affected by the presence of AB, whereas the concomitant treatment of tissue sacs with the NOS inhibitor aminoguanidine attenuated these alterations. Taken together, our data suggest that intestinal barrier dysfunction in diet-induced NAFLD in mice may not be predominantly dependent on changes in intestinal microbiota but rather that fructose-induced alterations of intestinal NO-homeostasis might be critically involved.}, }
@article {pmid37866247, year = {2023}, author = {Kleikamp, HBC and Grouzdev, D and Schaasberg, P and van Valderen, R and van der Zwaan, R and Wijgaart, RV and Lin, Y and Abbas, B and Pronk, M and van Loosdrecht, MCM and Pabst, M}, title = {Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome.}, journal = {Water research}, volume = {246}, number = {}, pages = {120700}, doi = {10.1016/j.watres.2023.120700}, pmid = {37866247}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; RNA, Ribosomal, 16S/genetics ; Bioreactors ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.}, }
@article {pmid37860776, year = {2023}, author = {Yitbarek, S and Guittar, J and Knutie, SA and Ogbunugafor, CB}, title = {Deconstructing taxa x taxa xenvironment interactions in the microbiota: A theoretical examination.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107875}, pmid = {37860776}, issn = {2589-0042}, abstract = {A major objective of microbial ecology is to identify how the composition of microbial taxa shapes host phenotypes. However, most studies focus on pairwise interactions and ignore the potentially significant effects of higher-order microbial interactions.Here, we quantify the effects of higher-order interactions among taxa on host infection risk. We apply our approach to an in silico dataset that is built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite across a breadth of nutrient environmental contexts.We find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Furthermore, we show that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.Our approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes.}, }
@article {pmid37858824, year = {2024}, author = {Niu, S and Xie, J and Wang, G and Li, Z and Zhang, K and Li, H and Xia, Y and Tian, J and Yu, E and Xie, W and Gong, W}, title = {Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167913}, doi = {10.1016/j.scitotenv.2023.167913}, pmid = {37858824}, issn = {1879-1026}, mesh = {Wastewater ; Bacteria ; *Microbiota ; Aquaculture ; *Water Purification ; }, abstract = {Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.}, }
@article {pmid37855643, year = {2023}, author = {Villabona, N and Moran, N and Hammer, T and Reyes, A}, title = {Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0013923}, pmid = {37855643}, issn = {2379-5042}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Ecology ; }, abstract = {Social bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.}, }
@article {pmid37852481, year = {2024}, author = {Zammit, I and Badia, S and Mejías-Molina, C and Rusiñol, M and Bofill-Mas, S and Borrego, CM and Corominas, L}, title = {Zooming in to the neighborhood level: A year-long wastewater-based epidemiology monitoring campaign for COVID-19 in small intraurban catchments.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167811}, doi = {10.1016/j.scitotenv.2023.167811}, pmid = {37852481}, issn = {1879-1026}, mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2 ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {In recent years, wastewater-based epidemiology (WBE) has emerged as a valuable and cost-effective tool for monitoring the prevalence of COVID-19. Large-scale monitoring efforts have been implemented in numerous countries, primarily focusing on sampling at the entrance of wastewater treatment plants (WWTPs) to cover a large population. However, sampling at a finer spatial scale, such as at the neighborhood level (NGBs), pose new challenges, including the absence of composite sampling infrastructure and increased uncertainty due to the dynamics of small catchments. This study aims to investigate the feasibility and accuracy of WBE when deployed at the neighborhood level (sampling in sewers) compared to the city level (sampling at the entrance of a WWTP). To achieve this, we deployed specific WBE sampling stations at the intraurban scale within three NGBs in Barcelona, Spain. The study period covers the 5th and the 6th waves of COVID-19 in Spain, spanning from March 2021 to March 2022, along with the WWTP downstream from the NGBs. The results showed a strong correlation between the dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 loads at both the NGB and city levels. Notably, during the 5th wave, which was dominated by the Delta SARS-CoV-2 variant, wastewater loads were higher than during the 6th wave (Omicron variant), despite a lower number of clinical cases recorded during the 5th wave. The correlations between wastewater loads and clinical cases at the NGB level were stronger than at the WWTP level. However, the early warning potential varied across neighborhoods and waves, with some cases showing a one-week early warning and others lacking any significant early warning signal. Interestingly, the prevalence of COVID-19 did not exhibit major differences among NGBs with different socioeconomic statuses.}, }
@article {pmid37848722, year = {2023}, author = {Rizaludin, MS and Garbeva, P and Zwart, M and Hu, J}, title = {Microbial volatiles mediate bacterial evolutionary dynamics.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2144-2146}, pmid = {37848722}, issn = {1751-7370}, }
@article {pmid37844340, year = {2023}, author = {Li, Z and Ma, H and Hong, Z and Zhang, T and Cao, M and Cui, F and Grossart, HP}, title = {Phytoplankton interspecific interactions modified by symbiotic fungi and bacterial metabolites under environmentally relevant hydrogen peroxide concentrations stress.}, journal = {Water research}, volume = {246}, number = {}, pages = {120739}, doi = {10.1016/j.watres.2023.120739}, pmid = {37844340}, issn = {1879-2448}, mesh = {Phytoplankton ; Hydrogen Peroxide/pharmacology ; Symbiosis ; *Chlorella vulgaris ; *Cyanobacteria ; *Microcystis/metabolism ; Water ; Fungi ; Microcystins/metabolism ; }, abstract = {Hydrogen peroxide (H2O2), which accumulates in water and triggers oxidative stress for aquatic microbes, has been shown to have profound impacts on planktonic microbial community dynamics including cyanobacterial bloom formation. Yet, potential effects of H2O2 on interspecific relationships of phytoplankton-microbe symbiotic interactions remain unclear. Here, we investigated effects of environmentally relevant H2O2 concentrations on interspecific microbial relationships in algae-microbe symbiosis. Microbes play a crucial role in the competition between M. aeruginosa and Chlorella vulgaris at low H2O2 concentrations (∼400 nM), in which fungi and bacteria protect Microcystis aeruginosa from oxidative stress. Moreover, H2O2 stimulated the synthesis and release of extracellular microcystin-LR from Microcystis aeruginosa, while intracellular microcystin-LR concentrations remained at a relatively constant level. In the presence of H2O2, loss of organoheterocyclic compounds, organic acids and ketones contributed to the growth of M. aeruginosa, but the reduction of vitamins inhibited it. Regulation of interspecific relationships by H2O2 is achieved by its action on fungal species and bacterial secretory metabolites. This study explored the response of phytoplankton interspecific relationships in symbiotic phytoplankton-microbe interactions to environmentally relevant H2O2 concentrations stress, providing a theoretical basis for understanding the formation of harmful-algae blooming and impact of photochemical properties of water on aquatic ecological safety and stability.}, }
@article {pmid37843656, year = {2023}, author = {Znamínko, M and Falteisek, L and Vrbická, K and Klímová, P and Christiansen, JR and Jørgensen, CJ and Stibal, M}, title = {Methylotrophic Communities Associated with a Greenland Ice Sheet Methane Release Hotspot.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3057-3067}, pmid = {37843656}, issn = {1432-184X}, support = {A32524//Hartmann Fonden/ ; 0135-00229B//Danish Independent Research Fund/ ; LL2004 'MARCH4G'//Czech Ministry of Education, Youth and Sports/ ; }, mesh = {Greenland ; *Ice Cover/microbiology ; *Methane/analysis ; Climate ; Seasons ; }, abstract = {Subglacial environments provide conditions suitable for the microbial production of methane, an important greenhouse gas, which can be released from beneath the ice as a result of glacial melting. High gaseous methane emissions have recently been discovered at Russell Glacier, an outlet of the southwestern margin of the Greenland Ice Sheet, acting not only as a potential climate amplifier but also as a substrate for methane consuming microorganisms. Here, we describe the composition of the microbial assemblage exported in meltwater from the methane release hotspot at Russell Glacier and its changes over the melt season and as it travels downstream. We found that a substantial part (relative abundance 27.2% across the whole dataset) of the exported assemblage was made up of methylotrophs and that the relative abundance of methylotrophs increased as the melt season progressed, likely due to the seasonal development of the glacial drainage system. The methylotrophs were dominated by representatives of type I methanotrophs from the Gammaproteobacteria; however, their relative abundance decreased with increasing distance from the ice margin at the expense of type II methanotrophs and/or methylotrophs from the Alphaproteobacteria and Betaproteobacteria. Our results show that subglacial methane release hotspot sites can be colonized by microorganisms that can potentially reduce methane emissions.}, }
@article {pmid37843655, year = {2023}, author = {Sudhakari, PA and Ramisetty, BCM}, title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3068-3081}, pmid = {37843655}, issn = {1432-184X}, mesh = {Humans ; Lysogeny ; Prophages/genetics ; Escherichia coli/genetics ; *Superinfection/genetics ; Wastewater ; *Bacteriophages/genetics ; Genome, Bacterial ; }, abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.}, }
@article {pmid37836513, year = {2023}, author = {Perreau, C and Thabuis, C and Verstrepen, L and Ghyselinck, J and Marzorati, M}, title = {Ex Vivo Colonic Fermentation of NUTRIOSE[®] Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects.}, journal = {Nutrients}, volume = {15}, number = {19}, pages = {}, pmid = {37836513}, issn = {2072-6643}, support = {//Roquette/ ; }, mesh = {Humans ; *Dextrins ; Fermentation ; *Lipopolysaccharides/metabolism ; Caco-2 Cells ; Colon/metabolism ; Fatty Acids, Volatile/metabolism ; Immunity ; Anti-Inflammatory Agents/pharmacology/metabolism ; }, abstract = {NUTRIOSE[®] (Roquette, Lestrem, France) is a resistant dextrin with well-established prebiotic effects. This study evaluated the indirect effects of pre-digested NUTRIOSE[®] on host immune response and gut barrier integrity. Fecal samples from eight healthy donors were inoculated in a Colon-on-a-plate[®] system (ProDigest, Ghent, Belgium) with or without NUTRIOSE[®] supplementation. Following 48 h fermentation, colonic suspensions were tested in a Caco-2/THP1-Blue™ co-culture system to determine their effects on gut barrier activity (transepithelial electrical resistance) and immune response following lipopolysaccharide stimulation. Additionally, changes in short-chain fatty acid levels (SCFA) and microbial community composition following a 48 h fermentation in the Colon-on-a-plate[®] system were measured. Across all donors, immune-mediated intestinal barrier damage was significantly reduced with NUTRIOSE[®]-supplemented colonic suspensions versus blank. Additionally, IL-6 and IL-10 levels were significantly increased, and the level of the neutrophil chemoattractant IL-8 was significantly decreased with NUTRIOSE[®]-supplemented colonic suspensions versus blank in the co-culture models following lipopolysaccharide stimulation. These beneficial effects of NUTRIOSE[®] supplementation were likely due to increased acetate and propionate levels and the enrichment of SCFA-producing bacteria. NUTRIOSE[®] was well fermented by the colonic bacteria of all eight donors and had protective effects on inflammation-induced disruption of the intestinal epithelial barrier and strong anti-inflammatory effects.}, }
@article {pmid37833155, year = {2023}, author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Sex-specific intestinal dysbiosis persists after multicompartmental injury.}, journal = {Surgery}, volume = {174}, number = {6}, pages = {1453-1462}, doi = {10.1016/j.surg.2023.08.023}, pmid = {37833155}, issn = {1532-7361}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Male ; Rats ; Animals ; Rats, Sprague-Dawley ; *Dysbiosis/etiology ; RNA, Ribosomal, 16S ; *Multiple Trauma ; Computational Biology ; }, abstract = {BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n&#xa0;= 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or na&#xef;ve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.<br><br>RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P&#xa0;= .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.<br><br>CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.}, }
@article {pmid37831075, year = {2023}, author = {Xu, H and Xiao, Q and Dai, Y and Chen, D and Zhang, C and Jiang, Y and Xie, J}, title = {Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3043-3056}, pmid = {37831075}, issn = {1432-184X}, mesh = {*Rivers/chemistry ; *Carbon Sequestration ; Dissolved Organic Matter ; Leucine/metabolism ; Multiomics ; Carbon/metabolism ; Bacteria/genetics/metabolism ; Water/metabolism ; }, abstract = {Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.}, }
@article {pmid37830797, year = {2023}, author = {Stapelfeldt, HRD and Lanclos, VC and Henson, MW and Thrash, JC}, title = {Draft genome sequence of the BAL58 Betaproteobacteria representative strain LSUCC0117.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0062023}, pmid = {37830797}, issn = {2576-098X}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; }, abstract = {Here, we present the draft genome sequence of strain LSUCC0117, a representative of the abundant aquatic BAL58 Betaproteobacteria group which we isolated from a coastal site in the northern Gulf of Mexico. The genome is estimated at over 99% complete, with a genome size of 2,687,225 bp.}, }
@article {pmid37828283, year = {2023}, author = {Kothamasi, D and Vermeylen, S and Deepika, S}, title = {Are ecological processes that select beneficial traits in agricultural microbes nature's intellectual property rights?.}, journal = {Nature biotechnology}, volume = {41}, number = {10}, pages = {1381-1384}, pmid = {37828283}, issn = {1546-1696}, support = {894188//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Intellectual Property ; *Agriculture ; Bacteria ; }, }
@article {pmid37823651, year = {2023}, author = {Tran, WC and Sullivan, B and Kitzmiller, CE and Choudoir, M and Simoes, R and Dayarathne, N and DeAngelis, KM}, title = {Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0037323}, pmid = {37823651}, issn = {2576-098X}, support = {DEB-1749206, DEB-1456610, DEB-1832210//National Science Foundation (NSF)/ ; }, abstract = {Paenibacillus sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.}, }
@article {pmid37822474, year = {2023}, author = {Callewaert, C and Pezavant, M and Vandaele, R and Meeus, B and Vankrunkelsven, E and Van Goethem, P and Plumacker, A and Misset, B and Darcis, G and Piret, S and De Vleeschouwer, L and Staelens, F and Van Varenbergh, K and Tombeur, S and Ottevaere, A and Montag, I and Vandecandelaere, P and Jonckheere, S and Vandekerckhove, L and Tobback, E and Wieers, G and Marot, JC and Anseeuw, K and D'Hoore, L and Tuyls, S and De Tavernier, B and Catteeuw, J and Lotfi, A and Melnik, A and Aksenov, A and Grandjean, D and Stevens, M and Gasthuys, F and Guyot, H}, title = {Sniffing out safety: canine detection and identification of SARS-CoV-2 infection from armpit sweat.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1185779}, pmid = {37822474}, issn = {2296-858X}, abstract = {Detection dogs were trained to detect SARS-CoV-2 infection based on armpit sweat odor. Sweat samples were collected using cotton pads under the armpits of negative and positive human patients, confirmed by qPCR, for periods of 15-30 min. Multiple hospitals and organizations throughout Belgium participated in this study. The sweat samples were stored at -20°C prior to being used for training purposes. Six dogs were trained under controlled atmosphere conditions for 2-3 months. After training, a 7-day validation period was conducted to assess the dogs' performances. The detection dogs exhibited an overall sensitivity of 81%, specificity of 98%, and an accuracy of 95%. After validation, training continued for 3 months, during which the dogs' performances remained the same. Gas chromatography/mass spectrometry (GC/MS) analysis revealed a unique sweat scent associated with SARS-CoV-2 positive sweat samples. This scent consisted of a wide variety of volatiles, including breakdown compounds of antiviral fatty acids, skin proteins and neurotransmitters/hormones. An acceptability survey conducted in Belgium demonstrated an overall high acceptability and enthusiasm toward the use of detection dogs for SARS-CoV-2 detection. Compared to qPCR and previous canine studies, the detection dogs have good performances in detecting SARS-CoV-2 infection in humans, using frozen sweat samples from the armpits. As a result, they can be used as an accurate pre-screening tool in various field settings alongside the PCR test.}, }
@article {pmid37821698, year = {2023}, author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and ,  and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC}, title = {Unraveling the functional dark matter through global metagenomics.}, journal = {Nature}, volume = {622}, number = {7983}, pages = {594-602}, pmid = {37821698}, issn = {1476-4687}, support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; }, abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.}, }
@article {pmid37821652, year = {2023}, author = {Yost, RT and Fowler, AE and Adler, LS}, title = {Gut Transplants from Bees Fed an Antipathogenic Pollen Diet Do Not Confer Pathogen Resistance to Recipients.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3133-3137}, pmid = {37821652}, issn = {1432-184X}, support = {2128221//National Science Foundation/ ; NE2001//U.S. Department of Agriculture/ ; }, mesh = {Bees ; Animals ; Pollen ; Diet/veterinary ; *Microbiota ; *Gastrointestinal Microbiome ; Crithidia ; *Biological Products ; }, abstract = {Pollinators are threatened by diverse stressors, including microbial pathogens such as Crithidia bombi. Consuming sunflower pollen dramatically reduces C. bombi infection in the bumble bee Bombus impatiens, but the mechanism behind this medicinal effect is unclear. We asked whether diet mediates resistance to C. bombi through changes in the gut microbiome. We hypothesized that sunflower pollen changes the gut microbiome, which in turn reduces Crithidia infection. To test this, we performed a gut transplant experiment. We fed donor bees either a sunflower pollen treatment or buckwheat pollen as a control treatment and then inoculated recipient bees with homogenized guts from either sunflower-fed or buckwheat-fed donor bees. All recipient bees were then fed a wildflower pollen diet. Two days after the transplant, we infected recipients with C. bombi, and 2 days later, we provided another donor gut transplant. To quantify infection, we performed both fecal screens and dissections of the recipient bees. We found no significant differences in C. bombi infection intensity or presence between bees that received sunflower-fed microbiomes versus buckwheat-fed microbiomes. This suggests that sunflower pollen's effects on pathogen resistance are not mediated by gut microbiota.}, }
@article {pmid37820474, year = {2023}, author = {Ma, L and Roman, M and Alhadidi, A and Jia, M and Martini, F and Xue, Y and Verliefde, A and Gutierrez, L and Cornelissen, E}, title = {Fate of organic micropollutants during brackish water desalination for drinking water production in decentralized capacitive electrodialysis.}, journal = {Water research}, volume = {245}, number = {}, pages = {120625}, doi = {10.1016/j.watres.2023.120625}, pmid = {37820474}, issn = {1879-2448}, mesh = {*Drinking Water ; *Water Purification ; Sodium Chloride ; Ions ; Adsorption ; Saline Waters ; }, abstract = {Capacitive electrodialysis (CED) is an emerging and promising desalination technology for decentralized drinking water production. Brackish water, often used as a drinking water source, may contain organic micropollutants (OMPs), thus raising environmental and health concerns. This study investigated the transport of OMPs in a fully-functional decentralized CED system for drinking water production under realistic operational conditions. Eighteen environmentally-relevant OMPs (20 µg L[-1]) with different physicochemical properties (charge, size, hydrophobicity) were selected and added to the feed water. The removal of OMPs was significantly lower than that of salts (∼94%), mainly due to their lower electrical mobility and higher steric hindrance. The removal of negatively-charged OMPs reached 50% and was generally higher than that of positively-charged OMPs (31%), whereas non-charged OMPs were barely transported. Marginal adsorption of OMPs was found under moderate water recovery (50%), in contrast to significant adsorption of charged OMPs under high water recovery (80%). The five-month operation demonstrated that the CED system could reliably produce water with low salt ions and TOC concentrations, meeting the respective WHO requirements. The specific energy consumption of the CED stack under 80% water recovery was 0.54 kWh m[-3], which is competitive to state-of-the-art RO, ED, and emerging MCDI in brackish water desalination. Under this condition, the total OPEX was 2.43 € m[-3], of which the cost of membrane replacement contributed significantly. Although the CED system proved to be a robust, highly adaptive, and fully automated technology for decentralized drinking water production, it was not highly efficient in removing OMPs, especially non-charged OMPs.}, }
@article {pmid37819096, year = {2023}, author = {Khot, V and Strous, M and Dong, X and Kiesser, AK}, title = {Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0221723}, pmid = {37819096}, issn = {2165-0497}, support = {//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Alberta Innovates (AI)/ ; Alberta Graduate Excellence//Government of Alberta (Alberta Government)/ ; Faculty of Graduate Studies Doctoral Scholarship//University of Calgary (U of C)/ ; }, mesh = {CRISPR-Cas Systems ; *Cyanobacteria/genetics ; *Viruses ; }, abstract = {Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.}, }
@article {pmid37819078, year = {2023}, author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP}, title = {Competitive interactions facilitate resistance development against antimicrobials.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0115523}, pmid = {37819078}, issn = {1098-5336}, mesh = {*Anti-Infective Agents/pharmacology ; Biofilms ; Bacteria/genetics ; Phenotype ; Sulfathiazoles/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.}, }
@article {pmid37818230, year = {2023}, author = {Grander, C and Meyer, M and Steinacher, D and Claudel, T and Hausmann, B and Pjevac, P and Grabherr, F and Oberhuber, G and Grander, M and Brigo, N and Jukic, A and Schwärzler, J and Weiss, G and Adolph, TE and Trauner, M and Tilg, H}, title = {24-Norursodeoxycholic acid ameliorates experimental alcohol-related liver disease and activates hepatic PPARγ.}, journal = {JHEP reports : innovation in hepatology}, volume = {5}, number = {11}, pages = {100872}, pmid = {37818230}, issn = {2589-5559}, support = {P 29379/FWF_/Austrian Science Fund FWF/Austria ; P 33070/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND &amp; AIMS: Alcohol-related liver disease (ALD) is a global healthcare challenge with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a synthetic bile acid with anti-inflammatory properties in experimental and human cholestatic liver diseases. In the present study, we explored the efficacy of norUDCA in experimental ALD.<br><br>METHODS: NorUDCA was tested in a preventive and therapeutic setting in an experimental ALD model (Lieber-DeCarli diet enriched with ethanol). Liver disease was phenotypically evaluated using histology and biochemical methods, and anti-inflammatory properties and peroxisome proliferator-activated receptor gamma activation by norUDCA were evaluated in cellular model systems.<br><br>RESULTS: NorUDCA administration ameliorated ethanol-induced liver injury, reduced hepatocyte death, and reduced the expression of hepatic pro-inflammatory cytokines including tumour necrosis factor (Tnf), Il-1&#x3b2;, Il-6, and Il-10. NorUDCA shifted hepatic macrophages towards an anti-inflammatory M2 phenotype. Further, norUDCA administration altered the composition of the intestinal microbiota, specifically increasing the abundance of Roseburia, Enterobacteriaceae, and Clostridum spp. In a&#xa0;therapeutic model, norUDCA also ameliorated ethanol-induced liver injury. Moreover, norUDCA suppressed lipopolysaccharide-induced IL-6 expression in human peripheral blood mononuclear cells and evoked peroxisome proliferator-activated receptor gamma activation.<br><br>CONCLUSIONS: NorUDCA ameliorated experimental ALD, protected against hepatic inflammation, and affected gut microbial commensalism. NorUDCA could serve as a novel therapeutic agent in the future management of patients with ALD.<br><br>IMPACT AND IMPLICATIONS: Alcohol-related liver disease is a global healthcare concern with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a modified bile acid, which was proven to be effective in human cholestatic liver diseases. In the present study, we found a protective effect of norUDCA in experimental alcoholic liver disease. For patients with ALD, norUDCA could be a potential new treatment option.}, }
@article {pmid37816903, year = {2023}, author = {Abdolahpur Monikh, F and Baun, A and Hartmann, NB and Kortet, R and Akkanen, J and Lee, JS and Shi, H and Lahive, E and Uurasjärvi, E and Tufenkji, N and Altmann, K and Wiesner, Y and Grossart, HP and Peijnenburg, W and Kukkonen, JVK}, title = {Exposure protocol for ecotoxicity testing of microplastics and nanoplastics.}, journal = {Nature protocols}, volume = {18}, number = {11}, pages = {3534-3564}, pmid = {37816903}, issn = {1750-2799}, support = {965367//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 964766//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *Microplastics/analysis/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/analysis/chemistry/toxicity ; }, abstract = {Despite the increasing concern about the harmful effects of micro- and nanoplastics (MNPs), there are no harmonized guidelines or protocols yet available for MNP ecotoxicity testing. Current ecotoxicity studies often use commercial spherical particles as models for MNPs, but in nature, MNPs occur in variable shapes, sizes and chemical compositions. Moreover, protocols developed for chemicals that dissolve or form stable dispersions are currently used for assessing the ecotoxicity of MNPs. Plastic particles, however, do not dissolve and also show dynamic behavior in the exposure medium, depending on, for example, MNP physicochemical properties and the medium's conditions such as pH and ionic strength. Here we describe an exposure protocol that considers the particle-specific properties of MNPs and their dynamic behavior in exposure systems. Procedure 1 describes the top-down production of more realistic MNPs as representative of MNPs in nature and particle characterization (e.g., using thermal extraction desorption-gas chromatography/mass spectrometry). Then, we describe exposure system development for short- and long-term toxicity tests for soil (Procedure 2) and aquatic (Procedure 3) organisms. Procedures 2 and 3 explain how to modify existing ecotoxicity guidelines for chemicals to target testing MNPs in selected exposure systems. We show some examples that were used to develop the protocol to test, for example, MNP toxicity in marine rotifers, freshwater mussels, daphnids and earthworms. The present protocol takes between 24 h and 2 months, depending on the test of interest and can be applied by students, academics, environmental risk assessors and industries.}, }
@article {pmid37816747, year = {2023}, author = {Rahlff, J and Esser, SP and Plewka, J and Heinrichs, ME and Soares, A and Scarchilli, C and Grigioni, P and Wex, H and Giebel, HA and Probst, AJ}, title = {Marine viruses disperse bidirectionally along the natural water cycle.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6354}, pmid = {37816747}, issn = {2041-1723}, mesh = {*Ecosystem ; Water Cycle ; Seawater/analysis ; *Viruses/genetics ; Aerosols/analysis ; }, abstract = {Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.}, }
@article {pmid37816673, year = {2023}, author = {Byers, AK and Condron, LM and O'Callaghan, M and Waller, L and Dickie, IA and Wakelin, SA}, title = {Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, pmid = {37816673}, issn = {1574-6941}, mesh = {*Soil Microbiology ; Phylogeny ; Soil ; *Microbiota ; Bacteria/genetics ; Plants/microbiology ; Plant Roots/microbiology ; Rhizosphere ; }, abstract = {The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.}, }
@article {pmid37814279, year = {2023}, author = {Liu, W and Liu, H and Wang, Y and Zhao, Z and Balasubramanian, B and Jha, R}, title = {Effects of Enteromorpha prolifera polysaccharides on growth performance, intestinal barrier function and cecal microbiota in yellow-feathered broilers under heat stress.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {132}, pmid = {37814279}, issn = {1674-9782}, support = {32002196//National Nature Science Foundation of China/ ; }, abstract = {BACKGROUND: Global warming leading to heat stress (HS) is becoming a major challenge for broiler production. This study aimed to explore the protective effects of seaweed (Enteromorpha prolifera) polysaccharides (EPS) on the intestinal barrier function, microbial ecology, and performance of broilers under HS. A total of 144 yellow-feathered broilers (male, 56 days old) with 682.59 ± 7.38 g were randomly assigned to 3 groups: 1) TN (thermal neutral zone, 23.6 ± 1.8 °C), 2) HS (heat stress, 33.2 ± 1.5 °C for 10 h/d), and 3) HSE (HS + 0.1% EPS). Each group contained 6 replicates with 8 broilers per replicate. The study was conducted for 4 weeks; feed intake and body weights were measured at the end of weeks 2 and 4. At the end of the feeding trial, small intestine samples were collected for histomorphology, antioxidant, secretory immunoglobulin A (sIgA) content, apoptosis, gene and protein expression analysis; cecal contents were also collected for microbiota analysis based on 16S rDNA sequencing.<br><br>RESULTS: Dietary EPS promoted the average daily gain (ADG) of broilers during 3-4 weeks of HS (P&#x2009;<&#x2009;0.05). At the end of HS on broilers, the activity of total superoxide dismutase (T-SOD), glutathione S-transferase (GST), and the content of sIgA in jejunum were improved by EPS supplementation (P&#x2009;<&#x2009;0.05). Besides, dietary EPS reduced the epithelial cell apoptosis of jejunum and ileum in heat-stressed broilers (P&#x2009;<&#x2009;0.05). Addition of EPS in HS group broilers' diet upregulated the relative mRNA expression of Occludin, ZO-1, &#x3b3;-GCLc and IL-10 of the jejunum (P&#x2009;<&#x2009;0.05), whereas downregulated the relative mRNA expression of NF-&#x3ba;B p65, TNF-&#x3b1; and IL-1&#x3b2; of the jejunum (P&#x2009;<&#x2009;0.05). Dietary EPS increased the protein expression of Occludin and ZO-1, whereas it reduced the protein expression of NF-&#x3ba;B p65 and MLCK (P&#x2009;<&#x2009;0.01) and tended to decrease the protein expression of TNF-&#x3b1; (P&#x2009;=&#x2009;0.094) in heat-stressed broilers. Furthermore, the proportions of Bacteroides and Oscillospira among the three groups were positively associated with jejunal apoptosis and pro-inflammatory cytokine expression (P&#x2009;<&#x2009;0.05) and negatively correlated with jejunal Occludin level (P&#x2009;<&#x2009;0.05). However, the proportions of Lactobacillus, Barnesiella, Subdoligranulum, Megasphaera, Collinsella, and Blautia among the three groups were positively related to ADG (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: EPS can be used as a feed additive in yellow-feathered broilers. It effectively improves growth performance and alleviates HS-induced intestinal injury by relieving inflammatory damage and improving the tight junction proteins expression. These beneficial effects may be related to inhibiting NF-&#x3ba;B/MLCK signaling pathway activation and regulation of cecal microbiota.}, }
@article {pmid37813267, year = {2024}, author = {Biagioli, F and Coleine, C and Delgado-Baquerizo, M and Feng, Y and Saiz-Jimenez, C and Selbmann, L}, title = {Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167674}, doi = {10.1016/j.scitotenv.2023.167674}, pmid = {37813267}, issn = {1879-1026}, mesh = {Caves/microbiology ; Bacteria/metabolism ; *Microbiota ; Geography ; *Mycobiome ; }, abstract = {The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.}, }
@article {pmid37812012, year = {2023}, author = {Kocurek, B and Ramachandran, P and Grim, CJ and Morin, P and Howard, L and Ottesen, A and Timme, R and Leonard, SR and Rand, H and Strain, E and Tadesse, D and Pettengill, JB and Lacher, DW and Mammel, M and Jarvis, KG}, title = {Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0148223}, pmid = {37812012}, issn = {2165-0497}, mesh = {Humans ; *Listeria monocytogenes/genetics ; Food Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Seafood ; }, abstract = {In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.}, }
@article {pmid37812006, year = {2023}, author = {Phillips, EK and Shaffer, JMC and Henson, MW and Coelho, JT and Martin, MO and Thrash, JC}, title = {Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0066723}, pmid = {37812006}, issn = {2576-098X}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279, EF-2125191//National Science Foundation (NSF)/ ; }, abstract = {Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.}, }
@article {pmid37811990, year = {2023}, author = {He, D and Yao, X and Zhang, P and Liu, W and Huang, J and Sun, H and Wang, N and Zhang, X and Wang, H and Zhang, H and Ao, X and Xie, F}, title = {Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0178623}, pmid = {37811990}, issn = {2165-0497}, support = {LJKZ0678//Project of Scientific Research in Education Department of Liaoning Province, China/ ; 22-318-2-05//Project of Science and technology of Shenyang, China/ ; LJKZ0630//Project of Scientific Research in Education Department of Liaoning province, China/ ; }, mesh = {*Soil ; *Mycobiome ; Glycine max ; Rhizosphere ; Soil Microbiology ; Crops, Agricultural/microbiology ; }, abstract = {Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.}, }
@article {pmid37810791, year = {2023}, author = {McKenney, EA and Nichols, LM and Alvarado, S and Hardy, S and Kemp, K and Polmanteer, R and Shoemaker, A and Dunn, RR}, title = {Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16163}, pmid = {37810791}, issn = {2167-8359}, mesh = {*Flour/microbiology ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/genetics ; Lactobacillus/genetics ; }, abstract = {The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2-6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10-14) characterized by acid-tolerant taxa and fruity (p < 3.03e-03), sour (p < 1.60e-01), and fermented (p < 1.47e-05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.}, }
@article {pmid37807043, year = {2023}, author = {Hayes, MG and Langille, MGI and Gu, H}, title = {Cross-study analyses of microbial abundance using generalized common factor methods.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {380}, pmid = {37807043}, issn = {1471-2105}, support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; }, abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.<br><br>RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.<br><br>CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.}, }
@article {pmid37805972, year = {2023}, author = {Pandit, B and Moin, A and Mondal, A and Banik, A and Alam, M}, title = {Characterization of a biofilm-forming, amylase-producing, and heavy-metal-bioremediating strain Micrococcus sp. BirBP01 isolated from oligotrophic subsurface lateritic soil.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {351}, pmid = {37805972}, issn = {1432-072X}, mesh = {Micrococcus/genetics/metabolism ; Soil ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Metals, Heavy/metabolism ; Bacteria/genetics ; Biofilms ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; }, abstract = {Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have isolated and partially characterized a bacterial strain BirBP01 from a lead, calcium, and magnesium-rich, oligotrophic subsurface lateritic soil-sample collected from 12-feet deep horizon of a laterite mining pit in Birbhum district, India. The isolate is a biofilm-forming, Gram-positive bacterium having a sarcinae arrangement, mesophilic, slightly alkaliphilic, able to produce amylase, and resistant against multiple heavy-metals. BirBP01 has the ability to bioremediate 51% of Pb, 30% of Zn, and 22% of Cu through biosorption, possibly into the biofilm matrix. The bioremediating ability of the bacterium alleviated the inhibitory effect of heavy-metals on the germination of chickpea (Cicer arietinum L.) seeds. 16S rRNA gene-based phylogenetic analysis revealed that BirBP01 is a member of the genus Micrococcus. It showed more than 99% identity of the 16S rRNA gene sequence, and clustered within the same branch of the phylogenetic tree, with strains of M. yunnanensis, M. endophyticus, and M. luteus. The ability to produce amylase, and bioremediate heavy-metals signify that Micrococcus sp. BirBP01 could be potentially a good candidate for industrial applications, and to clean up heavy-metal contaminated sites.}, }
@article {pmid37804686, year = {2024}, author = {Çömlekcioğlu, U and Jezierska, S and Opsomer, G and Pascottini, OB}, title = {Uterine microbial ecology and disease in cattle: A review.}, journal = {Theriogenology}, volume = {213}, number = {}, pages = {66-78}, doi = {10.1016/j.theriogenology.2023.09.016}, pmid = {37804686}, issn = {1879-3231}, mesh = {Female ; Cattle ; Animals ; Dysbiosis/veterinary ; *Cattle Diseases/prevention &amp; control/microbiology ; Uterus/microbiology ; *Endometritis/veterinary ; Bacteria ; *Uterine Diseases/veterinary/microbiology ; }, abstract = {Due to the critical contribution of the uterine-associated microbiota in reproductive health, physiology, and performance, culture-independent methods have been increasingly employed to unravel key aspects of microbial ecology in the uterus of cattle. Nowadays, we know that bacterial diversity is crucial to maintain uterine health, however, there is still no consensus on the exact composition of a healthy uterine microbiota (or eubiosis). Generally, loss of bacterial diversity (or dysbiosis) contributes to the development of uterine infections, associated with increased relative abundances of Bacteroides, Fusobacterium, Trueperella, and Porphyromonas. Uterine infections are highly prevalent and gravely influence the profitability of cattle operations, animal welfare, and public health. Thus, understanding the dynamics of uterine microbial ecology is essential to develop effective strategies focused on preventing and mitigating the adverse effects of uterine dysbiosis as well as assisting in the process of restoring the core, healthy uterine microbiota. The aim of this review is to summarize research conducted in the microbial ecology of bovine uteri. We discuss the origin of the uterine microflora of healthy cows and the factors influencing its composition. In addition, we review the biology of specific pathogens that are known to increase in abundance during the occurrence of uterine disease. Lastly, we provide an overview of the bacterial biofilm in the bovine endometrium, and we briefly summarize the rationale for the use of probiotics to prevent uterine disease in cattle.}, }
@article {pmid37803760, year = {2023}, author = {Tadielo, LE and Dos Santos, EAR and Possebon, FS and Schmiedt, JA and Juliano, LCB and Cerqueira-Cézar, CK and de Oliveira, JP and Sampaio, ANDCE and Melo, PRL and Caron, EFF and Pinto, JPAN and Bersot, LDS and Pereira, JG}, title = {Characterization of microbial ecology, Listeria monocytogenes, and Salmonella sp. on equipment and utensil surfaces in Brazilian poultry, pork, and dairy industries.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113422}, doi = {10.1016/j.foodres.2023.113422}, pmid = {37803760}, issn = {1873-7145}, mesh = {Animals ; Swine ; *Listeria monocytogenes ; Poultry ; Food Microbiology ; Dairying ; *Pork Meat ; Brazil ; RNA, Ribosomal, 16S ; *Red Meat ; Escherichia coli ; Salmonella/genetics ; }, abstract = {This study aimed to evaluate the level of counting by indicator microorganisms, identify the microbial ecology, detect Listeria monocytogenes and Salmonella sp., and determine the presence of virulence genes and biofilm formation. A total of 480 samples were collected from the surfaces of the equipment and utensils using sterile swabs for the detection of L. monocytogenes and Salmonella sp. and counting mesophilic aerobes, Enterobacteriaceae, Escherichia coli, and Pseudomonas sp. The microbial ecology was evaluated by sequencing the 16S rRNA gene. Genes for virulence and biofilm formation were analyzed and adhesion capacity was evaluated for L. monocytogenes and Salmonella sp. The mesophilic aerobe count was the highest in the dairy processing facility, followed by the pork and poultry slaughterhouses. L. monocytogenes was detected in all facilities, with the highest detection in the pork slaughterhouse, followed by the poultry and dairy facilities. Salmonella sp. was only detected in the dairy. Isolates of L. monocytogenes and Salmonella sp. showed poor adhesion to polystyrene surfaces, virulence genes, and biofilm formation. The frequent contaminants in the slaughterhouses were Pseudomonas, Acinetobacter, and Aeromonas in poultry, Acinetobacter, Pseudomonas, and Brevundimonas in pork, and Pseudomonas, Kocuria, and Staphylococcus in dairy. Our results provide useful information to understand the microbiological risks associated with contamination.}, }
@article {pmid37803713, year = {2023}, author = {Podduturi, R and da Silva David, G and da Silva, RJ and Hyldig, G and Jørgensen, NOG and Agerlin Petersen, M}, title = {Characterization and finding the origin of off-flavor compounds in Nile tilapia cultured in net cages in hydroelectric reservoirs, São Paulo State, Brazil.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113375}, doi = {10.1016/j.foodres.2023.113375}, pmid = {37803713}, issn = {1873-7145}, mesh = {Animals ; *Cichlids ; Brazil ; *Volatile Organic Compounds ; Naphthols/analysis/chemistry ; }, abstract = {An increasing demand for fish products has led to an intensive aquaculture production in Brazil, and cultivation of fish constituted 860 × 10[3] tons in 2022, contributing to the 87% of total fish consumption. Nile tilapia constitutes almost half of the aquaculture production, and most tilapia farms use floating net cages. One of the major constraints of intensive fish production is production of off-flavors. Release of nutrients by the fish leads to deterioration of the water quality and stimulates growth of microorganisms, also including off-flavor producing species. The objective of this study was to determine levels of taste and odor compounds (geosmin, 2-MIB and a selection of volatile compounds) and their impact on the flavor quality of Nile tilapia produced in net cages in reservoirs in São Paulo State, Brazil. GC-MS analysis of fish and water from six different farms showed concentrations of geosmin in the water from 1 to 8 ng/L, while geosmin in fish flesh ranged from 40 to 750 ng/kg. The level of 2-MIB in water was 2 to 25 ng/L, and 0 to 800 ng/kg fish. The GC-MS analysis also revealed presence of more than 100 volatile organic compounds in the fish flesh, consisting of aldehydes, alcohols, benzene derivatives, hydrocarbons, ketones and few other compounds. Geosmin and 2-MIB related flavor notes were detected in all fish by a sensory panel, and a high correlation between the chemical and sensory analyses was found. The potential impact of the volatile organic compounds on the fish flavor is discussed. Analysis of the water quality in the reservoirs indicated that levels of geosmin and 2-MIB levels were highly influenced by the nutrient levels in the water.}, }
@article {pmid37802356, year = {2024}, author = {Sarkodie, EK and Jiang, L and Li, K and Guo, Z and Yang, J and Shi, J and Peng, Y and Wu, X and Huang, S and Deng, Y and Jiang, H and Liu, H and Liu, X}, title = {The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167535}, doi = {10.1016/j.scitotenv.2023.167535}, pmid = {37802356}, issn = {1879-1026}, mesh = {Humans ; Cadmium/analysis ; Cysteine ; Soil/chemistry ; *Microbiota ; Sulfur ; Nitrogen ; *Soil Pollutants/analysis ; *Oryza ; }, abstract = {Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.}, }
@article {pmid37800904, year = {2023}, author = {Ettinger, CL and Wu-Woods, J and Kurbessoian, T and Brown, DJ and Souza Pacheco, Id and Vindiola, BG and Walling, LL and Atkinson, PW and Byrne, FJ and Redak, R and Stajich, JE}, title = {Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0026723}, pmid = {37800904}, issn = {2379-5042}, mesh = {Xylella ; RNA, Ribosomal, 16S/genetics ; *Mycobiome ; *Microbiota ; Animals ; *Hemiptera/microbiology ; Geography ; }, abstract = {The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.}, }
@article {pmid37799598, year = {2023}, author = {Wang, H and Yan, B and Wu, Y and Yin, M and Wang, M and Fu, C}, title = {Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1218806}, pmid = {37799598}, issn = {1664-302X}, abstract = {River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.}, }
@article {pmid37798675, year = {2023}, author = {Avila Santos, AP and Kabiru Nata'ala, M and Kasmanas, JC and Bartholomäus, A and Keller-Costa, T and Jurburg, SD and Tal, T and Camarinha-Silva, A and Saraiva, JP and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Rocha, U}, title = {The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {48}, pmid = {37798675}, issn = {2524-4671}, abstract = {BACKGROUND: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research.<br><br>RESULTS: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. &#xa0;Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries.&#xa0;From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers).<br><br>CONCLUSION: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .}, }
@article {pmid37796897, year = {2023}, author = {Diao, M and Dyksma, S and Koeksoy, E and Ngugi, DK and Anantharaman, K and Loy, A and Pester, M}, title = {Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {5}, pages = {}, pmid = {37796897}, issn = {1574-6976}, support = {P 31996-B/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Oxidation-Reduction ; *Bacteria/metabolism ; *Archaea/metabolism ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/metabolism ; Phylogeny ; }, abstract = {Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.}, }
@article {pmid37794496, year = {2023}, author = {Lühken, R and Becker, N and Dyczko, D and Sauer, FG and Kliemke, K and Schmidt-Chanasit, J and Rydzanicz, K}, title = {First record of Anopheles (Anopheles) hyrcanus (Pallas 1771) (Diptera: Culicidae) in Poland.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {345}, pmid = {37794496}, issn = {1756-3305}, support = {BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Culicidae ; *Anopheles/parasitology ; Poland ; Mosquito Vectors ; Climate ; Europe ; }, abstract = {The spatial distribution of mosquito species in the course of globalization and climate warming is highly dynamic. Different studies have demonstrated the spread and establishment of thermophilic mosquito species, potentially increasing the prevalence of 'nuisance' mosquitoes and the local transmission of pathogens. Here we report the first recorded sampling of Anopheles hyrcanus in Wrocław, southwest Poland. This is the most northern detection of this species to date in Europe. Future spread and population development of this potential vector of malaria parasites, viruses or zoonotic helminths, such as Dirofilaria spp., must be monitored carefully. Potential factors underlying the spread of this species are discussed.}, }
@article {pmid37794421, year = {2023}, author = {Xiang, S and Chen, Z and Dai, Z and Wang, F}, title = {Global burden of lower respiratory infections attributable to secondhand smoke among children under 5 years of age, 2010-2019: a systematic analysis of the global burden of disease study 2019.}, journal = {BMC public health}, volume = {23}, number = {1}, pages = {1920}, pmid = {37794421}, issn = {1471-2458}, mesh = {Humans ; Child ; Child, Preschool ; Global Burden of Disease ; *Tobacco Smoke Pollution/adverse effects ; Quality-Adjusted Life Years ; *Respiratory Tract Infections/epidemiology ; Risk Factors ; Global Health ; }, abstract = {BACKGROUND: Epidemiological trends of lower respiratory infections (LRIs) attributable to secondhand smoke (SHS) among children under 5 years since smoking bans have been increasingly applied globally remain unclear. Here, we aimed to estimate the spatiotemporal trends of the global, regional, and national burden of LRIs attributable to SHS among children under 5 years old between 2010 and 2019.<br><br>METHODS: Data on the deaths, and disability adjusted life years (DALYs) of the disease burden was retrieved from the Global Burden of Disease (GBD) 2019 for 204 countries and territories between 2010 and 2019. The rates per 100,000 population, along with 95% uncertainty intervals, as well as population-attributable fraction (PAF) was presented for each estimate.<br><br>RESULTS: In 2019, an estimated 6.94% (3.80-10.12%) of under-5 LRIs deaths were attributable to SHS globally, with an under-5 mortality rate of 7.02 per 100,000, a decrease of 5.77% since 2010. Similarly, 6.95% (3.81-10.13%) of LRIs DALYs were due to SHS among children under 5 years, with a rate in under-5s of 619.36 DALYs per 100,000, and also a 5.77% decrease since 2010. Azerbaijan, Turkmenistan, and Papua New Guinea showed the highest under-5 mortality and DALYs burden rates of LRIs attributable to SHS in 2019. In contrast, the PAF was stagnant over the past ten years and there is even a year-on-year upward trend in South Asia. Nationally, in 2019, Bosnia and Herzegovina, Armenia, and Montenegro showed the highest PAFSHS of LRIs burden among children under 5 years of age. In addition, the burden was heavier in children under 1 year of age and was significantly negatively associated with sociodemographic index.<br><br>CONCLUSIONS: SHS remains a risk factor that cannot be ignored for LRIs burden worldwide. Hence, governments and health systems should continue to take steps to reduce SHS pollution among young children to mitigate this burden.}, }
@article {pmid37794084, year = {2023}, author = {Hettiarachchi, A and Cnockaert, M and Joossens, M and Gekière, A and Meeus, I and Vereecken, NJ and Michez, D and Smagghe, G and Vandamme, P}, title = {The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3013-3026}, pmid = {37794084}, issn = {1432-184X}, mesh = {Bees ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Mycobiome ; Bacteria ; *Spiroplasma ; }, abstract = {We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.}, }
@article {pmid37794025, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Author Correction: Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6188}, doi = {10.1038/s41467-023-41564-4}, pmid = {37794025}, issn = {2041-1723}, }
@article {pmid37792090, year = {2023}, author = {Rippel, TM and Wimp, GM}, title = {Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3003-3012}, pmid = {37792090}, issn = {1432-184X}, mesh = {*Mycobiome ; Ecosystem ; Fungi/physiology ; Soil Microbiology ; Plant Leaves/microbiology ; Biomass ; Plants ; Soil ; }, abstract = {Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.}, }
@article {pmid37792089, year = {2023}, author = {Sun, J and Zhou, H and Cheng, H and Chen, Z and Yang, J and Wang, Y and Jing, C}, title = {Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3027-3042}, pmid = {37792089}, issn = {1432-184X}, mesh = {*Bacteria/genetics ; *Manganese ; Geologic Sediments/microbiology ; Nickel ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cobalt ; }, abstract = {Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.}, }
@article {pmid37791342, year = {2023}, author = {Kamiya, S}, title = {Microbial ecology between Clostridioides difficile and gut microbiota.}, journal = {Bioscience of microbiota, food and health}, volume = {42}, number = {4}, pages = {229-235}, pmid = {37791342}, issn = {2186-6953}, abstract = {Clostridioides difficile colonizes a polymicrobial environment in the intestine and is a causative agent for antibiotic-associated diarrhea (AAD) and pseudomembranous colitis (PMC). The most important virulence factors of C. difficile are bacterial toxins, and three toxins (toxin A, toxin B, and binary toxin) are produced by toxigenic strains. Other virulence factors include spores, flagella, capsules, biofilms, hydrolytic enzymes and adhesins. C. difficile infection (CDI) is specifically diagnosed by anaerobic culture and toxin detection by either nucleic acid amplification test (NAAT) or enzyme-linked immunosorbent assay (ELISA). For treatment of CDI, metronidazole, vancomycin and fidaxomicin are used based on the severity of CDI. Mutual interaction between C. difficile and gut microbiota is associated with pathogenesis of CDI, and decreased microbial diversity with altered gut microbiome was detected in CDI patients. Restoration of certain gut microbiota is considered to be potentially effective for the prevention and treatment of CDI, and an ideal goal for CDI patients is restoration of the gut microbiota to a healthy state. Fecal microbiota transplantation (FMT) is a highly successful method of microbiome restoration and has been reported to be effective for the prevention of recurrent CDI. In addition, approaches to restoring the gut microbiota by using probioitcs and live biotherapeutic products (LBPs) are currently being studied to examine the effect on CDI. Further microbial ecological research on C. difficile and gut microbiota could lead to a better understanding of the pathogenesis and treatment of CDI.}, }
@article {pmid37783827, year = {2023}, author = {Skwara, A and Gowda, K and Yousef, M and Diaz-Colunga, J and Raman, AS and Sanchez, A and Tikhonov, M and Kuehn, S}, title = {Statistically learning the functional landscape of microbial communities.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {11}, pages = {1823-1833}, pmid = {37783827}, issn = {2397-334X}, support = {R01 GM151538/GM/NIGMS NIH HHS/United States ; T32 GM150375/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Biomass ; Soil ; Models, Theoretical ; }, abstract = {Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.}, }
@article {pmid37782571, year = {2023}, author = {Schnyder, E and Bodelier, PLE and Hartmann, M and Henneberger, R and Niklaus, PA}, title = {Experimental erosion of microbial diversity decreases soil CH4 consumption rates.}, journal = {Ecology}, volume = {104}, number = {12}, pages = {e4178}, doi = {10.1002/ecy.4178}, pmid = {37782571}, issn = {1939-9170}, support = {144065 to Pascal A. Niklaus.//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Ecosystem ; *Soil ; Bacteria/genetics ; Biodiversity ; Wetlands ; Methane ; Soil Microbiology ; }, abstract = {Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10[1] -10[7] -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.}, }
@article {pmid37779539, year = {2022}, author = {Caparrós, E and Cenit, MC and Muriel, J and Benítez-Páez, A and Moreno, MV and González-Delgado, P and Rubio, G and Sanz, Y and Fernández, J}, title = {Intestinal microbiota is modified in pediatric food protein-induced enterocolitis syndrome.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {1}, number = {4}, pages = {217-224}, pmid = {37779539}, issn = {2772-8293}, abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food hypersensitivity that affects the gastrointestinal system, especially in children, who often present with more severe clinical manifestations than adults do. Although its pathogenesis is poorly understood and biomarkers are still lacking, scientific evidence suggests that gut microbiota may play an important role in the development of FPIES.<br><br>OBJECTIVE: We aimed to compare the composition of gut microbiota in children with FPIES with that in age- and sex-matched healthy controls.<br><br>METHODS: We analyzed the gut microbiota profiles in fecal samples of 17 patients with FPIES (case patients) and 12 age-matched healthy children (controls) by tag sequencing of the 16S ribosomal RNA gene hypervariable V4-V5 regions. Subjects' sociodemographic, clinical, and food diary variables were described and compared between groups by using inferential statistical tests. Nonparametric linear discriminant analysis was performed for intestinal microbiota data.<br><br>RESULTS: Patients with confirmed cases FPIES (n&#xa0;= 17; average patient age, 7.5&#xa0;&#xb1; 3.2 years) and controls without FPIES or any atopy (n&#xa0;= 12, average patient age, 6.9&#xa0;&#xb1; 2.7 years) were included. Fish was the main FPIES-inducing allergen in 65% of the cases. The patients with FPIES showed higher proportions of Lachnospiraceae spp (P&#xa0;< .0286) and a lower proportion of Ruminococcaceae spp (P&#xa0;< .0066), Lactobacillaceae spp (P&#xa0;< .0075), and Leuconostocaceae spp (P&#xa0;< .0173) than the controls.<br><br>CONCLUSIONS: Our data clearly show a different gut microbial signature in patients with FPIES, suggesting a new potential avenue for aiding the diagnosis and clinical management of FPIES. Larger studies are needed to confirm these results.}, }
@article {pmid37778560, year = {2024}, author = {Buenaño-Vargas, C and Gagliano, MC and Paulo, LM and Bartle, A and Graham, A and van Veelen, HPJ and O'Flaherty, V}, title = {Acclimation of microbial communities to low and moderate salinities in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167470}, doi = {10.1016/j.scitotenv.2023.167470}, pmid = {37778560}, issn = {1879-1026}, mesh = {*Wastewater ; Anaerobiosis ; Sewage/microbiology ; Waste Disposal, Fluid ; Salinity ; Bioreactors/microbiology ; Bacteria ; *Microbiota ; }, abstract = {In recent years anaerobic digestion (AD) has been investigated as suitable biotechnology to treat wastewater at elevated salinities. However, when starting up AD reactors with inocula that are not adapted to salinity, low concentrations of sodium (Na[+]) in the influent can already cause disintegration of microbial aggregates and wash-out. This study investigated biomass acclimation to 5 g Na[+/]L of two different non-adapted inocula in two lab-scale hybrid expanded granular sludge bed (EGSB)-anaerobic filter (AF) reactors fed with synthetic wastewater. After an initial biomass disintegration, new aggregates were formed relatively fast (i.e., after 95 days of operation), indicating microbial community adaptation. The newly formed microbial aggregates accumulated Na[+] at the expense of calcium (Ca[2+]), but this did not hamper biomass retention or process performance. The hybrid reactor configuration, including a pumice stone filter in the upper section, and the low up-flow velocities applied, were key features for retaining the biomass within the system. This reactor configuration can be easily applied and represents a low-cost alternative for acclimating biomass to saline effluents, even in existing digesters. When the acclimated biomass was transferred from EGSB to an up-flow anaerobic sludge blanket (UASB) reactor configuration also fed with saline synthetic wastewater, more dense aggregates in the form of granules were obtained. The performances of the UASB inoculated with the acclimated biomass were comparable to another reactor seeded with saline-adapted granular sludge from a full-scale plant. Regardless of the inoculum origin, a defined core microbiome of Bacteria (Thermovirga, Bacteroidetes vadinHA17, Blvii28 wastewater-sludge group, Mesotoga, and Synergistaceae) and Archaea (Methanosaeta and Methanobacterium) was detected, highlighting the importance of these microbial groups in developing halotolerance and maintaining AD process stability.}, }
@article {pmid37778079, year = {2023}, author = {Sabach, O and Buhnik-Rosenblau, K and Kesten, I and Freilich, S and Freilich, S and Kashi, Y}, title = {The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties.}, journal = {International journal of food microbiology}, volume = {407}, number = {}, pages = {110402}, doi = {10.1016/j.ijfoodmicro.2023.110402}, pmid = {37778079}, issn = {1879-3460}, mesh = {Saccharomyces cerevisiae/genetics/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Yeast, Dried ; Bacteria ; Pediococcus ; Bread/microbiology ; Flour/microbiology ; Food Microbiology ; }, abstract = {Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period.}, }
@article {pmid37778064, year = {2023}, author = {Niu, G and Wang, R and Zhou, H and Yang, J and Lu, X and Han, X and Huang, J}, title = {Nitrogen addition and mowing had only weak interactive effects on macronutrients in plant-soil systems of a typical steppe in Inner Mongolia.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119121}, doi = {10.1016/j.jenvman.2023.119121}, pmid = {37778064}, issn = {1095-8630}, mesh = {*Ecosystem ; *Soil ; Nitrogen ; Plants ; China ; Nutrients ; Grassland ; }, abstract = {Effective management of macronutrients is pivotal in the optimization and provisioning of ecosystem services in grassland areas, particularly in degraded grasslands. In such instances where mowing and nitrogen (N) fertilization have emerged as predominant management strategies, nutrient management is especially important. However, the precise effects of these concurrent practices on the distribution of macronutrients in plant-soil systems remain unclear. Here we evaluated the effects of 12 years of N addition (2, 10, and 50 g N m[-2] year[-1]) and mowing on the concentrations and pools of six macronutrients (i.e., N; phosphorus P; sulfur S, calcium Ca, magnesium Mg, and potassium K) in three plant components (aboveground plants, litter, and belowground roots) at the community level and in the soil in a typical steppe in Inner Mongolia. Our results revealed that N addition generally raised the N concentration in the entire plant-soil system, regardless of whether plots were mowed. Higher N addition (10 and 50 g N m[-2] year[-1]) also led to higher concentrations of P (+22%, averaging two N addition rates), S (+16%), K (+22%), Ca (+22%), and Mg (+24%) in plants but lower concentrations of these nutrients in the litter. Similar decreases in K (-9%), Ca (-46%), and Mg (-8%) were observed in the roots. In light of the observed increases in vegetation biomass and the lack of pronounced changes in soil bulk density, we found that the ecosystem N enrichment resulted in increased pools of all measured macronutrients in plants, litter, and roots (with the exception of Ca in the roots) while concurrently decreased the pools of P (-20%, averaging two higher N addition rates), S (-12%), K (-10%), Ca (-37%), and Mg (-19%) in the soil, with no obvious effect of the mowing practice. Overall, mowing exhibited a very limited capacity to alleviate the effects of long-term N addition on macronutrients in the plant-soil system. These findings highlight the importance of considering the distribution of macronutrients across distinct plant organs and the dynamic nutrient interplay between plants and soil, particularly in the context of long-term fertilization and mowing practices, when formulating effective grassland management strategies.}, }
@article {pmid37777451, year = {2023}, author = {Tsirigotaki, M and Galanakis, E}, title = {Impact of vaccines on Staphylococcus aureus colonization: A systematic review and meta-analysis.}, journal = {Vaccine}, volume = {41}, number = {44}, pages = {6478-6487}, doi = {10.1016/j.vaccine.2023.09.034}, pmid = {37777451}, issn = {1873-2518}, abstract = {BACKGROUND: Concerns regarding vaccine effects on microbial ecology have led to interest in the non-targeted effects of vaccinations.<br><br>OBJECTIVES: To systematically review the literature related to the impact of vaccines on S. aureus carriage.<br><br>METHODS: We conducted a systematic search of MEDLINE, Scopus and clinical trials.gov for studies that assessed vaccine effects on S. aureus carriage in children and adults using predefined inclusion and exclusion criteria. Generic inverse variance meta-analysis was done using random-effects models.<br><br>RESULTS: Of 1,686 studies screened, 34 were eligible for inclusion, of which 22 were observational and 12 randomized controlled studies (RCTs). 88.2% (30/34) provided data on pneumococcal conjugate vaccines (PCV), 23.5% on influenza vaccines (8/34), 6% on other vaccines (2/34) and 20.6% on more than one vaccine (7/34). Most studies tested nasopharyngeal specimens (82.3%, 28/34). Among children aged more than 18-24&#xa0;months, evidence suggested no effect of PCV on S. aureus colonization [2 RCTs, pooled OR 1.09 (95% CI 0.94-1.25), p 0.25; 7 observational studies, pooled OR: 1.02 (95% CI 0.83-1.25), p 0.86]. A transient increase in S. aureus carriage in PCV-vaccinated infants 9-15&#xa0;months was shown [2 RCTs, pooled OR 1.11 (95% CI 1.00-1.23), p 0.06; 4 observational studies, pooled OR 1.64 (95% CI 1.00-2.68), p 0.05]. A reduction in S. aureus carriage was observed after influenza vaccination [4 observational studies; OR 0.85 (95% CI 0.78-0.94), p 0.0001]. Based on the Grading of Recommendations Assessment, Development and Evaluation, the quality of evidence was considered low for randomized and very low for non-randomized trials.<br><br>CONCLUSION: Evidence did not suggest long-term effects of pneumococcal vaccinations on S. aureus nasopharyngeal carriage in children, however transient niche changes may occur in infants. Influenza vaccination was related to decreased rates of S. aureus carriage. Data regarding other vaccines is scarce. Further research and ongoing surveillance are needed to monitor colonization changes.}, }
@article {pmid37775010, year = {2023}, author = {Shen, Z and Yu, B and Shao, K and Gao, G and Tang, X}, title = {Warming reduces microeukaryotic diversity, network complexity and stability.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117235}, doi = {10.1016/j.envres.2023.117235}, pmid = {37775010}, issn = {1096-0953}, mesh = {*Ecosystem ; *Climate Change ; Analysis of Variance ; Temperature ; }, abstract = {Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P＜0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P＞0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.}, }
@article {pmid37774017, year = {2023}, author = {Wielscher, M and Pfisterer, K and Samardzic, D and Balsini, P and Bangert, C and Jäger, K and Buchberger, M and Selitsch, B and Pjevac, P and Willinger, B and Weninger, W}, title = {The phageome in normal and inflamed human skin.}, journal = {Science advances}, volume = {9}, number = {39}, pages = {eadg4015}, pmid = {37774017}, issn = {2375-2548}, mesh = {Humans ; *Virome ; Skin/microbiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; DNA, Viral/genetics ; }, abstract = {Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.}, }
@article {pmid37771751, year = {2023}, author = {Arikawa, K and Hosokawa, M}, title = {Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4508-4518}, pmid = {37771751}, issn = {2001-0370}, abstract = {Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.}, }
@article {pmid37771273, year = {2023}, author = {Staller, K and Olén, O and Söderling, J and Roelstraete, B and Törnblom, H and Kuo, B and Nguyen, LH and Ludvigsson, JF}, title = {Antibiotic use as a risk factor for irritable bowel syndrome: Results from a nationwide, case-control study.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {58}, number = {11-12}, pages = {1175-1184}, doi = {10.1111/apt.17736}, pmid = {37771273}, issn = {1365-2036}, support = {K23DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Irritable Bowel Syndrome/drug therapy/epidemiology/diagnosis ; Case-Control Studies ; Anti-Bacterial Agents/adverse effects ; Risk Factors ; Sweden/epidemiology ; }, abstract = {BACKGROUND: The microbiome plays an important role in the pathophysiology of irritable bowel syndrome (IBS). Antibiotic use can fundamentally alter gut microbial ecology. We examined the association of antibiotic use with IBS in a large population-based investigation.<br><br>METHODS: A case-control study with prospectively collected data on 29,111 adult patients diagnosed with IBS in Sweden between 2007 and 2016 matched with 135,172 controls. Using a comprehensive histopathology cohort, the Swedish Patient Register, and the Prescribed Drug Register, we identified all consecutive cases of IBS in addition to cumulative antibiotic dispensations accrued until 1&#x2009;year prior to IBS (exclusionary period) for cases and time of matching for up to five general population controls matched on the basis of age, sex, country and calendar year. Conditional logistic regression estimated multivariable-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of IBS.<br><br>RESULTS: Patients with IBS (n&#x2009;=&#x2009;29,111) were more likely than controls (n&#x2009;=&#x2009;135,172) to have used antibiotics up to 1&#x2009;year prior to diagnosis (74.9% vs. 57.8%). After multivariable adjustment, this translated to a more than twofold increased odds of IBS (OR 2.21, 95% CI 2.14-2.28) that did not differ according to age, sex, year of IBS diagnosis or IBS subtype. Compared to none, 1-2 (OR 1.67, 95% CI 1.61-1.73) and &#x2265;3 antibiotics dispensations (OR 3.36, 95% CI 3.24-3.49) were associated with increased odds of IBS (p for trend <0.001) regardless of the antibiotic class.<br><br>CONCLUSIONS: Prior antibiotics use was associated with an increased odds of IBS with the highest risk among people with multiple antibiotics dispensations.}, }
@article {pmid38868338, year = {2023}, author = {Wan, W and Grossart, HP and He, D and Liu, W and Wang, S and Yang, Y}, title = {Differentiation strategies for planktonic bacteria and eukaryotes in response to aggravated algal blooms in urban lakes.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e84}, pmid = {38868338}, issn = {2770-596X}, abstract = {Aggravated algal blooms potentially decreased environmental heterogeneity. Different strategies of planktonic bacteria and eukaryotes in response to aggravated algal blooms. Environmental constraints of plankton showed different patterns over time.}, }
@article {pmid38818334, year = {2023}, author = {Zhu, YG and Zhu, D and Rillig, MC and Yang, Y and Chu, H and Chen, QL and Penuelas, J and Cui, HL and Gillings, M}, title = {Ecosystem Microbiome Science.}, journal = {mLife}, volume = {2}, number = {1}, pages = {2-10}, pmid = {38818334}, issn = {2770-100X}, abstract = {The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field.}, }
@article {pmid38868331, year = {2023}, author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J}, title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e79}, pmid = {38868331}, issn = {2770-596X}, abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.}, }
@article {pmid38868349, year = {2023}, author = {Fu, S and Wang, R and Xu, Z and Zhou, H and Qiu, Z and Shen, L and Yang, Q}, title = {Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e77}, pmid = {38868349}, issn = {2770-596X}, abstract = {A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.}, }
@article {pmid38665803, year = {2023}, author = {Schilling, OS and Nagaosa, K and Schilling, TU and Brennwald, MS and Sohrin, R and Tomonaga, Y and Brunner, P and Kipfer, R and Kato, K}, title = {Revisiting Mt Fuji's groundwater origins with helium, vanadium and environmental DNA tracers.}, journal = {Nature water}, volume = {1}, number = {1}, pages = {60-73}, pmid = {38665803}, issn = {2731-6084}, abstract = {Known locally as the water mountain, for millennia Japan's iconic Mt Fuji has provided safe drinking water to millions of people via a vast network of groundwater and freshwater springs. Groundwater, which is recharged at high elevations, flows down Fuji's flanks within three basaltic aquifers, ultimately forming countless pristine freshwater springs among Fuji's foothills. Here we challenge the current conceptual model of Fuji being a simple system of laminar groundwater flow with little to no vertical exchange between its three aquifers. This model contrasts strongly with Fuji's extreme tectonic instability due to its unique location on top of the only known continental trench-trench-trench triple junction, its complex geology and its unusual microbial spring water communities. On the basis of a unique combination of microbial environmental DNA, vanadium and helium tracers, we provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Fuji's freshwater springs. The most substantial deep groundwater upwelling has been found along Japan's most tectonically active region, the Fujikawa-kako Fault Zone. Our findings broaden the hydrogeological understanding of Fuji and demonstrate the vast potential of combining environmental DNA, on-site noble gas and trace element analyses for groundwater science.}, }
@article {pmid38665197, year = {2023}, author = {Simister, RL and Iulianella Phillips, BP and Wickham, AP and Cayer, EM and Hart, CJR and Winterburn, PA and Crowe, SA}, title = {DNA sequencing, microbial indicators, and the discovery of buried kimberlites.}, journal = {Communications earth &amp; environment}, volume = {4}, number = {1}, pages = {387}, pmid = {38665197}, issn = {2662-4435}, abstract = {Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.}, }
@article {pmid38665180, year = {2023}, author = {Naz, N and Harandi, BF and Newmark, J and Kounaves, SP}, title = {Microbial growth in actual martian regolith in the form of Mars meteorite EETA79001.}, journal = {Communications earth &amp; environment}, volume = {4}, number = {1}, pages = {381}, pmid = {38665180}, issn = {2662-4435}, abstract = {Studies to understand the growth of organisms on Mars are hampered by the use of simulants to duplicate martian mineralogy and chemistry. Even though such materials are improving, no terrestrial simulant can replace a real martian sample. Here we report the use of actual martian regolith, in the form of Mars meteorite EETA79001 sawdust, to demonstrate its ability to support the growth of four microorganisms, E. coli. Eucapsis sp., Chr20-20201027-1, and P. halocryophilus, for up to 23 days under terrestrial conditions using regolith:water ratios from 4:1 to 1:10. If the EETA79001 sawdust is widely representative of regolith on the martian surface, our results imply that microbial life under appropriate conditions could have been present on Mars in the past and/or today in the subsurface, and that the regolith does not contain any bactericidal agents. The results of our study have implications not only for putative martian microbial life but also for building bio-sustainable human habitats on Mars.}, }
@article {pmid38867909, year = {2022}, author = {Zhu, YX and Yang, R and Wang, XY and Wen, T and Gong, MH and Shen, Y and Xu, JY and Zhao, DS and Du, YZ}, title = {Gut microbiota composition in the sympatric and diet-sharing Drosophila simulans and Dicranocephalus wallichii bowringi shaped largely by community assembly processes rather than regional species pool.}, journal = {iMeta}, volume = {1}, number = {4}, pages = {e57}, pmid = {38867909}, issn = {2770-596X}, abstract = {Clarifying the mechanisms underlying microbial community assembly from regional microbial pools is a central issue of microbial ecology, but remains largely unexplored. Here, we investigated the gut bacterial and fungal microbiome assembly processes and potential sources in Drosophila simulans and Dicranocephalus wallichii bowringi, two wild, sympatric insect species that share a common diet of waxberry. While some convergence was observed, the diversity, composition, and network structure of the gut microbiota significantly differed between these two host species. Null model analyses revealed that stochastic processes (e.g., drift, dispersal limitation) play a principal role in determining gut microbiota from both hosts. However, the strength of each ecological process varied with the host species. Furthermore, the source-tracking analysis showed that only a minority of gut microbiota within D. simulans and D. wallichii bowringi are drawn from a regional microbial pool from waxberries, leaves, or soil. Results from function prediction implied that host species-specific gut microbiota might arise partly through host functional requirement and specific selection across host-microbiota coevolution. In conclusion, our findings uncover the importance of community assembly processes over regional microbial pools in shaping sympatric insect gut microbiome structure and function.}, }
@article {pmid37938751, year = {2022}, author = {Jia, X and Dini-Andreote, F and Salles, JF}, title = {Unravelling the interplay of ecological processes structuring the bacterial rare biosphere.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {96}, pmid = {37938751}, issn = {2730-6151}, abstract = {Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.}, }
@article {pmid37938754, year = {2022}, author = {Díaz Rodríguez, CA and Díaz-García, L and Bunk, B and Spröer, C and Herrera, K and Tarazona, NA and Rodriguez-R, LM and Overmann, J and Jiménez, DJ}, title = {Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {89}, pmid = {37938754}, issn = {2730-6151}, abstract = {The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.}, }
@article {pmid38818216, year = {2022}, author = {Guo, X and Yuan, M and Lei, J and Shi, Z and Zhou, X and Li, J and Deng, Y and Yang, Y and Wu, L and Luo, Y and Tiedje, JM and Zhou, J}, title = {Climate warming restructures seasonal dynamics of grassland soil microbial communities.}, journal = {mLife}, volume = {1}, number = {3}, pages = {245-256}, pmid = {38818216}, issn = {2770-100X}, abstract = {Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R [2] = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle.}, }
@article {pmid38234686, year = {2022}, author = {Crous, PW and Boers, J and Holdom, D and Osieck, ER and Steinrucken, TV and Tan, YP and Vitelli, JS and Shivas, RG and Barrett, M and Boxshall, AG and Broadbridge, J and Larsson, E and Lebel, T and Pinruan, U and Sommai, S and Alvarado, P and Bonito, G and Decock, CA and De la Peña-Lastra, S and Delgado, G and Houbraken, J and Maciá-Vicente, JG and Raja, HA and Rigueiro-Rodríguez, A and Rodríguez, A and Wingfield, MJ and Adams, SJ and Akulov, A and Al-Hidmi, T and Antonín, V and Arauzo, S and Arenas, F and Armada, F and Aylward, J and Bellanger, JM and Berraf-Tebbal, A and Bidaud, A and Boccardo, F and Cabero, J and Calledda, F and Corriol, G and Crane, JL and Dearnaley, JDW and Dima, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Fine, M and Ganzert, L and García, D and Torres-Garcia, D and Gené, J and Gutiérrez, A and Iglesias, P and Istel, &#x141; and Jangsantear, P and Jansen, GM and Jeppson, M and Karun, NC and Karich, A and Khamsuntorn, P and Kokkonen, K and Kolařík, M and Kubátová, A and Labuda, R and Lagashetti, AC and Lifshitz, N and Linde, C and Loizides, M and Luangsa-Ard, JJ and Lueangjaroenkit, P and Mahadevakumar, S and Mahamedi, AE and Malloch, DW and Marincowitz, S and Mateos, A and Moreau, PA and Miller, AN and Molia, A and Morte, A and Navarro-Ródenas, A and Nebesářová, J and Nigrone, E and Nuthan, BR and Oberlies, NH and Pepori, AL and Rämä, T and Rapley, D and Reschke, K and Robicheau, BM and Roets, F and Roux, J and Saavedra, M and Sakolrak, B and Santini, A and Ševčíková, H and Singh, PN and Singh, SK and Somrithipol, S and Spetik, M and Sridhar, KR and Starink-Willemse, M and Taylor, VA and van Iperen, AL and Vauras, J and Walker, AK and Wingfield, BD and Yarden, O and Cooke, AW and Manners, AG and Pegg, KG and Groenewald, JZ}, title = {Fungal Planet description sheets: 1383-1435.}, journal = {Persoonia}, volume = {48}, number = {}, pages = {261-371}, pmid = {38234686}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis × E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.) on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.) from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.) from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.) endophytic in roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands, Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.) on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.) on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa, Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum lauri-silvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa, Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on overwintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Boers J, Holdom D, et al. 2022. Fungal Planet description sheets: 1383-1435. Persoonia 48: 261-371. https://doi.org/10.3767/persoonia.2022.48.08.}, }
@article {pmid37938693, year = {2022}, author = {Zauner, S and Vogel, M and Polzin, J and Yuen, B and Mußmann, M and El-Hacen, EM and Petersen, JM}, title = {Microbial communities in developmental stages of lucinid bivalves.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {56}, pmid = {37938693}, issn = {2730-6151}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 31010/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.}, }
@article {pmid37938753, year = {2022}, author = {Alcolombri, U and Pioli, R and Stocker, R and Berry, D}, title = {Single-cell stable isotope probing in microbial ecology.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {55}, pmid = {37938753}, issn = {2730-6151}, support = {P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.}, }
@article {pmid38868712, year = {2022}, author = {Xi, J and Lei, B and Liu, YX and Ding, Z and Liu, J and Xu, T and Hou, L and Han, S and Qian, X and Ma, Y and Xue, Q and Gao, J and Gu, J and Tiedje, JM and Lin, Y}, title = {Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana.}, journal = {iMeta}, volume = {1}, number = {3}, pages = {e31}, pmid = {38868712}, issn = {2770-596X}, abstract = {Orobanche cumana Wallr. is a holoparasite weed that extracts water and nutrients from its host the sunflower, thereby causing yield reductions and quality losses. However, the number of O. cumana parasites in the same farmland is distinctly different. The roots of some hosts have been heavily parasitized, while others have not been parasitized. What are the factors contributing to this phenomenon? Is it possible that sunflower interroot microorganisms are playing a regulatory role in this phenomenon? The role of the microbial community in this remains unclear. In this study, we investigated the rhizosphere soil microbiome for sunflowers with different degrees of O. cumana parasitism, that is, healthy, light infection, moderate infection, and severe infection on the sunflower roots. The microbial structures differed significantly according to the degree of parasitism, where Xanthomonadaceae was enriched in severe infections. Metagenomic analyses revealed that amino acid, carbohydrate, energy, and lipid metabolism were increased in the rhizosphere soils of severely infected sunflowers, which were attributed to the proliferation of Lysobacter. Lysobacter antibioticus (HX79) was isolated and its capacity to promote O. cumana seed germination and increase the germ tube length was confirmed by germination and pot experiments. Cyclo(Pro-Val), an active metabolite of strain HX79, was identified and metabolomic and molecular docking approaches confirmed it was responsible for promoting O. cumana seed germination and growth. And we found that Pseudomonas mandelii HX1 inhibited the growth of O. cumana in the host rhizosphere soil. Our findings clarify the role of rhizosphere microbiota in regulating the parasite O. cumana to possibly facilitate the development of a new weed suppression strategy.}, }
@article {pmid37938683, year = {2022}, author = {Marasco, R and Fusi, M and Ramond, JB and Van Goethem, MW and Seferji, K and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {47}, pmid = {37938683}, issn = {2730-6151}, abstract = {Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.}, }
@article {pmid37938286, year = {2022}, author = {Yeh, YC and Fuhrman, JA}, title = {Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {36}, pmid = {37938286}, issn = {2730-6151}, support = {1737409//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 3779//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 549943//Simons Foundation/ ; }, abstract = {Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.}, }
@article {pmid37938248, year = {2022}, author = {Song, J and Beule, L and Jongmans-Hochschulz, E and Wichels, A and Gerdts, G}, title = {The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {35}, pmid = {37938248}, issn = {2730-6151}, support = {03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.}, }
@article {pmid39131681, year = {2022}, author = {Movva, R and Murtaza, N and Giri, R and Png, CW and Davies, J and Alabbas, S and Oancea, I and O'Cuiv, P and Morrison, M and Begun, J and Florin, TH}, title = {Successful Manipulation of the Gut Microbiome to Treat Spontaneous and Induced Murine Models of Colitis.}, journal = {Gastro hep advances}, volume = {1}, number = {3}, pages = {359-374}, pmid = {39131681}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: There is clinical interest in the sustainability or otherwise of prebiotic, microbial, and antibiotic treatments to both prevent and treat inflammatory bowel diseases. This study examined the role of antibiotic manipulation of the gut microbiome to treat spontaneous and induced murine models of colitis.<br><br>METHODS: Symptomatic, histological, molecular, and microbial ecology and bioinformatic readouts were used to study the effect of a 10-day antibiotic cocktail and then follow-up over 2 months in the spontaneous Winnie colitis mouse preclinical model of ulcerative colitis and also the indirect antibiotic and Winnie microbiotic gavage effects in an acute dextran sodium sulfate-induced colitis model in wild-type mice.<br><br>RESULTS: The antibiotics elicited a striking reduction in both colitis symptoms and blinded histological colitis scores, together with a convergence of the microbial taxonomy of the spontaneous colitis and wild-type control mice, toward a taxonomic phenotype usually considered to be dysbiotic. The improvement in colitis was sustained over the following 8 weeks although the microbial taxonomy changed. In&#xa0;vitro, fecal waters from the antibiotic-treated colitis and wild-type mice suppressed the inflammatory tenor of colonic epithelial cells, and gavaged cecal slurries from these mice moderated the acute induced colitis.<br><br>CONCLUSION: The results clearly show the possibility of a sustained remission of colitis by microbial manipulation, which is relevant to clinical management of inflammatory bowel diseases. The beneficial effects appeared to depend on the microbial metabolome rather than its taxonomy.}, }
@article {pmid38647867, year = {2022}, author = {Dzulkarnain, ELN and Audu, JO and Wan Dagang, WRZ and Abdul-Wahab, MF}, title = {Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook.}, journal = {Bioresources and bioprocessing}, volume = {9}, number = {1}, pages = {16}, pmid = {38647867}, issn = {2197-4365}, support = {MyBrainSC scholarship//Ministry of Higher Education, Malaysia/ ; 05G24//Universiti Teknologi Malaysia/ ; 09G86//Universiti Teknologi Malaysia/ ; }, abstract = {Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.}, }
@article {pmid38867731, year = {2022}, author = {Jiao, S and Chu, H and Zhang, B and Wei, X and Chen, W and Wei, G}, title = {Linking soil fungi to bacterial community assembly in arid ecosystems.}, journal = {iMeta}, volume = {1}, number = {1}, pages = {e2}, pmid = {38867731}, issn = {2770-596X}, abstract = {Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.}, }
@article {pmid37938679, year = {2022}, author = {Junkins, EN and McWhirter, JB and McCall, LI and Stevenson, BS}, title = {Environmental structure impacts microbial composition and secondary metabolism.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {15}, pmid = {37938679}, issn = {2730-6151}, support = {80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.}, }
@article {pmid37938685, year = {2022}, author = {Jiang, G and Zhang, Y and Gan, G and Li, W and Wan, W and Jiang, Y and Yang, T and Zhang, Y and Xu, Y and Wang, Y and Shen, Q and Wei, Z and Dini-Andreote, F}, title = {Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {10}, pmid = {37938685}, issn = {2730-6151}, abstract = {The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.}, }
@article {pmid38089065, year = {2022}, author = {Berkhout, M and Zoetendal, E and Plugge, C and Belzer, C}, title = {Use of synthetic communities to study microbial ecology of the gut.}, journal = {Microbiome research reports}, volume = {1}, number = {1}, pages = {4}, pmid = {38089065}, issn = {2771-5965}, abstract = {The application of in vitro synthetic microbial communities is an excellent approach to model the ecological interactions between microbes in the human gastrointestinal tract. Although DNA-based studies have provided a wealth of information, they do not consider the ecological properties of the human gut microbiota. Ecological interactions between gut microbes of interest can be studied by applying synthetic communities. This review describes the considerations that should be taken into account when constructing a synthetic community by discussing example research questions that can be answered by using a synthetic microbial community, the choice of microbial species, the growth conditions, possible reactor setups, and the parameters to analyze.}, }
@article {pmid37938641, year = {2021}, author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K}, title = {Null-model-based network comparison reveals core associations.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {36}, pmid = {37938641}, issn = {2730-6151}, support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.}, }
@article {pmid37938227, year = {2021}, author = {Reitmeier, S and Hitch, TCA and Treichel, N and Fikas, N and Hausmann, B and Ramer-Tait, AE and Neuhaus, K and Berry, D and Haller, D and Lagkouvardos, I and Clavel, T}, title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {31}, pmid = {37938227}, issn = {2730-6151}, abstract = {16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.}, }
@article {pmid37938246, year = {2021}, author = {Hill, JE and Raaijmakers, JM and Smidt, H}, title = {Editorial.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {10}, doi = {10.1038/s43705-021-00013-3}, pmid = {37938246}, issn = {2730-6151}, }
@article {pmid37769814, year = {2023}, author = {Zinzula, L and Scholz, J and Nagy, I and Di Guardo, G and Orsini, M}, title = {Biophysical characterization of the cetacean morbillivirus haemagglutinin glycoprotein.}, journal = {Virus research}, volume = {336}, number = {}, pages = {199231}, pmid = {37769814}, issn = {1872-7492}, abstract = {Cetacean morbillivirus (CeMV) is an enveloped, non-segmented, negative-stranded RNA virus that infects marine mammals, spreading across species and causing lethal disease outbreaks worldwide. Among the eight proteins encoded by the CeMV genome, the haemagglutinin (H) glycoprotein is responsible for the virus attachment to host cell receptors. CeMV H represents an attractive target for antiviral and diagnostic research, yet the elucidation of the molecular mechanisms underlying its role in infection and inter-species transmission was hampered thus far due to the unavailability of recombinant versions of the protein. Here we present the cloning, expression and purification of a recombinant CeMV H ectodomain (rH-ecto), providing an initial characterization of its biophysical and structural properties. Sodium dodecyl sulphate - polyacrylamide gel electrophoresis (PAGE) combined to Western blot analysis and periodic acid Schiff assay showed that CeMV rH-ecto is purifiable at homogeneity from insect cells as a secreted, soluble and glycosylated protein. Miniaturized differential scanning fluorimetry, Blue Native PAGE and size exclusion chromatography coupled to multiangle light scattering revealed that CeMV rH-ecto is globularly folded, thermally stable and exists in solution in the oligomeric states of dimer and multiple of dimers. Furthermore, negative stain electron microscopy single particle analysis allowed us to delineate a low-resolution molecular architecture of the CeMV rH-ecto dimer, which recapitulates native assemblies from other morbilliviral H proteins, such as those from measles virus and canine distemper virus. This set of experiments by orthogonal techniques validates the CeMV rH-ecto as an experimental model for future biochemical studies on its structure and functions.}, }
@article {pmid37768303, year = {2023}, author = {Kiewra, D and Krysmann, A}, title = {Interactions between hard ticks (Ixodidae) and bacterial tick-borne pathogens.}, journal = {Annals of parasitology}, volume = {69}, number = {1}, pages = {7-16}, doi = {10.17420/ap6901.502}, pmid = {37768303}, issn = {2299-0631}, mesh = {Animals ; Humans ; *Ixodidae ; *Tick-Borne Diseases ; *Rickettsia/genetics ; *Ticks ; Europe ; *Ixodes ; }, abstract = {In Europe, ticks are particularly important vectors of pathogens known as tick-borne pathogens (TBP). TBP can influence hosts, including domestic animals and humans as well as ticks. This review focuses on interactions between hard ticks and medically and veterinary significant bacterial pathogens i.e. Borrelia burgdorferi s.l., Anaplasma spp, and Rickettsia spp. The interactions between ticks and bacteria include among others the impact on gene expression and tick behaviour. Infection with TBP may influence tick salivary proteins and midgut receptors. Infection with B. burgdorferi s.l. changes the bahaviour of the tick allowing them for longer questing and increased mobility, while A. phagocytophilum increases survive in low temperatures by upregulating the expression of antifreeze glycoprotein (IAFGP). Whereas Rickettsia spp. increases ticks attraction towards the 900 MHz electromagnetic field.}, }
@article {pmid37768099, year = {2023}, author = {Ghesquière, J and Simoens, K and Koos, E and Boon, N and Teughels, W and Bernaerts, K}, title = {Spatiotemporal monitoring of a periodontal multispecies biofilm model: demonstration of prebiotic treatment responses.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0108123}, pmid = {37768099}, issn = {1098-5336}, mesh = {Humans ; *Bacteria ; Streptococcus gordonii/physiology ; Fusobacterium nucleatum ; Streptococcus sanguis ; Streptococcus oralis ; Biofilms ; *Periodontitis ; Arginine/metabolism ; Porphyromonas gingivalis/physiology ; }, abstract = {Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community.ImportancePeriodontitis is a multifactorial chronic inflammatory disease in the oral cavity associated with the accumulation of microorganisms in a biofilm. Not the presence of the biofilm as such, but changes in the microbiota (i.e., dysbiosis) drive the development of periodontitis, resulting in the destruction of tooth-supporting tissues. In this respect, novel treatment approaches focus on maintaining the health-associated homeostasis of the resident oral microbiota. To get insight in dynamic biofilm responses, our research presents the establishment of a periodontal biofilm model including Streptococcus gordonii, Streptococcus oralis, Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis. The added value of the model setup is the combination of simulating continuously changing natural mouth conditions with spatiotemporal biofilm profiling using non-destructive characterization tools. These applications are limited for periodontal biofilm research and would contribute in understanding treatment mechanisms, short- or long-term exposure effects, the adaptation potential of the biofilm and thus treatment strategies.}, }
@article {pmid37767604, year = {2023}, author = {Bustos-Lobato, L and Rus, MJ and Saúco, C and Simon-Soro, A}, title = {Oral microbial biomap in the drought environment: Sjogren's syndrome.}, journal = {Molecular oral microbiology}, volume = {38}, number = {5}, pages = {400-407}, doi = {10.1111/omi.12435}, pmid = {37767604}, issn = {2041-1014}, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Droughts ; Ecosystem ; Saliva/microbiology ; }, abstract = {Sjogren's syndrome (SS) is an autoimmune disease that affects primarily the salivary glands, making perturbations in the oral ecosystem and potential factors of salivary flow that influence the onset and development of the disease. The oral cavity contains diverse microorganisms that inhabit various niches such as the oral microbial "biomap." It does not seem specific enough to establish a characteristic microbiome, given the diversity of clinical manifestations, variable rates of salivary secretion, and influential risk factors in patients with SS. This review discusses the biogeography of the oral microbiome in patients with SS such as saliva, tongue, tooth, mucosa, and gum. The microorganisms that were more abundant in the different oral niches were Gram-positive species, suggesting a higher survival of cell wall bacteria in this arid oral environment. Reduced salivary flow appears not to be linked to the cause of dysbiosis alone but influences host-associated risk factors. However, much work remains to be done to establish the role of the microbiome in the etiopathogenesis of autoimmune diseases such as SS. Future studies of the microbiome in autoimmunity will shed light on the role of specific microorganisms that have never been linked before with SS.}, }
@article {pmid37767299, year = {2023}, author = {Cai, J and Pan, R and Lin, J and Liu, J and Zhang, L and Wen, X and Chen, X and Zhang, X}, title = {Improved EfficientNet for corn disease identification.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1224385}, pmid = {37767299}, issn = {1664-462X}, abstract = {INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.<br><br>METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.<br><br>RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.<br><br>DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.}, }
@article {pmid37766415, year = {2023}, author = {Bohórquez-Herrera, J and Abad Matías, ID and Gutiérrez Castañeda, CG}, title = {Impact of different environmental pollution processes on bacterial key-indicators in tropical rivers: scoping review.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad098}, pmid = {37766415}, issn = {1574-6968}, support = {//Universidad de Cartagena/ ; }, abstract = {Freshwater ecosystems are an essential resource for human use and natural populations, but they are exposed to different sources of man-made pollution. This study analyses how different environmental pollution processes influence the structure of bacterial communities in tropical rivers. A scoping review was performed to characterize the bacterial communities in freshwater ecosystems in tropical regions that have been reported to be associated with pollution of different kinds. The statistical analyses allowed us to categorize the genera found into three large groups (pollution generalists, middle types, and pollution specialists) according to the types of pollutants with which they were associated. The results show that Escherichia has a greater association with fecal contamination, while Enterococcus is more associated with domestic wastewater and organic and synthetic chemicals. The present study proposes Streptomyces as a potential indicator of waters with microbial contamination, as well as some other genera as possible indicators of waters with heavy metal contamination.}, }
@article {pmid37760211, year = {2023}, author = {Verstrepen, L and Calatayud-Arroyo, M and Duysburgh, C and De Medts, J and Ekmay, RD and Marzorati, M}, title = {Amino Acid Digestibility of Different Formulations of Torula Yeast in an In Vitro Porcine Gastrointestinal Digestion Model and Their Protective Effects on Barrier Function and Inflammation in a Caco-2/THP1Co-Culture Model.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {18}, pages = {}, pmid = {37760211}, issn = {2076-2615}, support = {//Arbiom Inc./ ; }, abstract = {Single-cell protein from torula yeast (Cyberlindnera jadinii) grown on lignocellulosic biomass has been proven to be an excellent alternative protein source for animal feed. This study aimed to evaluate the amino acid (AA) digestibility by estimating intestinal absorption from three yeast-based ingredients, produced by cultivating C. jadinii on hydrolysate, using either mixed woody species (drum- (WDI) or spray-dried (WSI)) or corn dextrose (drum-dried (DDI)) as the carbon source. Further, the protective effect of intestinal digests on activated THP1-Blue™-induced epithelial damage and cytokine profile was evaluated. Total protein content from these three ingredients ranged from 34 to 45%, while the AA dialysis showed an estimated bioaccessibility between 41 and 58%, indicating good digestibility of all test products. A protective effect against epithelial-induced damage was observed for two of the three tested products. Torula yeast cultivated on wood and drum-dried (WDI) and torula yeast cultivated on wood and spray-dried (WSI) significantly increased transepithelial electrical resistance (TEER) values (111-147%, p < 0.05), recovering the epithelial barrier from the inflammation-induced damage in a dose-dependent manner. Further, WSI digests significantly reduced IL8 (250.8 ± 28.1 ng/mL), IL6 (237.9 ± 1.8 pg/mL) and TNF (2797.9 ± 216.3 pg/mL) compared to the blank control (IL8 = 485.7 ± 74.4 ng/mL, IL6 = 478.7 ± 58.9 pg/mL; TNF = 4273.5 ± 20.9 pg/mL) (p < 0.05). These results align with previous in vivo studies, supporting torula yeast-based ingredients as a high-quality protein source for pigs, protecting the intestinal barrier from inflammatory damage, and reducing the pro-inflammatory response. We provided novel insights into the mechanisms behind the health improvement of pigs fed on torula yeast-based ingredients, with potential applications for designing nutritional interventions to recover intestinal homeostasis during critical production periods, such as weaning.}, }
@article {pmid37756318, year = {2023}, author = {Zhang, X and Yao, C and Zhang, B and Tan, W and Gong, J and Wang, GY and Zhao, J and Lin, X}, title = {Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {40}, pages = {15014-15025}, doi = {10.1021/acs.est.3c03994}, pmid = {37756318}, issn = {1520-5851}, mesh = {Nitrates/analysis ; Chlorophyll A ; Seasons ; Organic Chemicals ; *Ammonium Compounds ; Nitrogen/analysis ; *Microbiota ; Oxygen ; Denitrification ; }, abstract = {Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, [15]N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L[-1]), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.}, }
@article {pmid37755230, year = {2023}, author = {Bareia, T and Pollak, S and Guler, P and Puyesky, S and Eldar, A}, title = {Major distinctions between the two oligopeptide permease systems of Bacillus subtilis with respect to signaling, development and evolutionary divergence.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {9}, pages = {}, pmid = {37755230}, issn = {1465-2080}, mesh = {*Bacillus subtilis/genetics ; Biological Evolution ; *Biological Phenomena ; Signal Transduction ; Oligopeptides ; }, abstract = {Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.}, }
@article {pmid37754985, year = {2023}, author = {Marsaux, B and Moens, F and Marzorati, M and Van de Wiele, T}, title = {The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME[®] Model.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37754985}, issn = {2309-608X}, support = {812969//Marie Sklodowska-Curie/ ; BOF22/GOA/031//UGent special research fund/ ; }, abstract = {From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME[®] gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME[®]-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME[®] reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.}, }
@article {pmid37754764, year = {2023}, author = {Barbosa, C and Tamayo-Leiva, J and Alcorta, J and Salgado, O and Daniele, L and Morata, D and Díez, B}, title = {Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0024923}, pmid = {37754764}, issn = {2165-0497}, abstract = {Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 [2-] and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 [2-] gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.}, }
@article {pmid37754664, year = {2023}, author = {Djemiel, C and Dequiedt, S and Bailly, A and Tripied, J and Lelièvre, M and Horrigue, W and Jolivet, C and Bispo, A and Saby, N and Valé, M and Maron, P-A and Ranjard, L and Terrat, S}, title = {Biogeographical patterns of the soil fungal:bacterial ratio across France.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0036523}, pmid = {37754664}, issn = {2379-5042}, mesh = {Humans ; *Soil/chemistry ; *Environmental Biomarkers ; Soil Microbiology ; Bacteria/genetics ; France ; Carbon ; }, abstract = {Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.}, }
@article {pmid37752280, year = {2023}, author = {Dong, M and Kuramae, EE and Zhao, M and Li, R and Shen, Q and Kowalchuk, GA}, title = {Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {104}, pmid = {37752280}, issn = {2730-6151}, support = {41977044//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202006850020//China Scholarship Council (CSC)/ ; }, abstract = {Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.}, }
@article {pmid37750468, year = {2023}, author = {Wang, Z and Ishii, S and Novak, PJ}, title = {Quantification of depth-dependent microbial growth in encapsulated systems.}, journal = {Microbial biotechnology}, volume = {16}, number = {11}, pages = {2094-2104}, pmid = {37750468}, issn = {1751-7915}, mesh = {In Situ Hybridization, Fluorescence ; *Biofilms ; *Alginates ; }, abstract = {Encapsulated systems have been widely used in environmental applications to selectively retain and protect microorganisms. The permeable matrix used for encapsulation, however, limits the accessibility of existing analytical methods to study the behaviour of the encapsulated microorganisms. Here, we present a novel method that overcomes these limitations and enables direct observation and enumeration of encapsulated microbial colonies over a range of spatial and temporal scales. The method involves embedding, cross-sectioning, and analysing the system via fluorescence in situ hybridization and retains the structure of encapsulants and the morphology of encapsulated colonies. The major novelty of this method lies in its ability to distinguish between, and subsequently analyse, multiple microorganisms within a single encapsulation matrix across depth. Our results demonstrated the applicability and repeatability of this method with alginate-encapsulated pure (Nitrosomonas europaea) and enrichment cultures (anammox enrichment). The use of this method can potentially reveal interactions between encapsulated microorganisms and their surrounding matrix, as well as quantitatively validate predictions from mathematical models, thereby advancing our understanding of microbial ecology in encapsulated or even biofilm systems and facilitating the optimization of these systems.}, }
@article {pmid37749300, year = {2023}, author = {Mueller, AJ and Daebeler, A and Herbold, CW and Kirkegaard, RH and Daims, H}, title = {Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2123-2133}, pmid = {37749300}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria ; Ammonia/metabolism ; Nitrification ; Genomics ; Phylogeny ; }, abstract = {Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.}, }
@article {pmid37748600, year = {2023}, author = {Lamprea Pineda, PA and Demeestere, K and González-Cortés, JJ and Alvarado-Alvarado, AA and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C}, title = {Effect of inoculum type, packing material and operational conditions on the biofiltration of a mixture of hydrophobic volatile organic compounds in air.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {167326}, doi = {10.1016/j.scitotenv.2023.167326}, pmid = {37748600}, issn = {1879-1026}, mesh = {*Volatile Organic Compounds/analysis ; Filtration/methods ; Hexanes ; Biodegradation, Environmental ; Cyclohexanes ; Toluene ; *Air Pollutants/analysis ; Bioreactors/microbiology ; }, abstract = {The emission of volatile organic compounds (VOCs) into the atmosphere causes negative environmental and health effects. Biofiltration is known to be an efficient and cost-effective treatment technology for the removal of VOCs in waste gas streams. However, little is known on the removal of VOC mixtures and the effect of operational conditions, particularly for hydrophobic VOCs, and on the microbial populations governing the biofiltration process. In this study, we evaluated the effect of inoculum type (acclimated activated sludge (A-AS) versus Rhodococcus erythropolis) and packing material (mixture of compost and wood chips (C + WC) versus expanded perlite) on the removal of a mixture of hydrophobic VOCs (toluene, cyclohexane and hexane) in three biofilters (BFs), i.e., BF1: C + WC and R. erythropolis; BF2: C + WC and A-AS; and BF3: expanded perlite and R. erythropolis. The BFs were operated for 374 days at varying inlet loads (ILs) and empty bed residence times (EBRTs). The results showed that the VOCs were removed in the following order: toluene > cyclohexane > hexane, which corresponds to their air-water partitioning coefficient and thus bioavailability of each VOC. Toluene is the most hydrophilic VOC, while hexane is the most hydrophobic. BF2 outperformed BF1 and BF3 in each operational phase, with average maximum elimination capacities (ECmax) of 21 ± 3 g toluene m[-3] h[-1] (removal efficiency (RE): 100 %; EBRT: 82 s), 11 ± 2 g cyclohexane m[-3] h[-1] (RE: 86 ± 6 %; EBRT: 163 s) and 6.2 ± 0.9 g hexane m[-3] h[-1] (RE: 96 ± 4 %; EBRT: 245 s). Microbial analysis showed that despite having different inocula, the genera Rhodococcus, Mycobacterium and/or Pseudonocardia dominated in all BFs but at different relative abundances. This study provides new insights into the removal of difficult-to-degrade VOC mixtures with limited research to date on biofiltration.}, }
@article {pmid37748072, year = {2023}, author = {Maegele, I and Rupp, S and Özbek, S and Guse, A and Hambleton, EA and Holstein, TW}, title = {A predatory gastrula leads to symbiosis-independent settlement in Aiptasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {40}, pages = {e2311872120}, pmid = {37748072}, issn = {1091-6490}, mesh = {Animals ; *Sea Anemones ; Symbiosis ; Gastrula ; *Anthozoa ; *Asteraceae ; *Dinoflagellida ; Larva ; }, abstract = {The planula larvae of the sea anemone Aiptasia have so far not been reported to complete their life cycle by undergoing metamorphosis into adult forms. This has been a major obstacle in their use as a model for coral-dinoflagellate endosymbiosis. Here, we show that Aiptasia larvae actively feed on crustacean nauplii, displaying a preference for live prey. This feeding behavior relies on functional stinging cells, indicative of complex neuronal control. Regular feeding leads to significant size increase, morphological changes, and efficient settlement around 14 d postfertilization. Surprisingly, the presence of dinoflagellate endosymbionts does not affect larval growth or settlement dynamics but is crucial for sexual reproduction. Our findings finally close Aiptasia's life cycle and highlight the functional nature of its larvae, as in Haeckel's Gastrea postulate, yet reveal its active carnivory, thus contributing to our understanding of early metazoan evolution.}, }
@article {pmid37747940, year = {2023}, author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ}, title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.}, journal = {PLoS biology}, volume = {21}, number = {9}, pages = {e3002292}, pmid = {37747940}, issn = {1545-7885}, mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.}, }
@article {pmid37746209, year = {2022}, author = {Yamaguchi, S and Fujioka, T and Yoshimi, A and Kumagai, T and Umemura, M and Abe, K and Machida, M and Kawai, K}, title = {Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1081179}, pmid = {37746209}, issn = {2673-6128}, abstract = {KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.}, }
@article {pmid37746167, year = {2022}, author = {Koizumi, A and Miyazawa, K and Ogata, M and Takahashi, Y and Yano, S and Yoshimi, A and Sano, M and Hidaka, M and Nihira, T and Nakai, H and Kimura, S and Iwata, T and Abe, K}, title = {Cleavage of α-1,4-glycosidic linkages by the glycosylphosphatidylinositol-anchored α-amylase AgtA decreases the molecular weight of cell wall α-1,3-glucan in Aspergillus oryzae.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1061841}, pmid = {37746167}, issn = {2673-6128}, abstract = {Aspergillus fungi contain α-1,3-glucan with a low proportion of α-1,4-glucan as a major cell wall polysaccharide. Glycosylphosphatidylinositol (GPI)-anchored α-amylases are conserved in Aspergillus fungi. The GPI-anchored α-amylase AmyD in Aspergillus nidulans has been reported to directly suppress the biosynthesis of cell wall α-1,3-glucan but not to degrade it in vivo. However, the detailed mechanism of cell wall α-1,3-glucan biosynthesis regulation by AmyD remains unclear. Here we focused on AoAgtA, which is encoded by the Aspergillus oryzae agtA gene, an ortholog of the A. nidulans amyD gene. Similar to findings in A. nidulans, agtA overexpression in A. oryzae grown in submerged culture decreased the amount of cell wall α-1,3-glucan and led to the formation of smaller hyphal pellets in comparison with the wild-type strain. We analyzed the enzymatic properties of recombinant (r)AoAgtA produced in Pichia pastoris and found that it degraded soluble starch, but not linear bacterial α-1,3-glucan. Furthermore, rAoAgtA cleaved 3-α-maltotetraosylglucose with a structure similar to the predicted boundary structure between the α-1,3-glucan main chain and a short spacer composed of α-1,4-linked glucose residues in cell wall α-1,3-glucan. Interestingly, rAoAgtA randomly cleaved only the α-1,4-glycosidic bonds of 3-α-maltotetraosylglucose, indicating that AoAgtA may cleave the spacer in cell wall α-1,3-glucan. Consistent with this hypothesis, heterologous overexpression of agtA in A. nidulans decreased the molecular weight of cell wall α-1,3-glucan. These in vitro and in vivo properties of AoAgtA suggest that GPI-anchored α-amylases can degrade the spacer α-1,4-glycosidic linkages in cell wall α-1,3-glucan before its insolubilization, and this spacer cleavage decreases the molecular weight of cell wall α-1,3-glucan in vivo.}, }
@article {pmid37746119, year = {2023}, author = {Tamano, K and Brown, DW and Yoshimi, A}, title = {Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi.}, journal = {Frontiers in fungal biology}, volume = {4}, number = {}, pages = {1178290}, pmid = {37746119}, issn = {2673-6128}, }
@article {pmid37744927, year = {2023}, author = {Frates, ES and Spietz, RL and Silverstein, MR and Girguis, P and Hatzenpichler, R and Marlow, JJ}, title = {Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1235906}, pmid = {37744927}, issn = {1664-302X}, abstract = {Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.}, }
@article {pmid37744490, year = {2023}, author = {Petrin, S and Orsini, M and Massaro, A and Olsen, JE and Barco, L and Losasso, C}, title = {Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1221351}, pmid = {37744490}, issn = {2296-2565}, mesh = {Animals ; Humans ; Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Phenotype ; Salmonella/genetics ; Italy ; Aminoglycosides ; }, abstract = {INTRODUCTION: The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined.<br><br>METHODS: Eighty-eight Italian Salmonella enterica strains (n&#x2009;=&#x2009;88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated.<br><br>RESULTS AND DISCUSSION: Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.}, }
@article {pmid37737949, year = {2023}, author = {Li, X and Chen, S and Zhao, L and Zeng, X and Liu, Y and Li, C and Yang, Q}, title = {Effect of lactic acid bacteria by different concentrations of copper based on non-target metabolomic analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {49}, pages = {107568-107579}, pmid = {37737949}, issn = {1614-7499}, mesh = {Animals ; Humans ; *Copper/chemistry ; *Lactobacillales ; Bacteria ; Intestines ; Mammals ; }, abstract = {Copper (Cu) is an essential element for mammals, but excess intake can have detrimental health consequences. However, Cu is no longer present in the "Limit of Contaminants in Foods" promulgated in 2022. The potential impact of different Cu (II) concentrations on human health remains unclear. In this study, a strain of lactic acid bacteria (LAB), namely, Lactiplantibacillus plantarum CICC 23121 (L23121), was selected as a prebiotic indicator strain to indirectly assess the effects of food-limited Cu (II) concentrations (issued by Tolerance limit of copper in foods in 1994) on the functions of intestinal microbes. We used non-target metabolomics, automatic growth curve detector, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) to investigate the effects of Cu (II) on L23121. The study revealed shows that the 50% minimum inhibitory concentration (MIC50) of Cu (II) for most lactic acid bacteria was 4 mg/L. At low Cu (II) concentrations (≤ 4 mg/L), the pentose phosphate pathway and pyrimidine metabolism of the lactic acid bacteria were affected, resulting in a decrease in the content of beneficial secondary metabolites and a significant decrease in the cell activity. As Cu (II) concentrations increase (≥ 6 mg/L), the key amino acid and lipid metabolisms were affected, leading to the inhibition of growth and primary metabolite production of the bacteria. Under high concentration of Cu (II) (6 mg/L), the surface adhesion of the bacteria was distorted and covered with significantly large particles, and the functional groups of the cells were significantly shifted. As a probiotic, the abundance of lactic acid bacteria in the intestine is significantly reduced, which will inevitably seriously damage intestinal homeostasis. Thus, to protect human intestinal microbes' health, it is recommended to limit the concentration of Cu in food to less than 4 mg/L.}, }
@article {pmid37737839, year = {2023}, author = {Lee, HJ and Whang, KS}, title = {Oryzibacter oryziterrae gen. nov., sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006033}, pmid = {37737839}, issn = {1466-5034}, mesh = {*Oryza ; Base Composition ; Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Soil ; }, abstract = {A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58[T], was isolated from rice paddy soil. Strain COJ-58[T] grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58[T] forms a distinct lineage within the family Pleomorphomonadaceae, with highest similarity to Pleomorphomonas carboxyditropha SVCO-16[T] (95.9 %), Pleomorphomonas koreensis Y9[T] (95.8 %), Pleomorphomonas oryzae F-7[T] (95.7 %) and Pleomorphomonas diazotrophica R5-392[T] (95.6 %), respectively. The average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and percentage of conserved proteins values between the genomes of strain COJ-58[T] and its closely related taxa are ≤77.2 %, ≤21.6 %, ≤68.3 % and ≤61.3 %, respectively. The genome size of strain COJ-58[T] is 4.9 Mb and the genomic DNA G + C content is 63.7 mol%. The major fatty acids are C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The differential phenotypic and genotypic characteristics of strain COJ-58[T] indicate that it represents a novel genus and species, for which the name Oryzibacter oryziterrae gen. nov., sp. nov. is proposed, with strain COJ-58[T] (=KACC 22108[T]=JCM 34744[T]) as the type strain.}, }
@article {pmid37737625, year = {2023}, author = {Turner, TL and Mitra, SD and Kochan, TJ and Pincus, NB and Lebrun-Corbin, M and Cheung, BH and Gatesy, SW and Afzal, T and Nozick, SH and Ozer, EA and Hauser, AR}, title = {Taxonomic characterization of Pseudomonas hygromyciniae sp. nov., a novel species discovered from a commercially purchased antibiotic.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0183821}, pmid = {37737625}, issn = {2165-0497}, support = {K24 AI104831/AI/NIAID NIH HHS/United States ; R01 AI118257/AI/NIAID NIH HHS/United States ; R21 AI153953/AI/NIAID NIH HHS/United States ; R21 AI164254/AI/NIAID NIH HHS/United States ; }, abstract = {In an attempt to identify novel bacterial species, microbiologists have examined a wide range of environmental niches. We describe the serendipitous discovery of a novel gram-negative bacterial species from a different type of extreme niche: a purchased vial of antibiotic. The vial of antibiotic hygromycin B was found to be factory contaminated with a bacterial species, which we designate Pseudomonas hygromyciniae sp. nov. The proposed novel species belongs to the P. fluorescens complex and is most closely related to P. brenneri, P. proteolytica, and P. fluorescens. The type strain Pseudomonas hygromyciniae sp. nov. strain SDM007[T] (SDM007[T]) harbors a novel 250 kb megaplasmid which confers resistance to hygromycin B and contains numerous other genes predicted to encode replication and conjugation machinery. SDM007[T] grows in hygromycin concentrations of up to 5 mg/mL but does not use the antibiotic as a carbon or nitrogen source. While unable to grow at 37°C ruling out its ability to infect humans, it grows and survives at temperatures between 4 and 30°C. SDM007[T] can infect plants, as demonstrated by the lettuce leaf model, and is highly virulent in the Galleria mellonella infection model but is unable to infect mammalian A549 cells. These findings indicate that commercially manufactured antibiotics represent another extreme environment that may support the growth of novel bacterial species. IMPORTANCE Physical and biological stresses in extreme environments may select for bacteria not found in conventional environments providing researchers with the opportunity to not only discover novel species but to uncover new enzymes, biomolecules, and biochemical pathways. This strategy has been successful in harsh niches such as hot springs, deep ocean trenches, and hypersaline brine pools. Bacteria belonging to the Pseudomonas species are often found to survive in these unusual environments, making them relevant to healthcare, food, and manufacturing industries. Their ability to survive in a variety of environments is mainly due to the high genotypic and phenotypic diversity displayed by this genus. In this study, we discovered a novel Pseudomonas sp. from a desiccated environment of a sealed antibiotic bottle that was considered sterile. A close genetic relationship with its phylogenetic neighbors reiterated the need to use not just DNA-based tools but also biochemical characteristics to accurately classify this organism.}, }
@article {pmid37737001, year = {2023}, author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE}, title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).}, journal = {Infectious disease reports}, volume = {15}, number = {5}, pages = {549-563}, pmid = {37737001}, issn = {2036-7430}, abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.}, }
@article {pmid37725513, year = {2023}, author = {Yang, J and Bowring, JZ and Krusche, J and Lehmann, E and Bejder, BS and Silva, SF and Bojer, MS and Grunert, T and Peschel, A and Ingmer, H}, title = {Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus.}, journal = {Cell reports}, volume = {42}, number = {9}, pages = {113154}, doi = {10.1016/j.celrep.2023.113154}, pmid = {37725513}, issn = {2211-1247}, mesh = {Humans ; Staphylococcus aureus/metabolism ; *Bacteriophages/metabolism ; Staphylococcus/metabolism ; Glycosyltransferases/metabolism ; *Staphylococcal Infections ; Bacterial Proteins/metabolism ; Quorum Sensing ; }, abstract = {Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.}, }
@article {pmid37725094, year = {2023}, author = {Rossetto Marcelino, V}, title = {The value of connections.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37725094}, issn = {2050-084X}, mesh = {*Gastrointestinal Microbiome ; }, abstract = {High proportions of gut bacteria that produce their own food can be an indicator for poor gut health.}, }
@article {pmid37724869, year = {2023}, author = {Leroux, N and Sylvain, FE and Holland, A and Luis Val, A and Derome, N}, title = {Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0275522}, pmid = {37724869}, issn = {2165-0497}, abstract = {A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.}, }
@article {pmid37724866, year = {2023}, author = {van der Loos, LM and De Coninck, L and Zell, R and Lequime, S and Willems, A and De Clerck, O and Matthijnssens, J}, title = {Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0025523}, pmid = {37724866}, issn = {2165-0497}, abstract = {Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.}, }
@article {pmid37723328, year = {2023}, author = {Sasi, R and Suchithra, TV}, title = {Wastewater microbial diversity versus molecular analysis at a glance: a mini-review.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {4}, pages = {3033-3039}, pmid = {37723328}, issn = {1678-4405}, mesh = {*Wastewater ; Phylogeny ; *Microbiota ; Genomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.}, }
@article {pmid37723166, year = {2023}, author = {Ye, H and Borusak, S and Eberl, C and Krasenbrink, J and Weiss, AS and Chen, SC and Hanson, BT and Hausmann, B and Herbold, CW and Pristner, M and Zwirzitz, B and Warth, B and Pjevac, P and Schleheck, D and Stecher, B and Loy, A}, title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5533}, pmid = {37723166}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; Animals ; Mice ; *Affect ; Bile Acids and Salts ; *Salmonella enterica ; Taurine ; Sulfur ; }, abstract = {Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.}, }
@article {pmid37722685, year = {2023}, author = {Jacobovitz, MR and Hambleton, EA and Guse, A}, title = {Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach.}, journal = {Annual review of genetics}, volume = {57}, number = {}, pages = {411-434}, doi = {10.1146/annurev-genet-072320-125436}, pmid = {37722685}, issn = {1545-2948}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; *Anthozoa/genetics ; Symbiosis/genetics ; Ecosystem ; *Dinoflagellida/genetics ; Systems Analysis ; }, abstract = {Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.}, }
@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37717747, year = {2023}, author = {Farrell, ML and Chueiri, A and Maguire, M and Kovářová, A and Miliotis, G and O'Connor, L and McDonagh, F and Duane, S and Cormican, M and Devane, G and Tuohy, A and DeLappe, N and De Bock, F and Burke, LP and Morris, D}, title = {Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167100}, doi = {10.1016/j.scitotenv.2023.167100}, pmid = {37717747}, issn = {1879-1026}, mesh = {Humans ; *Escherichia coli/genetics ; Enterobacteriaceae/genetics ; Ireland/epidemiology ; beta-Lactamases/genetics ; Feces ; *Anti-Infective Agents ; Anti-Bacterial Agents ; }, abstract = {The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.}, }
@article {pmid37717325, year = {2023}, author = {Sandeep, R and Muscolino, JF and Macêdo, WV and Piculell, M and Christensson, M and Poulsen, JS and Nielsen, JL and Vergeynst, L}, title = {Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor.}, journal = {Water research}, volume = {245}, number = {}, pages = {120599}, doi = {10.1016/j.watres.2023.120599}, pmid = {37717325}, issn = {1879-2448}, abstract = {Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550-1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40-58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34-60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100-500 µm, at which the phosphorus accumulating bacteria have the highest activity.}, }
@article {pmid37715042, year = {2023}, author = {Candry, P and Chadwick, GL and Caravajal-Arroyo, JM and Lacoere, T and Winkler, MH and Ganigué, R and Orphan, VJ and Rabaey, K}, title = {Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2014-2022}, pmid = {37715042}, issn = {1751-7370}, mesh = {*Carboxylic Acids ; *Biofilms ; Bacteria ; Lactic Acid ; Sugars ; }, abstract = {Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of [15]N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.}, }
@article {pmid37713796, year = {2023}, author = {Cai, X and Hu, Y and Zhou, S and Meng, D and Xia, S and Wang, H}, title = {Unraveling bacterial and eukaryotic communities in secondary water supply systems: Dynamics, assembly, and health implications.}, journal = {Water research}, volume = {245}, number = {}, pages = {120597}, doi = {10.1016/j.watres.2023.120597}, pmid = {37713796}, issn = {1879-2448}, mesh = {Water ; Eukaryota ; Bacteria ; Water Supply ; *Amoeba ; *Microbiota ; }, abstract = {Secondary water supply systems (SWSSs) are crucial water supply infrastructures for high-rise buildings in metropolitan cities. In recent years, they have garnered public attention due to increased microbial risks. However, our understanding of SWSS microbial ecology, particularly concerning the composition of eukaryotes and the underlying mechanisms driving microbial dynamics and assembly in SWSSs, remains elusive. Herein, we conducted a comprehensive investigation on both eukaryotes and bacteria along the water transportation pathway and across various microbial habitats (water, biofilm, and sediment) in SWSSs. Sequencing results revealed that eukaryotes within SWSSs predominantly consist of protists (average abundance: 31.23%) and metazoans (20.91%), while amoebae accounted for 4.71% of the total. During water transportation from the distribution mains to taps, both bacterial and eukaryotic communities exhibited significant community shifts, and higher degrees of variation were observed for eukaryotic community among different locations within SWSSs. The normalized stochasticity ratio (NST) analysis demonstrated that bacterial community assembly was governed by stochastic processes, while eukaryotic community assembly was primarily shaped by deterministic processes. Within SWSS tanks, bacterial communities significantly varied across water, biofilm, and sediment, whereas eukaryotic communities showed minor differences among these habitats. The co-occurrence networks analysis revealed that tank biofilm and sediment harbored more eukaryote-bacterium linkages than water, suggesting biofilm and sediment might be hotspots for inter-kingdom interactions. We also applied FEAST analysis to track the source of tap water microbiota, results of which showed that household-tap bacteria mainly originated from tank water. In contrast, tank biofilm was identified as the primary microbial source to eukaryotes in household tap water. Additionally, engineering factors such as tank materials significantly affected amoeba community, and the SWSS configuration was found to influence Legionella and Mycobacterium abundances in SWSSs. Overall, results of our study shed light on the microbial ecology in SWSS and provide insights into SWSS management and health risk control.}, }
@article {pmid37712979, year = {2023}, author = {Li, Y and Yang, H and Su, Y and Gong, X and Yao, B and Cheng, L}, title = {Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2993-3002}, pmid = {37712979}, issn = {1432-184X}, mesh = {*Ecosystem ; *Soil/chemistry ; Grassland ; Nitrogen/chemistry ; Phosphorus ; Bacteria/genetics ; Soil Microbiology ; China ; }, abstract = {Nitrogen (N) and phosphorus (P) addition, either individually or in combination, has been demonstrated to enhance plant productivity in grassland ecosystems. Soil bacterial community, which is the driver of litter decomposition and nutrient cycling, is assumed to control responses of terrestrial ecosystem structure and function to N and P addition. Using a high-throughput Illumina MiSeq sequencing platform, we conducted a 9-year field experiment of N (0, 5, 10, and 20 g N m[-2] yr[-1]) and P (0 and 10 g P m[-2] yr[-1]) additions in the Inner Mongolian steppes to elucidate long-term effects of N and P addition on soil bacterial richness, diversity and composition. We found that N addition reduced the relative abundance of Acidobacteria, Chloroflexi, and Nitrospirae, while increased that of Bacteroides. The results showed that the bacterial biomarker was enriched in P addition treatments, either individually or combined with N addition. Both N and P addition altered the bacterial community structure, while only N addition greatly decreased bacterial richness and diversity. More importantly, we showed that all of these effects were most significant in N3P treatment (20 g N m[-2] yr[-1] and 10 g P m[-2] yr[-1]), implying that P coupled with a high-level N addition exerted a great influence on soil bacterial community. Structural equation models revealed that N and P addition had a great direct effect on soil bacterial community and an indirect effect on it mainly by changing the litter biomass. Our findings highlighted that severe niche differentiation was induced by P along with a high-level N, further emphasizing the importance of simultaneously evaluating response of soil bacterial community to N and P addition, especially in the context of increasing anthropogenic nutrient additions.}, }
@article {pmid37711620, year = {2023}, author = {Rosel-Pech, C and Pinto-Cardoso, S and Chávez-Torres, M and Montufar, N and Osuna-Padilla, I and Ávila-Ríos, S and Reyes-Terán, G and Aguirre-Alvarado, C and Matías Juan, NA and Pérez-Lorenzana, H and Vázquez-Rosales, JG and Bekker-Méndez, VC}, title = {Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1244473}, pmid = {37711620}, issn = {1664-3224}, mesh = {Adult ; Child ; Humans ; Female ; Male ; *HIV Infections ; RNA, Ribosomal, 16S/genetics ; *Aging, Premature ; Anti-Bacterial Agents ; Disease Progression ; }, abstract = {INTRODUCTION: Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children.<br><br>METHODS: We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata.<br><br>RESULTS: Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively).<br><br>CONCLUSION: The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.}, }
@article {pmid37711139, year = {2023}, author = {Vijay, S and Nair, RR and Sharan, D and Jakkala, K and Ajitkumar, P}, title = {Percoll discontinuous density gradient centrifugation method for the fractionation of the subpopulations of Mycobacterium smegmatis and Mycobacterium tuberculosis from in vitro cultures.}, journal = {MethodsX}, volume = {11}, number = {}, pages = {102344}, pmid = {37711139}, issn = {2215-0161}, abstract = {Bacterial populations in the in vitro laboratory cultures, environment, and patients contain metabolically different subpopulations that respond differently to stress agents, including antibiotics, and emerge as stress tolerant or resistant strains. To contain the emergence of such strains, it is important to study the features of the metabolic status and response of the subpopulations to stress agents. For this purpose, an efficient method is required for the fractionation and isolation of the subpopulations from the cultures. Here we describe in detail the manual setting up of a simple, easy-to-do, reproducibly robust Percoll discontinuous density gradient centrifugation for the fractionation of subpopulations of short-sized cells (SCs) and normal/long-sized cells (NCs) from Mycobacterium smegmatis and Mycobacterium tuberculosis cultures, which we had reported earlier. About 90-98% enrichment was obtained respectively for SCs and NCs for M. smegmatis and 69-67% enrichment was obtained respectively for the SCs and NCs for M. tuberculosis.•The Percoll discontinuous density gradient centrifugation helps the fractionation and isolation of mycobacterial subpopulations that differ in density.•The method offers a consistently reproducible high enrichment of the subpopulations of SCs and NCs from the in vitro cultures of M. smegmatis and M. tuberculosis.•Our earlier reports on the consistency in the differential response of the subpopulations, enriched using the method, to oxidative, nitrite, and antibiotic stress proves its validity.}, }
@article {pmid37708771, year = {2023}, author = {Sentenac, H and Loyau, A and Zoccarato, L and Jassey, VEJ and Grossart, HP and Schmeller, DS}, title = {Biofilm community composition is changing in remote mountain lakes with a relative increase in potentially toxigenic algae.}, journal = {Water research}, volume = {245}, number = {}, pages = {120547}, doi = {10.1016/j.watres.2023.120547}, pmid = {37708771}, issn = {1879-2448}, abstract = {Mountain lakes provide clear drinking water to humankind but are strongly impacted by global change. Benthic biofilms are crucial for maintaining water quality in these oligotrophic lakes, yet little is known about the effects of global change on mountain biofilm communities. By combining analyses of metabarcoding data on 16S and 18S rRNA genes with climatic and environmental data, we investigated global change effects on the composition of biofilm prokaryotic and micro-eukaryotic assemblages in a five-year monitoring program of 26 Pyrenean lakes (2016-2020). Using time-decay relationships and within-lake dissimilarity modelling, we show that the composition of both prokaryotic and micro-eukaryotic biofilm communities significantly shifted and their biodiversity declined from 2016 to 2020. In particular, analyses of temporal trends with linear mixed models indicated an increase in the richness and relative abundance of cyanobacteria, including potentially toxigenic cyanobacteria, and a concomitant decrease in diatom richness and relative abundance. While these compositional shifts may be due to several drivers of global change acting simultaneously on mountain lake biota, water pH and hardness were, from our data, the main environmental variables associated with changes for both prokaryotic and micro-eukaryotic assemblages. Water pH and hardness increased in our lakes over the study period, and are known to increase in Pyrenean lakes due to the intensification of rock weathering as a result of climate change. Given predicted climate trends and if water pH and hardness do cause some changes in benthic biofilms, those changes might be further exacerbated in the future. Such biofilm compositional shifts may induce cascading effects in mountain food webs, threatening the resilience of the entire lake ecosystem. The rise in potentially toxigenic cyanobacteria also increases intoxication risks for humans, pets, wild animals, and livestock that use mountain lakes. Therefore, our study has implications for water quality, ecosystem health, public health, as well as local economies (pastoralism, tourism), and highlights the possible impacts of global change on mountain lakes.}, }
@article {pmid37708391, year = {2023}, author = {Ionescu, D and Volland, JM and Contarini, PE and Gros, O}, title = {Genomic Mysteries of Giant Bacteria: Insights and Implications.}, journal = {Genome biology and evolution}, volume = {15}, number = {9}, pages = {}, pmid = {37708391}, issn = {1759-6653}, mesh = {*Genomics ; Bacteria/genetics ; Archaea/genetics ; Biological Evolution ; }, abstract = {Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.}, }
@article {pmid37705860, year = {2024}, author = {Mills, S and Trego, AC and Prevedello, M and De Vrieze, J and O'Flaherty, V and Lens, PNL and Collins, G}, title = {Unifying concepts in methanogenic, aerobic, and anammox sludge granulation.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100310}, pmid = {37705860}, issn = {2666-4984}, abstract = {The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.}, }
@article {pmid37702500, year = {2023}, author = {Deng, T and He, Z and Xu, M and Dong, M and Guo, J and Sun, G and Huang, H}, title = {Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0156723}, pmid = {37702500}, issn = {2150-7511}, mesh = {*Ecosystem ; Nitrates ; *Microbiota ; Sulfur ; Phenotype ; Oxidation-Reduction ; }, abstract = {Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.}, }
@article {pmid37695394, year = {2023}, author = {Wei, N and Tan, J}, title = {Correction to: Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2869}, doi = {10.1007/s00248-023-02300-z}, pmid = {37695394}, issn = {1432-184X}, }
@article {pmid37692385, year = {2023}, author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X}, title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1222844}, pmid = {37692385}, issn = {1664-302X}, abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.}, }
@article {pmid37692384, year = {2023}, author = {Mermans, F and Mattelin, V and Van den Eeckhoudt, R and García-Timermans, C and Van Landuyt, J and Guo, Y and Taurino, I and Tavernier, F and Kraft, M and Khan, H and Boon, N}, title = {Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233705}, pmid = {37692384}, issn = {1664-302X}, abstract = {New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.}, }
@article {pmid37692382, year = {2023}, author = {Amon, CER and Fossou, RK and Ebou, AET and Koua, DK and Kouadjo, CG and Brou, YC and Voko Bi, DRR and Cowan, DA and Zézé, A}, title = {The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220655}, pmid = {37692382}, issn = {1664-302X}, abstract = {The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.}, }
@article {pmid37691494, year = {2023}, author = {Mödl, B and Awad, M and Zwolanek, D and Scharf, I and Schwertner, K and Milovanovic, D and Moser, D and Schmidt, K and Pjevac, P and Hausmann, B and Krauß, D and Mohr, T and Svinka, J and Kenner, L and Casanova, E and Timelthaler, G and Sibilia, M and Krieger, S and Eferl, R}, title = {Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease.}, journal = {EMBO reports}, volume = {24}, number = {10}, pages = {e57084}, pmid = {37691494}, issn = {1469-3178}, support = {ERC-2015-AdG TNT-Tumors 694883//EC | European Research Council (ERC)/ ; P35069-B//Austrian Science Fund (FWF)/ ; P33430//Austrian Science Fund (FWF)/ ; P 32900/FWF_/Austrian Science Fund FWF/Austria ; P32900-B//Austrian Science Fund (FWF)/ ; DOC 59-833//Austrian Science Fund (FWF)/ ; 766214//EC | Horizon 2020 Framework Programme (H2020)/ ; }, mesh = {Animals ; Mice ; *Microvilli/metabolism/pathology ; Humans ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; *Intestinal Mucosa/metabolism/pathology ; Colitis/chemically induced/metabolism/pathology/genetics ; Cadherins/metabolism/genetics ; Mice, Knockout ; Enterocytes/metabolism/pathology ; Disease Models, Animal ; Dextran Sulfate ; Epithelial Cells/metabolism/pathology ; Permeability ; Mice, Inbred C57BL ; }, abstract = {Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.}, }
@article {pmid37690780, year = {2023}, author = {Cantu-Jungles, TM and Hamaker, BR}, title = {Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber.}, journal = {The Journal of nutrition}, volume = {153}, number = {11}, pages = {3156-3163}, doi = {10.1016/j.tjnut.2023.09.001}, pmid = {37690780}, issn = {1541-6100}, mesh = {*Gastrointestinal Microbiome ; Health Promotion ; Motivation ; Dietary Fiber/pharmacology ; *Microbiota ; }, abstract = {Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.}, }
@article {pmid37689957, year = {2023}, author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Wang, S and Zhang, B and Huang, Q}, title = {Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113215}, doi = {10.1016/j.foodres.2023.113215}, pmid = {37689957}, issn = {1873-7145}, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Resistant Starch ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Dysbiosis ; Microspheres ; Obesity ; Starch/pharmacology ; Amylose ; }, abstract = {The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice. MS more efficiently controlled body weight as well as adipose tissue mass compared to HAMS. Furthermore, MS significantly reduced blood glucose, insulin, lipid and pro-inflammatory cytokine levels compared to the high-fat diet, while the effects of HAMS were less pronounced. The MS-altered gut microbiota composition favoring Streptococcaceae, Bacilli, Firmicutes and unclassified Clostridiales was predicted to promote fatty acid, pantothenate and Coenzyme A biosynthesis. In line with this, elevated fecal short chain fatty acid (SCFA), in particular, propionate concentration was observed in MS-fed mice. Our study provides novel insights into the mechanistic action of MS on intestinal homeostasis, providing a basis for future dietary therapeutic applications.}, }
@article {pmid37688636, year = {2023}, author = {Garrido, AG and Machado, LF and Pereira, CM and Abrantes, DP and Calderon, EN and Zilberberg, C}, title = {Marine Heatwave Caused Differentiated Dysbiosis in Photosymbiont Assemblages of Corals and Hydrocorals During El Niño 2015/2016.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2959-2969}, pmid = {37688636}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa ; El Nino-Southern Oscillation ; Dysbiosis ; Coral Reefs ; Climate Change ; }, abstract = {Reef corals have been threatened by climate change, with more frequent and intense bleaching events leading to extensive coral mortality and loss of coral cover worldwide. In the face of this, the corals' photosymbiont assemblages have received special attention as a key to better understand the bleaching process and its recovery. To assess the effects of thermal anomalies, the coral Mussismilia harttii and the hydrocoral Millepora alcicornis were monitored through the El Niño 2015/2016 at a Southwestern Atlantic (SWA) coral reef. A severe bleaching event (57% of colonies bleached) was documented, triggered by a < 3 °C-week heatwave, but no mortality was detected. The hydrocoral was more susceptible than the scleractinian, displaying bleaching symptoms earlier and experiencing a longer and more intense bleaching event. The composition of photosymbionts in the M. alcicornis population was affected only at the rare biosphere level (< 5% relative abundance), with the emergence of new symbionts after bleaching. Conversely, a temporary dysbiosis was observed in the M. harttii population, with one of the dominant symbiodiniaceans decreasing in relative abundance at the peak of the bleaching, which negatively affected the total β-diversity. After colonies' complete recovery, symbiodiniaceans' dominances returned to normal levels in both hosts. These results highlight critical differences in how the two coral species cope with bleaching and contribute to the understanding of the role of photosymbionts throughout the bleaching-recovery process.}, }
@article {pmid37687396, year = {2023}, author = {Galinytė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Naginienė, R and Baranauskienė, D and Šulinskienė, J and Kudlinskienė, I and Savickas, A and Savickienė, N}, title = {Determination of Heavy Metal Content: Arsenic, Cadmium, Mercury, and Lead in Cyano-Phycocyanin Isolated from the Cyanobacterial Biomass.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, pmid = {37687396}, issn = {2223-7747}, abstract = {Cyano-phycocyanin (C-PC) is a light-absorbing biliprotein found in cyanobacteria, commonly known as blue-green algae. Due to its antioxidative, anti-inflammatory, and anticancer properties, this protein is a promising substance in medicine and pharmaceuticals. However, cyanobacteria tend to bind heavy metals from the environment, making it necessary to ensure the safety of C-PC for the development of pharmaceutical products, with C-PC isolated from naturally collected cyanobacterial biomass. This study aimed to determine the content of the most toxic heavy metals, arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb) in C-PC isolated from different cyanobacterial biomasses collected in the Kaunas Lagoon during 2019-2022, and compare them with the content of heavy metals in C-PC isolated from cultivated Spirulina platensis (S. platensis). Cyanobacteria of Aphanizomenon flos-aquae (A. flos-aquae) dominated the biomass collected in 2019, while the genus Microcystis dominated the biomasses collected in the years 2020 and 2022. Heavy metals were determined using inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS analysis revealed higher levels of the most investigated heavy metals (Pb, Cd, and As) in C-PC isolated from the biomass with the dominant Microcystis spp. compared to C-PC isolated from the biomass with the predominant A. flos-aquae. Meanwhile, C-PC isolated from cultivated S. platensis exhibited lower concentrations of As and Pb than C-PC isolated from naturally collected cyanobacterial biomass.}, }
@article {pmid37687181, year = {2023}, author = {Tom, A and Jacob, J and Mathews, M and Rajagopal, R and Alfarhan, A and Barcelo, D and Narayanankutty, A}, title = {Synthesis of Bis-Chalcones and Evaluation of Its Effect on Peroxide-Induced Cell Death and Lipopolysaccharide-Induced Cytokine Production.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {17}, pages = {}, pmid = {37687181}, issn = {1420-3049}, mesh = {*Antioxidants/pharmacology ; *Chalcones/pharmacology ; Lipopolysaccharides/pharmacology ; Cell Death ; Peroxides ; Cytokines ; }, abstract = {Plant secondary metabolites are important sources of biologically active compounds with wide pharmacological potentials. Among the different classes, the chalcones form integral pharmacologically active agents. Natural chalcones and bis-chalcones exhibit high antioxidant and anti-inflammatory properties in various experiments. Studies are also underway to explore more biologically active bis-chalcones by chemical synthesis of these compounds. In this study, the effects of six synthetic bis-chalcones were evaluated in intestinal epithelial cells (IEC-6); further, the anti-inflammatory potentials were studied in lipopolysaccharide-induced cytokine production in macrophages. The synthesized bis-chalcones differ from each other first of all by the nature of the aromatic cores (functional group substitution, and their position) and by the size of a central alicycle. The exposure of IEC-6 cells to peroxide radicals reduced the cell viability; however, pre-treatment with the bis-chalcones improved the cell viability in these cells. The mechanism of action was observed to be the increased levels of glutathione and antioxidant enzyme activities. Further, these bis-chalcones also inhibited the LPS-stimulation-induced inflammatory cytokine production in RAW 264.7 macrophages. Overall, the present study indicated the cytoprotective and anti-inflammatory abilities of synthetic bis-chalcones.}, }
@article {pmid37684546, year = {2023}, author = {Liu, N and Huang, Z and Fang, Y and Dong, Z}, title = {Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2981-2992}, pmid = {37684546}, issn = {1432-184X}, mesh = {*Ecosystem ; *Nuclear Power Plants ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Drainage ; Carbon ; }, abstract = {As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.}, }
@article {pmid37684545, year = {2023}, author = {Huang, R and Tang, C and Zhao, Y and Liu, L and Chen, J and Shi, Z and Yan, Z}, title = {Unveiling the Biochar-Respiratory Growth of Methanosarcina acetivorans Involving Extracellular Polymeric Substances.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2970-2980}, pmid = {37684545}, issn = {1432-184X}, support = {22008142//National Natural Science Foundation of China/ ; ZR2022YQ31//Natural Science Foundation of Shandong Province/ ; BK20200232//Natural Science Foundation of Jiangsu Province/ ; Qilu Youth Talent Program//Shandong University/ ; }, mesh = {*Methanosarcina/genetics ; *Extracellular Polymeric Substance Matrix ; Electron Transport ; Methane ; }, abstract = {Biochar can be applied to diverse natural and engineered anaerobic systems. Biochar plays biogeochemical roles during its production, storage, and environmental dynamics, one of which is related to the global methane flux governed by methanotrophs and methanogens. Our understanding of relevant mechanisms is currently limited to the roles of biochar in methanotrophic growth, but less is known about the roles of biochar in methanogenic growth. Here, we demonstrated that biochar enhanced the methanogenic growth of a model methanogen, Methanosarcina acetivorans, and the role of biochar as an electron acceptor during methanogenic growth was confirmed, which is referred to as biochar-respiratory growth. The biochar-respiratory growth of M. acetivorans promoted the secretion of extracellular polymeric substances (EPS) with augmented electron transfer capabilities, and the removal of EPS significantly attenuated extracellular electron transfer. Identification and quantification of prosthetic cofactors for EPS suggest an important role of flavin and F420 in extracellular electron transfer. Transcriptomic analysis provided additional insights into the biochar-respiratory growth of M. acetivorans, showing that there was a positive response in transcriptional regulation to the favorable growth environment provided by biochar, which stimulated global methanogenesis. Our results shed more light on the in situ roles of biochar in the ecophysiology of methanogens in diverse anaerobic environments.}, }
@article {pmid37682693, year = {2024}, author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Withall, DM and Wäckers, F and Birkett, MA and Jacquemyn, H and Lievens, B}, title = {Effects of root inoculation of entomopathogenic fungi on olfactory-mediated behavior and life-history traits of the parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae).}, journal = {Pest management science}, volume = {80}, number = {2}, pages = {307-316}, doi = {10.1002/ps.7762}, pmid = {37682693}, issn = {1526-4998}, support = {1S79919N//Fonds Wetenschappelijk Onderzoek/ ; C24E/19/052//KU Leuven/ ; BB/X010953/1//Growing Health Institute Strategic Programme funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/OS/CP/000001//Industrial Strategy Challenge Fund funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Parasites ; Pest Control, Biological ; *Wasps/physiology ; Plants ; Nicotiana ; *Aphids/physiology ; *Capsicum ; }, abstract = {BACKGROUND: Although most biological control programs use multiple biological agents to manage pest species, to date only a few programs have combined the use of agents from different guilds. Using sweet pepper (Capsicum annuum L.), the entomopathogenic fungus Akanthomyces muscarius ARSEF 5128, the tobacco peach aphid Myzus persicae var. nicotianae and the aphid parasitoid Aphidius ervi as the experimental model, we explored whether root inoculation with an entomopathogenic fungus is compatible with parasitoid wasps for enhanced biocontrol of aphids.<br><br>RESULTS: In dual-choice behavior experiments, A. ervi was significantly attracted to the odor of M. persicae-infested C. annuum plants that had been inoculated with A. muscarius, compared to noninoculated infested plants. There was no significant difference in attraction to the odor of uninfested plants. Myzus persicae-infested plants inoculated with A. muscarius emitted significantly higher amounts of indole, (E)-nerolidol, (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene and one unidentified terpene compared to noninoculated infested plants. Coupled gas chromatography-electroantennography, using the antennae of A. ervi, confirmed the physiological activity of these elevated compounds. Inoculation of plants with A. muscarius did not affect parasitism rate nor parasitoid longevity, but significantly increased the speed of mummy formation in parasitized aphids on fungus-inoculated plants.<br><br>CONCLUSION: Our data suggest that root inoculation of C. annuum with A. muscarius ARSEF 5128 alters the olfactory-mediated behavior of parasitoids, but has little effect on parasitism efficiency or life-history parameters. However, increased attraction of parasitoids towards M. persicae-infested plants when inoculated by entomopathogenic fungi can accelerate host localization and hence improve biocontrol efficacy. &#xa9; 2023 Society of Chemical Industry.}, }
@article {pmid37680522, year = {2023}, author = {You, Y and Zhang, W and Cai, M and Guo, Q and Wang, J and Cai, Y and Lin, J}, title = {Discovery of fecal microbial signatures in patients with ankylosing spondylitis.}, journal = {Archives of rheumatology}, volume = {38}, number = {2}, pages = {217-229}, pmid = {37680522}, issn = {2618-6500}, abstract = {OBJECTIVES: This study aimed to investigate the characteristics of the gut microbiota in Chinese patients with ankylosing spondylitis (AS) and healthy controls in Quanzhou aiming to explore the correlation between microbiome changes and AS activities.<br><br>PATIENTS AND METHODS: In this study, high-throughput sequencing of the gene of 16S ribosomal RNA (16S rRNA) in fecal samples from 40 AS patients and 40 healthy controls, for a total of 80 participants (70 males, 10 females; mean age 33.7&#xb1;10.7 years; range, 15 to 58 years), was conducted between January 2018 and January 2019. Alpha and beta diversity were analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) software, and differences were analyzed using Student's t-test, linear discriminant analysis coupled with effect size and Metastats. Finally, a correlation network was constructed using Pearson's analysis.<br><br>RESULTS: The alpha index values of the AS group were not significantly different from those of the control group. At the genus level, eight genera, Ruminiclostridium_9, Fusicatenibacter, Adlercreutzia, CAG-56, Intestinimonas, Lachnospira, Bacteroides, and Pseudoflavonifractor, were significantly enriched in patients with AS, whereas the abundance of uncultured_bacterium_f_Saccharimonadaceae, Prevotella_7, uncultured_bacterium_f_ Enterobacteriaceae, Cronobacter, Prevotellaceae_NK3B31_group, and Weissella were significantly decreased in patients with AS. In addition, diseaserelated gut microbial communities were detected in patients with AS.<br><br>CONCLUSION: We found differences in the gut microbiome between the patients with AS and controls and identified potential disease activity-related bacterial communities.}, }
@article {pmid37676325, year = {2023}, author = {Sun, P and Wang, M and Zheng, W and Li, S and Zhu, X and Chai, X and Zhao, S}, title = {Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance.}, journal = {Stress biology}, volume = {3}, number = {1}, pages = {20}, pmid = {37676325}, issn = {2731-0450}, abstract = {Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.}, }
@article {pmid37676037, year = {2023}, author = {Danevčič, T and Spacapan, M and Dragoš, A and Kovács, &#xc1;T and Mandic-Mulec, I}, title = {DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0090823}, pmid = {37676037}, issn = {2165-0497}, abstract = {Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.}, }
@article {pmid37675430, year = {2023}, author = {Edwards, J and Hoffbeck, C and West, AG and Pas, A and Taylor, MW}, title = {16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1239167}, pmid = {37675430}, issn = {1664-302X}, abstract = {The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.}, }
@article {pmid37674014, year = {2023}, author = {Cornish, CM and Bergholz, P and Schmidt, K and Sweetman, J}, title = {How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2949-2958}, pmid = {37674014}, issn = {1432-184X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *Herbicides/pharmacology ; *Microbiota ; Glyphosate ; }, abstract = {Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.}, }
@article {pmid37671861, year = {2023}, author = {Roller, BRK and Hellerschmied, C and Wu, Y and Miettinen, TP and Gomez, AL and Manalis, SR and Polz, MF}, title = {Single-cell mass distributions reveal simple rules for achieving steady-state growth.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0158523}, pmid = {37671861}, issn = {2150-7511}, support = {Life Sciences Project Award-572792//Simons Foundation (SF)/ ; }, mesh = {Reproducibility of Results ; Cell Division ; *Bacteria ; Culture Media ; Biomass ; }, abstract = {Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.}, }
@article {pmid37669892, year = {2023}, author = {Hellal, J and Lise, B and Annette, B and Aurélie, C and Giulia, C and Simon, C and Cristiana, CL and Caroline, C and Nicolas, G and Marina, H and Fabrice, ML and Jean, M and Soizic, M and Carmen, P and Stéphane, P and Agnès, R and Stéphane, V}, title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {10}, pages = {}, pmid = {37669892}, issn = {1574-6941}, mesh = {Ecotoxicology ; *Environmental Pollutants/toxicity ; Environmental Pollution ; *Environmental Restoration and Remediation ; Risk Assessment ; }, abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.}, }
@article {pmid37668400, year = {2023}, author = {Du, H and Pan, J and Zhang, C and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and Qu, W and Jiang, C and Tian, Y and He, Z and Liu, Y and Li, M}, title = {Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0157723}, pmid = {37668400}, issn = {2165-0497}, abstract = {As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.}, }
@article {pmid37668159, year = {2023}, author = {Van den Eeckhoudt, R and Christiaens, AS and Ceyssens, F and Vangalis, V and Verstrepen, KJ and Boon, N and Tavernier, F and Kraft, M and Taurino, I}, title = {Full-electric microfluidic platform to capture, analyze and selectively release single cells.}, journal = {Lab on a chip}, volume = {23}, number = {19}, pages = {4276-4286}, doi = {10.1039/d3lc00645j}, pmid = {37668159}, issn = {1473-0189}, mesh = {*Microfluidics ; Automation ; Cell Movement ; Cell Size ; *Dielectric Spectroscopy ; Saccharomyces cerevisiae ; }, abstract = {Current single-cell technologies require large and expensive equipment, limiting their use to specialized labs. In this paper, we present for the first time a microfluidic device which demonstrates a combined method for full-electric cell capturing, analyzing, and selectively releasing with single-cell resolution. All functionalities are experimentally demonstrated on Saccharomyces cerevisiae. Our microfluidic platform consists of traps centered around a pair of individually accessible coplanar electrodes, positioned under a microfluidic channel. Using this device, we validate our novel Two-Voltage method for trapping single cells by positive dielectrophoresis (pDEP). Cells are attracted to the trap when a high voltage (VH) is applied. A low voltage (VL) holds the already trapped cell in place without attracting additional cells, allowing full control over the number of trapped cells. After trapping, the cells are analyzed by broadband electrochemical impedance spectroscopy. These measurements allow the detection of single cells and the extraction of cell parameters. Additionally, these measurements show a strong correlation between average phase change and cell size, enabling the use of our system for size measurements in biological applications. Finally, our device allows selectively releasing trapped cells by turning off the pDEP signal in their trap. The experimental results show the techniques potential as a full-electric single-cell analysis tool with potential for miniaturization and automation which opens new avenues towards small-scale, high throughput single-cell analysis and sorting lab-on-CMOS devices.}, }
@article {pmid37667323, year = {2023}, author = {Rodríguez-Pastor, R and Hasik, AZ and Knossow, N and Bar-Shira, E and Shahar, N and Gutiérrez, R and Zaman, L and Harrus, S and Lenski, RE and Barrick, JE and Hawlena, H}, title = {Bartonella infections are prevalent in rodents despite efficient immune responses.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {315}, pmid = {37667323}, issn = {1756-3305}, support = {DEB-1813069//National Science Foundation/ ; 1391/15//Israel Science Foundation/ ; }, mesh = {Animals ; *Bartonella Infections/epidemiology/veterinary ; *Bartonella ; Immunoglobulin G ; Kinetics ; Immunity ; }, abstract = {BACKGROUND: Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel's northwestern Negev Desert. We chose to study this system because, in this region, 75-100% of rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least one of these hosts exhibits a waning immune response to Bartonella, which allows reinfections.<br><br>METHODS: We inoculated captive animals of all three rodent species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific immunoglobulin G antibody kinetics over a period of 139&#xa0;days after the primary inoculation, and then for 60&#xa0;days following reinoculation with the same strain.<br><br>RESULTS: Contrary to our hypothesis, we found a strong, long-lasting immunoglobulin G antibody response, with protective immunological memory in all three rodent species. That response prevented reinfection upon exposure of the rodents to the same Bartonella strain.<br><br>CONCLUSIONS: This study constitutes an initial step toward understanding how the interplay between traits of Bartonella and their hosts influences the epidemiological dynamics of these pathogens in nature.}, }
@article {pmid37667132, year = {2023}, author = {Lv, H and Li, X and He, D and Chen, X and Liu, M and Lan, Y and Zhao, J and Wang, H and Yan, Z}, title = {Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2934-2948}, pmid = {37667132}, issn = {1432-184X}, mesh = {*Salvia miltiorrhiza/genetics/metabolism ; Fungi/genetics ; Endophytes/genetics ; *Microbiota/genetics ; Soil ; Seedlings ; Plant Roots/microbiology ; }, abstract = {The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.}, }
@article {pmid37666974, year = {2023}, author = {Lin, Q and Li, L and De Vrieze, J and Li, C and Fang, X and Li, X}, title = {Functional conservation of microbial communities determines composition predictability in anaerobic digestion.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1920-1930}, pmid = {37666974}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal ; Bioreactors ; Microbial Consortia/genetics ; }, abstract = {A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.}, }
@article {pmid37664629, year = {2023}, author = {Simon, LM and Flocco, C and Burkart, F and Methner, A and Henke, D and Rauer, L and Müller, CL and Vogel, J and Quaisser, C and Overmann, J and Simon, S}, title = {Microbial fingerprints reveal interaction between museum objects, curators, and visitors.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107578}, pmid = {37664629}, issn = {2589-0042}, abstract = {Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.}, }
@article {pmid37662195, year = {2023}, author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR}, title = {Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37662195}, issn = {2692-8205}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.}, }
@article {pmid37658881, year = {2023}, author = {Owashi, Y and Minami, T and Kikuchi, T and Yoshida, A and Nakano, R and Kageyama, D and Adachi-Hagimori, T}, title = {Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2923-2933}, pmid = {37658881}, issn = {1432-184X}, mesh = {Humans ; Animals ; Biological Control Agents ; *Hemiptera/genetics ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; *Spiroplasma ; *Wolbachia/genetics ; *Microbiota ; Symbiosis ; }, abstract = {Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.}, }
@article {pmid37659544, year = {2023}, author = {Kazmi, SSUH and Saqib, HSA and Pastorino, P and Grossart, HP and Yaseen, ZM and Abualreesh, MH and Liu, W and Wang, Z}, title = {Influence of the antibiotic nitrofurazone on community dynamics of marine periphytic ciliates: Evidence from community-based bioassays.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166687}, doi = {10.1016/j.scitotenv.2023.166687}, pmid = {37659544}, issn = {1879-1026}, mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Anti-Bacterial Agents/toxicity ; Environmental Monitoring ; Biodiversity ; *Ciliophora ; }, abstract = {Marine periphytic ciliates play a pivotal role in shaping coastal ecosystems dynamics, thereby acting as robust biological indicators of aquatic ecosystem health and functionality. However, the understanding of the effects of veterinary antibiotics on composition and structure of periphytic ciliate communities remains limited. Therefore, this research investigates the influence of the veterinary antibiotic nitrofurazone on the community dynamics of marine periphytic ciliates through bioassay experiments conducted over a one-year cycle. Various concentrations of nitrofurazone were administered to the tested ciliate assemblages, and subsequent changes in community composition, abundance, and diversity were quantitatively analyzed. The research revealed significant alterations in periphytic ciliate communities following exposure to nitrofurazone. Concentration-dependent (0-8 mg L[-1]) decrease in ciliates abundance, accompanied by shifts in species composition, community structure, and community patterns were observed. Comprehensive assessment of diversity metrics indicated significant changes in species richness and evenness in the presence of nitrofurazone, potentially disrupting the stability of ciliate communities. Furthermore, nitrofurazone significantly influenced the community structure of ciliates in all seasons (winter: R[2] = 0.489; spring: R[2] = 0.666; summer: R[2] = 0.700, autumn: R[2] = 0.450), with high toxic potential in treatments 4 and 8 mg L[-1]. Differential abundances of ciliates varied across seasons and nitrofurazone treatments, some orders like Pleurostomatida were consistently affected, while others (i.e., Strombidida and Philasterida) showed irregular distributions or were evenly affected (e.g., Urostylida and Synhymeniida). Retrieved contrasting patterns between nitrofurazone and community responses underscore the broad response repertoire exhibited by ciliates to antibiotic exposure, suggesting potential cascading effects on associated ecological processes in the periphyton community. These findings significantly enhance the understanding of the ecological impacts of nitrofurazone on marine periphytic ciliate communities, emphasizing the imperative for vigilant monitoring and regulation of veterinary antibiotics to protect marine ecosystem health and biodiversity. Further research is required to explore the long-term effects of nitrofurazone exposure and evaluate potential strategies to reduce the ecological repercussions of antibiotics in aquatic environments, with a particular focus on nitrofurazone.}, }
@article {pmid37659520, year = {2023}, author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K}, title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166740}, doi = {10.1016/j.scitotenv.2023.166740}, pmid = {37659520}, issn = {1879-1026}, mesh = {*Rivers ; *Nitrates/analysis ; Ecosystem ; Environmental Monitoring/methods ; Nitrogen/analysis ; Eutrophication ; Harmful Algal Bloom ; Water ; }, abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.}, }
@article {pmid37658593, year = {2023}, author = {Ahmmed, MK and Bhowmik, S and Ahmmed, F and Giteru, SG and Islam, SS and Hachem, M and Hussain, MA and Kanwugu, ON and Agyei, D and Defoirdt, T}, title = {Utilisation of probiotics for disease management in giant freshwater prawn (Macrobrachium rosenbergii): Administration methods, antagonistic effects and immune response.}, journal = {Journal of fish diseases}, volume = {46}, number = {12}, pages = {1321-1336}, doi = {10.1111/jfd.13850}, pmid = {37658593}, issn = {1365-2761}, support = {//Bijzonder Onderzoeksfonds UGent/ ; //University of Otago/ ; //Ural Federal University/ ; }, mesh = {Animals ; *Palaemonidae ; *Fish Diseases ; *Probiotics/therapeutic use ; Fresh Water ; Immunity ; Disease Management ; }, abstract = {The giant freshwater prawn (Macrobrachium rosenbergii) is a high-yielding prawn variety well-received worldwide due to its ability to adapt to freshwater culture systems. Macrobrachium rosenbergii is an alternative to shrimp typically obtained from marine and brackish aquaculture systems. However, the use of intensive culture systems can lead to disease outbreaks, particularly in larval and post-larval stages, caused by pathogenic agents such as viruses, bacteria, fungi, yeasts and protozoans. White tail disease (viral), white spot syndrome (viral) and bacterial necrosis are examples of economically significant diseases. Given the increasing antibiotic resistance of disease-causing microorganisms, probiotics have emerged as promising alternatives for disease control. Probiotics are live active microbes that are introduced into a target host in an adequate number or dose to promote its health. In the present paper, we first discuss the diseases that occur in M. rosenbergii production, followed by an in-depth discussion on probiotics. We elaborate on the common methods of probiotics administration and explain the beneficial health effects of probiotics as immunity enhancers. Moreover, we discuss the antagonistic effects of probiotics on pathogenic microorganisms. Altogether, this paper provides a comprehensive overview of disease control in M. rosenbergii aquaculture through the use of probiotics, which could enhance the sustainability of prawn culture.}, }
@article {pmid37657296, year = {2023}, author = {Fu, S and Zhang, Y and Wang, R and Qiu, Z and Song, W and Yang, Q and Shen, L}, title = {A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118737}, doi = {10.1016/j.jenvman.2023.118737}, pmid = {37657296}, issn = {1095-8630}, mesh = {*Metagenome ; *Drinking Water ; Phylogeny ; Anti-Bacterial Agents ; Risk Management ; }, abstract = {Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.}, }
@article {pmid37656873, year = {2023}, author = {Cantoran, A and Maillard, F and Baldrian, P and Kennedy, PG}, title = {Defining a core microbial necrobiome associated with decomposing fungal necromass.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {9}, pages = {}, doi = {10.1093/femsec/fiad098}, pmid = {37656873}, issn = {1574-6941}, mesh = {Animals ; Carbon ; Ecosystem ; Forests ; *Mycobiome ; *Mycorrhizae ; }, abstract = {Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.}, }
@article {pmid37656196, year = {2023}, author = {Fagre, AC and Islam, A and Reeves, WK and Kading, RC and Plowright, RK and Gurley, ES and McKee, CD}, title = {Bartonella Infection in Fruit Bats and Bat Flies, Bangladesh.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2910-2922}, pmid = {37656196}, issn = {1432-184X}, mesh = {Animals ; Phylogeny ; Bangladesh/epidemiology ; *Chiroptera ; Genetic Variation ; *Bartonella Infections/epidemiology/veterinary/microbiology ; *Bartonella/genetics ; DNA ; }, abstract = {Bats harbor diverse intracellular Bartonella bacteria, but there is limited understanding of the factors that influence transmission over time. Investigation of Bartonella dynamics in bats could reveal general factors that control transmission of multiple bat-borne pathogens, including viruses. We used molecular methods to detect Bartonella DNA in paired bat (Pteropus medius) blood and bat flies in the family Nycteribiidae collected from a roost in Faridpur, Bangladesh between September 2020 and January 2021. We detected high prevalence of Bartonella DNA in bat blood (35/55, 64%) and bat flies (59/60, 98%), with sequences grouping into three phylogenetic clades. Prevalence in bat blood increased over the study period (33% to 90%), reflecting an influx of juvenile bats in the population and an increase in the prevalence of bat flies. Discordance between infection status and the clade/genotype of detected Bartonella was also observed in pairs of bats and their flies, providing evidence that bat flies take blood meals from multiple bat hosts. This evidence of bat fly transfer between hosts and the changes in Bartonella prevalence during a period of increasing nycteribiid density support the role of bat flies as vectors of bartonellae. The study provides novel information on comparative prevalence and genetic diversity of Bartonella in pteropodid bats and their ectoparasites, as well as demographic factors that affect Bartonella transmission and potentially other bat-borne pathogens.}, }
@article {pmid37655448, year = {2023}, author = {Wang, Y and Li, Q and Zhang, J and Liu, P and Zheng, H and Chen, L and Wang, Z and Tan, C and Zhang, M and Zhang, H and Miao, W and Wang, Y and Xuan, X and Yi, G and Wang, P}, title = {Ring1a protects against colitis through regulating mucosal immune system and colonic microbial ecology.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2251646}, pmid = {37655448}, issn = {1949-0984}, mesh = {Animals ; Mice ; *Colitis/genetics/microbiology ; *Gastrointestinal Microbiome ; Immune System ; Metronidazole/pharmacology ; Prevotella/genetics ; }, abstract = {Inflammatory bowel disease (IBD) represents a prominent chronic immune-mediated inflammatory disorder, yet its etiology remains poorly comprehended, encompassing intricate interactions between genetics, immunity, and the gut microbiome. This study uncovers a novel colitis-associated risk gene, namely Ring1a, which regulates the mucosal immune response and intestinal microbiota. Ring1a deficiency exacerbates colitis by impairing the immune system. Concomitantly, Ring1a deficiency led to a Prevotella genus-dominated pathogenic microenvironment, which can be horizontally transmitted to co-housed wild type (WT) mice, consequently intensifying dextran sodium sulfate (DSS)-induced colitis. Furthermore, we identified a potential mechanism linking the altered microbiota in Ring1aKO mice to decreased levels of IgA, and we demonstrated that metronidazole administration could ameliorate colitis progression in Ring1aKO mice, likely by reducing the abundance of the Prevotella genus. We also elucidated the immune landscape of DSS colitis and revealed the disruption of intestinal immune homeostasis associated with Ring1a deficiency. Collectively, these findings highlight Ring1a as a prospective candidate risk gene for colitis and suggest metronidazole as a potential therapeutic option for clinically managing Prevotella genus-dominated colitis.}, }
@article {pmid37655346, year = {2023}, author = {Gutierrez, T and Liu, H}, title = {Editorial: Rising stars in aquatic microbiology: 2022.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265720}, doi = {10.3389/fmicb.2023.1265720}, pmid = {37655346}, issn = {1664-302X}, }
@article {pmid37653502, year = {2023}, author = {Zehentner, B and Scherer, S and Neuhaus, K}, title = {Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {243}, pmid = {37653502}, issn = {1471-2180}, mesh = {*Escherichia coli O157/genetics ; Transcription Initiation Site ; *Enterohemorrhagic Escherichia coli ; Cell Cycle ; Culture Media ; }, abstract = {Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.}, }
@article {pmid37653010, year = {2023}, author = {Gralka, M and Pollak, S and Cordero, OX}, title = {Genome content predicts the carbon catabolic preferences of heterotrophic bacteria.}, journal = {Nature microbiology}, volume = {8}, number = {10}, pages = {1799-1808}, pmid = {37653010}, issn = {2058-5276}, mesh = {*Carbon/metabolism ; Bacteria ; Heterotrophic Processes ; *Microbiota/genetics ; Genomics ; }, abstract = {Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.}, }
@article {pmid37652144, year = {2023}, author = {Low, KE and Tingley, JP and Klassen, L and King, ML and Xing, X and Watt, C and Hoover, SER and Gorzelak, M and Abbott, DW}, title = {Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates.}, journal = {Biotechnology advances}, volume = {69}, number = {}, pages = {108245}, doi = {10.1016/j.biotechadv.2023.108245}, pmid = {37652144}, issn = {1873-1899}, mesh = {Animals ; *Carbohydrates/chemistry ; Carbohydrate Metabolism ; Agriculture ; Soil/chemistry ; *Microbiota ; }, abstract = {Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.}, }
@article {pmid37650927, year = {2023}, author = {Ho, HVN and Dunigan, DD and Salsbery, ME and Agarkova, IV and Al Ameeli, Z and Van Etten, JL and DeLong, JP}, title = {Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2904-2909}, pmid = {37650927}, issn = {1432-184X}, support = {1736030//Directorate for Biological Sciences/ ; }, mesh = {*Paramecium ; Chemotaxis ; *Phycodnaviridae ; Symbiosis ; }, abstract = {Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.}, }
@article {pmid37649628, year = {2023}, author = {Levante, A and Bertani, G and Marrella, M and Mucchetti, G and Bernini, V and Lazzi, C and Neviani, E}, title = {The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1196879}, pmid = {37649628}, issn = {1664-302X}, abstract = {INTRODUCTION: Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem.<br><br>METHODS: In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps.<br><br>RESULTS AND DISCUSSION: All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.}, }
@article {pmid37649327, year = {2024}, author = {Mariën, Q and Regueira, A and Ganigué, R}, title = {Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14321}, pmid = {37649327}, issn = {1751-7915}, support = {ERDF (UE)//Galician Competitive Research Group/ ; GRC ED431C 2021/37//Galician Competitive Research Group/ ; BOF19/STA/044//Bijzonder Onderzoeksfonds UGent/ ; 1SC5722N//Fonds Wetenschappelijk Onderzoek/ ; ED481B-2021-012//Xunta de Galicia/ ; }, mesh = {Butyric Acid/metabolism ; *Isobutyrates ; *Carbon Dioxide ; Acetic Acid ; Fermentation ; *Clostridium ; }, abstract = {Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.}, }
@article {pmid37643688, year = {2023}, author = {McEvoy, N and O'Connor, A and McDonagh, F and Lonappan, AM and Farrell, ML and Kovarova, A and Burke, L and Ryan, K and Hallahan, B and Miliotis, G}, title = {Complete genome of an inhibitor-resistant blaTEM-30 encoding Escherichia coli sequence type 127 isolate identified in human saliva with a high genotypic virulence load.}, journal = {Journal of global antimicrobial resistance}, volume = {35}, number = {}, pages = {44-47}, doi = {10.1016/j.jgar.2023.08.014}, pmid = {37643688}, issn = {2213-7173}, mesh = {Humans ; *Escherichia coli ; Virulence/genetics ; *Escherichia coli Infections ; Phylogeny ; Saliva ; Virulence Factors/genetics ; Genotype ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 127 is a pandemic lineage that belongs to the extraintestial pathogenic (ExPEC) family, mainly associated with urinary tract infections and bloodstream infections. Here, we report the complete genome of an E. coli ST 127 isolate which was identified in the saliva of a patient with treatment-resistant schizophrenia (TRS) exhibiting no signs of infection. The objective of this work is to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) that contribute to the pathogenicity of such ST127 isolates.<br><br>METHODS: Whole-genome sequencing (WGS) of isolate GABEEC10 was performed using DNABseq and Nanopore MinION platforms. Hybrid assembly of GABEEC10 was conducted with Unicycler v. 0.5.0. and annotated using PROKKA v1.14.5. Comparative genomics and phylogenomics were conducted using average nucleotide identity (ANI) and approximately-maximum-likelihood phylogenetic inference. ARGs, VFs, and serotyping were identified with Abricate v1.0.0 using CARD, vfdb, and EcOH databases, respectively.<br><br>RESULTS: Escherichia coli salivary isolate GABEEC10 was identified to belong to phylogroup B2 and have a serotype of O6 H31 with a total genome length of 4,940,530 bp and a mean guanine-cytosine (GC) content of 50.40 %. GABEEC10 was identified to have a highly virulent genotype with the presence of 84 VFs in addition to 44 ARGs, including an acquired blaTEM-30. The strain was identified to additionally carry four mobilisable plasmids.<br><br>CONCLUSION: We report the complete genome of E. coli GABAEEC10 that can be used for gaining insights into the pathogenicity, drug resistance mechanisms, and dissemination patterns of the emerging pandemic lineage ST 127.}, }
@article {pmid37640259, year = {2023}, author = {Ikeda, T and Ogawa, T and Aono, T}, title = {Dethiobiotin uptake and utilization by bacteria possessing bioYB operon.}, journal = {Research in microbiology}, volume = {174}, number = {8}, pages = {104131}, doi = {10.1016/j.resmic.2023.104131}, pmid = {37640259}, issn = {1769-7123}, mesh = {*Biotin/metabolism ; Biological Transport ; *Operon ; Bacteria/genetics/metabolism ; }, abstract = {Biotin is an essential vitamin for all organisms. Some bacteria cannot synthesize biotin and live by acquiring biotin from the environment. Bacterial biotin transporters (BioY) are classified into three mechanistic types. The first forms the BioMNY complex with ATPase (BioM) and transmembrane protein (BioN). The second relies on a promiscuous energy coupling module. The third functions independently. One-third of bioY genes spread in bacteria cluster with bioM and bioN on the genomes, and the rest does not. Interestingly, some bacteria have the bioY gene clustering with bioB gene, which encodes biotin synthase, an enzyme that converts dethiobiotin to biotin, on their genome. This bioY-bioB cluster is observed even though these bacteria cannot synthesize biotin. Azorhizobium caulinodans ORS571, a rhizobium of tropical legume Sesbania rostrata, is one of such bacteria. In this study using this bacterium, we demonstrated that the BioY linked to BioB could transport not only biotin but also dethiobiotin, and the combination of BioY and BioB contributed to the growth of A. caulinodans ORS571 in a biotin-deficient but dethiobiotin-sufficient environment. We propose that such environment universally exists in the natural world, and the identification of such environment will be a new subject in the field of microbial ecology.}, }
@article {pmid37639796, year = {2023}, author = {Mei, Z and Fu, Y and Wang, F and Xiang, L and Hu, F and Harindintwali, JD and Wang, M and Virta, M and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132388}, doi = {10.1016/j.jhazmat.2023.132388}, pmid = {37639796}, issn = {1873-3336}, mesh = {Humans ; *Sodium Chloride ; *Anti-Bacterial Agents/pharmacology ; Plant Leaves ; Soil ; Vegetables ; Magnetic Phenomena ; }, abstract = {Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.}, }
@article {pmid37637623, year = {2023}, author = {Ratna, HVK and Jeyaraman, M and Yadav, S and Jeyaraman, N and Nallakumarasamy, A}, title = {Is Dysbiotic Gut the Cause of Low Back Pain?.}, journal = {Cureus}, volume = {15}, number = {7}, pages = {e42496}, pmid = {37637623}, issn = {2168-8184}, abstract = {Low back pain (LBP) is the foremost cause of disability that affects the day-to-day activities of millions of people worldwide. The putative trigger of LBP is linked to the gut microbiome (GM) and its dysbiotic environment. With the concept of GM, various disease pathogenesis has been revisited with plausible crosstalks and micromolecular mimicry. In the normal intervertebral disc (IVD), Firmicutes and Actinobacteria were found in abundance. The blood-disc barrier protects IVD from systemic infection, resists inflammation, and halts the immune surveillance of the inner aspects of IVD. The insights into microbial ecology will broaden our horizons in GM and IVD degeneration in LBP cases. However, an improved understanding of GM and back pain has to be explored in large-scale individuals with varied timescales to validate the above findings. The role of GM (diet, prebiotics, probiotics, and fecal microbiota transplantation) in pain modulation can form novel therapies in cases of LBP.}, }
@article {pmid37637134, year = {2023}, author = {White, C and Antell, E and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, W and Alvarez-Cohen, L}, title = {Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1243410}, pmid = {37637134}, issn = {1664-302X}, abstract = {Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4[+]:NO2[-], where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4[+]:NO2[-] ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4[+]:NO2[-] ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4[+]:NO2[-] ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.}, }
@article {pmid37637113, year = {2023}, author = {Huang, J and Li, J and Zhou, W and Cheng, Y and Li, J}, title = {Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233815}, pmid = {37637113}, issn = {1664-302X}, abstract = {Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.}, }
@article {pmid37635954, year = {2024}, author = {Romans-Casas, M and Feliu-Paradeda, L and Tedesco, M and Hamelers, HVM and Bañeras, L and Balaguer, MD and Puig, S and Dessì, P}, title = {Selective butyric acid production from CO2 and its upgrade to butanol in microbial electrosynthesis cells.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100303}, pmid = {37635954}, issn = {2666-4984}, abstract = {Microbial electrosynthesis (MES) is a promising carbon utilization technology, but the low-value products (i.e., acetate or methane) and the high electric power demand hinder its industrial adoption. In this study, electrically efficient MES cells with a low ohmic resistance of 15.7 mΩ m[2] were operated galvanostatically in fed-batch mode, alternating periods of high CO2 and H2 availability. This promoted acetic acid and ethanol production, ultimately triggering selective (78% on a carbon basis) butyric acid production via chain elongation. An average production rate of 14.5 g m[-2] d[-1] was obtained at an applied current of 1.0 or 1.5 mA cm[-2], being Megasphaera sp. the key chain elongating player. Inoculating a second cell with the catholyte containing the enriched community resulted in butyric acid production at the same rate as the previous cell, but the lag phase was reduced by 82%. Furthermore, interrupting the CO2 feeding and setting a constant pH2 of 1.7-1.8 atm in the cathode compartment triggered solventogenic butanol production at a pH below 4.8. The efficient cell design resulted in average cell voltages of 2.6-2.8 V and a remarkably low electric energy requirement of 34.6 kWhel kg[-1] of butyric acid produced, despite coulombic efficiencies being restricted to 45% due to the cross-over of O2 and H2 through the membrane. In conclusion, this study revealed the optimal operating conditions to achieve energy-efficient butyric acid production from CO2 and suggested a strategy to further upgrade it to valuable butanol.}, }
@article {pmid37635262, year = {2023}, author = {Zhai, X and Castro-Mejía, JL and Gobbi, A and Aslampaloglou, A and Kot, W and Nielsen, DS and Deng, L}, title = {The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {193}, pmid = {37635262}, issn = {2049-2618}, mesh = {Humans ; *Bacteriophages/genetics ; DNA, Bacterial ; Feces ; Metagenome ; RNA ; }, abstract = {BACKGROUND: There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.<br><br>RESULTS: We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4&#xa0;&#xb0;C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100&#xa0;days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100&#xa0;days. Prolonged storage time (500&#xa0;days) at -&#xa0;80&#xa0;&#xb0;C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.<br><br>CONCLUSION: Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4&#xa0;&#xb0;C for the isolation of viruses and at -&#xa0;80&#xa0;&#xb0;C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.}, }
@article {pmid37635076, year = {2024}, author = {Barman, D and Dkhar, MS}, title = {Purification and characterization of moderately thermostable raw-starch digesting α-amylase from endophytic Streptomyces mobaraensis DB13 associated with Costus speciosus.}, journal = {The Journal of general and applied microbiology}, volume = {69}, number = {6}, pages = {293-300}, doi = {10.2323/jgam.2023.08.001}, pmid = {37635076}, issn = {1349-8037}, mesh = {*alpha-Amylases/metabolism/chemistry/isolation &amp; purification ; *Streptomyces/enzymology ; *Enzyme Stability ; *Starch/metabolism ; Hydrogen-Ion Concentration ; *Molecular Weight ; Kinetics ; *Temperature ; Endophytes/enzymology/metabolism/genetics ; Substrate Specificity ; Bacterial Proteins/metabolism/chemistry/isolation &amp; purification/genetics ; Electrophoresis, Polyacrylamide Gel ; }, abstract = {Endophytic actinobacteria are known to produce various enzymes with potential industrial applications. Alpha-amylase is an important class of industrial enzyme with a multi-dimensional utility. The present experiment was designed to characterize a moderately thermostable α-amylase producing endophytic Streptomyces mobaraensis DB13 isolated from Costus speciosus (J. Koenig) Sm. The enzyme was purified using 60% ammonium sulphate precipitation, dialysis, and Sephadex G-100 column chromatography. Based on 12% SDS-PAGE, the molecular weight of the purified α-amylase was estimated to be 55 kDa. The maximum α-amylase activity was achieved at pH 7.0, 50°C and it retained 80% of its activity at both pH 7.0 and 8.0 after incubation for 2 h. The α-mylase activity is strongly enhanced by Ca[2+], Mg[2+], and inhibited by Ba[2+]. The activity remains stable in the presence of Tween-80, SDS, PMSF, and Triton X-100; however, β-mercaptoethanol, EDTA, and H2O2 reduced the activity. The kinetic parameters Km and Vmax values for this α-amylase were calculated as 2.53 mM and 29.42 U/mL respectively. The α-amylase had the ability to digest various raw starches at a concentration of 10 mg/mL at pH 7.0, 50°C, where maize and rice are the preferred substrates. The digestion starts after 4 h of incubation, which reaches maximum after 48 h of incubation. These results suggest that S. mobaraensis DB13 is a potential source of moderately thermostable α-amylase enzyme, that effciently hydrolyzes raw starch. It suggesting that this α-amylase is a promising candidate to be use for industrial purposes.}, }
@article {pmid37633274, year = {2023}, author = {Pérez-Cobas, AE and Ginevra, C and Rusniok, C and Jarraud, S and Buchrieser, C}, title = {The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia.}, journal = {Cell reports. Medicine}, volume = {4}, number = {9}, pages = {101167}, pmid = {37633274}, issn = {2666-3791}, mesh = {Humans ; *Pneumonia, Bacterial/diagnosis ; Respiratory System ; *Coinfection ; Dysbiosis ; *Microbiota ; }, abstract = {Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.}, }
@article {pmid37633148, year = {2024}, author = {Guo, T and Wang, T and Chen, L and Zheng, B}, title = {Whole-grain highland barley premade biscuit prepared by hot-extrusion 3D printing: Printability and nutritional assessment.}, journal = {Food chemistry}, volume = {432}, number = {}, pages = {137226}, doi = {10.1016/j.foodchem.2023.137226}, pmid = {37633148}, issn = {1873-7072}, mesh = {*Nutrition Assessment ; *Hordeum ; Functional Food ; Corn Oil ; Printing, Three-Dimensional ; }, abstract = {In this study, to explore the possibility of applying whole-grain highland barley (HB) in functional food, HB premade biscuit was created by hot-extrusion 3D printing (HEP) for the first time, and its printability and nutritional functions were evaluated. The rheology results showed 20% (w/w) HB suspension with 9% corn oil addition had better printability due to the formation of a structure with higher elasticity and stronger resistance to deformation. Moreover, the obtained premade biscuit had lower predicted glycemic index (pGI) and starch digestibility. Meanwhile, in vivo experiment results showed it could affect the glycolipid metabolism, ameliorate the high fat diet (HFD)-induced metabolic disorders and maintain the balance of the gut microbial ecology. This could be attributed to the decrease in Firmicutes/Bacteroidetes ratio and the proliferation of propionate-producing probiotics, especially Veilonella, Weissella and Desulfovibrio. Overall, this study could provide basic data and innovative approaches to prepare nutritional whole-grain foods.}, }
@article {pmid37632540, year = {2023}, author = {Seward, J and Bräuer, S and Beckett, P and Roy-Léveillée, P and Emilson, E and Watmough, S and Basiliko, N}, title = {Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2894-2903}, pmid = {37632540}, issn = {1432-184X}, mesh = {Ecosystem ; *Sphagnopsida ; Soil/chemistry ; *Metals, Heavy ; Ontario ; }, abstract = {Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.}, }
@article {pmid37630470, year = {2023}, author = {Won, S and Shin, C and Kang, HY}, title = {Potential Self-Attenuation of Arsenic by Indigenous Microorganisms in the Nakdong River.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630470}, issn = {2076-2607}, support = {NRF- 2020R1I1A3068585//National Research Foundation of Korea/ ; }, abstract = {The toxic element arsenic (As) has become the major focus of global research owing to its harmful effects on human health, resulting in the establishment of several guidelines to prevent As contamination. The widespread industrial use of As has led to its accumulation in the environment, increasing the necessity to develop effective remediation technologies. Among various treatments, such as chemical, physical, and biological treatments, used to remediate As-contaminated environments, biological methods are the most economical and eco-friendly. Microbial oxidation of arsenite (As(III)) to arsenate (As(V)) is a primary detoxification strategy for As remediation as it reduces As toxicity and alters its mobility in the environment. Here, we evaluated the self-detoxification potential of microcosms isolated from Nakdong River water by investigating the autotrophic and heterotrophic oxidation of As(III) to As(V). Experimental data revealed that As(III) was oxidized to As(V) during the autotrophic and heterotrophic growth of river water microcosms. However, the rate of oxidation was significantly higher under heterotrophic conditions because of the higher cell growth and density in an organic-matter-rich environment compared to that under autotrophic conditions without the addition of external organic matter. At an As(III) concentration > 5 mM, autotrophic As(III) oxidation remained incomplete, even after an extended incubation time. This inhibition can be attributed to the toxic effect of the high contaminant concentration on bacterial growth and the acidification of the growth medium with the oxidation of As(III) to As(V). Furthermore, we isolated representative pure cultures from both heterotrophic- and autotrophic-enriched cultures. The new isolates revealed new members of As(III)-oxidizing bacteria in the diversified bacterial community. This study highlights the natural process of As attenuation within river systems, showing that microcosms in river water can detoxify As under both organic-matter-rich and -deficient conditions. Additionally, we isolated the bacterial strains HTAs10 and ATAs5 from the microcosm which can be further investigated for potential use in As remediation systems. Our findings provide insights into the microbial ecology of As(III) oxidation in river ecosystems and provide a foundation for further investigations into the application of these bacteria for bioremediation.}, }
@article {pmid37624441, year = {2023}, author = {Pinheiro Alves de Souza, Y and Schloter, M and Weisser, W and Schulz, S}, title = {Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2882-2893}, pmid = {37624441}, issn = {1432-184X}, mesh = {Biomass ; *Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; }, abstract = {Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.}, }
@article {pmid37624156, year = {2023}, author = {Cao, Y and Wang, R and Liu, Y and Li, Y and Jia, L and Yang, Q and Zeng, X and Li, X and Wang, Q and Wang, R and Riaz, L}, title = {Improved Calculations of Heavy Metal Toxicity Coefficients for Evaluating Potential Ecological Risk in Sediments Based on Seven Major Chinese Water Systems.}, journal = {Toxics}, volume = {11}, number = {8}, pages = {}, pmid = {37624156}, issn = {2305-6304}, support = {U1904205//Key Project of the National Natural Science Foundation of China-Henan Joint Fund/ ; NSFC 42277409//National Natural Science Foundation of China/ ; 22B180006//Educational Commission of the Henan Province of China/ ; 21A180014//Key Project of Natural Science of the Education Department of Henan Province of China/ ; 212102110322//Science and Technology Project of Henan Province/ ; }, abstract = {Several methods have been used to assess heavy metal contamination in sediments. However, an assessment that considers both composite heavy metal speciation and concentration is necessary to accurately study ecological risks. This study improved the potential ecological risk index method and calculated the toxicity coefficients of seven heavy metals: Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn). The newly calculated toxicity coefficients were validated by using previously published heavy metal distribution data of the Henan section of the Yellow River. The calculation procedure is based on the principle that the abundance of heavy metals in the environment and their bioavailable forms affect the toxicity of heavy metals. The toxicity coefficients for the seven heavy metals were calculated as follows: As = 10, Cd = 20, Cr = 5, Cu = 2, Ni = 5, Pb = 5, Zn = 1. Ecological risk assessment of the Henan section of the Yellow River using the improved toxicity coefficients revealed that the ecological risk of Cd and total heavy metals is higher than previous calculations, reaching the strength and moderate risk levels, respectively. The improved potential ecological risk index method is more sensitive to heavy metal pollution and thus provides a better indication of ecological risk. This is a necessary improvement to provide more accurate pollution assessments.}, }
@article {pmid37620628, year = {2023}, author = {Chen, X and Li, Q and Chen, D and Zhao, L and Xiao, C}, title = {Restoration Measures of Fencing after Tilling Guided Succession of Grassland Soil Microbial Community Structure to Natural Grassland in the Sanjiangyuan Agro-pasture Ecotone of the Qinghai-Tibetan Plateau.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2870-2881}, pmid = {37620628}, issn = {1432-184X}, support = {2019QZKK040104//the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 2021FY100705//the Special Project on National Science and Technology Basic Resources Investigation of China/ ; 31770501//the National Natural Science Foundation of China/ ; }, mesh = {*Soil/chemistry ; Grassland ; Tibet ; Soil Microbiology ; Plants ; *Microbiota ; }, abstract = {In the fragile Sanjiangyuan (SJY) agro-pasture ecotone of the Qinghai-Tibetan Plateau (QTP), planting and fencing have been used to alleviate grassland degradation and to provide high-quality grass seeds for the implementation of the project of "grain for green". The soil microbe is the major driving factor in maintaining plant productivity and soil nutrient cycling. However, few studies have explored the effects of planting and fencing on soil microorganisms in the SJY agro-pasture ecotone. We explored the effects of tilling (TG) and fencing after tilling (FTG) on soil microbial communities to reveal the effects of restoration measures on soil microbes and to provide a reference in assessing and improving ecosystem structure. The results showed that restoration measures increased soil microbial species diversity and significantly changed their community structure. We found, the microbial composition was more complex under FTG, and its fungal variability was higher and more similar to that of natural grassland. Additionally, restoration measures resulted in fungal co-occurrence network was more edges, higher density, larger diameter and more positive interactions. This was due to the management of the vegetation-soil microenvironment by FTG inducing a differentiation of microbial community structure. In summary, the implementation of FTG could change the microenvironment in the SJY agro-pasture ecotone, so that variation in the structure of microbial community tended toward that of natural grassland, and increased the stability of microbial co-occurrence network, which was more obvious in the fungal community. HIGHLIGHTS: • Restoration measures have changed the vegetation characteristics and soil microenvironment. • Fencing after tilling (FTG) has brought the microenvironment closer to natural grassland. • FTG significantly increased microbial unique ASVs. The number of fungal unique ASVs was similar to that of natural grassland. • FTG resulted in changes in microbial community structure towards natural grasslands and increased the stability of the microbial co-occurrence network, which was more apparent in the fungal community.}, }
@article {pmid37620398, year = {2023}, author = {De Micco, V and Amitrano, C and Mastroleo, F and Aronne, G and Battistelli, A and Carnero-Diaz, E and De Pascale, S and Detrell, G and Dussap, CG and Ganigué, R and Jakobsen, &#xd8;M and Poulet, L and Van Houdt, R and Verseux, C and Vlaeminck, SE and Willaert, R and Leys, N}, title = {Plant and microbial science and technology as cornerstones to Bioregenerative Life Support Systems in space.}, journal = {NPJ microgravity}, volume = {9}, number = {1}, pages = {69}, pmid = {37620398}, issn = {2373-8065}, abstract = {Long-term human space exploration missions require environmental control and closed Life Support Systems (LSS) capable of producing and recycling resources, thus fulfilling all the essential metabolic needs for human survival in harsh space environments, both during travel and on orbital/planetary stations. This will become increasingly necessary as missions reach farther away from Earth, thereby limiting the technical and economic feasibility of resupplying resources from Earth. Further incorporation of biological elements into state-of-the-art (mostly abiotic) LSS, leading to bioregenerative LSS (BLSS), is needed for additional resource recovery, food production, and waste treatment solutions, and to enable more self-sustainable missions to the Moon and Mars. There is a whole suite of functions crucial to sustain human presence in Low Earth Orbit (LEO) and successful settlement on Moon or Mars such as environmental control, air regeneration, waste management, water supply, food production, cabin/habitat pressurization, radiation protection, energy supply, and means for transportation, communication, and recreation. In this paper, we focus on air, water and food production, and waste management, and address some aspects of radiation protection and recreation. We briefly discuss existing knowledge, highlight open gaps, and propose possible future experiments in the short-, medium-, and long-term to achieve the targets of crewed space exploration also leading to possible benefits on Earth.}, }
@article {pmid37619629, year = {2023}, author = {Wang, SH and Yuan, SW and Che, FF and Wan, X and Wang, YF and Yang, DH and Yang, HJ and Zhu, D and Chen, P}, title = {Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {116954}, doi = {10.1016/j.envres.2023.116954}, pmid = {37619629}, issn = {1096-0953}, abstract = {Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R[2] = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.}, }
@article {pmid37615431, year = {2023}, author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD}, title = {Machine learning classification by fitting amplicon sequences to existing OTUs.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0033623}, pmid = {37615431}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; R01CA215574/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Algorithms ; *Microbiota/genetics ; }, abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.}, }
@article {pmid37614461, year = {2023}, author = {Kandeel, SA and Megahed, AA}, title = {Editorial: Infectious diseases, microbial ecology, and antimicrobial resistance dynamics in food animals.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1266980}, pmid = {37614461}, issn = {2297-1769}, }
@article {pmid37610498, year = {2023}, author = {Wei, N and Tan, J}, title = {Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2858-2868}, pmid = {37610498}, issn = {1432-184X}, support = {030869//Holden Arboretum/ ; LEQSF(2023-26)-RD-A-14//Louisiana Board of Regents/ ; 10635//Gordon and Betty Moore Foundation/ ; }, mesh = {*Microbiota/genetics ; Bacteria/genetics ; *Araceae/microbiology ; }, abstract = {To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.}, }
@article {pmid37608162, year = {2023}, author = {Fecchio, A and Bell, JA and Williams, EJ and Dispoto, JH and Weckstein, JD and de Angeli Dutra, D}, title = {Co-infection with Leucocytozoon and Other Haemosporidian Parasites Increases with Latitude and Altitude in New World Bird Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2838-2846}, pmid = {37608162}, issn = {1432-184X}, support = {DEB-1503804//National Science Foundation/ ; }, mesh = {Animals ; *Parasites ; *Coinfection/veterinary ; Bayes Theorem ; Altitude ; *Bird Diseases/epidemiology/parasitology ; Birds ; *Haemosporida ; Prevalence ; }, abstract = {Establishing how environmental gradients and host ecology drive spatial variation in infection rates and diversity of pathogenic organisms is one of the central goals in disease ecology. Here, we identified the predictors of concomitant infection and lineage richness of blood parasites in New Word bird communities. Our multi-level Bayesian models revealed that higher latitudes and elevations played a determinant role in increasing the probability of a bird being co-infected with Leucocytozoon and other haemosporidian parasites. The heterogeneity in both single and co-infection rates was similarly driven by host attributes and temperature, with higher probabilities of infection in heavier migratory host species and at cooler localities. Latitude, elevation, host body mass, migratory behavior, and climate were also predictors of Leucocytozoon lineage richness across the New World avian communities, with decreasing parasite richness at higher elevations, rainy and warmer localities, and in heavier and resident host species. Increased parasite richness was found farther from the equator, confirming a reverse Latitudinal Diversity Gradient pattern for this parasite group. The increased rates of Leucocytozoon co-infection and lineage richness with increased latitude are in opposition with the pervasive assumption that pathogen infection rates and diversity are higher in tropical host communities.}, }
@article {pmid37607924, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5090}, pmid = {37607924}, issn = {2041-1723}, mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; }, abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.}, }
@article {pmid37607131, year = {2023}, author = {Klapper, FA and Kiel, C and Bellstedt, P and Vyverman, W and Pohnert, G}, title = {Structure Elucidation of the First Sex-Inducing Pheromone of a Diatom.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {62}, number = {43}, pages = {e202307165}, doi = {10.1002/anie.202307165}, pmid = {37607131}, issn = {1521-3773}, support = {FWO G001521N, BOF/GOA No. 01G01715//European Marine Biological Resource Centre Belgium/ ; Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Diatoms are abundant unicellular microalgae, responsible for ≈20 % of global photosynthetic CO2 fixation. Nevertheless, we know little about fundamental aspects of their biology, such as their sexual reproduction. Pheromone-mediated chemical communication is crucial for successful mating. An attraction pheromone was identified in the diatom Seminavis robusta, but metabolites priming cells for sex and synchronizing search and mating behavior remained elusive. These sex-inducing pheromones (SIP) induce cell cycle arrest and trigger the production of the attraction pheromone. Here we describe the challenging structure elucidation of an S. robusta SIP. Guided by metabolomics, a candidate metabolite was identified and elucidated by labeling experiments, NMR, ESI MS[n] analyses, and chemical transformations. The use of negative ion mode MS was essential to decipher the unprecedented hydroxyproline and β-sulfated aspartate-containing cyclic heptapeptide that acts in femtomolar concentrations.}, }
@article {pmid37606945, year = {2023}, author = {Ricks, KD and Ricks, NJ and Yannarell, AC}, title = {Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes.}, journal = {The American naturalist}, volume = {202}, number = {3}, pages = {276-287}, doi = {10.1086/725393}, pmid = {37606945}, issn = {1537-5323}, mesh = {Humans ; *Salinity ; Acclimatization ; *Infertility ; Phenotype ; Soil ; }, abstract = {AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.}, }
@article {pmid37606696, year = {2023}, author = {Theodorescu, M and Bucur, R and Bulzu, PA and Faur, L and Levei, EA and Mirea, IC and Cadar, O and Ferreira, RL and Souza-Silva, M and Moldovan, OT}, title = {Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2847-2857}, pmid = {37606696}, issn = {1432-184X}, mesh = {*Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Proteobacteria/genetics ; }, abstract = {Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.}, }
@article {pmid37604894, year = {2023}, author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L}, title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13635}, pmid = {37604894}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; }, abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.}, }
@article {pmid37604501, year = {2023}, author = {Kuzyk, SB and Messner, K and Plouffe, J and Ma, X and Wiens, K and Yurkov, V}, title = {Diverse aerobic anoxygenic phototrophs synthesize bacteriochlorophyll in oligotrophic rather than copiotrophic conditions, suggesting ecological niche.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2653-2665}, doi = {10.1111/1462-2920.16482}, pmid = {37604501}, issn = {1462-2920}, mesh = {Humans ; *Bacteriochlorophylls ; Phylogeny ; Bacteria, Aerobic/genetics ; Ecosystem ; Photosynthesis ; *Alphaproteobacteria ; }, abstract = {While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.}, }
@article {pmid37603734, year = {2023}, author = {Lee, H and Bloxham, B and Gore, J}, title = {Resource competition can explain simplicity in microbial community assembly.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {35}, pages = {e2212113120}, pmid = {37603734}, issn = {1091-6490}, mesh = {*Ecology ; Laboratories ; *Microbiota ; }, abstract = {Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using the harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.}, }
@article {pmid37601377, year = {2023}, author = {Flocco, CG and Methner, A and Burkart, F and Geppert, A and Overmann, J}, title = {Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1197837}, pmid = {37601377}, issn = {1664-302X}, abstract = {Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.}, }
@article {pmid37597041, year = {2023}, author = {Cleary, DFR and de Voogd, NJ and Stuij, TM and Swierts, T and Oliveira, V and Polónia, ARM and Louvado, A and Gomes, NCM and Coelho, FJRC}, title = {A Study of Sponge Symbionts from Different Light Habitats.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2819-2837}, pmid = {37597041}, issn = {1432-184X}, mesh = {Animals ; Biodiversity ; Phylogeny ; Bacteria/genetics ; Seawater/microbiology ; *Microbiota ; Water ; *Porifera ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.}, }
@article {pmid37594520, year = {2023}, author = {Martínez, LT and Marchant, M and Díaz, RTA and Arrojo, M&#xc1; and Muñoz, P}, title = {Benthic Foraminifera as Pollution Biomarkers: a Morphological Approach.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2802-2818}, pmid = {37594520}, issn = {1432-184X}, support = {1130511//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170124//Fondo de Equipamiento Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry ; *Foraminifera/chemistry ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Biomarkers ; }, abstract = {Coastal areas are often intervened by anthropic activities, which increase the contamination of toxic agents such as heavy metals. This causes adverse morphological effects on benthic microorganisms, such as foraminifera. This group is one of the most susceptible to environmental deterioration, so they can be used as pollution biomarkers by identifying shell abnormalities. Therefore, 28 sediment samples from northern Chile were analyzed, calculating the Abnormality Index-FAI and its spatio-temporal distributions in benthic foraminifera, as well as the minimum and maximum abnormality percentages and their relationship with heavy metal concentrations, using a generalized non-linear model and a principal component analysis. The results indicated a proportion of abnormal shells within the ranges described for polluted areas conditions, revealing environmental stress conditions. This reflected a change in the environmental conditions in the most recent sediments of the bay. The highest FAI values were observed to the southwest of the bay, caused by the local current system. The species Bolivina seminuda, Buliminella elegantissima, and Epistominella exigua presented a greater number of deformities, allowing them to be used as contamination biomarkers. A significant correlation was found between Ti, Mn, Ni, Va, and Ba with decreased chamber sizes, wrong coiling, scars, and number of abnormality types. This suggests the effect of the particular geochemical conditions of the area on the heavy metals that cause toxic effects on foraminifera. These analyses are an efficient tool for identifying the effects of environmental stress before they occur in higher organisms, mitigating the environmental impact on marine biodiversity.}, }
@article {pmid37594170, year = {2023}, author = {Hambleton, EA}, title = {How corals get their nutrients.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37594170}, issn = {2050-084X}, mesh = {Animals ; *Nutrients ; *Anthozoa ; Cell Wall ; }, abstract = {Algae living inside corals provide sugars for their host by digesting their own cell walls.}, }
@article {pmid37590550, year = {2022}, author = {de Almeida, OGG and De Martinis, ECP}, title = {Multitargeted Analyses are Instrumental for Microbial Ecology Studies.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {187}, pages = {}, doi = {10.3791/64789}, pmid = {37590550}, issn = {1940-087X}, }
@article {pmid37586176, year = {2023}, author = {Bai, X and Dinkla, IJT and Muyzer, G}, title = {Shedding light on the total and active core microbiomes in slow sand filters for drinking water production.}, journal = {Water research}, volume = {243}, number = {}, pages = {120404}, doi = {10.1016/j.watres.2023.120404}, pmid = {37586176}, issn = {1879-2448}, mesh = {Humans ; *Drinking Water ; Filtration/methods ; *Water Purification/methods ; *Microbiota ; Bacteria/genetics ; Silicon Dioxide/chemistry ; }, abstract = {Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.}, }
@article {pmid37579703, year = {2023}, author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X}, title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.}, journal = {Marine environmental research}, volume = {191}, number = {}, pages = {106131}, doi = {10.1016/j.marenvres.2023.106131}, pmid = {37579703}, issn = {1879-0291}, mesh = {*Marine Toxins ; Kainic Acid/toxicity ; Eukaryota ; *Microbiota ; }, abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.}, }
@article {pmid37573698, year = {2023}, author = {Song, Y and Zhang, S and Lu, J and Duan, R and Chen, H and Ma, Y and Si, T and Luo, M}, title = {Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118700}, doi = {10.1016/j.jenvman.2023.118700}, pmid = {37573698}, issn = {1095-8630}, mesh = {*Rhizosphere ; Wetlands ; Bacteria ; Archaea ; *Microbiota ; Plants ; Nutrients ; Geologic Sediments/chemistry ; }, abstract = {Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.}, }
@article {pmid37567875, year = {2023}, author = {Molbert, N and Ghanavi, HR and Johansson, T and Mostadius, M and Hansson, MC}, title = {An evaluation of DNA extraction methods on historical and roadkill mammalian specimen.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13080}, pmid = {37567875}, issn = {2045-2322}, mesh = {Animals ; *Chloroform ; *DNA/genetics ; Phenol ; Phenols ; Mammals/genetics ; Silicon Dioxide ; }, abstract = {Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.}, }
@article {pmid37567306, year = {2023}, author = {Schroll, M and Liu, L and Einzmann, T and Keppler, F and Grossart, HP}, title = {Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166205}, doi = {10.1016/j.scitotenv.2023.166205}, pmid = {37567306}, issn = {1879-1026}, abstract = {Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, eutrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in [13]C-CH4 and [2]H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with [13]C- and [2]H-labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emission to the atmosphere.}, }
@article {pmid37564072, year = {2023}, author = {Michoud, G and Kohler, TJ and Ezzat, L and Peter, H and Nattabi, JK and Nalwanga, R and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Marasco, R and Daffonchio, D and Bourquin, M and Busi, SB and Battin, TJ}, title = {The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.}, journal = {Royal Society open science}, volume = {10}, number = {8}, pages = {230329}, pmid = {37564072}, issn = {2054-5703}, abstract = {The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.}, }
@article {pmid37563275, year = {2023}, author = {Epp Schmidt, D and Maul, JE and Yarwood, SA}, title = {Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2790-2801}, pmid = {37563275}, issn = {1432-184X}, support = {1828910//NSF/ ; }, mesh = {*Bacteria/genetics ; Population Density ; *Microbiota/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.}, }
@article {pmid37555066, year = {2023}, author = {Mashamaite, L and Lebre, PH and Varliero, G and Maphosa, S and Ortiz, M and Hogg, ID and Cowan, DA}, title = {Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203216}, pmid = {37555066}, issn = {1664-302X}, abstract = {INTRODUCTION: The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.<br><br>METHODS: We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.<br><br>RESULTS AND DISCUSSION: Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.}, }
@article {pmid37552473, year = {2023}, author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z}, title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2781-2789}, pmid = {37552473}, issn = {1432-184X}, mesh = {*Nitrates ; Pacific Ocean ; Chlorophyll A ; *Thiosulfates ; Seawater/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Carbon ; Chitin ; Phylogeny ; }, abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.}, }
@article {pmid37550791, year = {2023}, author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Dimitroulia, E and Saroglou, G and Tsakris, A}, title = {Comparison of microbial colonization rates between central venous catheters and peripherally inserted central catheters.}, journal = {Antimicrobial resistance and infection control}, volume = {12}, number = {1}, pages = {74}, pmid = {37550791}, issn = {2047-2994}, mesh = {Humans ; *Central Venous Catheters/adverse effects ; *Catheterization, Central Venous/adverse effects/methods ; Retrospective Studies ; Critical Illness ; *Catheter-Related Infections/prevention &amp; control ; Risk Factors ; *Sepsis ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: Central venous catheters (CVCs) and peripherally inserted central catheters (PICCs), have been widely used as intravascular devices in critically ill patients. However, they might evoke complications, such as catheter colonization that has been considered as predisposing factor for central line-associated bloodstream infections (CLABSIs). Although numerous studies have compared the risk of bloodstream infections between PICCs and CVCs, comparative studies on their colonization rates are limited.<br><br>OBJECTIVES: The episodes of catheter colonization in critically ill patients with CVCs or PICCs were retrospectively analysed during a two-year period in a Greek tertiary care hospital and colonization rates, microbial profiles and antimicrobial susceptibility&#xa0;patterns were compared.<br><br>METHODS: Clinical and laboratory data of consecutive hospitalized critically-ill patients who underwent PICC and CVC placement between May 2017-May 2019 were analysed. All catheters were examined by the semiquantitative culture technique for bacterial pathogens, either as a routine process after catheter removal or after suspicion of infection. Species identification and antimicrobial resistance patterns were determined by the Vitek2 automated system.<br><br>RESULTS: During the survey period a total of 122/1187 (10.28%) catheter colonization cases were identified among CVCs and 19/639 (2.97%) cases among PICCs (p&#x2009;=&#x2009;0.001). The colonization rate was 12.48/1000 catheter-days for the&#xa0;CVC group and 1.71/1000 catheter-days for the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). The colonization rate per 1000 catheter-days due to multidrug-resistant organisms (MDROs) was 3.85 in all study cases, 7.26 (71/122) in the&#xa0;CVC group and 0.63 (7/19) in the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). Within the&#xa0;CVC group, the most common microorganism isolated was MDR Acinetobacter baumannii (n&#x2009;=&#x2009;38, 31.1%) followed by MDR Klebsiella pneumoniae (n&#x2009;=&#x2009;20, 16.4%). In the&#xa0;PICC group, the predominant microorganism isolated was Candida spp. (n&#x2009;=&#x2009;5, 23.8%) followed by MDR K. pneumoniae and MDR A. baumannii in equal numbers (n&#x2009;=&#x2009;3, 14.2%).<br><br>CONCLUSION: PICC lines were associated with significantly lower colonization rates comparing to the&#xa0;CVC&#xa0;ones. In addition, patterns of microbial colonization revealed a trend over the predominance of MDR gram-negatives in CVCs suggesting that PICCs might be a&#xa0;safer alternative for prolonged inpatient intravascular access. Prevention programs directed by local microbial ecology may diminish catheter colonization rates and CLABSIs.}, }
@article {pmid37550373, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH}, title = {Author Correction: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {9}, number = {8}, pages = {1370}, doi = {10.1038/s41477-023-01504-y}, pmid = {37550373}, issn = {2055-0278}, }
@article {pmid37548146, year = {2023}, author = {Ruiz, J and de Celis, M and Diaz-Colunga, J and Vila, JC and Benitez-Dominguez, B and Vicente, J and Santos, A and Sanchez, A and Belda, I}, title = {Predictability of the community-function landscape in wine yeast ecosystems.}, journal = {Molecular systems biology}, volume = {19}, number = {9}, pages = {e11613}, pmid = {37548146}, issn = {1744-4292}, mesh = {*Saccharomyces cerevisiae/genetics ; *Wine ; Ecosystem ; Phylogeny ; Fermentation ; Yeasts ; }, abstract = {Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.}, }
@article {pmid37547726, year = {2023}, author = {Gibson, E and Zimmerman, NB}, title = {Urban biogeography of fungal endophytes across San Francisco.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15454}, pmid = {37547726}, issn = {2167-8359}, mesh = {Humans ; Endophytes/genetics ; Cities ; San Francisco ; Hot Temperature ; *Fungi, Unclassified ; Plants/microbiology ; Trees/microbiology ; *Microbiota ; }, abstract = {In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.}, }
@article {pmid37544074, year = {2023}, author = {Fu, S and Wang, R and Zhang, J and Xu, Z and Yang, X and Yang, Q}, title = {Temporal variability of microbiome in the different plankton hosts revealed distinct environmental persistence of Vibrio parahaemolyticus in shrimp farms.}, journal = {Microbiological research}, volume = {275}, number = {}, pages = {127464}, doi = {10.1016/j.micres.2023.127464}, pmid = {37544074}, issn = {1618-0623}, mesh = {Plankton/genetics ; *Vibrio parahaemolyticus/genetics ; *Chlorella ; Hemolysin Proteins/genetics ; *Microbiota/genetics ; Aquaculture ; }, abstract = {Plankton-bacteria interactions may play essential roles in maintaining the persistence of pathogenic Vibrio spp. However, the actual plankton host of the toxigenic Vibrio parahaemolyticus that harbors thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) remains unclear. To answer this question, we measured the abundance of toxigenic and nontoxigenic Vibrio parahaemolyticus in different types of plankton by most probable number (MPN)-PCR. We next investigated the dynamics of the microbiomes of rearing water, copepods, Chlorella, four predominant diatom genera (Nitzschia, Melosira, Skeletonema and Chaetoceros) and the gut of the shrimp in two recirculated shrimp farming systems from April to September using high-throughput 16 S rRNA amplicon sequencing. The survival of trh-positive and trh-negative V. parahaemolyticus in seawater and different plankton hosts was examined under low temperature and starvation conditions. The results showed that copepods harbored the highest proportion of trh-positive V. parahaemolyticus, followed by diatoms. Chitinous diatoms (CD) harbored a high proportion of Vibrionaceae, of which a high abundance of V. parahaemolyticus was found in summer. In contrast, Vibrio spp. is rarely found in Chlorella and nonchitinous diatoms. Taxon-specific associations were also observed, including a relatively high abundance of Vibrio and Halodesulfovibrio on copepods and covariation of Aeromonas and Bacillus inside the Chlorella. The survival assays showed that, in comparison to trh-negative V. parahaemolyticus, trh-positive V. parahaemolyticus showed better survival in copepods and CD under starvation conditions and maintained high persistence in the above hosts at low temperature. In conclusion, the results herein suggested that chitinous plankton might provide protection for V. parahaemolyticus, especially trh-positive V. parahaemolyticus, and improve their persistence under harsh conditions. Our study provided in-depth insights into the persistence of V. parahaemolyticus in the environment, which would promote targeted disease prevention measures.}, }
@article {pmid37543702, year = {2023}, author = {Tang, L and O'Dwyer, J and Kimyon, &#xd6; and Manefield, MJ}, title = {Microbial community composition of food waste before anaerobic digestion.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12703}, pmid = {37543702}, issn = {2045-2322}, mesh = {Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; *Microbiota/genetics ; Bacteria/genetics ; Bioreactors/microbiology ; Methane ; Sewage/microbiology ; }, abstract = {Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.}, }
@article {pmid37542810, year = {2023}, author = {De Paepe, J and Garcia Gragera, D and Arnau Jimenez, C and Rabaey, K and Vlaeminck, SE and Gòdia, F}, title = {Continuous cultivation of microalgae yields high nutrient recovery from nitrified urine with limited supplementation.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118500}, doi = {10.1016/j.jenvman.2023.118500}, pmid = {37542810}, issn = {1095-8630}, mesh = {Humans ; *Microalgae/metabolism ; Calcium/metabolism ; Edetic Acid/metabolism ; Magnesium ; Nutrients ; Photobioreactors ; Phosphorus/metabolism ; Dietary Supplements ; Biomass ; Nitrogen/metabolism ; }, abstract = {Microalgae can play a key role in the bioeconomy, particularly in combination with the valorisation of waste streams as cultivation media. Urine is an example of a widely available nutrient-rich waste stream, and alkaline stabilization and subsequent full nitrification in a bioreactor yields a stable nitrate-rich solution. In this study, such nitrified urine served as a culture medium for the edible microalga Limnospira indica. In batch cultivation, nitrified urine without additional supplements yielded a lower biomass concentration, nutrient uptake and protein content compared to modified Zarrouk medium, as standard medium. To enhance the nitrogen uptake efficiency and biomass production, nitrified urine was supplemented with potentially limiting elements. Limited amounts of phosphorus (36 mg L[-1]), magnesium (7.9 mg L[-1]), calcium (12.2 mg L[-1]), iron (2.0 mg L[-1]) and EDTA (88.5 mg Na2-EDTA.2H2O L[-1]) rendered the nitrified urine matrix as effective as modified Zarrouk medium in terms of biomass production (OD750 of 1.2), nutrient uptake (130 mg N L[-1]) and protein yield (47%) in batch culture. Urine precipitates formed by alkalinisation could in principle supply enough phosphorus, calcium and magnesium, requiring only external addition of iron, EDTA and inorganic carbon. Subsequently, the suitability of supplemented nitrified urine as a culture medium was confirmed in continuous Limnospira cultivation in a CSTR photobioreactor. This qualifies nitrified urine as a valuable and sustainable microalgae growth medium, thereby creating novel nutrient loops on Earth and in Space, i.e., in regenerative life support systems for human deep-space missions.}, }
@article {pmid37542791, year = {2023}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Costa, OYA and Korthals, GW and de Boer, W and Bodelier, PLE}, title = {The intrinsic methane mitigation potential and associated microbes add product value to compost.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {17-32}, doi = {10.1016/j.wasman.2023.07.027}, pmid = {37542791}, issn = {1879-2456}, abstract = {Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 &amp; ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h[-1] g dw compost[-1] and 25.19 ± 6.75 pmol h[-1] g dw compost[-1], respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.}, }
@article {pmid37542538, year = {2023}, author = {Niu, J and Chen, D and Shang, C and Xiao, L and Wang, Y and Zeng, W and Zheng, X and Chen, Z and Du, X and Chen, X}, title = {Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2770-2780}, pmid = {37542538}, issn = {1432-184X}, mesh = {*Drinking Water ; Water Quality ; Bacteria/genetics ; Proteobacteria ; Biofilms ; Archaea/genetics ; *Bacillus ; Water Supply ; Water Microbiology ; }, abstract = {Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×10[3]~1.1×10[5] copies/cm[2]. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×10[3]~9.6×10[6] copies/cm[2]. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.}, }
@article {pmid37542537, year = {2023}, author = {Ren, Z and Ye, S and Li, H and Huang, X and Chen, L and Cao, S and Chen, T}, title = {Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2756-2769}, pmid = {37542537}, issn = {1432-184X}, mesh = {Animals ; *Permafrost ; Tibet ; Soil/chemistry ; *Microbiota ; *Arthropods ; Soil Microbiology ; *Ciliophora/genetics ; }, abstract = {Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.}, }
@article {pmid37541415, year = {2023}, author = {He, Q and Yan, X and Wang, H and Ji, Y and Li, J and Liu, L and Bi, P and Xu, P and Xu, B and Ma, J}, title = {Towards a better understanding of the anaerobic/oxic/anoxic-aerobic granular sludge process (AOA-AGS) for simultaneous low-strength wastewater treatment and in situ sludge reduction from ambient to winter temperatures.}, journal = {Environmental research}, volume = {236}, number = {Pt 2}, pages = {116822}, doi = {10.1016/j.envres.2023.116822}, pmid = {37541415}, issn = {1096-0953}, abstract = {The new anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) merits the advantages of effective carbon utilization and low-carbon treatment. However, low temperature poses stressing concerns and the resisting mechanism remains much unknown. Herein, an AOA-AGS process was configured for simultaneous nitrification, denitrification and phosphorus removal (SNDPR) with low-strength wastewater from ambient (>15 °C) to winter temperatures (<15 °C). Results showed that simultaneously advanced nutrients removal, and dramatic in situ sludge reduction (Yobs of 0.093 g MLSS/g COD) were gained regardless of seasonally decreasing temperatures. Winter temperatures even amplified Candidatus Competibacter predominating from 20.11% to 34.74%, which laid the core basis for endogenous denitrification, sludge minimization and temperature resistance. A removal model was thus proposed given the observed functional groups, and doubts were also raised for future investigations. This study would aid a better understanding on the microbial ecology and engineering aspects of the new AOA-AGS process treating low-strength wastewater at low temperatures.}, }
@article {pmid37537784, year = {2023}, author = {Guan, X and Zhao, Z and Jiang, J and Fu, L and Liu, J and Pan, Y and Gao, S and Wang, B and Chen, Z and Wang, X and Sun, H and Jiang, B and Dong, Y and Zhou, Z}, title = {Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient.}, journal = {Environmental microbiology reports}, volume = {15}, number = {6}, pages = {545-556}, pmid = {37537784}, issn = {1758-2229}, support = {2022JH2/101300155//Applied Basic Research Project of Liaoning Province/ ; 2022XTCX0504//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2021RT08//Innovation and Entrepreneurship Program for High-level Talent of Dalian/ ; 2021921071//Liaoning BaiQianWan Talents Program/ ; }, mesh = {*Archaea/genetics ; Salinity ; Prokaryotic Cells ; Seawater ; *Microbiota ; Sodium Chloride ; }, abstract = {Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.}, }
@article {pmid37537681, year = {2023}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Sepo, E and Gómez Expósito, R and Chiorato, AF and Mendes, R and Tsai, SM and Carrión, VJ}, title = {Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {68}, pmid = {37537681}, issn = {2524-6372}, support = {2014/03217-3, 2015/00251-9, 2020/00469-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 408191/2018-0, 307670/2021-0, 302591/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.185941/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.<br><br>RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.<br><br>CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.}, }
@article {pmid37535084, year = {2023}, author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW}, title = {Correction to: Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2183}, doi = {10.1007/s00248-023-02281-z}, pmid = {37535084}, issn = {1432-184X}, }
@article {pmid37535083, year = {2023}, author = {Šaraba, V and Milovanovic, J and Nikodinovic-Runic, J and Budin, C and de Boer, T and Ciric, M}, title = {Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2747-2755}, pmid = {37535083}, issn = {1432-184X}, mesh = {*Cellulose/metabolism ; Ecosystem ; Plastics ; Bacteria ; *Groundwater ; }, abstract = {The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3-Na + K and HCO3-Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.}, }
@article {pmid37533451, year = {2023}, author = {Pandey, S and Kim, ES and Cho, JH and Song, M and Doo, H and Kim, S and Keum, GB and Kwak, J and Ryu, S and Choi, Y and Kang, J and Lee, JJ and Kim, HB}, title = {Swine gut microbiome associated with non-digestible carbohydrate utilization.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1231072}, pmid = {37533451}, issn = {2297-1769}, abstract = {Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.}, }
@article {pmid37532947, year = {2023}, author = {Jabir, T and Jain, A and Vipindas, PV and Krishnan, KP}, title = {Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2733-2746}, pmid = {37532947}, issn = {1432-184X}, mesh = {*Estuaries ; *Water ; Svalbard ; Nitrogen Fixation/genetics ; Nitrogen ; Stochastic Processes ; }, abstract = {Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3[+]) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.}, }
@article {pmid37531050, year = {2023}, author = {Zhang, D and Sun, J and Wang, D and Peng, S and Wang, Y and Lin, X and Yang, X and Hua, Q and Wu, P}, title = {Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {41}, pages = {94347-94360}, pmid = {37531050}, issn = {1614-7499}, support = {BK20201110//Natural Science Foundation of Jiangsu Province/ ; 2021BEE02025//Key Research and Development Program of Ningxia/ ; NMKJXM202009//Science and Technology Major Project of Inner Mongolia/ ; }, mesh = {Animals ; Swine ; *Mycobiome ; Manure/microbiology ; Chickens/genetics ; *Composting ; RNA, Ribosomal, 16S ; Soil ; Bacteria/genetics ; *Actinomycetales/genetics ; }, abstract = {Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.}, }
@article {pmid37528183, year = {2023}, author = {Wang, L and Wang, J and Yuan, J and Tang, Z and Wang, J and Zhang, Y}, title = {Long-Term Organic Fertilization Strengthens the Soil Phosphorus Cycle and Phosphorus Availability by Regulating the pqqC- and phoD-Harboring Bacterial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2716-2732}, pmid = {37528183}, issn = {1432-184X}, mesh = {*Soil/chemistry ; *Phosphorus/metabolism ; Fertilizers/analysis ; Carbon ; Bacteria/genetics/metabolism ; Soil Microbiology ; Minerals ; Fertilization ; }, abstract = {The pqqC and phoD genes encode pyrroloquinoline quinone synthase and alkaline phosphomonoesterase (ALP), respectively. These genes play a crucial role in regulating the solubilization of inorganic phosphorus (Pi) and the mineralization of organic phosphorus (Po), making them valuable markers for P-mobilizing bacterial. However, there is limited understanding of how the interplay between soil P-mobilizing bacterial communities and abiotic factors influences P transformation and availability in the context of long-term fertilization scenarios. We used real-time polymerase chain reaction and high-throughput sequencing to explore the characteristics of soil P-mobilizing bacterial communities and their relationships with key physicochemical properties and P fractions under long-term fertilization scenarios. In a 38-year fertilization experiment, six fertilization treatments were selected. These treatments were sorted into three groups: the non-P-amended group, including no fertilization and mineral NK fertilizer; the sole mineral-P-amended group, including mineral NP and NPK fertilizer; and the organically amended group, including sole organic fertilizer and organic fertilizer plus mineral NPK fertilizer. The organically amended group significantly increased soil labile P (Ca2-P and enzyme-P) and Olsen-P content and proportion but decreased non-labile P (Ca10-P) proportion compared with the sole mineral-P-amended group, indicating enhanced P availability in the soil. Meanwhile, the organically amended group significantly increased soil ALP activity and pqqC and phoD gene abundances, indicating that organic fertilization promotes the activity and abundance of microorganisms involved in P mobilization processes. Interestingly, the organically amended group dramatically reshaped the community structure of P-mobilizing bacteria and increased the relative abundance of Acidiphilium, Panacagrimonas, Hansschlegelia, and Beijerinckia. These changes had a greater positive impact on ALP activity, labile P, and Olsen-P content compared to the abundance of P-mobilizing genes alone, indicating their importance in driving P mobilization processes. Structural equation modeling indicated that soil organic carbon and Po modulated the relationship between P-mobilizing bacterial communities and labile P and Olsen-P, highlighting the influence of SOC and Po on the functioning of P-mobilizing bacteria and their impact on P availability. Overall, our study demonstrates that organic fertilization has the potential to reshape the structure of P-mobilizing bacterial communities, leading to increased P mobilization and availability in the soil. These findings contribute to our understanding of the mechanisms underlying P cycling in agricultural systems and provide valuable insights for enhancing microbial P mobilization through organic fertilization.}, }
@article {pmid37527741, year = {2023}, author = {Antonelli, P and Peruzzo, A and Mancin, M and Boscolo Anzoletti, A and Dall'Ara, S and Orsini, M and Bordin, P and Arcangeli, G and Zanolin, B and Barco, L and Losasso, C}, title = {Tetrodotoxin in bivalve mollusks: An integrated study towards the comprehension of the influencing factors of a newly native phenomenon.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139682}, doi = {10.1016/j.chemosphere.2023.139682}, pmid = {37527741}, issn = {1879-1298}, mesh = {Animals ; Tetrodotoxin/toxicity ; *Tandem Mass Spectrometry ; Comprehension ; *Bivalvia ; Neurotoxins ; Phytoplankton ; }, abstract = {Tetrodotoxins (TTXs) are potent neurotoxins named after the Tetraodontidae fish family. The ingestion of TTX-contaminated flesh can cause neurotoxic symptoms and can lead to death. In 2017 symptoms the European Food Safety Authority (EFSA) recognized the threat to food safety resulting from TTX exposure via food consumption and, thus, proposed a safety limit of 44 μg/kg of TTX in marine gastropods and bivalves. To date, however, TTXs have not yet been included in the list of biotoxins to be monitored within the European Union, even though, in a few cases, levels of TTX found were higher than the EFSA limit. The origin of TTX production is debated and the roles of both biotic and abiotic factors on TTX-mediated toxic events remain unclear. In order to meet these knowledge requests the present study was aimed to investigate the role of seawater temperature, pH, water conductivity, and oxygen saturation, along with the marine phytoplankton community and the bacterial community of mussels and oysters on the accumulation of TTX and analogues in the bivalves. Abiotic parameters were measured by means of a multi-parametric probe, phytoplankton community was analyzed by optic microscopy while microbial community was described by amplicon metataxonomic sequencing, TTXs concentration in the collected matrices were measured by HILIC-MS/MS. A possible role of seawater pH and temperature, among the investigated abiotic factors, in regulating the occurrence of TTXs was found. Regarding biotic variables, a possible influence of Vibrio, Shewanella and Flavobacteriaceae in the occurrence of TTXs was found. Concurrently, Prorocentrum cordatum cell numbers were correlated to the incidence of TTX in mussels. The results herein collected suggest that environmental variables play a consistent part in the occurrence of TTX in the edible bivalve habitats, and there are also indications of a potential role played by specific bacteria taxa in association with phytoplankton.}, }
@article {pmid37527740, year = {2023}, author = {Wang, Y and Gao, Y and Lu, X and Gadow, SI and Zhuo, G and Hu, W and Song, Y and Zhen, G}, title = {Bioelectrochemical anaerobic membrane bioreactor enables high methane production from methanolic wastewater: Roles of microbial ecology and microstructural integrity of anaerobic biomass.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139676}, doi = {10.1016/j.chemosphere.2023.139676}, pmid = {37527740}, issn = {1879-1298}, mesh = {*Wastewater ; *Methanol ; Sewage/chemistry ; Anaerobiosis ; Biomass ; Methane/metabolism ; Bioreactors ; Waste Disposal, Fluid ; Membranes, Artificial ; }, abstract = {The disintegration of anaerobic sludge and blockage of membrane pores has impeded the practical application of anaerobic membrane bioreactor (AnMBR) in treating methanolic wastewater. In this study, bioelectrochemical system (BES) was integrated into AnMBR to alleviate sludge dispersion and membrane fouling as well as enhance bioconversion of methanol. Bioelectrochemical regulation effect induced by BES enhanced methane production rate from 4.94 ± 0.52 to 5.39 ± 0.37 L/Lreactor/d by accelerating the enrichment of electroactive microorganisms and the agglomeration of anaerobic sludge via the adhesive and chemical bonding force. 16 S rRNA gene high-throughput sequencing demonstrated that bioelectrochemical stimulation had modified the metabolic pathways by regulating the key functional microbial communities. Methanogenesis via the common methylotrophic Methanomethylovorans was partially substituted by the hydrogenotrophic Candidatus_Methanofastidiosum, etc. The metabolic behaviors of methanol are bioelectrochemistry-dependent, and controlling external voltage is thus an effective strategy for ensuring robust electron transfer, low membrane fouling, and long-term process stability.}, }
@article {pmid37525505, year = {2024}, author = {Effelsberg, N and Kobusch, I and Schollenbruch, H and Linnemann, S and Bang, C and Franke, A and Köck, R and Boelhauve, M and Mellmann, A}, title = {Pilot study on nasal microbiota dynamics and MRSA carriage of a pig cohort housed on straw bedding.}, journal = {Molecular microbiology}, volume = {122}, number = {3}, pages = {403-412}, doi = {10.1111/mmi.15136}, pmid = {37525505}, issn = {1365-2958}, support = {01KI2009A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01KI2009B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification ; Swine ; *Staphylococcal Infections/microbiology ; *Microbiota ; *Housing, Animal ; *RNA, Ribosomal, 16S/genetics ; *Carrier State/microbiology ; *Nose/microbiology ; Pilot Projects ; Bedding and Linens/microbiology ; Swine Diseases/microbiology ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing-in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA-negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow-up study including two different husbandry systems to further assess these effects.}, }
@article {pmid37523041, year = {2024}, author = {Li, S and Young, T and Archer, S and Lee, K and Alfaro, AC}, title = {Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {571-580}, pmid = {37523041}, issn = {1618-1905}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Perna ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Bacteria/genetics ; }, abstract = {Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.}, }
@article {pmid37520283, year = {2023}, author = {Wentzien, NM and Fernández-González, AJ and Villadas, PJ and Valverde-Corredor, A and Mercado-Blanco, J and Fernández-López, M}, title = {Thriving beneath olive trees: The influence of organic farming on microbial communities.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {3575-3589}, pmid = {37520283}, issn = {2001-0370}, abstract = {Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10[6] ± 1.62 × 10[5] (CM) to 4.54 × 10[6] ± 8.07 × 10[5] (OM) copies of the 18 S rRNA gene g[-1] soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.}, }
@article {pmid37516570, year = {2023}, author = {Parizadeh, M and Arrieta, MC}, title = {The global human gut microbiome: genes, lifestyles, and diet.}, journal = {Trends in molecular medicine}, volume = {29}, number = {10}, pages = {789-801}, doi = {10.1016/j.molmed.2023.07.002}, pmid = {37516570}, issn = {1471-499X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria ; *Microbiota ; Diet ; Life Style ; }, abstract = {A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.}, }
@article {pmid37515622, year = {2023}, author = {Mi, JX and Liu, KL and Ding, WL and Zhang, MH and Wang, XF and Shaukat, A and Rehman, MU and Jiao, XL and Huang, SC}, title = {Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {41}, pages = {93731-93743}, pmid = {37515622}, issn = {1614-7499}, support = {No. 32202876//National Natural Science Foundation of China/ ; No. 30501374//Special Support Fund for High-level Talents of Henan Agricultural University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Wetlands ; Ecosystem ; RNA, Ribosomal, 16S ; *Anseriformes ; Birds ; Ducks ; China ; }, abstract = {The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.}, }
@article {pmid37512939, year = {2023}, author = {Mourgela, RN and Kioukis, A and Pourjam, M and Lagkouvardos, I}, title = {Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512939}, issn = {2076-2607}, abstract = {The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.}, }
@article {pmid37512925, year = {2023}, author = {St-Pierre, B and Perez Palencia, JY and Samuel, RS}, title = {Impact of Early Weaning on Development of the Swine Gut Microbiome.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512925}, issn = {2076-2607}, support = {Hatch projects SD00H719-20 and SD00H682-19//South Dakota State University Agricultural Experiment Station / USDA National Institute of Food and Agriculture/ ; }, abstract = {Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.}, }
@article {pmid37512843, year = {2023}, author = {Cowan, DA and Cary, SC and DiRuggiero, J and Eckardt, F and Ferrari, B and Hopkins, DW and Lebre, PH and Maggs-Kölling, G and Pointing, SB and Ramond, JB and Tribbia, D and Warren-Rhodes, K}, title = {'Follow the Water': Microbial Water Acquisition in Desert Soils.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512843}, issn = {2076-2607}, support = {80256//National Research Foundation/ ; }, abstract = {Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.}, }
@article {pmid37511881, year = {2023}, author = {Walther-Antonio, M and Schulze-Makuch, D}, title = {The Hypothesis of a "Living Pulse" in Cells.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {37511881}, issn = {2075-1729}, abstract = {Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.}, }
@article {pmid37511821, year = {2023}, author = {Schulze-Makuch, D and Irwin, LN}, title = {Life Unknown: Preliminary Scheme for a Magnetotrophic Organism.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {37511821}, issn = {2075-1729}, abstract = {No magnetotrophic organism on Earth is known to use magnetic fields as an energy source or the storage of information. However, a broad diversity of life forms is sensitive to magnetic fields and employs them for orientation and navigation, among other purposes. If the magnetic field strength were much larger, such as that on planets around neutron stars or magnetars, metabolic energy could be obtained from these magnetic fields in principle. Here, we introduce three hypothetical models of magnetotrophic organisms that obtain energy via the Lorentz force. Even if an organism uses magnetic fields only as an energy source, but otherwise is relying on biochemistry, this organism would be by definition a magnetotrophic form of life as we do not know it.}, }
@article {pmid37511182, year = {2023}, author = {Turbant, F and Waeytens, J and Blache, A and Esnouf, E and Raussens, V and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511182}, issn = {1422-0067}, support = {101004806//Trans-National Access (TNA) of Molecular-Scale Biophysics Research Infrastructure (MOSBRI)/ ; 08254//IEA/PICS CNRS/ ; ANR-11-IDEX-0003-02//Investissements d'Avenir &#xbb; program, through the "ADI 2021 Paris Saclay/ ; 2016/21/N/NZ1/02850//National Science Center Poland/ ; 531-D020-D242-23//University of Gdansk/ ; }, mesh = {Escherichia coli/genetics/metabolism ; Circular Dichroism ; *Escherichia coli Proteins/genetics/metabolism ; *RNA, Small Untranslated/genetics ; Host Factor 1 Protein/genetics/metabolism ; RNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; }, abstract = {The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.}, }
@article {pmid37509218, year = {2023}, author = {Li, G and Jin, Y and Chen, B and Lin, A and Wang, E and Xu, F and Hu, G and Xiao, C and Liu, H and Hou, X and Zhang, B and Song, J}, title = {Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations.}, journal = {Cancers}, volume = {15}, number = {14}, pages = {}, pmid = {37509218}, issn = {2072-6694}, support = {Nos. 81873553//National Natural Science Foundation of China/ ; Nos. 81800465//National Natural Science Foundation of China/ ; }, abstract = {The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.}, }
@article {pmid37507629, year = {2024}, author = {Daba, G and Daelemans, R and Berecha, G and Geerinck, MWJ and Verreth, C and Crauwels, S and Lievens, B and Honnay, O}, title = {Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {525-534}, pmid = {37507629}, issn = {1618-1905}, mesh = {*Coffea/genetics/microbiology ; Ethiopia ; *Basidiomycota/genetics ; Polymorphism, Genetic ; Plant Diseases/microbiology ; }, abstract = {Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.}, }
@article {pmid37507489, year = {2023}, author = {Daraz, U and Erhunmwunse, AS and Dubeux, JCB and Mackowiak, C and Guerra, VA and Hsu, CM and Ma, J and Li, Y and Yang, X and Liao, HL and Wang, XB}, title = {Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2703-2715}, pmid = {37507489}, issn = {1432-184X}, mesh = {*Soil ; Seasons ; *Arachis/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.}, }
@article {pmid37507488, year = {2023}, author = {Gonçalves, OS and Santana, MF}, title = {Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2687-2702}, pmid = {37507488}, issn = {1432-184X}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; *Grassland ; Bacteria ; Genomics ; Soil Microbiology ; Phylogeny ; }, abstract = {One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.}, }
@article {pmid37507453, year = {2023}, author = {Villela, H and Modolon, F and Schultz, J and Delgadillo-Ordoñez, N and Carvalho, S and Soriano, AU and Peixoto, RS}, title = {Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12273}, pmid = {37507453}, issn = {2045-2322}, mesh = {*Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Petroleum/metabolism ; Bacteria/genetics ; Alkanes/metabolism ; Biodegradation, Environmental ; }, abstract = {Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.}, }
@article {pmid37507436, year = {2023}, author = {Melaugh, G and Martinez, VA and Baker, P and Hill, PJ and Howell, PL and Wozniak, DJ and Allen, RJ}, title = {Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {52}, pmid = {37507436}, issn = {2055-5008}, support = {BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI077628/AI/NIAID NIH HHS/United States ; R01 AI134895/AI/NIAID NIH HHS/United States ; R01 AI143916/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms ; *Pseudomonas aeruginosa ; Polysaccharides, Bacterial/metabolism ; DNA ; }, abstract = {Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.}, }
@article {pmid37505287, year = {2023}, author = {Feckler, A and Baudy-Groh, P and Friedrichs, L and Gonçalves, S and Lüderwald, S and Risse-Buhl, U and Bundschuh, M}, title = {Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2674-2686}, pmid = {37505287}, issn = {1432-184X}, support = {2017-0507//Vetenskapsr&#xe5;det/ ; }, mesh = {*Diatoms/metabolism ; Fungi/metabolism ; Rivers ; Plant Leaves/microbiology ; Carbon/metabolism ; Ecosystem ; }, abstract = {Heterotrophic microbial decomposers colonize submerged leaf litter in close spatial proximity to periphytic algae that exude labile organic carbon during photosynthesis. These exudates are conjectured to affect microbial decomposers' abundance, resulting in a stimulated (positive priming) or reduced (negative priming) leaf litter decomposition. Yet, the occurrence, direction, and intensity of priming associated with leaf material of differing recalcitrance remains poorly tested. To assess priming, we submerged leaf litter of differing recalcitrance (Alnus glutinosa [alder; less recalcitrant] and Fagus sylvatica [beech; more recalcitrant]) in microcosms and quantified bacterial, fungal, and diatom abundance as well as leaf litter decomposition over 30 days in absence and presence of light. Diatoms did not affect beech decomposition but reduced alder decomposition by 20% and alder-associated fungal abundance by 40% in the treatments including all microbial groups and light, thus showing negative priming. These results suggest that alder-associated heterotrophs acquired energy from diatom exudates rather than from leaf litter. Moreover, it is suggested that these heterotrophs have channeled energy to alternative (reproductive) pathways that may modify energy and nutrient availability for the remaining food web and result in carbon pools protected from decomposition in light-exposed stream sections.}, }
@article {pmid37505057, year = {2024}, author = {Choudhary, M and Minsavage, GV and Goss, EM and Timilsina, S and Coutinho, TA and Vallad, GE and Paret, ML and Jones, JB}, title = {Whole-Genome-Sequence-Based Classification of Xanthomonas euvesicatoria pv. eucalypti and Computational Analysis of the Type III Secretion System.}, journal = {Phytopathology}, volume = {114}, number = {1}, pages = {47-60}, doi = {10.1094/PHYTO-05-23-0150-R}, pmid = {37505057}, issn = {0031-949X}, mesh = {Type III Secretion Systems ; Phylogeny ; *Eucalyptus ; Plant Diseases/microbiology ; *Xanthomonas ; }, abstract = {Xanthomonas spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as X. perforans. However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized X. euvesicatoria pv. perforans (Xp) strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the Eucalyptus strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the Eucalyptus strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. They formed separate clades, which included X. euvesicatoria pv. alangii, X. euvesicatoria pv. citrumelonis, and X. euvesicatoria pv. alfalfae. Based on ANI, phylogenetic relationships, and pathogenicity, we designated these Eucalyptus strains as X. euvesicatoria pv. eucalypti (Xee). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic Xp and Xeu strains, was absent in the Xee strains. Comparison of the hrp clusters of Xee, Xp, and Xeu genomes revealed that HrpE in Xee strains was very different from that in Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in Xanthomonas spp., in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.}, }
@article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1619-1633}, pmid = {37500801}, issn = {2058-5276}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, }
@article {pmid37496156, year = {2022}, author = {Wolfsberger, W and Chhugani, K and Shchubelka, K and Frolova, A and Salyha, Y and Zlenko, O and Arych, M and Dziuba, D and Parkhomenko, A and Smolanka, V and Gümüş, ZH and Sezgin, E and Diaz-Lameiro, A and Toth, VR and Maci, M and Bortz, E and Kondrashov, F and Morton, PM and Łabaj, PP and Romero, V and Hlávka, J and Mangul, S and Oleksyk, TK}, title = {Scientists without borders: lessons from Ukraine.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37496156}, issn = {2047-217X}, support = {R33 CA263705/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Ukraine ; *Armed Conflicts ; *Science ; }, abstract = {Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.}, }
@article {pmid37491575, year = {2023}, author = {Kim, JM and Yoo, SY and An, JS and Woo, JJ and Cho, YD and Park, HE and Karm, MH}, title = {Effect of a multichannel oral irrigator on periodontal health and the oral microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12043}, pmid = {37491575}, issn = {2045-2322}, mesh = {Humans ; Administration, Oral ; Dental Plaque Index ; *Microbiota ; *Periodontal Diseases ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Oral biofilms or dental plaques are one of the major etiological factors for diverse oral diseases. We aimed to evaluate the effect of a multichannel oral irrigator (MCOI) on periodontal health in 29 participants randomly divided into two groups: the MCOI group and the control group. To evaluate the effect of the MCOI on periodontal health, the modified Quigley Hein Plaque Index (PI), Mühlemann-Son Sulcus Bleeding Index (SBI), bleeding on probing (BOP), and swelling were evaluated and compared before and after MCOI use for 3 days. Although PI and SBI showed statistically significant increases in the control group, the MCOI group showed no significant changes in either parameter. Moreover, the percentage of BOP was significantly lower in the MCOI group. Saliva samples were analyzed by 16s rRNA amplicon sequencing to investigate changes in the oral microbiome. Sequencing results showed that Porphyromonas spp. were significantly increased in the control group, whereas no significant change was detected in the MCOI group. Using the MCOI, enriched populations and functional pathways were detected in pioneer species comprising non-mutans streptococci. These findings provide evidence of the effectiveness of the MCOI in maintaining periodontal health and a healthy microbial ecology in the oral cavity.}, }
@article {pmid37486583, year = {2023}, author = {Zaman, R and Antonioli, F and Shah, A and Ullah, A and May, C and Klutsch, JG and Erbilgin, N}, title = {A Pine in Distress: How Infection by Different Pathogenic Fungi Affect Lodgepole Pine Chemical Defenses.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2666-2673}, pmid = {37486583}, issn = {1432-184X}, mesh = {Animals ; *Pinus/microbiology ; *Coleoptera/microbiology ; *Weevils ; Canada ; Terpenes ; }, abstract = {In North America, lodgepole pine is frequently subjected to attacks by various biotic agents that compromise its ability to defend against subsequent attacks by insect herbivores. We investigated whether infections of lodgepole pine by different pathogenic fungal species have varying effects on its defense chemistry. We selected two common pathogens, Atropellis canker, Atropellis piniphila, and western gall rust, Endocronartium harknessii, affecting mature lodgepole pine trees in western Canada. We also included three ophiostomatoid fungi Grosmannia clavigera, Ophiostoma montium, and Leptographium longiclavatum associated with the mountain pine beetle (Dendroctonus ponderosae), because they are commonly used to investigate induced defenses of host trees of bark beetles. We collected phloem samples from lodgepole pines infected with the rust or the canker and healthy lodgepole pines in the same stand. We also inoculated mature lodgepole pines with the three fungal symbionts and collected phloem samples 2 weeks later when the defense chemistry was at its highest level. Different fungal species differentially altered the terpene chemistry of lodgepole pine trees. E. harknessii and the fungal symbionts altered the terpene chemistry in a similar pattern while trees responded to the infection by the A. piniphila differently. Our study highlights the importance of considering specific biotic stress agents in tree susceptibility or resistance to the subsequent attacks by insect herbivores, such as mountain pine beetle.}, }
@article {pmid37485515, year = {2023}, author = {Němečková, K and Mareš, J and Procházková, L and Culka, A and Košek, F and Wierzchos, J and Nedbalová, L and Dudák, J and Tymlová, V and Žemlička, J and Kust, A and Zima, J and Nováková, E and Jehlička, J}, title = {Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175066}, pmid = {37485515}, issn = {1664-302X}, abstract = {In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.}, }
@article {pmid37485507, year = {2023}, author = {Thiele, S and Vader, A and Thomson, S and Saubrekka, K and Petelenz, E and Müller, O and Bratbak, G and Øvreås, L}, title = {Seasonality of the bacterial and archaeal community composition of the Northern Barents Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213718}, pmid = {37485507}, issn = {1664-302X}, abstract = {The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.}, }
@article {pmid37485503, year = {2023}, author = {Van Holm, W and Lauwens, K and De Wever, P and Schuermans, A and Zayed, N and Pamuk, F and Saghi, M and Fardim, P and Bernaerts, K and Boon, N and Teughels, W}, title = {Probiotics for oral health: do they deliver what they promise?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1219692}, pmid = {37485503}, issn = {1664-302X}, abstract = {Probiotics have demonstrated oral health benefits by influencing the microbiome and the host. Although promising, their current use is potentially constrained by several restrictions. One such limiting factor lies in the prevailing preparation of a probiotic product. To commercialize the probiotic, a shelf stable product is achieved by temporarily inactivating the live probiotic through drying or freeze drying. Even though a lyophilized probiotic can be kept dormant for an extended period of time, their viability can be severely compromised, making their designation as probiotics questionable. Additionally, does the application of an inactive probiotic directly into the oral cavity make sense? While the dormancy may allow for survival on its way towards the gut, does it affect their capacity for oral colonisation? To evaluate this, 21 probiotic product for oral health were analysed for the number of viable (probiotic), culturable (CFU) and dead (postbiotic) cells, to verify whether the commercial products indeed contain what they proclaim. After isolating and uniformly lyophilizing three common probiotic species in a simple yet effective lyoprotective medium, the adhesion to saliva covered hydroxyapatite discs of lyophilized probiotics was compared to fresh or reactivated lyophilized probiotics. Unfortunately, many of the examined products failed to contain the claimed amounts of viable cells, but also the strains used were inadequately characterized and lacked clinical evidence for that unknown strain, questioning their label of a 'probiotic'. Additionally, lyophilized probiotics demonstrated low adhesive capacity compared to their counterparts, prompting the question of why fresh or reactivated probiotics are not currently used.}, }
@article {pmid37482337, year = {2023}, author = {Santás-Miguel, V and Arias-Estévez, M and Rodríguez-Seijo, A and Arenas-Lago, D}, title = {Use of metal nanoparticles in agriculture. A review on the effects on plant germination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122222}, doi = {10.1016/j.envpol.2023.122222}, pmid = {37482337}, issn = {1873-6424}, mesh = {*Metal Nanoparticles/toxicity ; Silver/toxicity ; Agriculture/methods ; Soil ; *Nanoparticles ; Nanotechnology ; Germination ; }, abstract = {Agricultural nanotechnology has become a powerful tool to help crops and improve agricultural production in the context of a growing world population. However, its application can have some problems with the development of harvests, especially during germination. This review evaluates nanoparticles with essential (Cu, Fe, Ni and Zn) and non-essential (Ag and Ti) elements on plant germination. In general, the effect of nanoparticles depends on several factors (dose, treatment time, application method, type of nanoparticle and plant). In addition, pH and ionic strength are relevant when applying nanoparticles to the soil. In the case of essential element nanoparticles, Fe nanoparticles show better results in improving nutrient uptake, improving germination, and the possibility of magnetic properties could favor their use in the removal of pollutants. In the case of Cu and Zn nanoparticles, they can be beneficial at low concentrations, while their excess presents toxicity and negatively affects germination. About nanoparticles of non-essential elements, both Ti and Ag nanoparticles can be helpful for nutrient uptake. However, their potential effects depend highly on the crop type, particle size and concentration. Overall, nanotechnology in agriculture is still in its early stages of development, and more research is needed to understand potential environmental and public health impacts.}, }
@article {pmid37482010, year = {2023}, author = {Pan, Y and Sun, RZ and Wang, Y and Chen, GL and Fu, YY and Yu, HQ}, title = {Carbon source shaped microbial ecology, metabolism and performance in denitrification systems.}, journal = {Water research}, volume = {243}, number = {}, pages = {120330}, doi = {10.1016/j.watres.2023.120330}, pmid = {37482010}, issn = {1879-2448}, mesh = {*Carbon/chemistry ; *Denitrification ; Methanol ; Glycerol ; Bioreactors/microbiology ; Acetates ; Glucose ; Nitrogen/metabolism ; Nitrates/metabolism ; }, abstract = {The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.}, }
@article {pmid37482007, year = {2023}, author = {Wang, M and Wang, X and Zhou, S and Chen, Z and Chen, M and Feng, S and Li, J and Shu, W and Cao, B}, title = {Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem.}, journal = {Water research}, volume = {243}, number = {}, pages = {120343}, doi = {10.1016/j.watres.2023.120343}, pmid = {37482007}, issn = {1879-2448}, mesh = {*Ecosystem ; Mining ; *Microbiota ; Microbial Consortia ; Fresh Water ; Iron ; }, abstract = {Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.}, }
@article {pmid37480518, year = {2023}, author = {O'Brien, L and Siboni, N and Seymour, JR and Balzer, M and Mitrovic, S}, title = {Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2642-2654}, pmid = {37480518}, issn = {1432-184X}, mesh = {*Rivers/chemistry ; *Carbon ; Ecosystem ; Water ; Bacteria/genetics ; }, abstract = {Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.}, }
@article {pmid37480517, year = {2023}, author = {Aguado-López, D and Bartolomé, C and Lopes, AR and Henriques, D and Segura, SK and Maside, X and Pinto, MA and Higes, M and Martín-Hernández, R}, title = {Frequent Parasitism of Apis mellifera by Trypanosomatids in Geographically Isolated Areas with Restricted Beekeeping Movements.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2655-2665}, pmid = {37480517}, issn = {1432-184X}, support = {project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; Grant no. PRE2018-084878, RTA2017-00004-C02-01//Ministerio de Asuntos Econ&#xf3;micos y Transformaci&#xf3;n Digital/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/143627/2019//Funda&#xe7;ao para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0007/2021//SusTEC/ ; INCRECYT program//European Social Funds/ ; }, mesh = {Animals ; Bees ; *Beekeeping ; *Trypanosomatina/genetics/parasitology ; Crithidia/genetics/parasitology ; Symbiosis ; Azores ; }, abstract = {Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae did not shown any significant correlation with the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A high-throughput sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.}, }
@article {pmid37479828, year = {2023}, author = {Ravindhiran, R and Sivarajan, K and Sekar, JN and Murugesan, R and Dhandapani, K}, title = {Listeria monocytogenes an Emerging Pathogen: a Comprehensive Overview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial Interventions.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2231-2251}, pmid = {37479828}, issn = {1432-184X}, mesh = {Animals ; Humans ; *Listeria monocytogenes/genetics ; *Listeria ; Virulence ; Food Microbiology ; *Listeriosis/diagnosis/epidemiology/microbiology ; Virulence Factors/genetics ; }, abstract = {Listeria monocytogenes, the third most deleterious zoonotic pathogen, is a major causative agent of animal and human listeriosis, an infection related to the consumption of contaminated food products. Even though, this pathogen has been responsible for the outbreaks of foodborne infections in the early 1980s, the major outbreaks have been reported during the past two decades. Listeriosis infection in the host is a rare but life-threatening disease with major public health and economic implications. Extensive reports on listeriosis outbreaks are associated with milk and milk products, meat and meat products, and fresh produce. This bacterium can adapt to any environmental and stress conditions, making it a prime causative agent for major foodborne diseases. The pathogen could survive an antibiotic treatment and persist in the host cell, thereby escaping the standard diagnostic practices. The current review strives to provide concise information on the epidemiology, serotypes, and pathogenesis of the L. monocytogenes to decipher the knowledge on the endurance of the pathogen inside the host and food products as a vehicle for Listeria contaminations. In addition, various detection methods for Listeria species from food samples and frontline regimens of L. monocytogenes treatment have also been discussed.}, }
@article {pmid37479827, year = {2023}, author = {Hirata, K and Asahi, T and Kataoka, K}, title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2627-2641}, pmid = {37479827}, issn = {1432-184X}, mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome ; *Gryllidae ; RNA, Ribosomal, 16S/genetics ; *Cricket Sport ; Bacteria/genetics ; }, abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.}, }
@article {pmid37478594, year = {2023}, author = {Tang, Y and Wang, C and Holm, PE and Hansen, HCB and Brandt, KK}, title = {Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132067}, doi = {10.1016/j.jhazmat.2023.132067}, pmid = {37478594}, issn = {1873-3336}, mesh = {Humans ; Copper/toxicity ; *Trace Elements ; Biological Availability ; *Soil Pollutants/metabolism ; Charcoal ; Soil ; Triticum/metabolism ; }, abstract = {Trace element polluted soils pose risks to human and environmental health. Biochar can decrease trace element bioavailability in soils, but their resulting ability to reduce soil toxicity may vary significantly depending on feedstocks used, pyrolysis conditions, and the target pollutants. Chromated copper arsenate (CCA) polluted sites are common, but only very few types of biochar have been tested for these sites. Hence, we tested fourteen well-characterized biochar materials for their ability to bind Cu and reduce toxicity in a CCA polluted soil in a 56-day experiment. Biochar (1%, wt/wt) increased plant (wheat, Triticum aestivum L.) shoot and root growth by 6-58% and 0-73%, reduced soil toxicity to Arthrobacter globiformis by 7-55%, decreased bioavailable Cu (Pseudomonas fluorescens bioreporter) by 5-65%, and decreased free Cu[2+] ion activities by 27-89%. The A. globiformis solid-contact test constituted a sensitive ecotoxicological endpoint and deserves further attention for assessment of soil quality. Oil seed rape straw biochar generally performed better than other tested biochar materials. Biochar performance was positively correlated with its high cation exchange capacity, multiple surface functional groups, and high nitrogen and phosphorus content. Our results pave the way for future selection of feedstocks for creation of modified biochar materials with optimal performance in CCA polluted soil.}, }
@article {pmid37476672, year = {2023}, author = {Zhang, Y and Wang, R}, title = {The human gut phageome: composition, development, and alterations in disease.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213625}, pmid = {37476672}, issn = {1664-302X}, abstract = {The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.}, }
@article {pmid37474781, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH}, title = {Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {9}, number = {8}, pages = {1207-1220}, pmid = {37474781}, issn = {2055-0278}, mesh = {*Ecosystem ; *Zosteraceae/genetics ; Canada ; Phylogeography ; Oceans and Seas ; }, abstract = {Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.}, }
@article {pmid37470815, year = {2023}, author = {Lee, K and Bogdanova, A and Missaoui, A}, title = {Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2618-2626}, pmid = {37470815}, issn = {1432-184X}, mesh = {Endophytes/genetics ; *Lolium/genetics/microbiology ; *Epichloe/genetics ; Poaceae ; Seeds/microbiology ; *Festuca/microbiology ; }, abstract = {Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.}, }
@article {pmid37469593, year = {2023}, author = {Riedel, T and Bunk, B and Schröttner, P}, title = {Editorial: Characterization of rare and recently first described human pathogenic bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1212627}, pmid = {37469593}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/genetics ; *Genome, Bacterial ; }, }
@article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1789-1792}, pmid = {37468677}, issn = {1751-7370}, support = {863664/ERC_/European Research Council/International ; }, mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, }
@article {pmid37466247, year = {2024}, author = {Avasthi, I and Lerner, H and Grings, J and Gräber, C and Schleheck, D and Cölfen, H}, title = {Biodegradable Mineral Plastics.}, journal = {Small methods}, volume = {8}, number = {4}, pages = {e2300575}, doi = {10.1002/smtd.202300575}, pmid = {37466247}, issn = {2366-9608}, support = {//Carl-Zeiss Foundation/ ; }, abstract = {Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.}, }
@article {pmid37461605, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37461605}, issn = {2693-5015}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, abstract = {BACKGROUND: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).<br><br>RESULTS: The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including &#x3b2;-lactone and type III polyketide synthase (T3PKS) clusters.<br><br>CONCLUSIONS: Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (=NRRL B-65660[T]), Leifsonia virtsii, F6_8S_P_1A[T] (=NRRL B-65661[T]), Leifsonia williamsii, F6_8S_P_1B[T] (=NRRL B- 65662[T] and DSMZ 115932[T]), Paenibacillus vandeheii, F6_3S_P_1C[T](=NRRL B-65663[T] and DSMZ 115940[T]), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664[T] and DSMZ 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, }
@article {pmid37459919, year = {2023}, author = {Wang, L and Zhu, L and Liang, C and Huang, X and Liu, Z and Huo, J and Zhang, Y and Zhang, Y and Chen, L and Xu, H and Li, X and Xu, L and Kuang, M and Wong, CC and Yu, J}, title = {Targeting N6-methyladenosine reader YTHDF1 with siRNA boosts antitumor immunity in NASH-HCC by inhibiting EZH2-IL-6 axis.}, journal = {Journal of hepatology}, volume = {79}, number = {5}, pages = {1185-1200}, doi = {10.1016/j.jhep.2023.06.021}, pmid = {37459919}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: RNA N[6]-methyladenosine (m[6]A) reader protein YTHDF1 has been implicated in cancer; however, its role in hepatocellular carcinoma (HCC), especially in non-alcoholic steatohepatitis-associated HCC (NASH-HCC), remains unknown. Here, we investigated the functional role of YTHDF1 in NASH-HCC and its interplay with the tumor immune microenvironment.<br><br>METHODS: Hepatocyte-specific Ythdf1-overexpressing mice were subjected to a NASH-HCC-inducing diet. Tumor-infiltrating immune cells were profiled with single-cell RNA-sequencing, flow cytometry, and immunostaining. The molecular target of YTHDF1 was elucidated with RNA-sequencing, m[6]A-sequencing, YTHDF1 RNA immunoprecipitation-sequencing, proteomics, and ribosome-profiling. Ythdf1 in NASH-HCC models was targeted by lipid nanoparticle (LNP)-encapsulated small-interfering Ythdf1.<br><br>RESULTS: YTHDF1 is overexpressed in tumor tissues compared to adjacent peri-tumor tissues from patients with NASH-HCC. Liver-specific Ythdf1 overexpression drives tumorigenesis in dietary models of spontaneous NASH-HCC. Single-cell RNA-sequencing and flow cytometry revealed that Ythdf1 induced accumulation of myeloid-derived suppressor cells (MDSCs) and suppressed cytotoxic CD8[+] T-cell function. Mechanistically, Ythdf1 expression in NASH-HCC cells induced the secretion of IL-6, which mediated MDSC recruitment and activation, leading to CD8[+] T-cell dysfunction. EZH2 mRNA was identified as a key YTHDF1 target. YTHDF1 binds to m[6]A-modified EZH2 mRNA and promotes EZH2 translation. EZH2 in turn increased expression and secretion of IL-6. Ythdf1 knockout synergized with anti-PD-1 treatment to suppress tumor growth in NASH-HCC allografts. Furthermore, therapeutic targeting of Ythdf1 using LNP-encapsulated small-interfering RNA significantly increased the efficacy of anti-PD-1 blockade in NASH-HCC allografts.<br><br>CONCLUSIONS: We identified that YTHDF1 promotes NASH-HCC tumorigenesis via EZH2-IL-6 signaling, which recruits and activates MDSCs to cause cytotoxic CD8[+] T-cell dysfunction. YTHDF1 may be a novel therapeutic target to improve responses to anti-PD-1 immunotherapy in NASH-HCC.<br><br>IMPACT AND IMPLICATIONS: YTHDF1, a N[6]-methyladenosine reader, is upregulated in patients with non-alcoholic steatohepatitis (NASH)-associated hepatocellular carcinoma (HCC); however, its role in modulating the tumor immune microenvironment in NASH-HCC remains unclear. Here, we show that Ythdf1 mediates immunosuppression in NASH-HCC and that targeting YTHDF1 in combination with immune checkpoint blockade elicits robust antitumor immune responses. Our findings suggest novel therapeutic targets for potentiating the efficacy of immune checkpoint blockade in NASH-HCC and provide the rationale for developing YTHDF1 inhibitors for the treatment of NASH-HCC.}, }
@article {pmid37459796, year = {2023}, author = {Sabbe, K and D'Haen, L and Boon, N and Ganigué, R}, title = {Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting.}, journal = {Water research}, volume = {243}, number = {}, pages = {120323}, doi = {10.1016/j.watres.2023.120323}, pmid = {37459796}, issn = {1879-2448}, mesh = {Fermentation ; *Caproates ; Flow Cytometry ; Bioreactors/microbiology ; *Microbiota ; }, abstract = {As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R[2] > 0.87) and intermediate accuracy in the near future (R[2] > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.}, }
@article {pmid37458953, year = {2024}, author = {Vélez-Martínez, GA and Reyes-Ardila, WL and Duque-Zapata, JD and Rugeles-Silva, PA and Muñoz Flórez, JE and López-Álvarez, D}, title = {Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {377-391}, pmid = {37458953}, issn = {1618-1905}, mesh = {*Ecosystem ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Colombia ; Bacteria/genetics ; Forests ; Fungi/genetics ; Soil Microbiology ; }, abstract = {The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.}, }
@article {pmid37458790, year = {2023}, author = {Huang, S and Lentendu, G and Fujinuma, J and Shiono, T and Kubota, Y and Mitchell, EAD}, title = {Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2606-2617}, pmid = {37458790}, issn = {1432-184X}, support = {182531/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Soil ; *Biodiversity ; Soil Microbiology ; Japan ; Nitrogen ; }, abstract = {The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.}, }
@article {pmid37458590, year = {2023}, author = {Masuda, T and Inomura, K and Mareš, J and Kodama, T and Shiozaki, T and Matsui, T and Suzuki, K and Takeda, S and Deutsch, C and Prášil, O and Furuya, K}, title = {Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0400022}, pmid = {37458590}, issn = {2165-0497}, mesh = {Phytoplankton ; Ecosystem ; Seawater/microbiology ; Nitrates ; *Synechococcus ; Nitrogen ; *Ammonium Compounds ; }, abstract = {Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3[-] decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.}, }
@article {pmid37458207, year = {2023}, author = {Seto, M and Kondoh, M}, title = {Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity.}, journal = {Ecology letters}, volume = {26}, number = {10}, pages = {1714-1725}, doi = {10.1111/ele.14287}, pmid = {37458207}, issn = {1461-0248}, support = {JPMEERF20214103//Environmental Restoration and Conservation Agency/ ; JP19H05641//Japan Society for the Promotion of Science/ ; JP19K06853//Japan Society for the Promotion of Science/ ; JP21H05315//Japan Society for the Promotion of Science/ ; JP22K06390//Japan Society for the Promotion of Science/ ; JP23H04652//Japan Society for the Promotion of Science/ ; }, mesh = {*Ecosystem ; *Symbiosis/physiology ; Thermodynamics ; }, abstract = {Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.}, }
@article {pmid37454793, year = {2023}, author = {Qi, L and Li, R and Wu, Y and Ibeanusi, V and Chen, G}, title = {Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116584}, doi = {10.1016/j.envres.2023.116584}, pmid = {37454793}, issn = {1096-0953}, mesh = {*Ecosystem ; Phylogeny ; Florida ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fresh Water ; *Microbiota ; }, abstract = {Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.}, }
@article {pmid37453005, year = {2023}, author = {Nagpal, S and Mande, SS}, title = {Environmental insults and compensative responses: when microbiome meets cancer.}, journal = {Discover oncology}, volume = {14}, number = {1}, pages = {130}, pmid = {37453005}, issn = {2730-6011}, support = {PhD Sponsorship//Tata Consultancy Services/ ; }, abstract = {Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.}, }
@article {pmid37452612, year = {2024}, author = {Hoque, E and Fritscher, J}, title = {Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {5}, pages = {540-563}, doi = {10.1080/1040841X.2023.2224425}, pmid = {37452612}, issn = {1549-7828}, mesh = {*Anaerobiosis ; *Microbiota ; Biofilms ; *Environment ; Fossils/microbiology ; *Mucor/classification/genetics/isolation &amp; purification ; *Aquatic Organisms/isolation &amp; purification ; DNA, Fungal/genetics ; Geologic Sediments/microbiology ; Adaptation, Physiological ; Groundwater/microbiology ; }, abstract = {Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.}, }
@article {pmid37452527, year = {2023}, author = {Soder-Walz, JM and Wasmund, K and Deobald, D and Vicent, T and Adrian, L and Marco-Urrea, E}, title = {Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2604-2620}, doi = {10.1111/1462-2920.16464}, pmid = {37452527}, issn = {1462-2920}, mesh = {*Proteomics ; *Bacteria/genetics ; Genomics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.}, }
@article {pmid37449414, year = {2023}, author = {Ni, G and Leung, PM and Daebeler, A and Guo, J and Hu, S and Cook, P and Nicol, GW and Daims, H and Greening, C}, title = {Nitrification in acidic and alkaline environments.}, journal = {Essays in biochemistry}, volume = {67}, number = {4}, pages = {753-768}, pmid = {37449414}, issn = {1744-1358}, mesh = {*Nitrification ; *Ammonia/metabolism ; Ecosystem ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.}, }
@article {pmid37446198, year = {2023}, author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J}, title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446198}, issn = {1422-0067}, support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; }, mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; }, abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.}, }
@article {pmid37442613, year = {2023}, author = {Demarquest, G and Lajoie, G}, title = {Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {9}, pages = {}, doi = {10.1093/femsec/fiad079}, pmid = {37442613}, issn = {1574-6941}, mesh = {Humans ; *Ecosystem ; Endophytes ; *Acer ; Bacteria/genetics ; Plants ; Plant Leaves/microbiology ; }, abstract = {Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.}, }
@article {pmid37440561, year = {2023}, author = {Fiedler, S and Schrader, H and Theobalt, N and Hofmann, I and Geiger, T and Arndt, D and Wanke, R and Schwaiger, J and Blutke, A}, title = {Standardized tissue sampling guidelines for histopathological and molecular analyses of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288542}, pmid = {37440561}, issn = {1932-6203}, mesh = {Animals ; *Oncorhynchus mykiss ; Ecotoxicology ; Reproducibility of Results ; *Water Pollutants, Chemical/toxicity ; }, abstract = {In ecotoxicology, evaluation of toxicities and no observed effect concentrations (NOEC) of test compounds in experimental fish is commonly based on molecular-, biochemical- and analytical chemistry analyses of organ/tissue samples and the assessment of (histo-) pathological lesions. Standardization of organ/tissue sampling locations, sample numbers, and sample processing contributes to warrant the reproducibility and inter- and intra-study comparability of analysis results. The present article provides the first comprehensive tissue sampling guidelines specifically adapted to rainbow trout (Oncorhynchus mykiss) as a frequently used fish species in ecotoxicological studies. A broad spectrum of ~40 different organs and tissues is covered. Appropriate sampling locations, sample sizes and sample numbers for subsequent routine histopathological evaluation (all organs/tissue) and for molecular analyses (~30 organs/tissues) are described in detail and illustrated with schematic drawings and representative macroscopic and histological images. These field-proven sampling guidelines were developed based on the pertinent literature and practical experience in ecotoxicological fish studies. They are intended to serve as a standard reference for any routine ecotoxicological study using rainbow trout as a test system. A broad application of the featured tissue sampling procedures will help to improve the reproducibility of analyses and to reduce inter- and intra-study variability induced by sampling bias and (normal) inter-sample morphological variation, and will therefore provide a robust basis for reliable characterization of toxicity and NOEC identification of diverse test substances and aquatic pollutants.}, }
@article {pmid37438876, year = {2023}, author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I}, title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226921}, pmid = {37438876}, issn = {1949-0984}, support = {757922/ERC_/European Research Council/International ; RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; }, abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.}, }
@article {pmid37438797, year = {2023}, author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {49}, pmid = {37438797}, issn = {1756-994X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<br><br>METHODS: We profiled 127 hospitalized patients with COVID-19 (n&#x2009;=&#x2009;79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<br><br>RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.<br><br>CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, }
@article {pmid37438590, year = {2023}, author = {Nava, V and Chandra, S and Aherne, J and Alfonso, MB and Antão-Geraldes, AM and Attermeyer, K and Bao, R and Bartrons, M and Berger, SA and Biernaczyk, M and Bissen, R and Brookes, JD and Brown, D and Cañedo-Argüelles, M and Canle, M and Capelli, C and Carballeira, R and Cereijo, JL and Chawchai, S and Christensen, ST and Christoffersen, KS and de Eyto, E and Delgado, J and Dornan, TN and Doubek, JP and Dusaucy, J and Erina, O and Ersoy, Z and Feuchtmayr, H and Frezzotti, ML and Galafassi, S and Gateuille, D and Gonçalves, V and Grossart, HP and Hamilton, DP and Harris, TD and Kangur, K and Kankılıç, GB and Kessler, R and Kiel, C and Krynak, EM and Leiva-Presa, &#xc0; and Lepori, F and Matias, MG and Matsuzaki, SS and McElarney, Y and Messyasz, B and Mitchell, M and Mlambo, MC and Motitsoe, SN and Nandini, S and Orlandi, V and Owens, C and Özkundakci, D and Pinnow, S and Pociecha, A and Raposeiro, PM and Rõõm, EI and Rotta, F and Salmaso, N and Sarma, SSS and Sartirana, D and Scordo, F and Sibomana, C and Siewert, D and Stepanowska, K and Tavşanoğlu, &#xdc;N and Tereshina, M and Thompson, J and Tolotti, M and Valois, A and Verburg, P and Welsh, B and Wesolek, B and Weyhenmeyer, GA and Wu, N and Zawisza, E and Zink, L and Leoni, B}, title = {Plastic debris in lakes and reservoirs.}, journal = {Nature}, volume = {619}, number = {7969}, pages = {317-322}, pmid = {37438590}, issn = {1476-4687}, mesh = {Ecosystem ; *Lakes/chemistry ; *Plastics/analysis/classification ; *Water Pollution/analysis/statistics &amp; numerical data ; Surveys and Questionnaires ; Urbanization ; *Water Supply ; Human Activities ; }, abstract = {Plastic debris is thought to be widespread in freshwater ecosystems globally[1]. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging[2,3]. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris[4]. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.}, }
@article {pmid37436063, year = {2023}, author = {Smets, W and Chock, MK and Walsh, CM and Vanderburgh, CQ and Kau, E and Lindow, SE and Fierer, N and Koskella, B}, title = {Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0111123}, pmid = {37436063}, issn = {2150-7511}, mesh = {*Bacteria/genetics ; *Microbiota ; Plants/microbiology ; Plant Leaves/microbiology ; }, abstract = {Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.}, }
@article {pmid37434715, year = {2023}, author = {Trexler, RV and Van Goethem, MW and Goudeau, D and Nath, N and Malmstrom, RR and Northen, TR and Couradeau, E}, title = {BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1176751}, pmid = {37434715}, issn = {1664-302X}, abstract = {Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.}, }
@article {pmid37433981, year = {2023}, author = {Gomes, AFF and de Almeida, LG and Cônsoli, FL}, title = {Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2583-2605}, pmid = {37433981}, issn = {1432-184X}, support = {140835/2019-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2010/13714-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Spodoptera/genetics ; *Insecticides ; *Pesticides ; Larva ; Enterococcus/genetics ; Genomics ; DNA ; Zea mays ; }, abstract = {Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.}, }
@article {pmid37433980, year = {2023}, author = {Candelori, A and Di Giuseppe, G and Villalobo, E and Sjödin, A and Vallesi, A}, title = {Bipolar Biogeographical Distribution of Parafrancisella Bacteria Carried by the Ciliate Euplotes.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3128-3132}, pmid = {37433980}, issn = {1432-184X}, support = {PNRA18_00152//PNRA (Programma Nazionale di Ricerca in Antartide)/ ; }, mesh = {Phylogeny ; *Euplotes/genetics/microbiology ; *Francisella ; Cytoplasm ; Antarctic Regions ; }, abstract = {Parafrancisella adeliensis, a Francisella-like endosymbiont, was found to reside in the cytoplasm of an Antarctic strain of the bipolar ciliate species, Euplotes petzi. To inquire whether Euplotes cells collected from distant Arctic and peri-Antarctic sites host Parafrancisella bacteria, wild-type strains of the congeneric bipolar species, E. nobilii, were screened for Parafrancisella by in situ hybridization and 16S gene amplification and sequencing. Results indicate that all Euplotes strains analyzed contained endosymbiotic bacteria with 16S nucleotide sequences closely similar to the P. adeliensis 16S gene sequence. This finding suggests that Parafrancisella/Euplotes associations are not endemic to Antarctica, but are common in both the Antarctic and Arctic regions.}, }
@article {pmid37432727, year = {2023}, author = {Wang, J and Shi, K and Jing, Z and Ge, Y}, title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {29}, pages = {10640-10651}, doi = {10.1021/acs.est.3c02181}, pmid = {37432727}, issn = {1520-5851}, mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.}, }
@article {pmid37432469, year = {2023}, author = {DiPietro, AG and Bryant, SA and Zanger, MM and Williamson, KE}, title = {Understanding Viral Impacts in Soil Microbial Ecology Through the Persistence and Decay of Infectious Bacteriophages.}, journal = {Current microbiology}, volume = {80}, number = {9}, pages = {276}, pmid = {37432469}, issn = {1432-0991}, mesh = {*Bacteriophages ; Soil Microbiology ; Ecology ; Fresh Water ; Soil ; }, abstract = {Marine bacteriophages have been well characterized in terms of decay rates, population dynamics in relation to their hosts, and their impacts on biogeochemical cycles in the global ocean. Knowledge in soil bacteriophage ecology lags considerably behind, with few studies documenting population dynamics with hosts and even fewer reporting phage decay rates. By using sterile soil or aquatic microcosms inoculated with single bacteriophage isolates, phage decay rates (loss of infectivity over time) were determined, independent of host interactions, for 5 model phage isolates. Decay rates varied by phage from 0.11-2.07% h[-1] in soils to 0.07-0.28% h[-1] in aquatic microcosms. For phages incubated in both soil and aquatic microcosms, the observed decay rate was consistently higher in soil microcosms than in aquatic microcosms by at least a factor of two. However, when decay rates for soil phage isolates in the present study were compared to those reported for marine and freshwater phage isolates from previous studies, the decay constants for soil phages were, on average, 4 times lower than those for aquatic phages. Slower rates of phage decay in soils indicate a lower turnover rate, which may have subsequent and potentially far-reaching impacts on virus-mediated mortality and bacterial activity. The wide range of decay rates observed in the present study and the lack of information on this critical aspect of virus-host dynamics in soil emphasizes the need for continued research in this field.}, }
@article {pmid37431054, year = {2022}, author = {Seo, H and Lee, S and Park, H and Jo, S and Kim, S and Rahim, MA and Ul-Haq, A and Barman, I and Lee, Y and Seo, A and Kim, M and Jung, IY and Song, HY}, title = {Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37431054}, issn = {2304-8158}, support = {2021040D288//Gochang Bokbunja vinegar Research Project/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; }, abstract = {As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of "Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation". Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of "Komagataeibacter (90.2%) fermentation" were found. "Lactobacillus (92.2%) fermentation" characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.}, }
@article {pmid37428189, year = {2023}, author = {Rellegadla, S and Prajapat, G and Jain, S and Agrawal, A}, title = {Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5531-5544}, pmid = {37428189}, issn = {1432-0614}, support = {IMP/2018/000589//SERB Department of Science and Technology/ ; BT/PR25132/NER/95/1034/2017//Department of Biotechnology, Ministry of Science and Technology, India/ ; 09/1131(0028)/2019-EMR-I//CSIR India/ ; }, abstract = {The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.}, }
@article {pmid37426976, year = {2023}, author = {Wang, M and Cernava, T}, title = {Editorial: The phyllosphere microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1234843}, pmid = {37426976}, issn = {1664-462X}, }
@article {pmid37423403, year = {2023}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Quintanilla-Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM}, title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.}, journal = {Fish &amp; shellfish immunology}, volume = {140}, number = {}, pages = {108928}, doi = {10.1016/j.fsi.2023.108928}, pmid = {37423403}, issn = {1095-9947}, mesh = {Animals ; *Cichlids ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Diet/veterinary ; *Tilapia ; Animal Feed/analysis ; *Fish Diseases ; Dietary Supplements ; }, abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.}, }
@article {pmid37422225, year = {2023}, author = {Villar-dePablo, M and Ascaso, C and Rodríguez-Pérez, E and Urizal, M and Wierzchos, J and Pérez-Ortega, S and de Los Ríos, A}, title = {Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments.}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165318}, doi = {10.1016/j.scitotenv.2023.165318}, pmid = {37422225}, issn = {1879-1026}, mesh = {*Disinfectants/pharmacology ; *Cyanobacteria ; *Ascomycota ; Microscopy ; }, abstract = {The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.}, }
@article {pmid37419360, year = {2023}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Cuezva, S and Cañaveras, JC and Benavente, D and Duarte, E and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain).}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165218}, doi = {10.1016/j.scitotenv.2023.165218}, pmid = {37419360}, issn = {1879-1026}, mesh = {*Caves/microbiology ; Spain ; *Bacteria ; Ecology ; Biofilms ; }, abstract = {In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.}, }
@article {pmid37419243, year = {2023}, author = {Loyola-Fonseca, SC and Campello, AF and Rodrigues, RCV and Alves, FRF and Brasil, SC and Vilela, CLS and Gonçalves, LS and Provenzano, JC and Siqueira, JF and Rôças, IN}, title = {Disinfection and Shaping of Vertucci Class II Root Canals after Preparation with Two Instrument Systems and Supplementary Ultrasonic Activation of Sodium Hypochlorite.}, journal = {Journal of endodontics}, volume = {49}, number = {9}, pages = {1183-1190}, doi = {10.1016/j.joen.2023.06.017}, pmid = {37419243}, issn = {1878-3554}, mesh = {*Dental Pulp Cavity/diagnostic imaging/microbiology ; *Sodium Hypochlorite/therapeutic use ; X-Ray Microtomography ; Disinfection ; Ultrasonics ; Root Canal Preparation ; }, abstract = {INTRODUCTION: This study compared disinfection and shaping after root canal preparation with either XP-endo Shaper or TruNatomy instrument systems, supplemented by ultrasonic activation of sodium hypochlorite (NaOCl) with either stainless-steel (SS) or nickel-titanium (NiTi) inserts.<br><br>METHODS: Mesial roots from mandibular molars with Vertucci class II configuration were divided into 2 groups (n&#xa0;=&#xa0;24) based on anatomically paired micro-computed tomography (micro-CT) analyses. Pre and postpreparation micro-CT scans were obtained to evaluate the shaping performance. The canals were contaminated with a mixed bacterial culture for 30&#xa0;days and then subjected to preparation with either XP-endo Shaper or TruNatomy instruments using NaOCl irrigation. Supplementary ultrasonic activation of NaOCl was conducted using either an SS (TruNatomy group) or NiTi (XP-endo Shaper group) insert. Bacteriological samples were taken from the canals before preparation (S1), after preparation (S2), and after the supplementary approach (S3). Bacterial reduction was evaluated using a quantitative real-time polymerase chain reaction.<br><br>RESULTS: Preparation with both instrument systems significantly reduced bacterial counts (P&#xa0;<&#xa0;.01). After preparation, 36% (TruNatomy) and 35% (XP-endo Shaper) were negative for bacteria. These values increased to 59% and 65% after ultrasonic activation with the SS and NiTi inserts, respectively. The quantitative data in S2 showed that XP-endo Shaper promoted a significantly higher bacterial reduction than TruNatomy (P&#xa0;<&#xa0;.05). No significant intragroup differences were observed after ultrasonic activation (P&#xa0;>&#xa0;.05), probably because the SS insert promoted a significantly higher S2-to-S3 reduction than the NiTi insert (P&#xa0;<&#xa0;.01). Micro-CT analysis revealed no significant differences in the unprepared areas between the groups (P&#xa0;>&#xa0;.05).<br><br>CONCLUSIONS: The XP-endo Shaper caused a significantly higher bacterial reduction than TruNatomy in Vertucci class II canals. Better antibacterial results after ultrasonic activation were observed for the SS ultrasonic inserts than for the NiTi inserts.}, }
@article {pmid37418833, year = {2024}, author = {Crump, BC and Bowen, JL}, title = {The Microbial Ecology of Estuarine Ecosystems.}, journal = {Annual review of marine science}, volume = {16}, number = {}, pages = {335-360}, doi = {10.1146/annurev-marine-022123-101845}, pmid = {37418833}, issn = {1941-0611}, mesh = {Animals ; Humans ; *Wetlands ; Estuaries ; Food Chain ; Carbon ; *Microbiota ; }, abstract = {Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.}, }
@article {pmid37417553, year = {2023}, author = {Jansma, J and Thome, NU and Schwalbe, M and Chatziioannou, AC and Elsayed, SS and van Wezel, GP and van den Abbeele, P and van Hemert, S and El Aidy, S}, title = {Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2232506}, pmid = {37417553}, issn = {1949-0984}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; *Probiotics/pharmacology ; Propionates/pharmacology ; Enterobacteriaceae ; }, abstract = {The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.}, }
@article {pmid37415044, year = {2023}, author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA}, title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2574-2582}, pmid = {37415044}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Kelp/microbiology ; Ecosystem ; Peru ; Bacteria/genetics ; Biodiversity ; *Microbiota ; }, abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.}, }
@article {pmid37415043, year = {2023}, author = {Shao, Q and Lin, Z and Xu, Z and Zhu, Z and Zhou, C and Yan, X}, title = {Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2560-2573}, pmid = {37415043}, issn = {1432-184X}, support = {2022J195//Natural Science Foundation of Ningbo/ ; 2022S116//Public Welfare Science and Technology Project of Ningbo/ ; 2018YFD0900702//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Ecosystem ; Plankton/genetics ; *Diatoms ; China ; *Dinoflagellida/genetics ; *Arthropods ; Shellfish ; }, abstract = {The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.}, }
@article {pmid37408642, year = {2023}, author = {Kasahara, K and Leygeber, M and Seiffarth, J and Ruzaeva, K and Drepper, T and Nöh, K and Kohlheyer, D}, title = {Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1198170}, pmid = {37408642}, issn = {1664-302X}, abstract = {Microfluidic cultivation devices that facilitate O2 control enable unique studies of the complex interplay between environmental O2 availability and mi