@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 & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10918},
pmid = {40025674},
issn = {1520-5851},
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 = {},
number = {},
pages = {107405},
doi = {10.1016/j.micpath.2025.107405},
pmid = {40024538},
issn = {1096-1208},
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 2,838 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 3,358 orthologous clusters, including 1,775 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},
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},
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 ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Agriculture/methods ; },
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.},
}

*Oryza/microbiology/metabolism
*Nitrous Oxide/metabolism
*Rhizosphere
*Microbiota/genetics
*Soil Microbiology
*Nitrogen Fixation
*Plant Roots/microbiology/metabolism
Domestication
Metagenomics
Soil/chemistry
Nitrogenase/metabolism/genetics
Nitrogen/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Agriculture/methods

@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 = {},
doi = {10.3390/microorganisms13020361},
pmid = {40005728},
issn = {2076-2607},
support = {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 = {},
doi = {10.3390/microorganisms13020240},
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 = {},
doi = {10.3390/microorganisms13020222},
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 = {},
doi = {10.3390/insects16020195},
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 = {},
doi = {10.3390/insects16020122},
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 ; *Seafood/analysis ; Europe ; Animals ; Humans ; *Food Contamination/analysis ; *Tetrodotoxin/analysis/toxicity ; Dietary Exposure/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.},
}

Risk Assessment
*Seafood/analysis
Europe
Animals
Humans
*Food Contamination/analysis
*Tetrodotoxin/analysis/toxicity
Dietary Exposure/analysis

@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 = {},
number = {},
pages = {},
doi = {10.1039/d4np00045e},
pmid = {39996333},
issn = {1460-4752},
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 = {},
number = {},
pages = {e0260324},
doi = {10.1128/spectrum.02603-24},
pmid = {39992142},
issn = {2165-0497},
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 = {},
number = {},
pages = {e0243724},
doi = {10.1128/aem.02437-24},
pmid = {39992122},
issn = {1098-5336},
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},
doi = {10.1111/1462-2920.70061},
pmid = {39988434},
issn = {1462-2920},
support = {APP1186140//National Health and Medical Research Council/ ; DP220103548//Australian Research Council/ ; },
mesh = {*Pseudomonas fluorescens/genetics/growth & development ; *Escherichia coli/genetics/growth & development/radiation effects ; *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.},
}

*Pseudomonas fluorescens/genetics/growth & development
*Escherichia coli/genetics/growth & development/radiation effects
*Coculture Techniques
Adaptation, Physiological
Genome, Bacterial
Whole Genome Sequencing

@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},
doi = {10.1111/1462-2920.70059},
pmid = {39987915},
issn = {1462-2920},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Adaptation, Physiological ; Soil Microbiology ; Genome, Bacterial ; Betaproteobacteria/genetics ; DNA, Bacterial/genetics ; Carbon/metabolism ; Ecosystem ; Sequence Analysis, DNA ; },
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.},
}

*Phylogeny
*RNA, Ribosomal, 16S/genetics
*Adaptation, Physiological
Soil Microbiology
Genome, Bacterial
Betaproteobacteria/genetics
DNA, Bacterial/genetics
Carbon/metabolism
Ecosystem
Sequence Analysis, DNA

@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 ; Uncertainty ; Male ; Female ; *Adaptation, Psychological ; *Inflammatory Bowel Diseases/psychology ; Adult ; Middle Aged ; *Mental Health ; Surveys and Questionnaires ; *Anxiety/psychology ; *Depression/psychology ; Young Adult ; Aged ; },
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.},
}

Humans
Uncertainty
Male
Female
*Adaptation, Psychological
*Inflammatory Bowel Diseases/psychology
Adult
Middle Aged
*Mental Health
Surveys and Questionnaires
*Anxiety/psychology
*Depression/psychology
Young Adult
Aged

@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 ; *Environmental Restoration and Remediation/methods ; Fungi/metabolism/genetics/physiology ; Biodiversity ; Cyanobacteria/metabolism ; Lichens/microbiology ; Microbiota ; Bryophyta/microbiology ; 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.},
}

*Soil Microbiology
*Soil/chemistry
*Ecosystem
*Environmental Restoration and Remediation/methods
Fungi/metabolism/genetics/physiology
Biodiversity
Cyanobacteria/metabolism
Lichens/microbiology
Microbiota
Bryophyta/microbiology
Biodegradation, Environmental

@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 = {},
number = {},
pages = {109867},
doi = {10.1016/j.jnutbio.2025.109867},
pmid = {39978646},
issn = {1873-4847},
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/ ; 741332//Horizon 2020/ ; PID2021-123184OA-I00//MICIN/AEI, Spain/ ; },
mesh = {*Fungi/classification/genetics/isolation & purification ; Norway ; *Housing ; *Air Pollution, Indoor/analysis ; *Yeasts/classification/isolation & purification/genetics ; *Mycobiome ; Humans ; *Child Day Care Centers ; Air Microbiology ; Dust/analysis ; 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.},
}

*Fungi/classification/genetics/isolation & purification
Norway
*Housing
*Air Pollution, Indoor/analysis
*Yeasts/classification/isolation & purification/genetics
*Mycobiome
Humans
*Child Day Care Centers
Air Microbiology
Dust/analysis
Child
Child, Preschool

@article {pmid39976447,
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 = {},
number = {},
pages = {e0009125},
doi = {10.1128/msystems.00091-25},
pmid = {39976447},
issn = {2379-5077},
}

@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 = {},
number = {},
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)./ ; },
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 {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},
doi = {10.1016/j.ebiom.2025.105608},
pmid = {39970705},
issn = {2352-3964},
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.

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.

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.

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.

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},
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 {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 = {},
number = {},
pages = {},
doi = {10.1146/annurev-biophys-081624-030543},
pmid = {39971349},
issn = {1936-1238},
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 {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},
doi = {10.1073/pnas.2423774122},
pmid = {39970001},
issn = {1091-6490},
support = {R01GM138533//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM106189//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31GM149174-01//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Escherichia coli/genetics/physiology ; *Chemotaxis/physiology ; *Adaptation, Physiological ; Phenotype ; Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; },
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.},
}

*Escherichia coli/genetics/physiology
*Chemotaxis/physiology
*Adaptation, Physiological
Phenotype
Escherichia coli Proteins/metabolism/genetics
Gene Expression Regulation, Bacterial

@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 ; Microbiota ; Water Microbiology ; Microplastics ; Ecosystem ; COVID-19 ; },
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.},
}

*Masks
Microbiota
Water Microbiology
Microplastics
Ecosystem
COVID-19

@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 = {},
number = {},
pages = {},
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/ ; },
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},
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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
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 ; *Quinolones/pharmacology ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Genomics ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; },
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.},
}

*Escherichia coli/genetics/drug effects
*Quinolones/pharmacology
*Escherichia coli Proteins/genetics
*Anti-Bacterial Agents/pharmacology
*Plasmids/genetics
Genomics
Drug Resistance, Bacterial/genetics
Genome, Bacterial

@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/isolation & purification/genetics ; China ; *Rivers/microbiology ; Biodiversity ; Ecosystem ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
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.},
}

*Soil Microbiology
*Ice Cover/microbiology
*Bacteria/classification/isolation & purification/genetics
China
*Rivers/microbiology
Biodiversity
Ecosystem
Soil/chemistry
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics

@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 & bioelectronics},
volume = {276},
number = {},
pages = {117232},
doi = {10.1016/j.bios.2025.117232},
pmid = {39954521},
issn = {1873-4235},
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},
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 {pmid39953673,
year = {2025},
author = {Kotsakis, GA and Ganesan, SM},
title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241307939},
doi = {10.1177/00220345241307939},
pmid = {39953673},
issn = {1544-0591},
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 = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.011},
pmid = {39952886},
issn = {1878-4372},
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 = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; },
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.},
}

*Metagenomics
*Vegetables/virology/microbiology
*Fermentation
*Bacteriophages/genetics/isolation & purification/classification
Microbiota
Brassica/microbiology/virology
Fermented Foods/microbiology/virology
Bacteria/genetics/classification/isolation & purification/virology
Biodiversity
Daucus carota/microbiology/virology
Food Microbiology
Viruses/isolation & purification/classification/genetics
Enterobacteriaceae/isolation & purification/genetics/virology/classification
Metagenome
Lactobacillaceae/isolation & purification/genetics/classification

@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 = {Animals ; *Pseudomonas fragi/genetics/metabolism/growth & development ; *Chickens/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Food Microbiology ; *Meat/microbiology ; Mutation ; Biofilms/growth & development ; Microbiota ; Food Storage ; Food Contamination/analysis ; },
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.},
}

Animals
*Pseudomonas fragi/genetics/metabolism/growth & development
*Chickens/microbiology
*Bacterial Proteins/genetics/metabolism
*Food Microbiology
*Meat/microbiology
Mutation
Biofilms/growth & development
Microbiota
Food Storage
Food Contamination/analysis

@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},
doi = {10.1073/pnas.2417075122},
pmid = {39951503},
issn = {1091-6490},
mesh = {*Models, Biological ; Population Dynamics ; Computer Simulation ; },
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.},
}

*Models, Biological
Population Dynamics
Computer Simulation

@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},
doi = {10.1002/eap.70007},
pmid = {39950593},
issn = {1051-0761},
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 ; *Fungi/physiology ; Environmental Restoration and Remediation/methods ; Microbiota ; Conservation of Natural Resources/methods ; },
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.},
}

*Soil Microbiology
*Trees
*Fungi/physiology
Environmental Restoration and Remediation/methods
Microbiota
Conservation of Natural Resources/methods

@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//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; },
mesh = {Humans ; South Africa/epidemiology ; Male ; Adult ; *Allergens ; Pilot Projects ; Female ; Young Adult ; Adolescent ; Prevalence ; Middle Aged ; *Air Pollutants/analysis ; Pollen ; Hypersensitivity/epidemiology ; 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.},
}

Humans
South Africa/epidemiology
Male
Adult
*Allergens
Pilot Projects
Female
Young Adult
Adolescent
Prevalence
Middle Aged
*Air Pollutants/analysis
Pollen
Hypersensitivity/epidemiology
Skin Tests

@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/ ; PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigación/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Científicas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; *Soil/chemistry ; Phylogeny ; Chlorophyta ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; },
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.},
}

*Soil Microbiology
Antarctic Regions
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Microbiota
*Soil/chemistry
Phylogeny
Chlorophyta
Nitrogen/analysis/metabolism
Carbon/analysis/metabolism

@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 = {},
doi = {10.3390/ani15030361},
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 = {},
doi = {10.3390/ma18030625},
pmid = {39942291},
issn = {1996-1944},
support = {ED481D-2021/016//Consellería de Cultura, Educación e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovación y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovación 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 = {},
doi = {10.3390/foods14030469},
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 ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; Microbiota ; Phylogeny ; Fresh Water/microbiology ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; },
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.},
}

*Geologic Sediments/microbiology
Brazil
*RNA, Ribosomal, 16S/genetics
Seawater/microbiology
Water Microbiology
Microbiota
Phylogeny
Fresh Water/microbiology
Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics

@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 = {},
number = {},
pages = {e14083},
doi = {10.1111/1755-0998.14083},
pmid = {39936183},
issn = {1755-0998},
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/growth & development ; *Amino Acids, Diamino/metabolism ; *Methane/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.},
}

*Biofuels
*Microalgae/metabolism/growth & development
*Amino Acids, Diamino/metabolism
*Methane/metabolism
Carbon Dioxide/metabolism

@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 = {},
number = {},
pages = {},
pmid = {39934529},
issn = {1678-4405},
support = {TNU/R&D/M/11//The Neotia University/ ; },
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},
doi = {10.1098/rsif.2024.0611},
pmid = {39933594},
issn = {1742-5662},
support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; },
mesh = {*Ecosystem ; *Models, Biological ; Bacteria/metabolism ; Anti-Bacterial Agents/pharmacology ; },
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.},
}

*Ecosystem
*Models, Biological
Bacteria/metabolism
Anti-Bacterial Agents/pharmacology

@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 ; *DNA, Bacterial/genetics ; *Sequence Analysis, DNA ; *Base Composition ; Bacterial Typing Techniques ; Fatty Acids ; Symbiosis ; DNA, Archaeal/genetics ; },
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.},
}

*Phylogeny
*RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics
*Sequence Analysis, DNA
*Base Composition
Bacterial Typing Techniques
Fatty Acids
Symbiosis
DNA, Archaeal/genetics

@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 ; Humans ; *Odorants/analysis ; Laundering/methods ; Volatile Organic Compounds/analysis ; Clothing ; Skin/microbiology ; },
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.

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.

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.},
}

*Microbiota
Humans
*Odorants/analysis
Laundering/methods
Volatile Organic Compounds/analysis
Clothing
Skin/microbiology

@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 = {*Anthozoa/microbiology ; Animals ; Malaysia ; *Microbiota ; *Symbiosis ; Biodiversity ; Bacteria/genetics/classification ; Climate Change ; Coral Reefs ; 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.},
}

*Anthozoa/microbiology
Animals
Malaysia
*Microbiota
*Symbiosis
Biodiversity
Bacteria/genetics/classification
Climate Change
Coral Reefs
Phylogeny
RNA, Ribosomal, 16S/genetics

@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 = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf022},
pmid = {39914458},
issn = {1574-6968},
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 three-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 like 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},
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, MÁ 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/physiology ; Biological Evolution ; Plants ; Conservation of Natural Resources ; },
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.},
}

Antarctic Regions
*Biodiversity
Animals
*Fresh Water
*Invertebrates/physiology
Vertebrates/physiology
Biological Evolution
Plants
Conservation of Natural Resources

@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 = {},
number = {},
pages = {e0216124},
doi = {10.1128/aem.02161-24},
pmid = {39912641},
issn = {1098-5336},
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 & biology education},
volume = {},
number = {},
pages = {e0011624},
doi = {10.1128/jmbe.00116-24},
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 ; *Soil/chemistry ; *Fungi/genetics/classification ; *Bacteria/classification/genetics/isolation & purification ; *Grassland ; Italy ; *Biodiversity ; *Carbon/analysis ; Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Climate Change ; 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.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/genetics/classification
*Bacteria/classification/genetics/isolation & purification
*Grassland
Italy
*Biodiversity
*Carbon/analysis
Microbiota
Nitrogen/analysis
Phosphorus/analysis
Forests
Hydrogen-Ion Concentration
Climate Change
Mycobiome

@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 = {Animals ; *Microbiota ; Antarctic Regions ; Food Chain ; Predatory Behavior ; },
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.

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.

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.},
}

Animals
*Microbiota
Antarctic Regions
Food Chain
Predatory Behavior

@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},
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 = {},
number = {},
pages = {e0219324},
doi = {10.1128/spectrum.02193-24},
pmid = {39902955},
issn = {2165-0497},
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.

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 ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation & purification ; },
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.},
}

*Porifera/microbiology
*Microbiota
Animals
*Fresh Water/microbiology
North Carolina
*Symbiosis
Bacteria/classification/genetics/isolation & purification

@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/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endophytes/isolation & purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; },
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.},
}

*Capsicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Endophytes/isolation & purification/classification/physiology/genetics
Plant Diseases/microbiology
Plant Roots/microbiology
Fungi/classification/genetics/isolation & purification/physiology

@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/physiology ; *Lung/microbiology/immunology ; 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.},
}

Humans
*Microbiota/immunology/physiology
*Lung/microbiology/immunology
Lung Diseases/immunology/microbiology

@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},
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 {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 ; *Phylogeny ; *Diet ; *Desert Climate ; *Microbiota ; Bacteria/genetics/classification ; Symbiosis ; Arizona ; },
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.},
}

Animals
*Drosophila/microbiology/genetics
*Phylogeny
*Diet
*Desert Climate
*Microbiota
Bacteria/genetics/classification
Symbiosis
Arizona

@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},
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 {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 = {},
number = {},
pages = {e0236824},
doi = {10.1128/aem.02368-24},
pmid = {39882875},
issn = {1098-5336},
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.

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 = {},
number = {},
pages = {e0220924},
doi = {10.1128/spectrum.02209-24},
pmid = {39882867},
issn = {2165-0497},
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 Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Agave/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; *Agriculture ; *RNA, Ribosomal, 16S/genetics ; Mexico ; Alcoholic Beverages/microbiology ; Biodiversity ; Rhizosphere ; },
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.},
}

*Agave/microbiology
*Soil Microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
*Agriculture
*RNA, Ribosomal, 16S/genetics
Mexico
Alcoholic Beverages/microbiology
Biodiversity
Rhizosphere

@article {pmid39880083,
year = {2025},
author = {Moortele, TV 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 & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100918},
doi = {10.1016/j.mcpro.2025.100918},
pmid = {39880083},
issn = {1535-9484},
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 case 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 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 = {},
number = {},
pages = {e0392824},
doi = {10.1128/mbio.03928-24},
pmid = {39878512},
issn = {2150-7511},
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.

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 & biology education},
volume = {},
number = {},
pages = {e0005624},
doi = {10.1128/jmbe.00056-24},
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 ; Female ; Male ; *Dental Implants/microbiology/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; 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.

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.

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 < 0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.

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.},
}

Humans
*Peri-Implantitis/microbiology
*Microbiota
Cross-Sectional Studies
Female
Male
*Dental Implants/microbiology/adverse effects
Middle Aged
RNA, Ribosomal, 16S/analysis
Adult
Aged

@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墨},
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},
doi = {10.1111/1758-2229.70069},
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 ; *Carbon/metabolism/analysis ; *Sulfates/metabolism ; *Ponds/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Phylogeny ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
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.},
}

*Wetlands
*Carbon/metabolism/analysis
*Sulfates/metabolism
*Ponds/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Phylogeny
Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Biodiversity

@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},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
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.},
}

Antarctic Regions
*Soil Microbiology
*Archaea/classification/genetics
*Bacteria/classification/isolation & purification/genetics
*Ecosystem
Microbiota
Phylogeny
Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics

@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 ; *Soil/chemistry ; *Forests ; *Carbon/metabolism ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Organic Chemicals/metabolism ; 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.},
}

*Soil Microbiology
*Soil/chemistry
*Forests
*Carbon/metabolism
Hydrogen-Ion Concentration
China
*Microbiota
Carbon Cycle
Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Organic Chemicals/metabolism
Microbial Interactions

@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 & purification/metabolism ; Reunion ; *Fungi/classification/genetics/isolation & purification/metabolism ; Seawater/microbiology ; Indian Ocean ; Seasons ; Biodiversity ; Environmental Monitoring/methods ; Islands ; Microalgae/classification/metabolism ; Geologic Sediments/microbiology ; },
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.},
}

*Coral Reefs
*Microbiota
*Anthozoa/microbiology
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
Reunion
*Fungi/classification/genetics/isolation & purification/metabolism
Seawater/microbiology
Indian Ocean
Seasons
Biodiversity
Environmental Monitoring/methods
Islands
Microalgae/classification/metabolism
Geologic Sediments/microbiology

@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 ; Bacteria/genetics/metabolism ; },
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.},
}

*Introduced Species
*Plants/microbiology
*Plant Diseases/microbiology
*Soil Microbiology
Host-Pathogen Interactions
Bacteria/genetics/metabolism

@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 = {},
doi = {10.1101/2025.01.15.633187},
pmid = {39868213},
issn = {2692-8205},
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 = {},
doi = {10.1101/2025.01.14.632972},
pmid = {39868180},
issn = {2692-8205},
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 P veg , 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 = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf043},
pmid = {39862387},
issn = {1367-4811},
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.

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/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
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 reorganisations 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 = {},
doi = {10.3390/biology14010028},
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/ ; 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/physiology ; *Bacteriophages/physiology ; *Fresh Water/virology ; Eutrophication ; Ecosystem ; Cyanobacteria/virology/physiology ; Photosynthesis ; Host Specificity ; },
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.},
}

*Microcystis/virology/physiology
*Bacteriophages/physiology
*Fresh Water/virology
Eutrophication
Ecosystem
Cyanobacteria/virology/physiology
Photosynthesis
Host Specificity

@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},
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},
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.},
}