@article {pmid34541249, year = {2017}, author = {Stuart, RK and Mayali, X and Thelen, MP and Pett-Ridge, J and Weber, PK}, title = {Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM).}, journal = {Bio-protocol}, volume = {7}, number = {9}, pages = {e2263}, doi = {10.21769/BioProtoc.2263}, pmid = {34541249}, issn = {2331-8325}, abstract = {To advance the understanding of microbial interactions, it is becoming increasingly important to resolve the individual metabolic contributions of microorganisms in complex communities. Organisms from biofilms can be especially difficult to separate, image and analyze, and methods to address these limitations are needed. High resolution imaging secondary ion mass spectrometry (NanoSIMS) generates single cell isotopic composition measurements, and can be used to quantify incorporation and exchange of an isotopically labeled substrate among individual organisms. Here, incorporation of cyanobacterial extracellular organic matter (EOM) by members of a cyanobacterial mixed species biofilm is used as a model to illustrate this method. Incorporation of stable isotope labeled (15N and 13C) EOM by two groups, cyanobacteria and associated heterotrophic microbes, are quantified. Methods for generating, preparing, and analyzing samples for quantifying uptake of stable isotope-labeled EOM in the biofilm are described.}, }
@article {pmid34540837, year = {2021}, author = {Tudela, H and Claus, SP and Saleh, M}, title = {Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {719072}, doi = {10.3389/fcell.2021.719072}, pmid = {34540837}, issn = {2296-634X}, abstract = {The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.}, }
@article {pmid34540373, year = {2021}, author = {Rodríguez-Barreras, R and Tosado-Rodríguez, EL and Godoy-Vitorino, F}, title = {Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12084}, doi = {10.7717/peerj.12084}, pmid = {34540373}, issn = {2167-8359}, abstract = {Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.}, }
@article {pmid34540243, year = {2021}, author = {Briggs, AA and Brown, AL and Osenberg, CW}, title = {Local versus site-level effects of algae on coral microbial communities.}, journal = {Royal Society open science}, volume = {8}, number = {9}, pages = {210035}, doi = {10.1098/rsos.210035}, pmid = {34540243}, issn = {2054-5703}, abstract = {Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.}, }
@article {pmid34537690, year = {2021}, author = {Bai, L and Ju, Q and Wang, C and Tian, L and Wang, C and Zhang, H and Jiang, H}, title = {Responses of steroid estrogen biodegradation to cyanobacterial organic matter biodegradability in the water column of a eutrophic lake.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150058}, doi = {10.1016/j.scitotenv.2021.150058}, pmid = {34537690}, issn = {1879-1026}, abstract = {The co-occurrence of cyanobacterial harmful algal blooms and contaminants is an increasing environmental concern in freshwater worldwide. Our field investigations coupled with laboratory incubations demonstrated that the microbial degradation potential of 17β-estradiol (E2) with estrone as the intermediate was primarily driven by increased dissolved organic matter (DOM) in the water column of a cyanobacterial bloom. To explain the intrinsic contribution of cyanobacterial-derived DOM (C-DOM) to estrogen biodegradation, a combination of methods including bioassay, ultrahigh-resolution mass spectrometry, and microbial ecology were applied. The results showed that preferential assimilation of highly biodegradable structures, including protein-, carbohydrate-, and unsaturated hydrocarbon-like molecules sustained bacterial growth, selected for more diverse microbes, and resulted in greater estrogen biodegradation compared to less biodegradable molecules (lignin- and tannin-like molecules). The biodegradability of C-DOM decreased from 78% to 1%, whereas the E2 biodegradation rate decreased dramatically at first, then increased with the accumulation of recalcitrant, bio-produced lipid-like molecules in C-DOM. This change was linked to alternative substrate-induced selection of the bacterial community under highly refractory conditions, as suggested by the greater biomass-normalized E2 biodegradation rate after a 24-h lag phase. In addition to the increased frequency of potential degraders, such as Sphingobacterium, the network analysis revealed that C-DOM molecules distributed in high H/C (protein- and lipid-like molecules) were the main drivers structuring the bacterial community, inducing strong deterministic selection of the community assemblage and upregulating the metabolic capacity for contaminants. These findings provide strong evidence that estrogen biodegradation in eutrophic water may be facilitated by cyanobacterial blooms and provide a theoretical basis for ecological remediation of estrogen pollution.}, }
@article {pmid34537275, year = {2021}, author = {Majlander, J and Anttila, VJ and Nurmi, W and Seppälä, A and Tiedje, J and Muziasari, W}, title = {Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals: focus on carbapenem resistance genes and genes associated with bacteria causing hospital acquired infections.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2021.09.008}, pmid = {34537275}, issn = {1532-2939}, abstract = {BACKGROUND: Wastewater-based monitoring represents a useful tool for antibiotic resistance surveillance.<br><br>AIM: This study investigates the prevalence and abundance of antibiotic resistance genes (ARGs) in hospital wastewater over time.<br><br>METHODS: We monitored wastewater from two hospitals in Finland (HUS1 and HUS2) weekly for nine weeks (weeks 25-33) in summer 2020. We used a high throughput real-time PCR (HT-qPCR) system to detect and quantify 216 ARGs and genes associated with mobile genetic elements (MGEs), integrons, and bacteria causing hospital acquired infections (HAIs), as well as the 16S rRNA gene. We analysed and visualised data from HT-qPCR using a novel digital platform, ResistApp. We focused on eight carbapenem resistance genes (blaGES, blaKPC, blaVIM, blaNDM, blaCMY, blaMOX, blaOXA48, and blaOXA51) and three genes associated with bacteria causing HAIs (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa).<br><br>FINDINGS: We detected a significantly higher number of ARGs at both hospitals in weeks 27-30 (174-191 genes) compared to other sampling weeks (151-171 genes). Our analyses also indicated that the two hospitals, which used different amounts of antibiotics, had significantly different resistance gene profiles. Carbapenem resistance genes were more prevalent and abundant in HUS1 than HUS2. Across both hospitals, blaGES and blaVIM were the most prevalent and abundant. We also found a strong positive association between blaKPC and K. pneumoniae in HUS1 wastewater.<br><br>CONCLUSION: Routine wastewater-based monitoring using ResistApp can provide valuable information on the prevalence and abundance of ARGs in hospitals. This helps hospitals understand the spread of antibiotic resistance in hospitals and identify potential areas for intervention.}, }
@article {pmid34536095, year = {2021}, author = {Gnat, S and Łagowski, D and Dyląg, M and Nowakiewicz, A}, title = {European Hedgehogs (Erinaceus europaeus L.) as a Reservoir of Dermatophytes in Poland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34536095}, issn = {1432-184X}, abstract = {The European hedgehog (Erinaceus europaeus Linnaeus) frequently colonises areas located close to human life in cities, as these are more suitable nest sites offering an abundance of food and allowing avoidance of predators. However, urbanisation has a significant impact on the epidemiology of infectious diseases, including dermatophytoses, the primary source of which are wild animals. In this study, we determined the spectrum of dermatophytes isolated from the European hedgehog and assessed their susceptibility profile to antifungal drugs. Symptomatic and asymptomatic dermatophyte infections were observed in 7.7% and 8% of the 182 examined free-living hedgehogs, respectively. In the pool of the isolated dermatophyte strains, Trichophyton erinacei was dominant (29.9%), followed by Trichophyton mentagrophytes (17.9%), Trichophyton benhamiae (13.4%), Nannizzia gypsea (11.9%), Microsporum canis (10.4%), Nannizzia nana (7.5%), Paraphyton cookei (6.0%), and Nannizzia fulva (3.0%). Susceptibility tests revealed the highest activity of luliconazole and the lowest of activity fluconazole among the azole drugs applied. Although terbinafine generally exhibited high efficacy, two Trichophyton mentagrophytes isolates showed resistance to this drug (MIC = 2 µg/ml) resulting from missense mutations in the SQLE gene corresponding to the amino acid substitution Leu393Phe. Summarising, our study has also revealed that such wildlife animals as hedgehogs can be a reservoir of pathogenic human dermatophytes, including harmful strains resistant to commonly used antifungal drugs.}, }
@article {pmid34530674, year = {2021}, author = {Neumann, M and Steimle, A and Grant, ET and Wolter, M and Parrish, A and Willieme, S and Brenner, D and Martens, EC and Desai, MS}, title = {Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1966263}, doi = {10.1080/19490976.2021.1966263}, pmid = {34530674}, issn = {1949-0984}, abstract = {The change of dietary habits in Western societies, including reduced consumption of fiber, is linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections between diet-induced microbiota changes that affect colonization resistance and enteric pathogen susceptibility are still emerging. We sought to investigate how a diet devoid of soluble plant fibers impacts the structure and function of a conventional gut microbiota in specific-pathogen-free (SPF) mice and how such changes alter susceptibility to a rodent enteric pathogen. We show that absence of dietary fiber intake leads to shifts in the abundances of specific taxa, microbiome-mediated erosion of the colonic mucus barrier, a reduction of intestinal barrier-promoting short-chain fatty acids, and increases in markers of mucosal barrier integrity disruption. Importantly, our results highlight that these low-fiber diet-induced changes in the gut microbial ecology collectively contribute to a lethal colitis by the mucosal pathogen Citrobacter rodentium, which is used as a mouse model for enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Our study indicates that modern, low-fiber Western-style diets might make individuals more prone to infection by enteric pathogens via the disruption of mucosal barrier integrity by diet-driven changes in the gut microbiota, illustrating possible implications for EPEC and EHEC infections.}, }
@article {pmid34530278, year = {2021}, author = {Li, W and Chen, X and Li, M and Cai, Z and Gong, H and Yan, M}, title = {Microplastics as an aquatic pollutant affect gut microbiota within aquatic animals.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt B}, pages = {127094}, doi = {10.1016/j.jhazmat.2021.127094}, pmid = {34530278}, issn = {1873-3336}, abstract = {The adverse impact of microplastics (MPs) on gut microbiota within aquatic animals depends on the overall effect of chemicals and biofilm of MPs. Thus, it is ideal to fully understand the influences that arise from each or even all of these characteristics, which should give us a whole picture of consequences that are brought by MPs. Harmful effects of MPs on gut microbiota within aquatic organisms start from the ingestion of MPs by aquatic organisms. According to this, the present review will discuss the ingestion of MPs and its following results on gut microbial communities within aquatic animals, in which chemical components, such as plastic polymers, heavy metals and POPs, and the biofilm of MPs would be involved. This review firstly analyzed the impacts of MPs on aquatic organisms in detail about its chemical components and biofilm based on previous relevant studies. At last, the significance of field studies, functional studies and complex dynamics of gut microbial ecology in the future research of MPs affecting gut microbiota is discussed.}, }
@article {pmid34528105, year = {2021}, author = {Zhang, J and Peng, S and Li, S and Song, J and Brunel, B and Wang, E and James, EK and Chen, W and Andrews, M}, title = {Arachis hypogaea L. from Acid Soils of Nanyang (China) Is Frequently Associated with Bradyrhizobium guangdongense and Occasionally with Bradyrhizobium ottawaense or Three Bradyrhizobium Genospecies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34528105}, issn = {1432-184X}, abstract = {Henan Province is a major area of peanut production in China but the rhizobia nodulating the crop in this region have not been described. A collection of 217 strains of peanut rhizobia was obtained from six field sites across four soil types in Henan Province, North China, by using peanut as a trap host under glasshouse conditions. The 217 strains separated into 8 distinct types on PCR-RFLP analysis of their IGS sequences. Phylogenetic analysis of the 16S rRNA, recA, atpD, and glnII genes of 11 representative strains of the 8 IGS types identified Bradyrhizobium guangdongense, B. ottawaense and three novel Bradyrhizobium genospecies. Bradyrhizobium guangdongense was dominant, accounting for 75.0% of the total isolates across the field sites while B. ottawaense covered 5.1% and the three novel Bradyrhizobium genospecies 4.1 to 8.8% of the total. The symbiosis-related nodA and nifH gene sequences were not congruent with the core genes on phylogenetic analysis and separated into three groups, two of which were similar to sequences of Bradyrhizobium spp. isolated from peanut in south-east China and the third identical to that of B. yuanmingense isolated from Lespedeza cuneata in northern China. A canonical correlation analysis between the distribution of IGS genotypes and soil physicochemical characteristics and climatic factors indicated that the occurrence of IGS types/species was mainly associated with soil pH and available phosphorus.}, }
@article {pmid34527661, year = {2021}, author = {Kerckhof, FM and Sakarika, M and Van Giel, M and Muys, M and Vermeir, P and De Vrieze, J and Vlaeminck, SE and Rabaey, K and Boon, N}, title = {From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {733753}, pmid = {34527661}, issn = {2296-4185}, abstract = {Increasing efforts are directed towards the development of sustainable alternative protein sources among which microbial protein (MP) is one of the most promising. Especially when waste streams are used as substrates, the case for MP could become environmentally favorable. The risks of using organic waste streams for MP production-the presence of pathogens or toxicants-can be mitigated by their anaerobic digestion and subsequent aerobic assimilation of the (filter-sterilized) biogas. Even though methane and hydrogen oxidizing bacteria (MOB and HOB) have been intensively studied for MP production, the potential benefits of their co-cultivation remain elusive. Here, we isolated a diverse group of novel HOB (that were capable of autotrophic metabolism), and co-cultured them with a defined set of MOB, which could be grown on a mixture of biogas and H2/O2. The combination of MOB and HOB, apart from the CH4 and CO2 contained in biogas, can also enable the valorization of the CO2 that results from the oxidation of methane by the MOB. Different MOB and HOB combinations were grown in serum vials to identify the best-performing ones. We observed synergistic effects on growth for several combinations, and in all combinations a co-culture consisting out of both HOB and MOB could be maintained during five days of cultivation. Relative to the axenic growth, five out of the ten co-cultures exhibited 1.1-3.8 times higher protein concentration and two combinations presented 2.4-6.1 times higher essential amino acid content. The MP produced in this study generally contained lower amounts of the essential amino acids histidine, lysine and threonine, compared to tofu and fishmeal. The most promising combination in terms of protein concentration and essential amino acid profile was Methyloparacoccus murrelli LMG 27482 with Cupriavidus necator LMG 1201. Microbial protein from M. murrelli and C. necator requires 27-67% less quantity than chicken, whole egg and tofu, while it only requires 15% more quantity than the amino acid-dense soybean to cover the needs of an average adult. In conclusion, while limitations still exist, the co-cultivation of MOB and HOB creates an alternative route for MP production leveraging safe and sustainably-produced gaseous substrates.}, }
@article {pmid34526978, year = {2021}, author = {Marvasi, M and Pangallo, D and Cavalieri, D and Poyatos-Jiménez, F}, title = {Editorial: Multi-Omics Revolution in Microbial Cultural Heritage Conservation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {720509}, pmid = {34526978}, issn = {1664-302X}, }
@article {pmid34526270, year = {2021}, author = {Barros, J and Seena, S}, title = {Plastisphere in freshwaters: An emerging concern.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {290}, number = {}, pages = {118123}, doi = {10.1016/j.envpol.2021.118123}, pmid = {34526270}, issn = {1873-6424}, abstract = {Plastisphere, an ecosystem of microbes thriving on floating plastic debris, has been extensively studied in marine waters since 2013. Currently, very little is known about the freshwater plastisphere. This review seeks to provide a broad insight into the freshwater science of plastisphere in the light of marine plastisphere, including research gaps, suggestions, and rising concerns, which would be of interest to the public, policymakers, and stakeholders. Given that freshwaters are endangered ecosystems, it is imperative to understand the role and impact of plastisphere on freshwaters. Plastic debris, especially microplastics (size <5 mm) in freshwater ecosystems, provide a stable, persistent, and buoyant substrate for microbes. Although current evidence suggests that freshwater environmental conditions and microplastics' physical and chemical properties significantly influence microbial colonisation, its role and integration in the aquatic ecosystems are unknown. Considering that the plastisphere biodiversity is unique, we seek to establish why and how many species co-exist in the plastisphere. Evaluating such fundamental questions should advance our basic understanding of the resilience of plastisphere to the changing environment. Plastisphere microbes, including the pathogenic bacteria, were found in both systems demonstrating their ability to survive on the plastic fragments from one ecosystem to another. A significant concern regarding plastisphere is the potential freshwater dispersal of anthropogenic pollutants and invasive or pathogenic species. Notably, microplastics aggregates may serve as a food source for grazers, which opens the question of the extent to which it can impact freshwater food webs. To gain a thorough understanding of the interplay between microplastics and the biogeochemical cycle, further insight into plastisphere microbes' functional role is needed. This would shed light on the unconsidered freshwater elemental cycling pathways. Given the complexity and universal nature of the plastisphere, strong interdisciplinary global research initiatives or networks are required to address the emerging concerns of plastisphere in freshwaters.}, }
@article {pmid34523560, year = {2021}, author = {Trego, AC and Conall Holohan, B and Keating, C and Graham, A and O'Connor, S and Gerardo, M and Hughes, D and Ijaz, UZ and O'Flaherty, V}, title = {First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater.}, journal = {Bioresource technology}, volume = {341}, number = {}, pages = {125786}, doi = {10.1016/j.biortech.2021.125786}, pmid = {34523560}, issn = {1873-2976}, abstract = {Municipal wastewater constitutes the largest fraction of wastewater, and yet treatment processes are largely removal-based. High-rate anaerobic digestion (AD) has revolutionised the sustainability of industrial wastewater treatment and could additionally provide an alternative for municipal wastewater. While AD of dilute municipal wastewater is common in tropical regions, the low temperatures of temperate climates has resulted in slow uptake. Here, we demonstrate for the first time, direct, high-rate, low-temperature AD of low-strength municipal wastewater at full-scale. An 88 m3 hybrid reactor was installed at the municipal wastewater treatment plant in Builth Wells, UK and operated for 290 days. Ambient temperatures ranged from 2 to 18 °C, but remained below 15 °C for > 100 days. Influent BOD fluctuated between 2 and 200 mg L-1. However, BOD removal often reached > 85%. 16S rRNA amplicon sequencing of DNA from the biomass revealed a highly adaptable core microbiome. These findings could provide the basis for the next-generation of municipal wastewater treatment.}, }
@article {pmid34523363, year = {2021}, author = {De Vuyst, L and Comasio, A and Kerrebroeck, SV}, title = {Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-33}, doi = {10.1080/10408398.2021.1976100}, pmid = {34523363}, issn = {1549-7852}, abstract = {Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.}, }
@article {pmid34522990, year = {2021}, author = {Matsumoto, S and Watanabe, K and Imamura, A and Tachibana, M and Shimizu, T and Watarai, M}, title = {Comparative Analysis Between Paramecium Strains with Different Syngens Using the RAPD Method.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34522990}, issn = {1432-184X}, support = {19K06383//Japan Society for the Promotion of Science/ ; 17H03914//Japan Society for the Promotion of Science/ ; }, abstract = {Paramecium spp. are a genus of free-living protists that live mainly in freshwater environments. They are ciliates with high motility and phagocytosis and have been used to analyze cell motility and as a host model for pathogens. Besides such biological characteristics, apart from the usual morphological and genetic classification of species, the existence of taxonomies (such as syngens) and mating types related to Paramecium's unique reproduction is known. In this study, we attempted to develop a simple method to identify Paramecium strains, which are difficult to distinguish morphologically, using random amplified polymorphic DNA (RAPD) analysis. Consequently, we can observe strain-specific band patterns. We also confirm that the presence of endosymbiotic Chlorella cells affects the band pattern of P. bursaria. Furthermore, the results of the RAPD analysis using several P. caudatum strains with different syngens show that it is possible to detect a band specific to a certain syngen. By improving the reaction conditions and random primers, based on the results of this study, RAPD analysis can be applied to the identification of Paramecium strains and their syngen confirmation tests.}, }
@article {pmid34519519, year = {2021}, author = {Putman, LI and Sabuda, MC and Brazelton, WJ and Kubo, MD and Hoehler, TM and McCollom, TM and Cardace, D and Schrenk, MO}, title = {Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030021}, doi = {10.1128/mSystems.00300-21}, pmid = {34519519}, issn = {2379-5077}, abstract = {In recent years, our appreciation of the extent of habitable environments in Earth's subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time. IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.}, }
@article {pmid34518545, year = {2021}, author = {Chen, Y and Wang, Y and Paez-Espino, D and Polz, MF and Zhang, T}, title = {Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5398}, pmid = {34518545}, issn = {2041-1723}, abstract = {As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.}, }
@article {pmid34515628, year = {2021}, author = {Undabarrena, A and Pereira, CF and Kruasuwan, W and Parra, J and Sélem-Mojica, N and Vind, K and Schniete, JK}, title = {Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21.}, journal = {Microbiology (Reading, England)}, volume = {167}, number = {9}, pages = {}, doi = {10.1099/mic.0.001084}, pmid = {34515628}, issn = {1465-2080}, abstract = {Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.}, }
@article {pmid34515591, year = {2021}, author = {Li, Q and Van de Wiele, T}, title = {Gut microbiota as a driver of the interindividual variability of cardiometabolic effects from tea polyphenols.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-27}, doi = {10.1080/10408398.2021.1965536}, pmid = {34515591}, issn = {1549-7852}, abstract = {Tea polyphenols have been extensively studied for their preventive properties against cardiometabolic diseases. Nevertheless, the evidence of these effects from human intervention studies is not always consistent, mainly because of a large interindividual variability. The bioavailability of tea polyphenols is low, and metabolism of tea polyphenols highly depends on individual gut microbiota. The accompanying reciprocal relationship between tea polyphenols and gut microbiota may result in alterations in the cardiometabolic effects, however, the underlying mechanism of which is little explored. This review summarizes tea polyphenols-microbiota interaction and its contribution to interindividual variability in cardiometabolic effects. Currently, only a few bacteria that can biodegrade tea polyphenols have been identified and generated metabolites and their bioactivities in metabolic pathways are not fully elucidated. A deeper understanding of the role of complex interaction necessitates fully individualized data, the ntegration of multiple-omics platforms and development of polyphenol-centered databases. Knowledge of this microbial contribution will enable the functional stratification of individuals in the gut microbiota profile (metabotypes) to clarify interindividual variability in the health effects of tea polyphenols. This could be used to predict individual responses to tea polyphenols consumption, hence bringing us closer to personalized nutrition with optimal dose and additional supplementation of specific microorganisms.}, }
@article {pmid34512595, year = {2021}, author = {Tavares, TCL and Bezerra, WM and Normando, LRO and Rosado, AS and Melo, VMM}, title = {Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {715991}, doi = {10.3389/fmicb.2021.715991}, pmid = {34512595}, issn = {1664-302X}, abstract = {Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.}, }
@article {pmid34512593, year = {2021}, author = {Zhao, J and Ma, J and Yang, Y and Yu, H and Zhang, S and Chen, F}, title = {Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714967}, doi = {10.3389/fmicb.2021.714967}, pmid = {34512593}, issn = {1664-302X}, abstract = {Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.}, }
@article {pmid34510242, year = {2021}, author = {Mikhailov, IS and Galachyants, YP and Bukin, YS and Petrova, DP and Bashenkhaeva, MV and Sakirko, MV and Blinov, VV and Titova, LA and Zakharova, YR and Likhoshway, YV}, title = {Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34510242}, issn = {1432-184X}, support = {0279-2021-0008//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0009//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0004//Ministry of Science and Higher Education of Russian Federation/ ; АААА-А17-117041250054-8//Integration project of the Irkutsk Scientific Center state/ ; }, abstract = {Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.}, }
@article {pmid34505915, year = {2021}, author = {LaForgia, ML and Kang, H and Ettinger, CL}, title = {Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34505915}, issn = {1432-184X}, abstract = {Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.}, }
@article {pmid34504476, year = {2021}, author = {Lammers, A and Zweers, H and Sandfeld, T and Bilde, T and Garbeva, P and Schramm, A and Lalk, M}, title = {Antimicrobial Compounds in the Volatilome of Social Spider Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {700693}, doi = {10.3389/fmicb.2021.700693}, pmid = {34504476}, issn = {1664-302X}, abstract = {Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the dense colony structure, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. Stegodyphus dumicola is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of S. dumicola, their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40% of the tentatively identified VOCs are known for their antimicrobial activity. Here, six VOCs were confirmed by analyzing pure compounds namely acetophenone, 1,3-benzothiazole, 1-decanal, 2-decanone, 1-tetradecene, and docosane and for five of these compounds the antimicrobial activity were proven. The nest and web volatilomes had many VOCs in common, whereas the spider volatilomes were more differentiated. Clear differences were identified between the volatilomes from the different sampling sites which is likely justified by differences in the microbiomes of the spiders and nests, the plants, and the different climatic conditions. The results indicate the potential relevance of the volatilomes for the ecological success of S. dumicola.}, }
@article {pmid34499191, year = {2021}, author = {Yaghoubi Khanghahi, M and Crecchio, C and Verbruggen, E}, title = {Shifts in the Rhizosphere and Endosphere Colonizing Bacterial Communities Under Drought and Salinity Stress as Affected by a Biofertilizer Consortium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34499191}, issn = {1432-184X}, abstract = {The present research asks how plant growth-promoting bacterial (PGPB) inoculants and chemical fertilizers change rhizosphere and root endophytic bacterial communities in durum wheat, and its dependence on environmental stress. A greenhouse experiment was carried out under drought (at 40% field capacity), or salinity (150 mM NaCl) conditions to investigate the effects of a chemical fertilizer (containing nitrogen, phosphorus, potassium and zinc) or a biofertilizer (a bacterial consortium of four PGPBs). High-throughput amplicon sequencing of the 16S rRNA of the rhizosphere, non-sterilized, or surface-sterilized roots, showed shifts in bacterial communities in response to stress treatments, which were greater for salinity than for drought and tended to show increased oligotrophs relative abundances compared to non-stress controls. The results also showed that Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Thaumarchaeota, Firmicutes, and Verrucomicrobia had a higher relative abundance in the rhizosphere, while Actinobacteria were more abundant on roots, while Candidatus_Saccharibacteria and Planctomycetes inside roots. The results indicated that the root endophytic bacterial communities were more affected by (bio-) fertilization treatments than those in the rhizosphere, particularly as affected by PGPB inoculation. This greater susceptibility of endophytes to (bio-) fertilizers was associated with increased abundance of the 16S rRNA and acdS genes in plant roots, especially under stress conditions. These changes in root endophytes, which coincided with an improvement in grain yield and photosynthetic capacity of plants, may be considered as one of the mechanisms by which PGPB affect plants.}, }
@article {pmid34498120, year = {2021}, author = {Silva, AMM and Estrada-Bonilla, GA and Lopes, CM and Matteoli, FP and Cotta, SR and Feiler, HP and Rodrigues, YF and Cardoso, EJBN}, title = {Does Organomineral Fertilizer Combined with Phosphate-Solubilizing Bacteria in Sugarcane Modulate Soil Microbial Community and Functions?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34498120}, issn = {1432-184X}, support = {01.13.0209.00//Financiadora de Estudos e Projetos/ ; 2016/18944-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem processes. Here, information on composition and functions of bacterial and fungal communities were evaluated at two phenological stages of sugarcane (six and twelve months, equivalent to the most intensive vegetative stage and to final maturation, respectively) when organomineral fertilizer, combined with phosphate-solubilizing bacteria (PSB), was added into the soil. Organic compost enriched with apatite (C + A) or phosphorite (C + P) and compost without phosphate enrichment (C) were used in the presence or absence of PSB. In addition, we used a control fertilized with soluble triple superphosphate. The differences were more related to the sampling period than to the type of organomineral fertilizer, being observed higher available phosphorus at six months than at twelve months. Only in the C treatment we observed the presence of Bacillaceae and Planococcaceae, while Pseudomonadaceae were only prevalent in inoculated C + A. As for fungi, the genera Chaetomium and Achroiostachys were only present in inoculated C + P, while the genus Naganishia was most evident in inoculated C + A and in uninoculated C + P. Soliccocozyma represented 75% of the total fungal abundance in uninoculated C while in inoculated C, it represented 45%. The bacterial community was more related to the degradation of easily decomposable organic compounds, while the fungal community was more related to degradation of complex organic compounds. Although the microbial community showed a resilient trait, subtle changes were detected in microbial community composition and function, and this may be related to the increase in yield observed.}, }
@article {pmid34498119, year = {2021}, author = {Yun, J and Jung, JY and Kwon, MJ and Seo, J and Nam, S and Lee, YK and Kang, H}, title = {Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34498119}, issn = {1432-184X}, support = {NRF-2019H1A2A1076239//Ministry of Education/ ; NRF-2016M1A5A1901770, PN20081//Ministry of Science and ICT of Korea/ ; NRF-2016M1A5A1901795//Ministry of Science and ICT of Korea/ ; NRF-2020M1A5A1110494//Ministry of Science and ICT of Korea/ ; }, abstract = {In Arctic soils, warming accelerates decomposition of organic matter and increases emission of greenhouse gases (GHGs), contributing to a positive feedback to climate change. Although microorganisms play a key role in the processes between decomposition of organic matter and GHGs emission, the effects of warming on temporal responses of microbial activity are still elusive. In this study, treatments of warming and precipitation were conducted from 2012 to 2018 in Cambridge Bay, Canada. Soils of organic and mineral layers were collected monthly from June to September in 2018 and analyzed for extracellular enzyme activities and bacterial community structures. The activity of hydrolases was the highest in June and decreased thereafter over summer in both organic and mineral layers. Bacterial community structures changed gradually over summer, and the responses were distinct depending on soil layers and environmental factors; water content and soil temperature affected the shift of bacterial community structures in both layers, whereas bacterial abundance, dissolved organic carbon, and inorganic nitrogen did so in the organic layer only. The activity of hydrolases and bacterial community structures did not differ significantly among treatments but among months. Our results demonstrate that temporal variations may control extracellular enzyme activities and microbial community structure rather than the small effect of warming over a long period in high Arctic soil. Although the effects of the treatments on microbial activity were minor, our study provides insight that microbial activity may increase due to an increase in carbon availability, if the growing season is prolonged in the Arctic.}, }
@article {pmid34498118, year = {2021}, author = {Minahan, NT and Chen, CH and Shen, WC and Lu, TP and Kallawicha, K and Tsai, KH and Guo, YL}, title = {Fungal Spore Richness in School Classrooms is Related to Surrounding Forest in a Season-Dependent Manner.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34498118}, issn = {1432-184X}, support = {MOST 108-2621-M-002-018//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Airborne fungal spores are important aeroallergens that are remarkably diverse in terms of taxonomic richness. Indoor fungal richness is dominated by outdoor fungi and is geographically patterned, but the influence of natural landscape is unclear. We aimed to elucidate the relationship between indoor fungal spore richness and natural landscape by examining the amount of surrounding forest cover. Passive sampling of airborne fungal spores was conducted in 24 schools in Taiwan during hot and cool seasons, and amplicon sequencing was used to study fungal spore (genus) richness targeting the internal transcribed spacer 2 (ITS2) region. In total, 693 fungal genera were identified, 12 of which were ubiquitous. Despite overall similarity of fungal spore richness between seasons, Basidiomycota and Ascomycota richness increased during the hot and cool seasons, respectively. Fungal spore richness in schools had a strong positive correlation with the amount of surrounding forest cover during the cool season, but not during the hot season. Fungal assemblages in schools were more similar during the hot season due to the increased ubiquity of Agaricomycetes genera. These observations indicate dispersal limitation at the kilometer scale during the cool season and increased long-distance dispersal during the hot season. Several allergenic fungi were commonly identified in schools, including some previously overlooked by conventional methods, which may be targeted as sensitizing agents in future investigations into atopic conditions. More generally, the relative importance of fungal spore richness in the development, chronicity, and severity of atopic conditions in children requires investigation.}, }
@article {pmid34495440, year = {2021}, author = {Xie, J and Wang, X and Xu, J and Xie, H and Cai, Y and Liu, Y and Ding, X}, title = {Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).}, journal = {Rice (New York, N.Y.)}, volume = {14}, number = {1}, pages = {79}, pmid = {34495440}, issn = {1939-8425}, support = {81960364//national natural science foundation of china/ ; 31560041//national natural science foundation of china/ ; 81501162//national natural science foundation of china/ ; 20171BCB23020//jiangxi province outstanding young talents funding scheme/ ; 9166-27060003-YB11//interdisciplinary innovation fund of nanchang university/ ; }, abstract = {BACKGROUND: Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress.<br><br>RESULTS: We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'.<br><br>CONCLUSIONS: Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.}, }
@article {pmid34495359, year = {2021}, author = {Agarwal, R and Gupta, M and Antony, A and Sen, R and Raychoudhury, R}, title = {In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34495359}, issn = {1432-184X}, abstract = {Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.}, }
@article {pmid34494852, year = {2021}, author = {Ma, L and Huang, X and Wang, H and Yun, Y and Cheng, X and Liu, D and Lu, X and Qiu, X}, title = {Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0115221}, doi = {10.1128/Spectrum.01152-21}, pmid = {34494852}, issn = {2165-0497}, abstract = {The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.}, }
@article {pmid34491099, year = {2021}, author = {Su, L and Qiu, P and Fang, Z and Mo, X and Sun, J and Liu, Y and Kuramae, E and Zhang, R and Shen, B and Shen, Q}, title = {Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-08-21-1601-RE}, pmid = {34491099}, issn = {0191-2917}, abstract = {Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soil-borne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we combined potassium phosphite (K-Phite), an environmentally friendly agricultural chemical, and the biocontrol agent Bacillus amyloliquefaciens QPF8 (strain F8) to manage tomato bacterial wilt disease. First, K-Phite at a concentration of 0.05% (w/v) could significantly inhibit the growth of Ralstonia solanacearum. Second, 0.05% K-Phite enhanced the antagonistic capability of B. amyloliquefaciens F8. Third, the greenhouse soil experiments showed that the control efficiency for tomato bacterial wilt in the combined treatment was significantly higher than that of the application of B. amyloliquefaciens F8 or K-Phite alone. Overall, our results highlighted a novel strategy for the control of tomato bacterial wilt disease via application and revealed a new integrated pattern depending on the enhancement of the antagonistic capability of biocontrol microbes by K-Phite.}, }
@article {pmid34490209, year = {2021}, author = {Medvecky, M and Mandalakis, M}, title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.}, journal = {Frontiers in chemistry}, volume = {9}, number = {}, pages = {722087}, doi = {10.3389/fchem.2021.722087}, pmid = {34490209}, issn = {2296-2646}, abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.}, }
@article {pmid34487274, year = {2021}, author = {Benedek, T and Szentgyörgyi, F and Gergócs, V and Menashe, O and Gonzalez, PAF and Probst, AJ and Kriszt, B and Táncsics, A}, title = {Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites.}, journal = {AMB Express}, volume = {11}, number = {1}, pages = {126}, pmid = {34487274}, issn = {2191-0855}, support = {TKP2020-IKA-12//ministry of innovation and technology/ ; 2018-2.1.16-TÉT-IL-2018-00002//nemzeti kutatási fejlesztési és innovációs hivatal/ ; FK 134439//otka young researcher excellence programme/ ; }, abstract = {Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l-1) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l-1) conditions using either individual (8 mg‧l-1) or a mixture of compounds (~ 1.3 mg‧l-1 of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP-Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l-1 per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13-alone or in co-culture with other BTEX degrading bacterial isolates-can be a new and efficient commercial bioremediation agent for BTEX contaminated sites.}, }
@article {pmid34487212, year = {2021}, author = {Wahdan, SFM and Hossen, S and Tanunchai, B and Sansupa, C and Schädler, M and Noll, M and Dawoud, TM and Wu, YT and Buscot, F and Purahong, W}, title = {Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34487212}, issn = {1432-184X}, abstract = {Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca2+, and pH) and future (C/N, N, P, K+, Ca2+, pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.}, }
@article {pmid34487211, year = {2021}, author = {Deng, J and Yu, D and Zhou, W and Zhou, L and Zhu, W}, title = {Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34487211}, issn = {1432-184X}, support = {E0381601//the Mission of Chinese Academy of Sciences/ ; }, abstract = {Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.}, }
@article {pmid34486723, year = {2021}, author = {Stephen, AS and Dhadwal, N and Nagala, V and Gonzales-Marin, C and Gillam, DG and Bradshaw, DJ and Burnett, GR and Allaker, RP}, title = {Interdental and subgingival microbiota may affect the tongue microbial ecology and oral malodour in health, gingivitis and periodontitis.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.12931}, pmid = {34486723}, issn = {1600-0765}, support = {//GlaxoSmithKline/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND AND OBJECTIVE: Oral malodour is often observed in gingivitis and chronic periodontitis patients, and the tongue microbiota is thought to play a major role in malodorous gas production, including volatile sulphur compounds (VSCs) such as hydrogen sulphide (H2 S) and methanethiol (CH3 SH). This study aimed to examine the link between the presence of VSCs in mouth air (as a marker of oral malodour) and the oral bacterial ecology in the tongue and periodontal niches of healthy, gingivitis and periodontitis patients.<br><br>METHODS: Participants were clinically assessed using plaque index, bleeding on probing (BOP) and periodontal probing depths, and VSC concentrations in their oral cavity measured using a portable gas chromatograph. Tongue scrapings, subgingival and interdental plaque were collected from healthy individuals (n = 22), and those with gingivitis (n = 14) or chronic periodontitis (n = 15). The bacterial 16S rRNA gene region V3-V4 in these samples was sequenced, and the sequences were analysed using the minimum entropy decomposition pipeline.<br><br>RESULTS: Elevated VSC concentrations and CH3 SH:H2 S were observed in periodontitis compared with health. Significant ecological differences were observed in the tongue microbiota of healthy subjects with high plaque scores compared to low plaque scores, suggesting a possible connection between the microbiota of the tongue and the periodontium and that key dysbiotic changes may be initiated in the clinically healthy individuals who have higher dental plaque accumulation. Greater subgingival bacterial diversity was positively associated with H2 S in mouth air. Periodontopathic bacteria known to be prolific VSC producers increased in abundance on the tongue associated with increased bleeding on probing (BOP) and total percentage of periodontal pockets >6 mm, supporting the suggestion that the tongue may become a reservoir for periodontopathogens.<br><br>CONCLUSION: This study highlights the importance of the periodontal microbiota in malodour and has detected dysbiotic changes in the tongue microbiota in periodontitis.}, }
@article {pmid34480872, year = {2021}, author = {Seki, D and Mayer, M and Hausmann, B and Pjevac, P and Giordano, V and Goeral, K and Unterasinger, L and Klebermaß-Schrehof, K and De Paepe, K and Van de Wiele, T and Spittler, A and Kasprian, G and Warth, B and Berger, A and Berry, D and Wisgrill, L}, title = {Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2021.08.004}, pmid = {34480872}, issn = {1934-6069}, abstract = {Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.}, }
@article {pmid34477968, year = {2021}, author = {Deepika, S and Kothamasi, D}, title = {Plant hosts may influence arbuscular mycorrhizal fungal community composition in mangrove estuaries.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, pmid = {34477968}, issn = {1432-1890}, support = {894188//h2020 marie skłodowska-curie actions/ ; }, abstract = {We investigated the role of plant host and soil variables in determining arbuscular mycorrhizal fungi (AMF) community composition in plant roots of two spatially separated mangrove estuaries on the rivers Aghanashini (14° 30' 30″ N-74° 22' 44″ E) and Gangavali (14° 35' 26″ N-74° 17' 51″ E) on the west coast of India. Both mangrove estuaries had similar plant species composition but differed in soil chemistries.We amplified a 550-bp portion of 18S small subunit (SSU) rDNA from mangrove plant roots and analysed it by restriction fragment length polymorphism (RFLP). Clones representing unique RFLP patterns were sequenced. A total of 736 clones were obtained from roots of seven and five plant species sampled at Aghanashini and Gangavali, respectively. AMF phylotype numbers in plant roots at Aghanashini (12) were higher than at Gangavali (9) indicating quantitative differences in the AMF community composition in plant roots at the two mangrove estuaries. Because both estuaries had similar plant species composition, the quantitative difference in AMF communities between the estuaries could be an attribute of the differences in rhizospheric chemistry between the two sites.Non-metric multidimensional scaling (NMDS) revealed overlap in the AMF communities of the two sites. Three and two AMF phylotypes had significant indicator value indices with specific hosts at Aghanashini and Gangavali, respectively. Environmental vector fitting to NMDS ordination did not reveal a significant effect of any soil variable on AMF composition at the two sites. However, significant effects of both plant hosts and sites were observed on rhizospheric P. Our results indicate that root AMF community composition may be an outcome of plant response to rhizospheric variables. This suggests that plant identity may have a primary role in shaping AMF communities in mangroves.}, }
@article {pmid34474030, year = {2021}, author = {Brennerova, MV and Zavala-Meneses, SG and Josefiova, J and Branny, P and Buriankova, K and Vetrovsky, T and Junca, H}, title = {A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons.}, journal = {Environmental research}, volume = {}, number = {}, pages = {111954}, doi = {10.1016/j.envres.2021.111954}, pmid = {34474030}, issn = {1096-0953}, abstract = {Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.}, }
@article {pmid34468785, year = {2021}, author = {Bazzicalupo, AL and Erlandson, S and Branine, M and Ratz, M and Ruffing, L and Nguyen, NH and Branco, S}, title = {Fungal Community Shift Along Steep Environmental Gradients from Geothermal Soils in Yellowstone National Park.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34468785}, issn = {1432-184X}, abstract = {Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.}, }
@article {pmid34468725, year = {2021}, author = {Varliero, G and Rafiq, M and Singh, S and Summerfield, A and Sgouridis, F and Cowan, DA and Barker, G}, title = {Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab127}, pmid = {34468725}, issn = {1574-6941}, abstract = {Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.}, }
@article {pmid34468165, year = {2021}, author = {Iburg, S and Izabel-Shen, D and Austin, ÅN and Hansen, JP and Eklöf, JS and Nascimento, FJA}, title = {Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0012721}, doi = {10.1128/mSphere.00127-21}, pmid = {34468165}, issn = {2379-5042}, abstract = {Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.}, }
@article {pmid34467445, year = {2021}, author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Kotetishvili, M}, title = {Bacteriophage-Mediated Risk Pathways Underlying the Emergence of Antimicrobial Resistance via Intrageneric and Intergeneric Recombination of Antibiotic Efflux Genes Across Natural populations of Human Pathogenic Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34467445}, issn = {1432-184X}, abstract = {Antimicrobial resistance continues to be a significant and growing threat to global public health, being driven by the emerging drug-resistant and multidrug-resistant strains of human and animal bacterial pathogens. While bacteriophages are generally known to be one of the vehicles of antibiotic resistance genes (ARGs), it remains largely unclear how these organisms contribute to the dissemination of the genetic loci encoding for antibiotic efflux pumps, especially those that confer multidrug resistance, in bacteria. In this study, the in-silico recombination analyses provided strong statistical evidence for bacteriophage-mediated intra-species recombination of ARGs, encoding mainly for the antibiotic efflux proteins from the MF superfamily, as well as from the ABC and RND families, in Salmonella enterica, Staphylococcus aureus, Staphylococcus suis, Pseudomonas aeruginosa, and Burkholderia pseudomallei. Events of bacteriophage-driven intrageneric recombination of some of these genes could be also elucidated among Bacillus thuringiensis, Bacillus cereus and Bacillus tropicus natural populations. Moreover, we could also reveal the patterns of intergeneric recombination, involving the MF superfamily transporter-encoding genetic loci, induced by a Mycobacterium smegmatis phage, in natural populations of Streptomyces harbinensis and Streptomyces chartreusis. The SplitsTree- (fit: 100; bootstrap values: 92.7-100; Phi p ≤ 0.2414), RDP4- (p ≤ 0.0361), and GARD-generated data strongly supported the above genetic recombination inferences in these in-silico analyses. Thus, based on this pilot study, it can be suggested that the above mode of bacteriophage-mediated recombination plays at least some role in the emergence and transmission of multidrug resistance across a fairly broad spectrum of bacterial species and genera including human pathogens.}, }
@article {pmid34466168, year = {2021}, author = {Crous, PW and Lombard, L and Sandoval-Denis, M and Seifert, KA and Schroers, HJ and Chaverri, P and Gené, J and Guarro, J and Hirooka, Y and Bensch, K and Kema, GHJ and Lamprecht, SC and Cai, L and Rossman, AY and Stadler, M and Summerbell, RC and Taylor, JW and Ploch, S and Visagie, CM and Yilmaz, N and Frisvad, JC and Abdel-Azeem, AM and Abdollahzadeh, J and Abdolrasouli, A and Akulov, A and Alberts, JF and Araújo, JPM and Ariyawansa, HA and Bakhshi, M and Bendiksby, M and Ben Hadj Amor, A and Bezerra, JDP and Boekhout, T and Câmara, MPS and Carbia, M and Cardinali, G and Castañeda-Ruiz, RF and Celis, A and Chaturvedi, V and Collemare, J and Croll, D and Damm, U and Decock, CA and de Vries, RP and Ezekiel, CN and Fan, XL and Fernández, NB and Gaya, E and González, CD and Gramaje, D and Groenewald, JZ and Grube, M and Guevara-Suarez, M and Gupta, VK and Guarnaccia, V and Haddaji, A and Hagen, F and Haelewaters, D and Hansen, K and Hashimoto, A and Hernández-Restrepo, M and Houbraken, J and Hubka, V and Hyde, KD and Iturriaga, T and Jeewon, R and Johnston, PR and Jurjević, Ž and Karalti, I and Korsten, L and Kuramae, EE and Kušan, I and Labuda, R and Lawrence, DP and Lee, HB and Lechat, C and Li, HY and Litovka, YA and Maharachchikumbura, SSN and Marin-Felix, Y and Matio Kemkuignou, B and Matočec, N and McTaggart, AR and Mlčoch, P and Mugnai, L and Nakashima, C and Nilsson, RH and Noumeur, SR and Pavlov, IN and Peralta, MP and Phillips, AJL and Pitt, JI and Polizzi, G and Quaedvlieg, W and Rajeshkumar, KC and Restrepo, S and Rhaiem, A and Robert, J and Robert, V and Rodrigues, AM and Salgado-Salazar, C and Samson, RA and Santos, ACS and Shivas, RG and Souza-Motta, CM and Sun, GY and Swart, WJ and Szoke, S and Tan, YP and Taylor, JE and Taylor, PWJ and Tiago, PV and Váczy, KZ and van de Wiele, N and van der Merwe, NA and Verkley, GJM and Vieira, WAS and Vizzini, A and Weir, BS and Wijayawardene, NN and Xia, JW and Yáñez-Morales, MJ and Yurkov, A and Zamora, JC and Zare, R and Zhang, CL and Thines, M}, title = {Fusarium: more than a node or a foot-shaped basal cell.}, journal = {Studies in mycology}, volume = {98}, number = {}, pages = {100116}, doi = {10.1016/j.simyco.2021.100116}, pmid = {34466168}, issn = {0166-0616}, abstract = {Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).}, }
@article {pmid34465761, year = {2021}, author = {Jia, KH and Liu, H and Zhang, RG and Xu, J and Zhou, SS and Jiao, SQ and Yan, XM and Tian, XC and Shi, TL and Luo, H and Li, ZC and Bao, YT and Nie, S and Guo, JF and Porth, I and El-Kassaby, YA and Wang, XR and Chen, C and Van de Peer, Y and Zhao, W and Mao, JF}, title = {Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {177}, pmid = {34465761}, issn = {2662-6810}, support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.}, }
@article {pmid34465293, year = {2021}, author = {De Vos, S and Rombauts, S and Coussement, L and Dermauw, W and Vuylsteke, M and Sorgeloos, P and Clegg, JS and Nambu, Z and Van Nieuwerburgh, F and Norouzitallab, P and Van Leeuwen, T and De Meyer, T and Van Stappen, G and Van de Peer, Y and Bossier, P}, title = {The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {635}, pmid = {34465293}, issn = {1471-2164}, abstract = {BACKGROUND: Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.<br><br>RESULTS AND DISCUSSION: Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions.<br><br>CONCLUSIONS: A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.}, }
@article {pmid34254826, year = {2021}, author = {Ha, AD and Moniruzzaman, M and Aylward, FO}, title = {High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0029321}, doi = {10.1128/mSystems.00293-21}, pmid = {34254826}, issn = {2379-5077}, support = {Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; 1918271//National Science Foundation (NSF)/ ; }, abstract = {Viruses belonging to the Nucleocytoviricota phylum are globally distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use these gene products to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. IMPORTANCE The discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here, we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.}, }
@article {pmid34463583, year = {2021}, author = {Dekas, AE}, title = {Quantifying Microbial Activity In Situ: the Link between Cells and Cycles.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075821}, doi = {10.1128/mSystems.00758-21}, pmid = {34463583}, issn = {2379-5077}, abstract = {Metagenomic sequencing of environmental samples has dramatically expanded our knowledge of microbial taxonomic and metabolic diversity and suggests metabolic interdependence is widespread. However, translating these insights into knowledge of ecosystem function and, therefore, implications for local and global chemistry, remains a challenge. In this commentary, I argue that making direct measurements of microbial activity in situ is an essential step to confirm gene-based hypotheses of microbial physiology and bridge advances in microbial ecology with a predicative understanding of global chemistry and climate. Making these measurements across a range of spatial scales and experimentally manipulated conditions contributes to a process-based understanding and, therefore, more robust predictions of how activity will respond to changing environmental conditions. I discuss recent advancements in quantifying microbial activity in situ and highlight several lines of research in marine microbiology that leverage complementary genomic and isotopic methods to connect microbes and global chemistry.}, }
@article {pmid34463567, year = {2021}, author = {Harrington, V and Lau, L and Seddu, K and Suez, J}, title = {Ecology and Medicine Converge at the Microbiome-Host Interface.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075621}, doi = {10.1128/mSystems.00756-21}, pmid = {34463567}, issn = {2379-5077}, abstract = {The human body is home to a dense and diverse population of bacteria, viruses, and eukaryotes, collectively termed the microbiome. Research on host-microbiome interactions continuously demonstrates the importance of this microbial community to human physiology and its involvement in a myriad of diseases. This, in turn, sparks great interest in developing means for beneficially modulating the microbiome, such as fecal microbiome transplantation and probiotics. However, these interventions show mixed efficacy in clinical trials and raise safety concerns. How these exogenous microorganisms interact with the microbiome might underlie the efficacy and safety of these therapeutics, yet the signaling mechanisms mediating microbe-microbe interactions between human-dwelling commensals are poorly understood. In this commentary, we discuss known and putative mechanisms of interactions between commensals in the gut and how they can be harnessed for improving microbiome-targeting therapeutics and facilitating translation of microbiome research to the clinic.}, }
@article {pmid34460265, year = {2021}, author = {Wang, S and Xia, J and De Paepe, K and Zhang, B and Fu, X and Huang, Q and Van de Wiele, T}, title = {Ultra-high Pressure Treatment Controls In Vitro Fecal Fermentation Rate of Insoluble Dietary Fiber from Rosa Roxburghii Tratt Pomace and Induces Butyrogenic Shifts in Microbiota Composition.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.1c03453}, pmid = {34460265}, issn = {1520-5118}, abstract = {Dietary fiber has been considered a key element in shaping the beneficial host-microbe symbiosis. In the present study, we identified Rosa roxburghii Tratt fruits as a promising dietary fiber source. The physicochemical properties and in vitro fermentability by human fecal microbes of R. roxburghii pomace water insoluble dietary fiber (RIDF) obtained from ultrasonic extraction and ultrahigh pressure (90 MPa)-treated RIDF (RIDF-90) were compared to those of R. roxburghii Tratt pomace (R). Ultrahigh pressure modification significantly increased the water holding, oil holding, and swelling capacity of RIDF-90 in comparison to R and RIDF. RIDF-90 displayed the slowest fermentation rate yet yielded the highest butyrate production. The superior butyrogenic properties of both RIDF-90 and, in part, RIDF were reflected by increased Coprococcus and Ruminococcus levels, demonstrating that ultrasonic extraction and/or further ultrahigh pressure treatment of insoluble fibers promotes the prebiotic value of R. roxburghii Tratt.}, }
@article {pmid34459553, year = {2021}, author = {Lindström, S and Timonen, S and Sundström, L}, title = {The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae).}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1201}, doi = {10.1002/mbo3.1201}, pmid = {34459553}, issn = {2045-8827}, support = {252411//Academy of Finland/ ; 284666//Academy of Finland/ ; }, abstract = {In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.}, }
@article {pmid34459548, year = {2021}, author = {Block, KR and O'Brien, JM and Edwards, WJ and Marnocha, CL}, title = {Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1228}, doi = {10.1002/mbo3.1228}, pmid = {34459548}, issn = {2045-8827}, abstract = {The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.}, }
@article {pmid34459543, year = {2021}, author = {Toubes-Rodrigo, M and Potgieter-Vermaak, S and Sen, R and Oddsdóttir, ES and Elliott, D and Cook, S}, title = {Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1200}, doi = {10.1002/mbo3.1200}, pmid = {34459543}, issn = {2045-8827}, support = {Research Accelerator//Manchester Metropolitan University/ ; Geographical Club Award//Royal Geographical Society/ ; }, abstract = {The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.}, }
@article {pmid34456379, year = {2020}, author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Larsson, E and Angelini, C and Brandrud, TE and Dearnaley, JDW and Dima, B and Dovana, F and Fechner, N and García, D and Gené, J and Halling, RE and Houbraken, J and Leonard, P and Luangsa-Ard, JJ and Noisripoom, W and Rea-Ireland, AE and Ševčíková, H and Smyth, CW and Vizzini, A and Adam, JD and Adams, GC and Alexandrova, AV and Alizadeh, A and Duarte, EÁ and Andjic, V and Antonín, V and Arenas, F and Assabgui, R and Ballarà, J and Banwell, A and Berraf-Tebbal, A and Bhatt, VK and Bonito, G and Botha, W and Burgess, TI and Caboň, M and Calvert, J and Carvalhais, LC and Courtecuisse, R and Cullington, P and Davoodian, N and Decock, CA and Dimitrov, R and Di Piazza, S and Drenth, A and Dumez, S and Eichmeier, A and Etayo, J and Fernández, I and Fiard, JP and Fournier, J and Fuentes-Aponte, S and Ghanbary, MAT and Ghorbani, G and Giraldo, A and Glushakova, AM and Gouliamova, DE and Guarro, J and Halleen, F and Hampe, F and Hernández-Restrepo, M and Iturrieta-González, I and Jeppson, M and Kachalkin, AV and Karimi, O and Khalid, AN and Khonsanit, A and Kim, JI and Kim, K and Kiran, M and Krisai-Greilhuber, I and Kučera, V and Kušan, I and Langenhoven, SD and Lebel, T and Lebeuf, R and Liimatainen, K and Linde, C and Lindner, DL and Lombard, L and Mahamedi, AE and Matočec, N and Maxwell, A and May, TW and McTaggart, AR and Meijer, M and Mešić, A and Mileto, AJ and Miller, AN and Molia, A and Mongkolsamrit, S and Cortés, CM and Muñoz-Mohedano, J and Morte, A and Morozova, OV and Mostert, L and Mostowfizadeh-Ghalamfarsa, R and Nagy, LG and Navarro-Ródenas, A and Örstadius, L and Overton, BE and Papp, V and Para, R and Peintner, U and Pham, THG and Pordel, A and Pošta, A and Rodríguez, A and Romberg, M and Sandoval-Denis, M and Seifert, KA and Semwal, KC and Sewall, BJ and Shivas, RG and Slovák, M and Smith, K and Spetik, M and Spies, CFJ and Syme, K and Tasanathai, K and Thorn, RG and Tkalčec, Z and Tomashevskaya, MA and Torres-Garcia, D and Ullah, Z and Visagie, CM and Voitk, A and Winton, LM and Groenewald, JZ}, title = {Fungal Planet description sheets: 1112-1181.}, journal = {Persoonia}, volume = {45}, number = {}, pages = {251-409}, doi = {10.3767/persoonia.2020.45.10}, pmid = {34456379}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.}, }
@article {pmid34455914, year = {2021}, author = {Molina Ortiz, JP and McClure, DD and Shanahan, ER and Dehghani, F and Holmes, AJ and Read, MN}, title = {Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1965698}, doi = {10.1080/19490976.2021.1965698}, pmid = {34455914}, issn = {1949-0984}, abstract = {The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.}, }
@article {pmid34453008, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {35}, pages = {}, doi = {10.1073/pnas.2108995118}, pmid = {34453008}, issn = {1091-6490}, }
@article {pmid34451540, year = {2021}, author = {Dos Santos, IMO and Abe, VY and de Carvalho, K and Barazetti, AR and Simionato, AS and de Almeida Pega, GE and Matis, SH and Cano, BG and Cely, MVT and Marcelino-Guimarães, FC and Chryssafidis, AL and Andrade, G}, title = {Secondary Metabolites of Pseudomonas aeruginosa LV Strain Decrease Asian Soybean Rust Severity in Experimentally Infected Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, doi = {10.3390/plants10081495}, pmid = {34451540}, issn = {2223-7747}, abstract = {Asian Soybean Rust (ASR), a disease caused by Phakopsora pachyrhizi, causing yield losses up to 90%. The control is based on the fungicides which may generate resistant fungi. The activation of the plant defense system, should help on ASR control. In this study, secondary metabolites of Pseudomonas aeruginosa LV strain were applied on spore germination and the expression of defense genes in infected soybean plants. The F4A fraction and the pure metabolites were used. In vitro, 10 µg mL-1 of F4A reduced spore germination by 54%, while 100 µg mL-1 completely inhibited. Overexpression of phenylalanine ammonia lyase (PAL), O-methyltransferase (OMT) and pathogenesis related protein-2 (PR-2; glucanases) defense-related genes were detected 24 and 72 h after soybean sprouts were sprayed with an organocopper antimicrobial compound (OAC). Under greenhouse conditions, the best control was observed in plants treated with 60 µg mL-1 of PCA, which reduced ASR severity and lesion frequency by 75% and 43%, respectively. Plants sprayed with 2 and 20 µg mL-1 of F4A also decreased severity (41%) and lesion frequency (32%). The significant reduction in spore germination ASR in plant suggested that the strain of these metabolites are effective against P. pachyrhizi, and they can be used for ASR control.}, }
@article {pmid34451391, year = {2021}, author = {Vigsnaes, LK and Ghyselinck, J and Van den Abbeele, P and McConnell, B and Moens, F and Marzorati, M and Bajic, D}, title = {2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, doi = {10.3390/pathogens10080927}, pmid = {34451391}, issn = {2076-0817}, support = {Cut-Off 10: reference number 8404//Eurostars/ ; }, abstract = {Clostridioides difficile (formerly Clostridium difficile) infection (CDI) is one of the most common hospital-acquired infections, which is often triggered by a dysbiosed indigenous gut microbiota (e.g., upon antibiotic therapy). Symptoms can be as severe as life-threatening colitis. The current study assessed the antipathogenic potential of human milk oligosaccharides (HMOs), i.e., 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and a combination thereof (MIX), against C. difficile ATCC 9689 using in vitro gut models that allowed the evaluation of both direct and, upon microbiota modulation, indirect effects. During a first 48 h fecal batch study, dysbiosis and CDI were induced by dilution of the fecal inoculum. For each of the three donors tested, C. difficile levels strongly decreased (with >4 log CFU/mL) upon treatment with 2'FL, LNnT and MIX versus untreated blanks, coinciding with increased acetate/Bifidobacteriaceae levels. Interindividual differences among donors at an intermediate time point suggested that the antimicrobial effect was microbiota-mediated rather than being a direct effect of the HMOs. During a subsequent 11 week study with the PathogutTM model (specific application of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)), dysbiosis and CDI were induced by clindamycin (CLI) treatment. Vancomycin (VNC) treatment cured CDI, but the further dysbiosis of the indigenous microbiota likely contributed to CDI recurrence. Upon co-supplementation with VNC, both 2'FL and MIX boosted microbial activity (acetate and to lesser extent propionate/butyrate). Moreover, 2'FL avoided CDI recurrence, potentially because of increased secondary bile acid production. Overall, while not elucidating the exact antipathogenic mechanisms-of-action, the current study highlights the potential of HMOs to combat CDI recurrence, help the gut microbial community recover after antibiotic treatment, and hence counteract the adverse effects of antibiotic therapies.}, }
@article {pmid34447362, year = {2021}, author = {Isaac, A and Francis, B and Amann, RI and Amin, SA}, title = {Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {718297}, doi = {10.3389/fmicb.2021.718297}, pmid = {34447362}, issn = {1664-302X}, abstract = {The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010-2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.}, }
@article {pmid34438891, year = {2021}, author = {You, I and Kim, MJ}, title = {Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {8}, pages = {}, doi = {10.3390/ani11082432}, pmid = {34438891}, issn = {2076-2615}, support = {#PJ015274022021//Rural Development Administration, South Korea/ ; }, abstract = {Since dogs are part of many peoples' lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to host health, limited information is available for canines. Therefore, this study characterized GM according to individual signatures (e.g., breed, age, and body condition score-BCS) of dogs living in the same environment. Fresh fecal samples from 96 healthy dogs were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. The major microbial phyla were Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. In the comparison by breeds, relative abundance of Fusobacterium was significantly differed. Interestingly, Fusobacterium perfoetens abundance was positively correlated with age (p = 0.018), being significantly more enriched in the 6-10-year-old group (14.3%) than in the 0.5-1-year-old group (7.2%). Moreover, despite the healthy appearance of dogs in all age (0.5-10 years) and BCS (3-6) groups, the gut microbial environment may be disadvantageous in older dogs or in dogs with an abnormal BCS. These findings broaden our understanding of gut microbial ecology according to individual characteristics of dogs and may be used as a reference for providing customized-care to companion animals.}, }
@article {pmid34436641, year = {2021}, author = {Jan, B and Reshi, ZA and Mohiddin, FA}, title = {Correction to: Site and Organ‑Specific Culture‑Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01847-z}, pmid = {34436641}, issn = {1432-184X}, }
@article {pmid34436640, year = {2021}, author = {Möhlmann, TWR and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM}, title = {Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34436640}, issn = {1432-184X}, support = {1300018161//ANIHWA-EraNet/ ; Global One Health strategic program//Wageningen University/ ; }, abstract = {Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis, endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterised. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into 6-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens.}, }
@article {pmid34434657, year = {2021}, author = {Leonard, LT and Brodie, EL and Williams, KH and Sharp, JO}, title = {Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11926}, doi = {10.7717/peerj.11926}, pmid = {34434657}, issn = {2167-8359}, abstract = {Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800-3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2-3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.}, }
@article {pmid34232732, year = {2021}, author = {Malki, K and Sawaya, NA and Tisza, MJ and Coutinho, FH and Rosario, K and Székely, AJ and Breitbart, M}, title = {Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida).}, journal = {Applied and environmental microbiology}, volume = {87}, number = {18}, pages = {e0064621}, doi = {10.1128/AEM.00646-21}, pmid = {34232732}, issn = {1098-5336}, support = {award no. 3900101301//National Science Foundation GRFP/ ; //Swedish Research Council Formas/ ; //Intramural Research Program of the NIH and NCI/ ; //Marie Curie International Outgoing Fellowship/ ; DEB-1555854//National Science Foundation (NSF)/ ; APOSTD/2018/186//Generalitat Valenciana Fellowship/ ; }, abstract = {Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.}, }
@article {pmid34432600, year = {2021}, author = {Roussel, C and De Paepe, K and Galia, W and de Bodt, J and Chalancon, S and Denis, S and Leriche, F and Vandekerkove, P and Ballet, N and Blanquet-Diot, S and Van de Wiele, T}, title = {Multi-targeted properties of the probiotic saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic escherichia coli (ETEC) H10407 pathogenesis across human gut models.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1953246}, doi = {10.1080/19490976.2021.1953246}, pmid = {34432600}, issn = {1949-0984}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of acute traveler's diarrhea. Adhesins and enterotoxins constitute the major ETEC virulence traits. With the dramatic increase in antibiotic resistance, probiotics are considered a wholesome alternative to prevent or treat ETEC infections. Here, we examined the antimicrobial properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against ETEC H10407 pathogenesis upon co-administration in the TNO gastrointestinal Model (TIM-1), simulating the physicochemical and enzymatic conditions of the human upper digestive tract and preventive treatment in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), integrating microbial populations of the ileum and ascending colon. Interindividual variability was assessed by separate M-SHIME experiments with microbiota from six human individuals. The probiotic did not affect ETEC survival along the digestive tract. However, ETEC pathogenicity was significantly reduced: enterotoxin encoding virulence genes were repressed, especially in the TIM-1 system, and a lower enterotoxin production was noted. M-SHIME experiments revealed that 18-days probiotic treatment stimulate the growth of Bifidobacterium and Lactobacillus in different gut regions (mucosal and luminal, ileum and ascending colon) while a stronger metabolic activity was noted in terms of short-chain fatty acids (acetate, propionate, and butyrate) and ethanol production. Moreover, the probiotic pre-treated microbiota displayed a higher robustness in composition following ETEC challenge compared to the control condition. We thus demonstrated the multi-inhibitory properties of the probiotic S. cerevisiae CNCM I-3856 against ETEC in the overall simulated human digestive tract, regardless of the inherent variability across individuals in the M-SHIME.}, }
@article {pmid34432103, year = {2021}, author = {Allsup, CM and Lankau, RA and Paige, KN}, title = {Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34432103}, issn = {1432-184X}, abstract = {We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.}, }
@article {pmid34432102, year = {2021}, author = {Babur, E and Dindaroğlu, T and Riaz, M and Uslu, OS}, title = {Seasonal Variations in Litter Layers' Characteristics Control Microbial Respiration and Microbial Carbon Utilization Under Mature Pine, Cedar, and Beech Forest Stands in the Eastern Mediterranean Karstic Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34432102}, issn = {1432-184X}, support = {KSU-2017/5-12D//Scientific Research Projects Commission/ ; }, abstract = {The forest floor is hotspot of several functions integral to the stability of forest ecosystems. However, seasonal variations in litter decomposition rate contribute to biochemical and structural heterogeneity in the forest floor carbon (C) and nutrient cycling. We investigated the influence of seasonal variations in litter layers' micro-climate (temperature and moisture content) and chemical characteristics such as pH, electrical conductivity (EC), total organic C (TOC), total nitrogen (TN), and C/N ratio on microbial respiration, biomass, and C use efficiency under mature (> 80 years stage age) pine, beech, and cedar forests in eastern Mediterranean Karstic ecosystems. In contrast to significantly higher microbial respiration in fall, winter, and spring under pine, beech, and cedar forests, the significantly lowest microbial biomass C (MBC) and microbial biomass N (MBN) were observed in winter under each forest. Microbial C use efficiency, measured as the metabolic quotient (qCO2 = CO2/MBC), varied strongly between forest stands and seasons but was generally higher in winter. The significant positive correlations between litter layer and microbial biomass C/N ratios, under beech and cedar forests, suggested strong CN stoichiometric coupling and microbial adaptation to substrate resource stoichiometry. qCO2 correlated significantly negatively with litter layers' temperature, positively with moisture content and EC. However, qCO2 had significant negative relationships with pH in pine and beech forests but significant positive under cedar forest. qCO2 showed significant positive relationships with C/N ratios under all forests but much stronger in beech and cedar forests suggesting higher C respired per unit MBC with an increase in C/N ratio. Despite variations between forest species, the highest MBC/TOC and MBN/TN ratios in fall indicated greater C and N incorporation into microbial biomass. Changes in MBC/MBN ratios under pine (9.62-10.6), beech (8.63-15.6), and cedar (7.32-16.2) forests indicated the shift in microbial communities as fungi have a higher C/N ratio than bacteria. Stepwise regression analysis further revealed that microbial respiration and biomass were controlled differently by litter layer characteristics in each forest. This study suggested that qCO2 independently or with other microbial indices can show litter layers' controls on organic matter turnover in Karst ecosystems and, taking into account the strong seasonal variations, can enhance the predictive potential of decomposition models.}, }
@article {pmid34431694, year = {2021}, author = {Moreno Morales, N and Patel, MT and Stewart, CJ and Sweeney, K and McClean, MN}, title = {Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0058121}, doi = {10.1128/mSphere.00581-21}, pmid = {34431694}, issn = {2379-5042}, support = {R35GM128873//HHS | National Institutes of Health (NIH)/ ; 2045493//National Science Foundation (NSF)/ ; }, abstract = {Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.}, }
@article {pmid34431166, year = {2021}, author = {Wang, Y and Chen, L and Xiang, W and Ouyang, S and Zhang, T and Zhang, X and Zeng, Y and Hu, Y and Luo, G and Kuzyakov, Y}, title = {Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15835}, pmid = {34431166}, issn = {1365-2486}, support = {31971457//National Natural Science Foundation of China/ ; 2016YFD0600202//National Key Research and Development Program of China/ ; 2020132080//State Forestry Administration of China/ ; 19B611//Scientific Research Foundation of Hunan Provincial Education Department/ ; //Ministry of Education/ ; //Kazan Federal University/ ; //RUDN University/ ; }, abstract = {Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO2 , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO2 , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.}, }
@article {pmid34428623, year = {2021}, author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G}, title = {Distribution of black carbon and PAHs in sediments of Peninsular Malaysia.}, journal = {Marine pollution bulletin}, volume = {172}, number = {}, pages = {112871}, doi = {10.1016/j.marpolbul.2021.112871}, pmid = {34428623}, issn = {1879-3363}, abstract = {Concentrations, sources and interactions between black carbon (BC) and polycyclic aromatic hydrocarbons (PAHs) were investigated in 42 sediment samples collected from riverine, coastal and shelf areas in Peninsular Malaysia. The concentrations of BC measured by benzene polycarboxylic acid (BPCA) method and PAHs showed broad spatial variations between the relatively pristine environment of the East coast and developed environment of the West and South coast ranging from 0.02 to 0.36% dw and 57.7 ng g-1 dw to 19,300 ng g-1 dw, respectively. Among diagnostic ratios of PAHs, the ratios of Ant/(Ant+Phe) and LMW/HMW drew the clearest distinctions between the East coast versus the West and South coast sediments indicating the predominance of petrogenic sources in the former versus pyrogenic sources in the latter. PAHs significantly correlated with BC and total organic carbon (TOC) in the sediments (p < 0.05) having similar correlation coefficients. BC accounted for 6.06 to 30.6% of TOC in sediments.}, }
@article {pmid34427721, year = {2021}, author = {Basanta, MD and Rebollar, EA and García-Castillo, MG and Parra Olea, G}, title = {Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34427721}, issn = {1432-184X}, support = {CN 18-127//University of California Institute for Mexico and the United States/ ; IN205521//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, abstract = {The skin microbiome in amphibians has gained a lot of attention as some of its members play a protective role against pathogens such as the fungus Batrachochytrium dendrobatidis (Bd). The composition of skin bacterial communities has been suggested as one of the factors explaining differences in susceptibility to Bd among amphibian species and populations. The boreal toad Anaxyrus boreas is known to be susceptible to Bd, and severe population declines in its southeastern range have been documented. However, throughout A. boreas distribution, populations present differences in susceptibility to Bd infections which may be associated with differences in skin microbial diversity. This study compared the skin bacterial diversity and Bd infection levels of A. boreas in one desert population and one pine forest population from Baja California, Mexico. We found that desert and pine forest toad populations exhibit differences in skin bacterial community structure but show similar Bd infection levels. Using a predictive method, we found that the abundance of bacteria with potential Bd-inhibitory properties differed between uninfected and infected individuals but not between populations. Our data suggest that several bacteria in the skin community may be offering protection from Bd infections in these A. boreas populations. This study provides foundational evidence for future studies seeking to understand the skin-microbial variation among boreal toads' populations and its relation with Bd susceptibility.}, }
@article {pmid34427533, year = {2021}, author = {Saw, JHW}, title = {Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0077321}, doi = {10.1128/mSystems.00773-21}, pmid = {34427533}, issn = {2379-5077}, abstract = {Microbial communities are frequently numerically dominated by just a few species. Often, the long "tail" of the rank-abundance plots of microbial communities constitutes the so-called "rare biosphere," microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.}, }
@article {pmid34427532, year = {2021}, author = {Scanlan, PD}, title = {Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0083221}, doi = {10.1128/mSystems.00832-21}, pmid = {34427532}, issn = {2379-5077}, abstract = {How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.}, }
@article {pmid34427521, year = {2021}, author = {Rodríguez-Verdugo, A}, title = {Evolving Interactions and Emergent Functions in Microbial Consortia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0077421}, doi = {10.1128/mSystems.00774-21}, pmid = {34427521}, issn = {2379-5077}, abstract = {Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.}, }
@article {pmid34426366, year = {2021}, author = {Leite, MFA and Dimitrov, MR and Freitas-Iório, RP and de Hollander, M and Cipriano, MAP and Andrade, SAL and da Silveira, APD and Kuramae, EE}, title = {Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149493}, doi = {10.1016/j.scitotenv.2021.149493}, pmid = {34426366}, issn = {1879-1026}, abstract = {The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.}, }
@article {pmid34426295, year = {2021}, author = {Nicomel, NR and Otero-Gonzalez, L and Williamson, A and Ok, YS and Van Der Voort, P and Hennebel, T and Du Laing, G}, title = {Selective copper recovery from ammoniacal waste streams using a systematic biosorption process.}, journal = {Chemosphere}, volume = {286}, number = {Pt 3}, pages = {131935}, doi = {10.1016/j.chemosphere.2021.131935}, pmid = {34426295}, issn = {1879-1298}, abstract = {Cu-NH3 bearing effluents arise from electroplating and metal extraction industries, requiring innovative and sustainable Cu recovery technologies to reduce their adverse environmental impact. CO32- and Zn are often co-occurring, and thus, selective Cu recovery from these complex liquid streams is required for economic viability. This study assessed 23 sustainable biosorbents classified as tannin-rich, lignin-rich, chitosan/chitin, dead biomass, macroalgae or biochar for their Cu adsorption capacity and selectivity in a complex NH3-bearing bioleachate. Under a preliminary screen with 12 mM Cu in 1 M ammoniacal solution, most biosorbents showed optimal Cu adsorption at pH 11, with pinecone remarkably showing high removal efficiencies (up to 68%) at all tested pH values. Further refinements on select biosorbents with pH, contact time, and presence of NH3, Zn and CO32- showed again that pinecone has a high maximum adsorption capacity (1.07 mmol g-1), worked over pH 5-12 and was Cu-selective with 3.97 selectivity quotient (KCu/Zn). Importantly, pinecone performance was maintained in a real Cu/NH3/Zn/CO32- bioleachate, with 69.4% Cu removal efficiency. Unlike synthetic adsorbents, pinecones require no pre-treatment, which together with its abundance, selectivity, and efficiency without the need for prior NH3 removal, makes it a competitive and sustainable Cu biosorbent for complex Cu-NH3 bearing streams. Overall, this study demonstrated the potential of integrating bioleaching and biosorption as a clean Cu recovery technology utilizing only sustainable resources (i.e., bio-lixiviant and biosorbents). This presents a closed-loop approach to Cu extraction and recovery from wastes, thus effectively addressing elemental sustainability.}, }
@article {pmid34424345, year = {2021}, author = {Bacha, L and Ventura, R and Barrios, M and Seabra, J and Tschoeke, D and Garcia, G and Masi, B and Macedo, L and Godoy, JMO and Cosenza, C and de Rezende, CE and Lima, V and Ottoni, AB and Thompson, C and Thompson, F}, title = {Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34424345}, issn = {1432-184X}, abstract = {The Guandu River, one of the main rivers in the state of Rio de Janeiro, provides water for more than nine million people in the metropolitan region. However, the Guandu has suffered from massive domestic and industrial pollution for more than two decades, leading to high levels of dissolved total phosphorus, cyanobacteria, and enteric bacteria observed during the summers of 2020 and 2021. The use of Phoslock, a palliative compound, was not effective in mitigating the levels of phosphorus in the Guandu River. Furthermore, potable water driven from the river had levels of 2-MIB/geosmin and a mud smell/taste. With all these problems, several solutions are proposed for improving the Guandu River water quality, including establishment of (i) sewage treatment plants (STPs), (ii) strict water quality monitoring, (iii) environmental recovery (e.g., reforestation), and (iv) permanent protected areas. The objective of this paper is to verify the poor water quality in the Guandu and the ineffectiveness and undesired effects of Phoslock.}, }
@article {pmid34422537, year = {2021}, author = {de Siqueira, KA and Liotti, RG and de Sousa, JR and Vendruscullo, SJ and de Souza, GB and de Vasconcelos, LG and Januário, AH and de Oliveira Mendes, TA and Soares, MA}, title = {Streptomyces griseocarneus R132 expresses antimicrobial genes and produces metabolites that modulate Galleria mellonella immune system.}, journal = {3 Biotech}, volume = {11}, number = {9}, pages = {396}, doi = {10.1007/s13205-021-02942-1}, pmid = {34422537}, issn = {2190-572X}, abstract = {Actinobacteria is a phylum composed of aerobic, Gram-positive, and filamentous bacteria with a broad spectrum of biological activity, including antioxidant, antitumor, and antibiotic. The crude extract of Streptomyces griseocarneus R132 was fractionated on a C18 silica column and the isolated compound was identified by 1H and 13C nuclear magnetic resonance as 3-(phenylprop-2-enoic acid), also known as trans-cinnamic acid. Antimicrobial activity against human pathogens was assayed in vitro (disk-diffusion qualitative test) and in vivo using Galleria mellonella larvae (RT-qPCR). The methanol fractions 132-F30%, 132-F50%, 132-F70%, and 132-F100% inhibited the Escherichia coli (ATCC 25922) and Staphylococcus aureus (MRSA) growth in vitro the most effectively. Compared with the untreated control (60-80% of larvae death), the fractions and isolated trans-cinnamic acid increased the survival rate and modulated the immune system of G. mellonella larvae infected with pathogenic microorganisms. The anti-infection effect of the S. griseocarneus R132 fermentation product led us to sequence its genome, which was assembled and annotated using the Rast and antiSMASH platforms. The assembled genome consisted of 227 scaffolds represented on a linear chromosome of 8.85 Mb and 71.3% of GC. We detected conserved domains typical of enzymes that produce molecules with biological activity, such as polyketides and non-ribosomal and ribosomal peptides, indicating a great potential for obtaining new antibiotics and molecules with biotechnological application.<br><br>Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02942-1.}, }
@article {pmid34421884, year = {2021}, author = {Carlson, HK and Vuono, DC and Glass, JB and Adams, MWW}, title = {Editorial: Selective Controls on Microbial Energy Metabolisms: From the Microscale to the Macroscale.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {728705}, doi = {10.3389/fmicb.2021.728705}, pmid = {34421884}, issn = {1664-302X}, }
@article {pmid34418848, year = {2021}, author = {Mei, Z and Xiang, L and Wang, F and Xu, M and Fu, Y and Wang, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment.}, journal = {Environment international}, volume = {157}, number = {}, pages = {106830}, doi = {10.1016/j.envint.2021.106830}, pmid = {34418848}, issn = {1873-6750}, abstract = {The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 104 and 1.1 × 106 in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 107 and 3.2 × 107 of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.}, }
@article {pmid34418788, year = {2021}, author = {Verstrepen, L and Van den Abbeele, P and Pignataro, G and Ribecco, C and Gramenzi, A and Hesta, M and Marzorati, M}, title = {Inclusion of small intestinal absorption and simulated mucosal surfaces further improve the Mucosal Simulator of the Canine Intestinal Microbial Ecosystem (M-SCIME™).}, journal = {Research in veterinary science}, volume = {140}, number = {}, pages = {100-108}, doi = {10.1016/j.rvsc.2021.08.011}, pmid = {34418788}, issn = {1532-2661}, abstract = {While a large set of in vitro models are available to study the effects of specific food ingredients (e.g. pre- and probiotics) on the human gut microbiome, the availability of such models for companion animals is limited. Since improving gut health of such animals is an emerging research field, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data. The current study presents a further improvement of this model by using an alternative method for feed preparation, i.e. by administering digestive enzymes to mimic upper gastro-intestinal digestion followed by a dialysis approach to mimic small intestinal absorption. As opposed to the previously implemented method, this resulted in a more optimal simulation of protein digestion and absorption. Further, upon entrance in the colon, increased production of the health-promoting butyrate and lower levels of Lactobacillus spp. and Bifidobacterium spp. were observed, which corresponded better with obtained in vivo data. A second model improvement consisted of the implementation of a mucosal environment to not only simulate luminal but also mucosal microbiota. In consistency with the human model for which this technology was previously validated, it was found that for all canine microbiota mucin beads were enriched with members of the Lachnospiraceae (~ Clostridium cluster XIVa), a family containing multiple well-known butyrate producers. The SCIME™ was thus upgraded to a so-called Mucosal SCIME™ (M-SCIME™). In conclusion, the current study presents improvements of the SCIME™, further increasing the relevance of obtained data with this in vitro model for dogs.}, }
@article {pmid34417850, year = {2021}, author = {Tang, Y and Ma, KY and Cheung, MK and Yang, CH and Wang, Y and Hu, X and Kwan, HS and Chu, KH}, title = {Correction to: Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01825-5}, pmid = {34417850}, issn = {1432-184X}, }
@article {pmid34417849, year = {2021}, author = {Sangwan, S and Prasanna, R}, title = {Mycorrhizae Helper Bacteria: Unlocking Their Potential as Bioenhancers of Plant-Arbuscular Mycorrhizal Fungal Associations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34417849}, issn = {1432-184X}, abstract = {The dynamic interactions of plants and arbuscular mycorrhizal fungi (AMF) that facilitate the efficient uptake of minerals from soil and provide protection from various environmental stresses (biotic and abiotic) are now also attributed to a third component of the symbiosis. These are the less investigated mycorrhizae helper bacteria (MHB), which constitute a dense, active bacterial community, tightly associated with AMF, and involved in the development and functioning of AMF. Although AMF spores are known to host several bacteria in their spore walls and cytoplasm, their role in promoting the ecological fitness and establishment of AMF symbiosis by influencing spore germination, mycelial growth, root colonization, metabolic diversity, and biocontrol of soil borne diseases is now being deciphered. MHB also promote the functioning of arbuscular mycorrhizal symbiosis by triggering various plant growth factors, leading to better availability of nutrients in the soil and uptake by plants. In order to develop strategies to promote mycorrhization by AMF, and particularly to stimulate the ability to utilize phosphorus from the soil, there is a need to decipher crucial metabolic signalling pathways of MHB and elucidate their functional significance as mycorrhiza helper bacteria. MHB, also referred to as AMF bioenhancers, also improve agronomic efficiency and formulations using AMF along with enriched population of MHB are a promising option. This review covers the aspects related to the specificity and mechanisms of action of MHB, which positively impact the formation and functioning of AMF in mycorrhizal symbiosis, and the need to advocate MHB as AMF bioenhancers towards their inclusion in integrated nutrient management practices in sustainable agriculture.}, }
@article {pmid34411359, year = {2021}, author = {Lajoie, G and Kembel, SW}, title = {Plant-bacteria associations are phylogenetically structured in the phyllosphere.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16131}, pmid = {34411359}, issn = {1365-294X}, abstract = {Determining whether and how global change will lead to novel interactions between hosts and microbes is an important issue in ecology and evolution. Understanding the contribution of host and microbial ecologies and evolutionary histories in driving their contemporary associations is an important step towards addressing this challenge and predicting the fitness consequences of novel associations. Using shotgun metagenomic and amplicon sequencing of bacterial communities from the leaf surfaces (phyllosphere) of trees, we investigated how phylogenetic relatedness among hosts and among their associated bacteria influences the distribution of bacteria among hosts. We also evaluated whether the functional traits of trees and bacteria explained these associations across multiple host species. We show that phylogenetically similar hosts tended to associate with the same bacteria and that phylogenetically similar bacteria tended to associate with the same host species. Phylogenetic interactions between tree and bacterial taxa also explained variation in their associations. The effect of host and symbiont evolutionary histories on bacterial distribution across hosts were observed across phylogenetic scales, but prominently explained variation among higher taxonomic categories of hosts and symbionts. These results suggest that ecological variation arising early in the plant and bacterial phylogenies have been particularly important for driving their contemporary associations. Variation in bacterial functional genes associated with the biosynthesis of aromatic amino acids and compounds and with cell motility were notably important in explaining bacterial community turnover among gymnosperm and angiosperm hosts. Overall, our results suggest an influence of host and bacterial traits and evolutionary histories in driving their contemporary associations.}, }
@article {pmid34410645, year = {2021}, author = {Baker, JL and Edlund, A}, title = {Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {161-189}, pmid = {34410645}, issn = {1940-6029}, abstract = {Small molecules are a primary communication media of the microbial world, and play crucial, yet largely unidentified, roles in microbial ecology and disease pathogenesis. Many small molecules are produced by biosynthetic gene clusters, which can be predicted and analyzed computationally given a genome. A recent study examined the biosynthetic repertoire of the oral microbiome and cross-referenced this information against the disease status of the human host, providing leads for biosynthetic gene clusters, and their natural products, which may be key in the oral microbial ecology affecting dental caries and periodontitis. This chapter provides a step-by-step tutorial to bioinformatically to locate biosynthetic gene clusters within genomes, predict the type of natural products that are produced, and cross-reference the identified biosynthetic gene clusters to microbiomes associated with disease or health.}, }
@article {pmid34410455, year = {2021}, author = {Atnafu, B and Desta, A and Assefa, F}, title = {Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34410455}, issn = {1432-184X}, abstract = {Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.}, }
@article {pmid34408269, year = {2021}, author = {Yuan, Z and Druzhinina, IS and Gibbons, JG and Zhong, Z and Van de Peer, Y and Rodriguez, RJ and Liu, Z and Wang, X and Wei, H and Wu, Q and Wang, J and Shi, G and Cai, F and Peng, L and Martin, FM}, title = {Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-021-01083-w}, pmid = {34408269}, issn = {1751-7370}, }
@article {pmid34406837, year = {2021}, author = {Cheng, XY and Liu, XY and Wang, HM and Su, CT and Zhao, R and Bodelier, PLE and Wang, WQ and Ma, LY and Lu, XL}, title = {USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0082021}, doi = {10.1128/Spectrum.00820-21}, pmid = {34406837}, issn = {2165-0497}, abstract = {Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 104 to 109 copies · g-1 dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink. IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 104 to 109 copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.}, }
@article {pmid34406835, year = {2021}, author = {Li, X and Wang, A and Wan, W and Luo, X and Zheng, L and He, G and Huang, D and Chen, W and Huang, Q}, title = {High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0136621}, doi = {10.1128/AEM.01366-21}, pmid = {34406835}, issn = {1098-5336}, abstract = {Salinization is considered as a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Herein, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered bacterial both alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, TN, and SOM were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased indicated that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. Miseq sequencing of 16S rRNA genes revealed that the abundance and composition of nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbe responds to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m-1). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized bacterial network. Moreover, variable selection (61-66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance in managing saline soils and maintaining a healthy ecosystem.}, }
@article {pmid34406446, year = {2021}, author = {Yu, HW and He, WM}, title = {Arbuscular Mycorrhizal Fungi Compete Asymmetrically for Amino Acids with Native and Invasive Solidago.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34406446}, issn = {1432-184X}, support = {31971552//National Natural Science Foundation of China/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and soil amino acids both affect plant performance. However, little is known about how AMF compete for amino acids with native and invasive congeners. We conducted a factorial experiment (inoculation, native and invasive species, and amino acids) to examine the competition for amino acids between soil microbes and both native and invasive congeners. The competition for amino acids between AMF and invasive Solidago canadensis was weaker than that observed between AMF and native S. decurrens. This asymmetric competition increased the growth advantage of S. canadensis over S. decurrens. The efficacy (biomass production per unit of nitrogen supply) of amino acids compared to ammonium was smaller in S. canadensis than in S. decurrens when both species were grown without inoculation, but the opposite was the case when both species were grown with AMF. AMF and all microbes differentially altered four phenotypic traits (plant height, leaf chlorophyll content, leaf number, and root biomass allocation) and the pathways determining the effects of amino acids on growth advantages. These findings suggest that AMF could enhance plant invasiveness through asymmetric competition for amino acids and that amino acid-driven invasiveness might be differentially regulated by different microbial guilds.}, }
@article {pmid34406445, year = {2021}, author = {Harris, RL and Vetter, MCYL and van Heerden, E and Cason, E and Vermeulen, JG and Taneja, A and Kieft, TL and DeCoste, CJ and Laevsky, GS and Onstott, TC}, title = {FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34406445}, issn = {1432-184X}, support = {DGE-1148900//U.S. National Science Foundation/ ; DEB-1441717//U.S. National Science Foundation/ ; EAR-1528492//U.S. National Science Foundation/ ; DEB-1442059//U.S. National Science Foundation/ ; DEB-1441646//U.S. National Science Foundation/ ; P30CA072720-5921//NCI-CCSG/ ; }, abstract = {Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.}, }
@article {pmid34405252, year = {2021}, author = {Whitaker, BK and Giauque, H and Timmerman, C and Birk, N and Hawkes, CV}, title = {Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34405252}, issn = {1432-184X}, support = {HATCH accesssion no 1018688//U.S. Department of Agriculture/ ; SCW1039//U.S. Department of Energy/ ; }, abstract = {Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.}, }
@article {pmid34405251, year = {2021}, author = {Sharma, R and Gal, L and Garmyn, D and Bru, D and Sharma, S and Piveteau, P}, title = {Plant Growth Promoting Bacterial Consortium Induces Shifts in Indigenous Soil Bacterial Communities and Controls Listeria monocytogenes in Rhizospheres of Cajanus cajan and Festuca arundinacea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34405251}, issn = {1432-184X}, abstract = {The rhizosphere is a dynamic and complex interface between plant roots and microorganisms. Owing to exudates, a web of interactions establishes among the microbial members of this micro-environment. The present study explored the impact of a bacterial consortium (Azotobacter chroococcum, Bacillus megaterium and Pseudomonas fluorescens, ABP), on the fate of a human pathogen, Listeria monocytogenes EGD-e, in soil and in the rhizospheres of Cajanus cajan and Festuca arundinacea, in addition to its plant growth promoting effect. The study further assessed the impact these bioinoculants exert on the autochthonous soil bacterial communities. Experiments in sterilised soil inoculated with bioinoculants and L. monocytogenes revealed the inhibition of L. monocytogenes by approximately 80-fold compared to that without the consortium. Subsequently, experiments were conducted in non-sterile soil microcosms planted with C. cajan and F. arundinacea, and in bulk soil. The consortium led to a significant increase in plant growth in both plants and prevented growth of L. monocytogenes. However, the presence of resident soil bacterial communities overshadowed this inhibitory effect, and a sharp decline in L. monocytogenes populations (5-6 log reduction) was recorded under non-sterile soil conditions. A shift in the soil resident bacterial communities was observed upon amendment with the bioinoculants. A significant increase of potential Plant Growth Promoting Rhizobacteria (PGPR) and biocontrol agents was observed, while the abundance of potential phytopathogens dropped. The present study opens up new avenues for the application of such a consortium given their dual benefits of plant growth promotion and restricting phytopathogens as well as human pathogen.}, }
@article {pmid34405250, year = {2021}, author = {Wang, Z and Xiao, R and Huang, J and Qin, X and Hu, D and Guo, E and Liu, C and Lu, F and You, L and Sun, C and Chen, G}, title = {The Diversity of Vaginal Microbiota Predicts Neoadjuvant Chemotherapy Responsiveness in Locally Advanced Cervical Cancer.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34405250}, issn = {1432-184X}, support = {81402163//the Nature and Science Foundation of China/ ; 81402164//the Nature and Science Foundation of China/ ; 81572569//the Nature and Science Foundation of China/ ; 81874106//the Nature and Science Foundation of China/ ; 2020JYCXJJ013//the Technology Innovation Foundation of Innovation Institute of Huazhong University of Science and Technology/ ; }, abstract = {The vaginal microbiota is closely related to HPV infection and cervical cancer (CC), but its relationship with platinum-based chemotherapy responsiveness is unknown. The study aimed to investigate the vaginal microbiota diversity of women with locally advanced cervical cancer (LACC) and compare the differences between responders and nonresponders. We characterized the 16S rRNA gene sequencing of vaginal microbiome of 66 vaginal samples, including 26 LACC patients before neoadjuvant chemotherapy and 40 healthy controls. Compared with the healthy controls, alpha diversity was significantly increased in CC patients (p <0.05) with more unconventionality bacterial colonization. Beta diversity also significantly differed between cervical cancer patients and controls (p <0.01). Within the CC patients, alpha diversity in vaginal samples was significantly higher in the nonresponders versus the responders (p <0.01), and the Ace index and Chao index were negatively correlated with mass reduction (p <0.001). Moreover, the Bacteroides genus enriched in the nonresponders had a ROC-plot AUC value reaching 0.84. The study suggests the vaginal microbiota in LACC patients is associated with platinum-based chemotherapy responsiveness. Alpha diversity and Bacteroides abundance have the potential of identifying platinum-resistant patients at an early time. These findings provide a basis for further research on the relationship between vaginal microbiome and chemotherapy effect in LACC.}, }
@article {pmid34405249, year = {2021}, author = {Pascoal, F and Costa, R and Assmy, P and Duarte, P and Magalhães, C}, title = {Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34405249}, issn = {1432-184X}, support = {2020.04453.BD//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/30997/2017//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4946/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04423/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04423/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04565/2020//Fundação para a Ciência e a Tecnologia/ ; Project N. 007317//Programa Operacional Regional de Lisboa/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; }, abstract = {The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.}, }
@article {pmid34403645, year = {2021}, author = {van de Peppel, LJJ and Nieuwenhuis, M and Auxier, B and Grum-Grzhimaylo, AA and Cárdenas, ME and de Beer, ZW and Lodge, DJ and Smith, ME and Kuyper, TW and Franco-Molano, AE and Baroni, TJ and Aanen, DK}, title = {Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2021.07.070}, pmid = {34403645}, issn = {1879-0445}, abstract = {The ancestor of termites relied on gut symbionts for degradation of plant material, an association that persists in all termite families.1,2 However, the single-lineage Macrotermitinae has additionally acquired a fungal symbiont that complements digestion of food outside the termite gut.3 Phylogenetic analysis has shown that fungi grown by these termites form a clade-the genus Termitomyces-but the events leading toward domestication remain unclear.4 To address this, we reconstructed the lifestyle of the common ancestor of Termitomyces using a combination of ecological data with a phylogenomic analysis of 21 related non-domesticated species and 25 species of Termitomyces. We show that the closely related genera Blastosporella and Arthromyces also contain insect-associated species. Furthermore, the genus Arthromyces produces asexual spores on the mycelium, which may facilitate insect dispersal when growing on aggregated subterranean fecal pellets of a plant-feeding insect. The sister-group relationship between Arthromyces and Termitomyces implies that insect association and asexual sporulation, present in both genera, preceded the domestication of Termitomyces and did not follow domestication as has been proposed previously. Specialization of the common ancestor of these two genera on an insect-fecal substrate is further supported by similar carbohydrate-degrading profiles between Arthromyces and Termitomyces. We describe a set of traits that may have predisposed the ancestor of Termitomyces toward domestication, with each trait found scattered in related taxa outside of the termite-domesticated clade. This pattern indicates that the origin of the termite-fungus symbiosis may not have required large-scale changes of the fungal partner.}, }
@article {pmid34399522, year = {2021}, author = {Bolívar, A and Tarlak, F and Costa, JCCP and Cejudo-Gómez, M and Bover-Cid, S and Zurera, G and Pérez-Rodríguez, F}, title = {A new expanded modelling approach for investigating the bioprotective capacity of Latilactobacillus sakei CTC494 against Listeria monocytogenes in ready-to-eat fish products.}, journal = {Food research international (Ottawa, Ont.)}, volume = {147}, number = {}, pages = {110545}, doi = {10.1016/j.foodres.2021.110545}, pmid = {34399522}, issn = {1873-7145}, abstract = {Understanding the role of food-related factors on the efficacy of protective cultures is essential to attain optimal results for developing biopreservation-based strategies. The aim of this work was to assess and model growth of Latilactobacillus sakei CTC494 and Listeria monocytogenes CTC1034, and their interaction, in two different ready-to-eat fish products (i.e., surimi-based product and tuna pâté) at 2 and 12 °C. The existing expanded Jameson-effect and a new expanded Jameson-effect model proposed in this study were evaluated to quantitatively describe the effect of microbial interaction. The inhibiting effect of the selected lactic acid bacteria strain on the pathogen growth was product dependent. In surimi product, a reduction of lag time of both strains was observed when growing in coculture at 2 °C, followed by the inhibition of the pathogen when the bioprotective L. sakei CTC494 reached the maximum population density, suggesting a mutualism-antagonism continuum phenomenon between populations. In tuna pâté, L. sakei CTC494 exerted a strong inhibition of L. monocytogenes at 2 °C (<0.5 log increase) and limited the growth at 12 °C (<2 log increase). The goodness-of-fit indexes indicated that the new expanded Jameson-effect model performed better and appropriately described the different competition patterns observed in the tested fish products. The proposed expanded competition model allowed for description of not only antagonistic but also mutualism-based interactions based on their influence on lag time.}, }
@article {pmid34399325, year = {2021}, author = {Barbosa, RG and Oliveira, FC and Andrés-Torres, M and Sleutels, T and Verstraete, W and Boon, N}, title = {Effective orthophosphate removal from surface water using hydrogen-oxidizing bacteria: Moving towards applicability.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149648}, doi = {10.1016/j.scitotenv.2021.149648}, pmid = {34399325}, issn = {1879-1026}, abstract = {Effective orthophosphate removal strategies are needed to counteract eutrophication and guarantee water quality. Previously, we established that hydrogen-oxidizing bacteria (HOB) have the ability to remove orthophosphate from artificial surface water. In the present study, we expand the application of the HOB orthophosphate removal strategy (1) to treat artificial surface water with low initial orthophosphate concentrations, (2) to treat real surface water and real wastewater effluent, and (3) to remove orthophosphate continuously. For synthetic surface water, irrespective of the initial concentration of 0.7, 0.5, 0.3, and 0.1 mg PO43--P/L, ultra-low concentrations (0.0058 ± 0.0028 mg PO43--P/L) were obtained. When artificial surface water was replaced by real surface water, without added nutrients or other chemicals, it was shown that over 90% orthophosphate could be removed within 30 min of operation in a batch configuration (0.031 ± 0.023 mg PO43--P/L). In continuous operation, orthophosphate removal from surface water left an average concentration of 0.040 ± 0.036 for 60 days, and the lowest orthophosphate concentration measured was 0.013 mg PO43-/L. Simultaneously, nitrate was continuously removed for 60 days below 0.1 mg/L. The ability to remove orthophosphate even under nitrogen limiting conditions might be related to the ability of HOB to fix nitrogen. This study brings valuable insights into the potential use of HOB biofilms for nutrient remediation and recovery.}, }
@article {pmid34399219, year = {2021}, author = {Du, P and He, H and Zhou, L and Dong, F and Liu, X and Zheng, Y}, title = {Different biodegradation potential and the impacted soil functions of epoxiconazole in two soils.}, journal = {Journal of hazardous materials}, volume = {422}, number = {}, pages = {126787}, doi = {10.1016/j.jhazmat.2021.126787}, pmid = {34399219}, issn = {1873-3336}, abstract = {Epoxiconazole is an effective pesticide to control Fusarium head blight (FHB), and the application will increase. To investigate the ecotoxicity of epoxiconazole to soil microbiome, we carried out an indoor experiment in which soils from two main regions of wheat production in China (Nanjing and Anyang) were treated with epoxiconazole (0, 0.0625, 0.625, or 6.25 mg kg-1) and incubated for 90 days. Under epoxiconazole stress, for bacteria and fungi, the abundance was increased and the diversity and community were impacted. In Anyang soil, the half-life of epoxiconazole was short with more increased species (linear discriminant analysis effect size biomarkers) and more increased xenobiotics biodegradation pathways in epoxiconazole treatments. The increased species mostly due to high abundance in initial state and more positive connections of the species. Co-occurrences revealed that epoxiconazole tightened bacterial connection, and increased positive correlations in Anyang soil. The N transformation was influenced with increased nifH and amoA; and the contents of NH4+-N and NO3--N were also increased. The functions of C, S, and manganese metabolisms were also impacted by epoxiconazole. This work expands our understanding about epoxiconazole degradation and help us to properly assess the risk of epoxiconazole in soil.}, }
@article {pmid34398256, year = {2021}, author = {Li, Y and Lin, H and Gao, P and Yang, N and Xu, R and Sun, X and Li, B and Xu, F and Wang, X and Song, B and Sun, W}, title = {Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34398256}, issn = {1432-184X}, support = {U20A20109//National Natural Science Foundation of China/ ; 2020GDASYL-20200102015//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103048//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200102014//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103041//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0103052//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200103082//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200402003//GDAS' Project of Science and Technology Development/ ; 202002020072//the Science and Technology Planning Project of Guangzhou/ ; 2017GC010570//the High-Level Talents Project of the Pearl River Talents Recruitment Program/ ; 2017BT01Z176//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; }, abstract = {Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N2 into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.}, }
@article {pmid34396460, year = {2021}, author = {Bamary, Z and Einali, A}, title = {Changes in Carbon Partitioning and Pattern of Antioxidant Enzyme Activity Induced by Arginine Treatment in the Green Microalga Dunaliella salina Under Long-Term Salinity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34396460}, issn = {1432-184X}, support = {27259//University of Sistan and Baluchestan/ ; }, abstract = {In this work, the effects of arginine (Arg) on biochemical responses and antioxidant enzyme activity in the green microalga Dunaliella salina grown at different salt concentrations were investigated. Suspensions adapted with the concentrations of 1, 2, and 3 M NaCl were treated at the exponential growth phase with a concentration of 5 mM Arg. Salt stress was associated with a large decrease in the number of cells and non-reducing sugar levels but accumulated higher amounts of chlorophyll, β-carotene, reducing sugar, starch, total protein, free amino acid, and glycerol. Increased levels of protein carbonylation, lipid peroxidation, proteolysis, hydrogen peroxide, and antioxidant enzyme activity also occurred during salinity. Arg treatment changed the pattern of biochemical responses in the cells grown at high salinity by directing carbon flow to the biosynthesis of non-reducing sugars instead of starch, lowering levels of hydrogen peroxide, and downregulating antioxidant enzyme activity, but the levels of lipid peroxidation, glycerol, and β-carotene remained nearly unchanged. These results suggest that Arg treatment alleviates salinity-induced oxidative stress in D. salina cells by modifying carbon partitioning and inducing signaling molecules rather than antioxidant enzymes.}, }
@article {pmid34394041, year = {2021}, author = {Chu, XL and Zhang, QG and Buckling, A and Castledine, M}, title = {Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {699190}, doi = {10.3389/fmicb.2021.699190}, pmid = {34394041}, issn = {1664-302X}, abstract = {Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.}, }
@article {pmid34394013, year = {2021}, author = {Danko, D and Malli Mohan, GB and Sierra, MA and Rucker, M and Singh, NK and Regberg, AB and Bell, MS and O'Hara, NB and Ounit, R and Mason, CE and Venkateswaran, K}, title = {Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {608478}, doi = {10.3389/fmicb.2021.608478}, pmid = {34394013}, issn = {1664-302X}, abstract = {Background: Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied.<br><br>Results: To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 102 colony forming units per 25 cm2 of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 105 to 106 copies per 25 cm2 of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented.<br><br>Conclusion: The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.}, }
@article {pmid34390303, year = {2021}, author = {Huang, Z and Liu, B and Yin, Y and Liang, F and Xie, D and Han, T and Liu, Y and Yan, B and Li, Q and Huang, Y and Liu, Q}, title = {Impact of Biocontrol Microbes on Soil Microbial Diversity in Ginger (Zingiber officinale Roscoe).}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.6595}, pmid = {34390303}, issn = {1526-4998}, abstract = {BACKGROUND: Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.<br><br>RESULTS: MiSeq sequencing of the 16S rRNA gene was employed to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentration. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.<br><br>CONCLUSION: The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should get noticed in plant disease management.}, }
@article {pmid34389059, year = {2021}, author = {Boeuf, D and Eppley, JM and Mende, DR and Malmstrom, RR and Woyke, T and DeLong, EF}, title = {Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {172}, pmid = {34389059}, issn = {2049-2618}, support = {#329108//Simons Foundation/ ; #721223//Simons Foundation/ ; GBMF #3777//Gordon and Betty Moore Foundation/ ; DE-AC02-05CH11231//Office of Science/ ; }, abstract = {BACKGROUND: Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth.<br><br>RESULTS: We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins.<br><br>CONCLUSIONS: Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.}, }
@article {pmid34388922, year = {2021}, author = {Rogiers, T and Merroun, ML and Williamson, A and Leys, N and Houdt, RV and Boon, N and Mijnendonckx, K}, title = {Cupriavidus metallidurans NA4 actively forms polyhydroxybutyrate-associated uranium-phosphate precipitates.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126737}, doi = {10.1016/j.jhazmat.2021.126737}, pmid = {34388922}, issn = {1873-3336}, abstract = {Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 µM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uranium-phosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4.}, }
@article {pmid34387704, year = {2021}, author = {de Siqueira, KA and Senabio, JA and Pietro-Souza, W and de Oliveira Mendes, TA and Soares, MA}, title = {Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {34387704}, issn = {1432-072X}, support = {568258/2014//Fundação de Amparo à Pesquisa do Estado de Mato Grosso/ ; 409062/2018-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Aspergillus sp. A31 and Curvularia geniculata P1 are endophytes that colonize the roots of Aeschynomene fluminensis Vell. and Polygonum acuminatum Kunth. in humid environments contaminated with mercury. The two strains mitigated mercury toxicity and promoted Oryza sativa L growth. C. geniculata P1 stood out for increasing the host biomass by fourfold and reducing the negative effects of the metal on photosynthesis. Assembling and annotation of Aspergillus sp. A31 and C. geniculata P1 genomes resulted in 28.60 Mb (CG% 53.1; 10,312 coding DNA sequences) and 32.92 Mb (CG% 50.72; 8,692 coding DNA sequences), respectively. Twelve and 27 genomes of Curvularia/Bipolaris and Aspergillus were selected for phylogenomic analyzes, respectively. Phylogenetic analysis inferred the separation of species from the genus Curvularia and Bipolaris into different clades, and the separation of species from the genus Aspergillus into three clades; the species were distinguished by occupied niche. The genomes had essential gene clusters for the adaptation of microorganisms to high metal concentrations, such as proteins of the phytoquelatin-metal complex (GO: 0090423), metal ion binders (GO: 0046872), ABC transporters (GO: 0042626), ATPase transporters (GO: 0016887), and genes related to response to reactive oxygen species (GO: 0000302) and oxidative stress (GO: 0006979). The results reported here help to understand the unique regulatory mechanisms of mercury tolerance and plant development.}, }
@article {pmid34387702, year = {2021}, author = {Qin, M and Jiang, L and Kholmatov, BR and Qiao, G and Chen, J}, title = {Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34387702}, issn = {1432-184X}, support = {No. 31772492//National Natural Science Foundation of China/ ; No. XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; Grant No. ANSO-CR-KP-2020-04//Key Collaborative Research Program of the Alliance of International Science Organizations/ ; No. 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, abstract = {Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.}, }
@article {pmid34387003, year = {2021}, author = {Yang, S and Liebner, S and Svenning, MM and Tøsdal Tveit, A}, title = {Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16118}, pmid = {34387003}, issn = {1365-294X}, abstract = {Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Tveit et al., 2015). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1 - 30 °C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomics-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.}, }
@article {pmid34385301, year = {2021}, author = {Shoemaker, WR and Jones, SE and Muscarella, ME and Behringer, MG and Lehmkuhl, BK and Lennon, JT}, title = {Microbial population dynamics and evolutionary outcomes under extreme energy limitation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {33}, pages = {}, doi = {10.1073/pnas.2101691118}, pmid = {34385301}, issn = {1091-6490}, abstract = {Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 100 to 105 y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.}, }
@article {pmid34384885, year = {2021}, author = {Marzorati, M and Calatayud, M and Rotsaert, C and Van Mele, M and Duysburgh, C and Durkee, S and White, T and Fowler, K and Jannin, V and Bellamine, A}, title = {Comparison of protection and release behavior of different capsule polymer combinations based on L. acidophilus survivability and function and caffeine release.}, journal = {International journal of pharmaceutics}, volume = {}, number = {}, pages = {120977}, doi = {10.1016/j.ijpharm.2021.120977}, pmid = {34384885}, issn = {1873-3476}, abstract = {Oral administration of active pharmaceutical ingredients, nutraceuticals, enzymes or probiotics requires an appropriate delivery system for optimal bioactivity and absorption. The harsh conditions during the gastrointestinal transit can degrade the administered products, hampering their efficacy. Enteric or delayed-release pharmaceutical formulations may help overcome these issues. In a Simulator of Human Intestinal Microbial Ecosystem model (SHIME) and using caffeine as a marker for release kinetics and L. acidophilus survivability as an indicator for protection, we compared the performance of ten capsule configurations, single or in DUOCAP® combinations. The function of L. acidophilus and its impact on the gut microbiota was further tested in three selected capsule types, combinations of DRcaps® capsule in DRcaps® capsule (DR-in-DR) and DRcaps® capsule in Vcaps® capsule (DR-in-VC) and single Vcaps® Plus capsule under colonic conditions. We found that under stomach and small intestine conditions, DR-in-DR and DR-in-VC led to the best performance both under fed and fasted conditions based on the slow caffeine release and the highest L. acidophilus survivability. The Vcaps® Plus capsule however, led the quickest caffeine and probiotic release. When DR-in-DR, DR-in-VC and single Vcaps® Plus capsules were tested through the whole gastrointestinal tract including under colonic conditions, caffeine release was found to be slower in capsules containing DRcaps® capsules compared to the single Vcaps® capsules. In addition, colonic survival of L. acidophilus was significantly increased under fasted conditions in DR-in-DR or DR-in-VC formulation compared to Vcaps® Plus capsule. To assess the impact of these formulations on the microbial function, acetate, butyrate and propionate as well as ammonia were measured. L. acidophilus released from DR-in-DR or DR-in-VC induced significant increase in butyrate and decrease in ammonia, suggesting a proliferation of butyrate-producing bacteria and reduction in ammonia-producing bacteria. These data suggest that L. acidophilus included in DR-in-DR or DR-in-VC reaching the colon is viable and functional, contributing to changes in colonic microbiota composition and diversity.}, }
@article {pmid34384375, year = {2021}, author = {Xi, J and Ding, D and Zhu, H and Wang, R and Su, F and Wu, W and Xiao, Z and Liang, X and Zhao, Q and Hong, Z and Fu, H and Xiao, Q}, title = {Disturbed microbial ecology in Alzheimer's disease: evidence from the gut microbiota and fecal metabolome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {226}, pmid = {34384375}, issn = {1471-2180}, support = {GWV-10.1-XK14//Shanghai Municipal Committee for Health and Family Planning/ ; 2016YFC1306402//National Chronic Disease Project/ ; 17411950701//Scientific Research Plan Project of Shanghai Science and Technology Committee/ ; 17411950106//Scientific Research Plan Project of Shanghai Science and Technology Committee/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; }, abstract = {BACKGROUND: Gut microbiota (GMB) alteration has been reported to influence the Alzheimer's disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis. In this study, the fecal microbiota and metabolome from 21 AD participants and 44 cognitively normal control participants were measured. Untargeted GMB taxa was analyzed through 16S ribosomal RNA gene profiling based on next-generation sequencing and fecal metabolites were quantified by using ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS).<br><br>RESULTS: Our analysis revealed that AD was characterized by 15 altered gut bacterial genera, of which 46.7% (7/15 general) was significantly associated with a series of metabolite markers. The predicted metabolic profile of altered gut microbial composition included steroid hormone biosynthesis, N-Acyl amino acid metabolism and piperidine metabolism. Moreover, a combination of 2 gut bacterial genera (Faecalibacterium and Pseudomonas) and 4 metabolites (N-Docosahexaenoyl GABA, 19-Oxoandrost-4-ene-3,17-dione, Trigofoenoside F and 22-Angeloylbarringtogenol C) was able to discriminate AD from NC with AUC of 0.955 in these 65 subjects.<br><br>CONCLUSIONS: These findings demonstrate that gut microbial alterations and related metabolic output changes may be associated with pathogenesis of AD, and suggest that fecal markers might be used as a non-invasive examination to assist screening and diagnosis of AD.}, }
@article {pmid34383807, year = {2021}, author = {Deng, S and Wang, B and Zhang, W and Su, S and Dong, H and Banat, IM and Sun, S and Guo, J and Liu, W and Wang, L and She, Y and Zhang, F}, title = {Elucidate microbial characteristics in a full-scale treatment plant for offshore oil produced wastewater.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0255836}, doi = {10.1371/journal.pone.0255836}, pmid = {34383807}, issn = {1932-6203}, abstract = {Oil-produced wastewater treatment plants, especially those involving biological treatment processes, harbor rich and diverse microbes. However, knowledge of microbial ecology and microbial interactions determining the efficiency of plants for oil-produced wastewater is limited. Here, we performed 16S rDNA amplicon sequencing to elucidate the microbial composition and potential microbial functions in a full-scale well-worked offshore oil-produced wastewater treatment plant. Results showed that microbes that inhabited the plant were diverse and originated from oil and marine associated environments. The upstream physical and chemical treatments resulted in low microbial diversity. Organic pollutants were digested in the anaerobic baffled reactor (ABR) dominantly through fermentation combined with sulfur compounds respiration. Three aerobic parallel reactors (APRs) harbored different microbial groups that performed similar potential functions, such as hydrocarbon degradation, acidogenesis, photosynthetic assimilation, and nitrogen removal. Microbial characteristics were important to the performance of oil-produced wastewater treatment plants with biological processes.}, }
@article {pmid34383127, year = {2021}, author = {Vieira, FR and Pecchia, JA}, title = {Bacterial Community Patterns in the Agaricus bisporus Cultivation System, from Compost Raw Materials to Mushroom Caps.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34383127}, issn = {1432-184X}, support = {PEN04741//United States Department of Agriculture (USDA/NIFA - National Institute of Food and Agriculture) and Hatch Appropriations/ ; }, abstract = {Different from other fungal species that can be largely cultivated in 'axenic conditions' using plant material (e.g., species of Lentinula and Pleurotus in 'sterile' straw-based substrate), the commercial Agaricus bisporus cultivation system relies heavily on ecological relationships with a broad range of microorganisms present in the system (compost and casing). Since the A. bisporus cultivation system consists of a microbial manipulation process, it is important to know the microbial community dynamics during the entire cultivation cycle to design further studies and/or crop management strategies to optimize this system. To capture the bacterial community 'flow' from compost raw materials to the casing to the formation and maturation of mushroom caps, community snapshots were generated by direct DNA recovery (amplicon sequencing). The 'bacterial community flow' revealed that compost, casing and mushrooms represent different niches for bacteria present in the cultivation system, but at the same time, a bacterial exchange between microenvironments can occur for a portion of the community. Within each microenvironment, compost showed intense bacterial populational dynamics, probably due to the environmental changes imposed by composting conditions. In casing, the colonization of A. bisporus appeared, to reshape the native bacterial community which later, with some other members present in compost, becomes the core community in mushroom caps. The current bacterial survey along with previous results provides more cues of specific bacteria groups that can be in association with A. bisporus development and health.}, }
@article {pmid34378984, year = {2021}, author = {Liu, D and Pérez-Moreno, J and He, X and Garibay-Orijel, R and Yu, F}, title = {Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0003921}, doi = {10.1128/mSphere.00039-21}, pmid = {34378984}, issn = {2379-5042}, abstract = {Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.}, }
@article {pmid34378947, year = {2021}, author = {Zhang, SY and Xiao, X and Chen, SC and Zhu, YG and Sun, GX and Konstantinidis, KT}, title = {High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0138321}, doi = {10.1128/AEM.01383-21}, pmid = {34378947}, issn = {1098-5336}, abstract = {Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.}, }
@article {pmid34378531, year = {2021}, author = {Marie, IJ and Brambilla, L and Azzouz, D and Chen, Z and Baracho, GV and Arnett, A and Li, HS and Liu, W and Cimmino, L and Chattopadhyay, P and Silverman, G and Watowich, SS and Khor, B and Levy, D}, title = {Tonic interferon restricts pathogenic IL-17-driven inflammatory disease via balancing the microbiome.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, doi = {10.7554/eLife.68371}, pmid = {34378531}, issn = {2050-084X}, support = {A!28900/NH/NIH HHS/United States ; AI133822/NH/NIH HHS/United States ; AR070591/NH/NIH HHS/United States ; CA016087/NH/NIH HHS/United States ; }, abstract = {Maintenance of immune homeostasis involves a synergistic relationship between the host and the microbiome. Canonical interferon (IFN) signaling controls responses to acute microbial infection, through engagement of the STAT1 transcription factor. However, the contribution of tonic levels of IFN to immune homeostasis in absence of acute infection remains largely unexplored. We report that STAT1 KO mice spontaneously developed an inflammatory disease marked by myeloid hyperplasia and splenic accumulation of hematopoietic stem cells. Moreover, these animals developed inflammatory bowel disease. Profiling gut bacteria revealed a profound dysbiosis in absence of tonic IFN signaling, which triggered expansion of TH17 cells and loss of splenic Treg cells. Reduction of bacterial load by antibiotic treatment averted the TH17 bias, and blocking IL17 signaling prevented myeloid expansion and splenic stem cell accumulation. Thus, tonic IFNs regulate gut microbial ecology, which is crucial for maintaining physiologic immune homeostasis and preventing inflammation.}, }
@article {pmid34245073, year = {2021}, author = {Hunter-Cevera, KR and Hamilton, BR and Neubert, MG and Sosik, HM}, title = {Seasonal environmental variability drives microdiversity within a coastal Synechococcus population.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15666}, pmid = {34245073}, issn = {1462-2920}, support = {GGA#934//Gordon and Betty Moore Foundation/ ; Hibbitt Early Career Fellowship//Marine Biological Laboratory/ ; NNX11AF07G/NASA/NASA/United States ; NNX13AC98G/NASA/NASA/United States ; OCE-0530830//National Science Foundation/ ; OCE-1655686//National Science Foundation/ ; 561126//Simons Foundation: Early Investigator Award in Marine Microbial Ecology and Evolution/ ; //U.S. Department of Defense: National Defense Science and Engineering Graduate Fellowship/ ; }, abstract = {Marine microbes often show a high degree of physiological or ecological diversity below the species level. This microdiversity raises questions about the processes that drive diversification and permit coexistence of diverse yet closely related marine microbes, especially given the theoretical efficiency of competitive exclusion. Here, we provide insight with an 8-year time series of diversity within Synechococcus, a widespread and important marine picophytoplankter. The population of Synechococcus on the Northeast U.S. Shelf is comprised of six main types, each of which displays a distinct and consistent seasonal pattern. With compositional data analysis, we show that these patterns can be reproduced with a simple model that couples differential responses to temperature and light with the seasonal cycle of the physical environment. These observations support the hypothesis that temporal variability in environmental factors can maintain microdiversity in marine microbial populations. We also identify how seasonal diversity patterns directly determine overarching Synechococcus population abundance features.}, }
@article {pmid34370735, year = {2021}, author = {Ghasemian, E and Inic-Kanada, A and Collingro, A and Mejdoubi, L and Alchalabi, H and Keše, D and Elshafie, BE and Hammou, J and Barisani-Asenbauer, T}, title = {Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {8}, pages = {e0009655}, doi = {10.1371/journal.pntd.0009655}, pmid = {34370735}, issn = {1935-2735}, abstract = {Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598·596) than A genovar (51·005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent.}, }
@article {pmid34370055, year = {2021}, author = {Travanty, NV and Vargo, EL and Apperson, CS and Ponnusamy, L}, title = {Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34370055}, issn = {1432-184X}, abstract = {The long-standing association between insects and microorganisms has been especially crucial to the evolutionary and ecological success of social insect groups. Notably, research on the interaction of the two social forms (monogyne and polygyne) of the red imported fire ant (RIFA), Solenopsis invicta Buren, with microbes in its soil habitat is presently limited. In this study, we characterized bacterial microbiomes associated with RIFA nest soils and native (RIFA-negative) soils to better understand the effects of colonization of RIFA on soil microbial communities. Bacterial community fingerprints of 16S rRNA amplicons using denaturing gradient gel electrophoresis revealed significant differences in the structure of the bacterial communities between RIFA-positive and RIFA-negative soils at 0 and 10 cm depths. Illumina sequencing of 16S rRNA amplicons provided fine-scale analysis to test for effects of RIFA colonization, RIFA social form, and soil depth on the composition of the bacterial microbiomes of the soil and RIFA workers. Our results showed the bacterial community structure of RIFA-colonized soils to be significantly different from native soil communities and to evidence elevated abundances of several taxa, including Actinobacteria. Colony social form was not found to be a significant factor in nest or RIFA worker microbiome compositions. RIFA workers and nest soils were determined to have markedly different bacterial communities, with RIFA worker microbiomes being characterized by high abundances of a Bartonella-like endosymbiont and Entomoplasmataceae. Cloning and sequencing of the 16S rRNA gene revealed the Bartonella sp. to be a novel bacterium.}, }
@article {pmid34368008, year = {2021}, author = {Josephs-Spaulding, J and Krogh, TJ and Rettig, HC and Lyng, M and Chkonia, M and Waschina, S and Graspeuntner, S and Rupp, J and Møller-Jensen, J and Kaleta, C}, title = {Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {562525}, doi = {10.3389/fcimb.2021.562525}, pmid = {34368008}, issn = {2235-2988}, abstract = {Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.}, }
@article {pmid34367868, year = {2021}, author = {Paul, P and Chakraborty, P and Sarker, RK and Chatterjee, A and Maiti, D and Das, A and Mandal, S and Bhattacharjee, S and Dastidar, DG and Tribedi, P}, title = {Tryptophan interferes with the quorum sensing and cell surface hydrophobicity of Staphylococcus aureus: a promising approach to inhibit the biofilm development.}, journal = {3 Biotech}, volume = {11}, number = {8}, pages = {376}, doi = {10.1007/s13205-021-02924-3}, pmid = {34367868}, issn = {2190-572X}, abstract = {Staphylococcus aureus, a Gram-positive bacterium has been implicated in a plethora of human infections by virtue of its biofilm-forming ability. Inhibition in microbial biofilm formation has been found to be a promising approach towards compromising microbial pathogenesis. In this regard, various natural and synthetic molecules have been explored to attenuate microbial biofilm. In this study, the role of an amino acid, L-tryptophan was examined against the biofilm-forming ability of S. aureus. The compound did not execute any antimicrobial characteristics, instead, showed strong antibiofilm activity with the highest biofilm inhibition at a concentration of 50 µg/mL. Towards understanding the underlying mechanism of the same, efforts were given to examine whether tryptophan could inhibit biofilm formation by interfering with the quorum-sensing property of S. aureus. A molecular docking analysis revealed an efficient binding between the quorum-sensing protein, AgrA, and tryptophan. Moreover, the expression of the quorum-sensing gene (agrA) got significantly reduced under the influence of the test compound. These results indicated that tryptophan could interfere with the quorum-sensing property of the organism thereby inhibiting its biofilm formation. Further study revealed that tryptophan could also reduce the cell surface hydrophobicity of S. aureus by downregulating the expression of dltA. Moreover, the tested concentrations of tryptophan did not show any significant cytotoxicity. Hence, tryptophan could be recommended as a potential antibiofilm agent to manage the biofilm-associated infections caused by S. aureus.<br><br>Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02924-3.}, }
@article {pmid34367102, year = {2021}, author = {Rapp, JZ and Sullivan, MB and Deming, JW}, title = {Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {701186}, doi = {10.3389/fmicb.2021.701186}, pmid = {34367102}, issn = {1664-302X}, abstract = {Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL-1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL-1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.}, }
@article {pmid34365235, year = {2021}, author = {Bourhane, Z and Lanzén, A and Cagnon, C and Ben Said, O and Mahmoudi, E and Coulon, F and Atai, E and Borja, A and Cravo-Laureau, C and Duran, R}, title = {Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126789}, doi = {10.1016/j.jhazmat.2021.126789}, pmid = {34365235}, issn = {1873-3336}, abstract = {Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.}, }
@article {pmid34364026, year = {2021}, author = {Rogińska, J and Perdicakis, M and Midoux, C and Bouchez, T and Despas, C and Liu, L and Tian, JH and Chaumont, C and P A Jorand, F and Tournebize, J and Etienne, M}, title = {Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {142}, number = {}, pages = {107895}, doi = {10.1016/j.bioelechem.2021.107895}, pmid = {34364026}, issn = {1878-562X}, abstract = {Microbial electrochemical snorkel (MES) is a short-circuited microbial fuel cell applicable to water treatment that does not produce energy but requires lower cost for its implementation. Few reports have already described its water treatment capabilities but no deeper electrochemical analysis were yet performed. We tested various materials (iron, stainless steel and porous graphite) and configurations of snorkel in order to better understand the rules that will control in a wetland the mixed potential of this self-powered system. We designed a model snorkel that was studied in laboratory and on the field. We confirmed the development of MES by identifying anodic and cathodic parts, by measuring the current between them and by analyzing microbial ecology in laboratory and field experiments. An important application is denitrification of surface water. Here we discuss the influence of nitrate on its electrochemical response and denitrification performances. Introducing nitrate caused the increase of the mixed potential of MES and of current at a potential value relatively more positive than for nitrate-reducing biocathodes described in the literature. The major criteria for promoting application of MES in artificial wetland dedicated to mitigation of non-point source nitrate pollution from agricultural water are considered.}, }
@article {pmid34363579, year = {2021}, author = {Ghosh, A and Bhadury, P}, title = {Exploring changes in bacterioplankton community structure in response to tannic acid, a major component of mangrove litterfall of Sundarbans mangrove ecosystem: a laboratory mesocosm approach.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {34363579}, issn = {1614-7499}, abstract = {Tannic acid is a secondary compound produced by vascular plants and is a major component of mangrove litterfall. Tannic acid is water soluble, leaches out from mangrove litterfall and contributes to DOC and DON pools in adjacent estuaries. About 50% of the litterfall may be degraded and channelized into the marine microbial loop. The influence of tannic acid on bacterioplankton community structure was tested by setting up laboratory-based barrel experiments. Estuarine water from Stn3 of Sundarbans Biological Observatory Time Series (SBOTS) was enriched with tannic acid, and the change in concentration of dissolved nutrients was determined on a daily basis over a span of 15 days. Concentrations of tannic acid, gallic acid and other dissolved nutrients such as nitrate and ortho-phosphate were determined using a UV-Vis spectrophotometer. Tannic acid significantly affected the concentrations of gallic acid and dissolved nitrate in the barrels. Degradation of tannic acid was tracked by a decrease in concentration of tannic acid and generation of gallic acid. The influence of tannic acid on bacterioplankton community structure was analysed on the start (day 0), intermediate (day 3, day 5, day 7 and day 9) and end (day 15) of the experiment. Bacterioplankton community structure was elucidated by sequencing the V3-V4 region of 16S ribosomal RNA on an Illumina MiSeq platform. Proteobacteria was found to be the most dominant bacterial phylum in control and tannic acid-enriched barrels (barrels 1 and 2) on day 0. With the progression of experiment, the abundance of Proteobacteria altered significantly in the control barrel indicating the possible role of this phylum in the breakdown of tannic acid within estuarine mangroves. The abundance of Proteobacteria in the tannic acid-enriched barrels remained high, indicating that members of Proteobacteria may be capable of using tannic acid as a source of carbon and nitrogen. Tannic acid appeared to inhibit most of the other bacterioplankton phyla including Actinobacteria, Acidobacteria and Verrucomicrobia that existed in large abundance in the control barrel on day 15 but were almost absent in the tannic acid-enriched barrels. At class level, Bacteroides was found to be present in highest abundance in the tannic acid-enriched barrels. Tannic acid appeared to strongly influence the abundant bacterioplankton phyla and families as indicated by Pearson's correlation coefficient and non-metric multidimensional scaling ordination plots. Gallic acid is one of the final products of tannic acid degradation. Breakdown of tannic acid could influence the marine nitrogen and carbon cycling by releasing DON and DOC, respectively, into the adjacent estuaries. Information of breakdown and remineralization of components of litterfall such as tannic acid would also be important for calculation of carbon and nitrogen budgets of coastal ecosystems including in mangroves.}, }
@article {pmid34363516, year = {2021}, author = {Su, Y and Du, Y and Xing, P}, title = {The Light-to-Nutrient Ratio in Alpine Lakes: Different Scenarios of Bacterial Nutrient Limitation and Community Structure in Lakes Above and Below the Treeline.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34363516}, issn = {1432-184X}, support = {31971475//National Natural Science Foundation of China/ ; 31722008//National Natural Science Foundation of China/ ; 31670461//National Natural Science Foundation of China/ ; }, abstract = {The light-to-nutrient hypothesis proposes that under high light-to-nutrient conditions, bacteria tend to be limited by phosphorus (P), while under relatively low light-to-nutrient conditions, bacteria are likely driven towards carbon (C) limitation. Exploring whether this light-to-nutrient hypothesis is fitting for alpine lakes has profound implications for predicting the impacts of climatic and environmental changes on the structures and processes of aquatic ecosystems in climate-sensitive regions. We investigated the environmental conditions and bacterioplankton community compositions of 15 high-elevation lakes (7 above and 8 below treeline). High light-to-nutrient conditions (denoted by the reciprocal value of the attenuation coefficient (1/K) to total phosphorus (TP)), high chlorophyll a (Chl a) concentrations, low TP concentrations and low ratios of the dissolved organic carbon concentration to the dissolved total nitrogen concentration (DOC:DTN) were detected in above-treeline lakes. Significant positive correlations between the bacterioplankton community compositions with 1/K:TP ratios and Chl a concentrations indicated that not only high light energy but also nutrient competition between phytoplankton and bacteria could induce P limitation for bacteria. In contrast, low light-to-nutrient conditions and high allochthonous DOC input in below-treeline lakes lessen P limitation and C limitation. The most abundant genus, Polynucleobacter, was significantly enriched, and more diverse oligotypes of Polynucleobacter operational taxonomic units were identified in the below-treeline lakes, indicating the divergence of niche adaptations among Polynucleobacter oligotypes. The discrepancies in the light-to-P ratio and the components of organic matter between the above-treeline and below-treeline lakes have important implications for the nutrient limitation of bacterioplankton and their community compositions.}, }
@article {pmid34363515, year = {2021}, author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Naidu, R and Megharaj, M}, title = {Impact of Nitrate and Ammonium Concentrations on Co-Culturing of Tetradesmus obliquus IS2 with Variovorax paradoxus IS1 as Revealed by Phenotypic Responses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34363515}, issn = {1432-184X}, abstract = {Mutual interactions in co-cultures of microalgae and bacteria are well known for establishing consortia and nutrient uptake in aquatic habitats, but the phenotypic changes in terms of morphological, physiological, and biochemical attributes that drive these interactions have not been clearly understood. In this novel study, we demonstrated the phenotypic response in a co-culture involving a microalga, Tetradesmus obliquus IS2, and a bacterium, Variovorax paradoxus IS1, grown with varying concentrations of two inorganic nitrogen sources. Modified Bold's basal medium was supplemented with five ratios (%) of NO3-N:NH4-N (100:0, 75:25, 50:50, 25:75, and 0:100), and by maintaining N:P Redfield ratio of 16:1. The observed morphological changes in microalga included an increase in granularity and a broad range of cell sizes under the influence of increased ammonium levels. Co-culturing in presence of NO3-N alone or combination with NH4-N up to equimolar concentrations resulted in complete nitrogen uptake, increased growth in both the microbial strains, and enhanced accumulation of carbohydrates, proteins, and lipids. Total chlorophyll content in microalga was also significantly higher when it was grown as a co-culture with NO3-N and NH4-N up to a ratio of 50:50. Significant upregulation in the synthesis of amino acids and sugars and downregulation of organic acids were evident with higher ammonium uptake in the co-culture, indicating the regulation of carbon and nitrogen assimilation pathways and energy synthesis. Our data suggest that the co-culture of strains IS1 and IS2 could be exploited for effluent treatment by considering the concentrations of inorganic sources, particularly ammonium, in the wastewaters.}, }
@article {pmid34361657, year = {2021}, author = {Al-Shaibani, MM and Radin Mohamed, RMS and Sidik, NM and Enshasy, HAE and Al-Gheethi, A and Noman, E and Al-Mekhlafi, NA and Zin, NM}, title = {Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {15}, pages = {}, doi = {10.3390/molecules26154504}, pmid = {34361657}, issn = {1420-3049}, abstract = {The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.}, }
@article {pmid34360485, year = {2021}, author = {Ramli, NA and Md Yusof, NFF and Zarkasi, KZ and Suroto, A}, title = {Chemical, Biological and Morphological Properties of Fine Particles during Local Rice Straw Burning Activities.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {15}, pages = {}, doi = {10.3390/ijerph18158192}, pmid = {34360485}, issn = {1660-4601}, support = {(1001/PAWAM/8014106)//Universiti Sains Malaysia/ ; }, abstract = {Rice straw is commonly burned openly after harvesting in Malaysia and many other Asian countries where rice is the main crop. This operation emits a significant amount of air pollution, which can have severe consequences for indoor air quality, public health, and climate change. Therefore, this study focuses on determining the compositions of trace elements and the morphological properties of fine particles. Furthermore, the species of bacteria found in bioaerosol from rice burning activities were discovered in this study. For morphological observation of fine particles, FESEM-EDX was used in this study. Two main categories of particles were found, which were natural particles and anthropogenic particles. The zinc element was found during the morphological observation and was assumed to come from the fertilizer used by the farmers. ICP-OES identifies the concentration of trace elements in the fine particle samples. A cultured method was used in this study by using nutrient agar. From this study, several bacteria were identified: Exiguobavterium indicum, Bacillus amyloliquefaciens, Desulfonema limicola str. Jadabusan, Exiguobacterium acetylicum, Lysinibacillus macrolides, and Bacillus proteolyticus. This study is important, especially for human health, and further research on the biological composition of aerosols should be conducted to understand the effect of microorganisms on human health.}, }
@article {pmid34358486, year = {2021}, author = {Wauters, L and Slaets, H and De Paepe, K and Ceulemans, M and Wetzels, S and Geboers, K and Toth, J and Thys, W and Dybajlo, R and Walgraeve, D and Biessen, E and Verbeke, K and Tack, J and Van de Wiele, T and Hellings, N and Vanuytsel, T}, title = {Efficacy and safety of spore-forming probiotics in the treatment of functional dyspepsia: a pilot randomised, double-blind, placebo-controlled trial.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2468-1253(21)00226-0}, pmid = {34358486}, issn = {2468-1253}, abstract = {BACKGROUND: Current treatments for functional dyspepsia have limited efficacy or present safety issues. We aimed to assess spore-forming probiotics in functional dyspepsia as monotherapy or add-on therapy to long-term treatment with proton-pump inhibitors.<br><br>METHODS: In this single-centre, randomised, double-blind, placebo-controlled pilot trial that took place at University Hospitals Leuven (Leuven, Belgium), adult patients (≥18 years) with functional dyspepsia (as defined by Rome IV criteria, on proton-pump inhibitors or off proton-pump inhibitors) were randomly assigned (1:1) via computer-generated blocked lists, stratified by proton-pump inhibitor status, to receive 8 weeks of treatment with probiotics (Bacillus coagulans MY01 and Bacillus subtilis MY02, 2·5 × 109 colony-forming units per capsule) or placebo consumed twice per day, followed by an open-label extension phase of 8 weeks. Individuals with a history of abdominal surgery, diabetes, coeliac or inflammatory bowel disease, active psychiatric conditions, and use of immunosuppressant drugs, antibiotics, or probiotics in the past 3 months were excluded. All patients and on-site study personnel were masked to treatment allocation in the first 8 weeks. Symptoms, immune activation, and faecal microbiota were assessed and recorded. The primary endpoint was a decrease of at least 0·7 in the postprandial distress syndrome (PDS) score of the Leuven Postprandial Distress Scale in patients with a baseline PDS score of 1 or greater (at least mild symptoms), assessed in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT04030780.<br><br>FINDINGS: Between June 3, 2019, and March 11, 2020, of 93 individuals assessed for eligibility, we included 68 patients with functional dyspepsia (51 [75%] women, mean age 40·1 years [SD 14·4], 34 [50%] on proton-pump inhibitors). We randomly assigned 32 participants to probiotics and 36 to placebo. The proportion of clinical responders was higher with probiotics (12 [48%] of 25) than placebo (six [20%] of 30; relative risk 1·95 [95% CI 1·07-4·11]; p=0·028). The number of patients with adverse events was similar with probiotics (five [16%] of 32) and placebo (12 [33%] of 36). Two serious adverse events occurring during the open-label phase (appendicitis and syncope in two separate patients) were assessed as unlikely to be related to the study product.<br><br>INTERPRETATION: In this exploratory study, B coagulans MY01 and B subtilis MY02 were efficacious and safe in the treatment of functional dyspepsia. Participants had potentially beneficial immune and microbial changes, which could provide insights into possible underlying mechanisms as future predictors or treatment targets.<br><br>FUNDING: MY HEALTH.}, }
@article {pmid34356506, year = {2021}, author = {Bapteste, E and Gérard, P and Larose, C and Blouin, M and Not, F and Campos, L and Aïdan, G and Selosse, MA and Adénis, MS and Bouchard, F and Dutreuil, S and Corel, E and Vigliotti, C and Huneman, P and Lapointe, FJ and Lopez, P}, title = {The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View.}, journal = {Biology}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/biology10070651}, pmid = {34356506}, issn = {2079-7737}, support = {REVMICNAT//Centre National de la Recherche Scientifique/ ; }, abstract = {Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An 'epistemic revolution induced by microbiome studies' seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.}, }
@article {pmid34354050, year = {2021}, author = {Cheng, SP and Jia, KH and Liu, H and Zhang, RG and Li, ZC and Zhou, SS and Shi, TL and Ma, AC and Yu, CW and Gao, C and Cao, GL and Zhao, W and Nie, S and Guo, JF and Jiao, SQ and Tian, XC and Yan, XM and Bao, YT and Yun, QZ and Wang, XZ and Porth, I and El-Kassaby, YA and Wang, XR and Li, Z and Van de Peer, Y and Mao, JF}, title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {188}, pmid = {34354050}, issn = {2662-6810}, support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.}, }
@article {pmid34351469, year = {2021}, author = {Vora, SM and Ankati, S and Patole, C and Podile, AR and Archana, G}, title = {Alterations of Primary Metabolites in Root Exudates of Intercropped Cajanus cajan-Zea mays Modulate the Adaptation and Proteome of Ensifer (Sinorhizobium) fredii NGR234.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34351469}, issn = {1432-184X}, abstract = {Legume-cereal intercropping systems, in the context of diversity, ecological function, and better yield have been widely studied. Such systems enhance nutrient phytoavailability by balancing root-rhizosphere interactions. Root exudates (RE) play an important role in the rhizospheric interactions of plant-plant and/or plant-microbiome interaction. However, the influence of the primary metabolites of RE on plant-rhizobia interactions in a legume-cereal intercrop system is not known. To understand the plant communication with rhizobia, Cajanus cajan-Zea mays intercropped plants and the broad host range legume nodulating Ensifer fredii NGR234 as the model plants and rhizobium used respectively. A metabolomics-based approach revealed a clear separation between intercropped and monocropped RE of the two plants. Intercropped C. cajan showed an increase in the myo-inositol, and proline, while intercropped Z. mays showed enhanced galactose, D-glucopyranoside, and arginine in the RE. Physiological assays of NGR234 with the RE of intercropped C. cajan exhibited a significant enhancement in biofilm formation, while intercropped Z. mays RE accelerated the bacterial growth in the late log phase. Further, using label-free proteomics, we identified a total of 2570 proteins of NGR234 covering 50% annotated protein sequences upon exposure to Z. mays RE. Furthermore, intercropped Z. mays RE upregulated bacterioferritin comigratory protein (BCP), putative nitroreductase, IlvD, LeuC, D (branched-chain amino acid proteins), and chaperonin proteins GroEL2. Identification offered new insights into the metabolome of the legume-cereal intercrop and proteome of NGR234-Z. mays interactions that underline the new molecular candidates likely to be involved in the fitness of rhizobium in the intercropping system.}, }
@article {pmid34349744, year = {2021}, author = {Gresse, R and Chaucheyras-Durand, F and Garrido, JJ and Denis, S and Jiménez-Marín, A and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S}, title = {Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {703421}, doi = {10.3389/fmicb.2021.703421}, pmid = {34349744}, issn = {1664-302X}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post-weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to be the consequence of various stress factors such as transient anorexia, dietary change or increase in intestinal inflammation and permeability, but the exact mechanisms remain to be elucidated. As the use of animal experiments raise more and more ethical concerns, we used a recently developed in vitro model of piglet colonic microbiome and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning transition and pathogen challenge at weaning. Our data suggested that the tested factors impacted the composition and functionality of the MPigut-IVM microbiota. The simulation of weaning transition led to an increase in relative abundance of the Prevotellaceae family which was further promoted by the presence of the ETEC strain. In contrast, several beneficial families such as Bacteroidiaceae or Ruminococcaceae and gut health related short chain fatty acids like butyrate or acetate were reduced upon simulated weaning. Moreover, the incubation of MPigut-IVM filtrated effluents with porcine intestinal cell cultures showed that ETEC challenge in the in vitro model led to an increased expression of pro-inflammatory genes by the porcine cells. This study provides insights about the etiology of a dysbiotic microbiota in post-weaning piglets.}, }
@article {pmid34347817, year = {2021}, author = {Menden-Deuer, S and Rowlett, J and Nursultanov, M and Collins, S and Rynearson, T}, title = {Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0254799}, doi = {10.1371/journal.pone.0254799}, pmid = {34347817}, issn = {1932-6203}, abstract = {Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.}, }
@article {pmid34347524, year = {2021}, author = {Kim, T and Behrens, S and LaPara, TM}, title = {Direct evidence for deterministic assembly of bacterial communities in full-scale municipal wastewater treatment facilities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0108621}, doi = {10.1128/AEM.01086-21}, pmid = {34347524}, issn = {1098-5336}, abstract = {In this study we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral- based theory (deterministic or stochastic) and whether bioreactor design (continuous-flow vs. fill-and-draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, one with triplicated fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity: μ = 0.48 ± 0.06 vs. 0.58 ± 0.08). Next, we compared our results to previously-used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index: μ = 3.3 ± 0.6 vs. 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously-used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because "replicate" experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more towards stochastic mechanisms compared to the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously-used indirect methods (synchronous community dynamics and an application of a null-model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.}, }
@article {pmid34347349, year = {2021}, author = {Bosch, J and Varliero, G and Hallsworth, JE and Dallas, TD and Hopkins, D and Frey, B and Kong, W and Lebre, P and Makhalanyane, TP and Cowan, DA}, title = {Microbial anhydrobiosis.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15699}, pmid = {34347349}, issn = {1462-2920}, abstract = {The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells. This article is protected by copyright. All rights reserved.}, }
@article {pmid34346368, year = {2021}, author = {Tulumello, J and Chabert, N and Rodriguez, J and Long, J and Nalin, R and Achouak, W and Heulin, T}, title = {Rhizobium alamii improves water stress tolerance in a non-legume.}, journal = {The Science of the total environment}, volume = {797}, number = {}, pages = {148895}, doi = {10.1016/j.scitotenv.2021.148895}, pmid = {34346368}, issn = {1879-1026}, abstract = {With the increasing demand for alternative solutions to replace or optimize the use of synthetic fertilizers and pesticides, the inoculation of bacteria that can contribute to the growth and health of plants (PGPR) is essential. The properties classically sought in PGPR are the production of phytohormones and other growth-promoting molecules, and more rarely the production of exopolysaccharides. We compared the effect of two strains of exopolysaccharide-producing Rhizobium alamii on rapeseed grown in a calcareous silty-clay soil under water stress conditions or not. The effect of factors 'water stress' and 'inoculation' were evaluated on plant growth parameters and the diversity of microbiota associated to root and root-adhering soil compartments. Water stress resulted in a significant decrease in leaf area, shoot biomass and RAS/RT ratio (root-adhering soil/root tissues), as well as overall beta-diversity. Inoculation with R. alamii YAS34 and GBV030 under water-stress conditions produced the same shoot dry biomass compared to uninoculated treatment in absence of water stress, and both strains increased shoot biomass under water-stressed conditions (+7% and +15%, respectively). Only R. alamii GBV030 significantly increased shoot biomass under unstressed or water-stressed conditions compared to the non-inoculated control (+39% and +15%, respectively). Alpha-diversity of the root-associated microbiota after inoculation with R. alamii YAS34 was significantly reduced. Beta-diversity was significantly modified after inoculation with R. alamii GBV030 under unstressed conditions. LEfSe analysis identified characteristic bacterial families, Flavobacteriaceae and Comamonadaceae, in the RT and RAS compartments for the treatment inoculated by R. alamii GBV030 under unstressed conditions, as well as Halomonadaceae (RT) and several species belonging to Actinomycetales (RAS). We showed that R. alamii GBV030 had a PGPR effect on rapeseed growth, increasing its tolerance to water stress, probably involving its capacity to produce exopolysaccharides, and other plant growth-promoting (PGP) traits.}, }
@article {pmid34345962, year = {2021}, author = {Chaitra, HS and Singh, A and Pandiyan, K and Kalia, VK}, title = {Sex Biased Variance in the Structural and Functional Diversity of the Midgut Bacterial Community of Last Instar Larvae of Pectinophora gossypiella (Lepidoptera: Gelechiidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34345962}, issn = {1432-184X}, abstract = {Elucidating the midgut bacterial diversity in an important cotton bollworm Pectinophora gossypiella can be a stepping stone in understanding the possible role of midgut bacteria in field evolved resistance against Bt cotton as well as to commonly used insecticides. Present study targeted metagenomics of 16S rRNA V3-V4 region to understand the influence of sex, if exists, in community diversity of gut microbes vis a vis their function in pink bollworm larvae. The results of the present study revealed that Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in the midgut of pink bollworm. Distinctive differences were found in the Shannon and Simpson diversity indices, ChaoI and ACE richness estimates in male and female larvae. The alpha diversity analysis showed that the gut bacteria of male were diverse and rich as compared to that of female. Further, beta diversity analysis indicated that the gut bacterial communities of both larval groups were unique from each other. These findings are the maiden report on sex-based variation in gut bacteria in P. gossypiella larvae. Role of candidate phyla OD1 (Parcubacteria) and TM7 (Saccharibacteria) in the living organisms needs to be studied, and their fairly significant composition in male and negligible composition in female larva raises question on their obvious role. Taxonomic to phenotypic mapping revealed that these gut bacteria play vital role in many metabolic and physiological activities of pink bollworm. Difference in potential functions of gut bacteria also varied with the sex.}, }
@article {pmid34342700, year = {2021}, author = {Chen, H and Verplaetse, E and Jauslin, T and Cosson, P and Slamti, L and Lereclus, D}, title = {The Fate of Bacteria of the Bacillus cereus Group in the Amoeba Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34342700}, issn = {1432-184X}, abstract = {The Bacillus cereus sensu lato group consists of several closely related species, including B. anthracis, B. cereus sensu stricto, and B. thuringiensis. Spores of these pathogenic bacteria are commonly found in the soil but evidence suggests that they are unable to grow in such a natural environment in the absence of nutrient input. Amoebas have been reported to be an amplifier for several species of pathogenic bacteria and their potential involvement to explain the large amount of B. thuringiensis and B. cereus spores in soil has been frequently proposed. Here, we studied the fate of Bacillus and amoebas when cultured together. We show that the virulence factors produced by B. thuringiensis and B. cereus do not affect the amoeba Acanthamoeba castellanii, which, on the contrary, can phagocytose and effectively digest vegetative Bacillus cells to grow and prevent the formation of cysts. Bacterial spores can germinate in the amoeba environment and the vegetative cells can then form chains or aggregates that appear to be less efficiently phagocyted by the amoeba. The use of transcriptional fusions between fluorescent reporter genes and stationary phase- and sporulation-specific promoters showed that the sporulation process occurs more efficiently in the presence of amoebas than in their absence. Moreover, our results showed the amoeba environment to promote spore germination and allow the bacteria to complete their developmental cycle. Overall, this study suggests that the amoeba-Bacillus interaction creates a virtuous circle in which each protagonist helps the other to develop.}, }
@article {pmid34342699, year = {2021}, author = {Ke, L and Yan, WY and Zhang, LZ and Zeng, ZJ and Evans, JD and Huang, Q}, title = {Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34342699}, issn = {1432-184X}, abstract = {Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.}, }
@article {pmid34342698, year = {2021}, author = {Jan, B and Reshi, ZA and Mohiddin, FA}, title = {Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34342698}, issn = {1432-184X}, abstract = {The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus. A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs (P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.}, }
@article {pmid34340552, year = {2021}, author = {Munoz-Munoz, J and Ndeh, D and Fernandez-Julia, P and Walton, G and Henrissat, B and Gilbert, HJ}, title = {Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius.}, journal = {mBio}, volume = {}, number = {}, pages = {e0136821}, doi = {10.1128/mBio.01368-21}, pmid = {34340552}, issn = {2150-7511}, abstract = {The human gut microbiota (HGM) contributes to the physiology and health of its host. The health benefits provided by dietary manipulation of the HGM require knowledge of how glycans, the major nutrients available to this ecosystem, are metabolized. Arabinogalactan proteins (AGPs) are a ubiquitous feature of plant polysaccharides available to the HGM. Although the galactan backbone and galactooligosaccharide side chains of AGPs are conserved, the decorations of these structures are highly variable. Here, we tested the hypothesis that these variations in arabinogalactan decoration provide a selection mechanism for specific Bacteroides species within the HGM. The data showed that only a single bacterium, B. plebeius, grew on red wine AGP (Wi-AGP) and seaweed AGP (SW-AGP) in mono- or mixed culture. Wi-AGP thus acts as a privileged nutrient for a Bacteroides species within the HGM that utilizes marine and terrestrial plant glycans. The B. plebeius polysaccharide utilization loci (PULs) upregulated by AGPs encoded a polysaccharide lyase, located in the enzyme family GH145, which hydrolyzed Rha-Glc linkages in Wi-AGP. Further analysis of GH145 identified an enzyme with two active sites that displayed glycoside hydrolase and lyase activities, respectively, which conferred substrate flexibility for different AGPs. The AGP-degrading apparatus of B. plebeius also contained a sulfatase, BpS1_8, active on SW-AGP and Wi-AGP, which played a pivotal role in the utilization of these glycans by the bacterium. BpS1_8 enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health. IMPORTANCE Dietary manipulation of the HGM requires knowledge of how glycans available to this ecosystem are metabolized. The variable structures that decorate the core component of plant AGPs may influence their utilization by specific organisms within the HGM. Here, we evaluated the ability of Bacteroides species to utilize a marine and terrestrial AGP. The data showed that a single bacterium, B. plebeius, grew on Wi-AGP and SW-AGP in mono- or mixed culture. Wi-AGP is thus a privileged nutrient for a Bacteroides species that utilizes marine and terrestrial plant glycans. A key component of the AGP-degrading apparatus of B. plebeius is a sulfatase that conferred the ability of the bacterium to utilize these glycans. The enzyme enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health.}, }
@article {pmid34340550, year = {2021}, author = {Goordial, J and D'Angelo, T and Labonté, JM and Poulton, NJ and Brown, JM and Stepanauskas, R and Früh-Green, GL and Orcutt, BN}, title = {Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.}, journal = {mBio}, volume = {}, number = {}, pages = {e0049021}, doi = {10.1128/mBio.00490-21}, pmid = {34340550}, issn = {2150-7511}, abstract = {The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (101 to 104 cells cm-3) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.}, }
@article {pmid34339990, year = {2021}, author = {Zhang, S and Lu, J and Wang, Y and Verstraete, W and Yuan, Z and Guo, J}, title = {Insights of metallic nanoparticles and ions in accelerating the bacterial uptake of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126728}, doi = {10.1016/j.jhazmat.2021.126728}, pmid = {34339990}, issn = {1873-3336}, abstract = {The increasing release of nanomaterials has attracted significant concerns for human and environmental health. Similarly, the dissemination of antimicrobial resistance (AMR) is a global health crisis affecting approximately 700,000 people a year. However, a knowledge gap persists between the spread of AMR and nanomaterials. This study aims to fill this gap by investigating whether and how nanomaterials could directly facilitate the dissemination of AMR through horizontal gene transfer. Our results show that commonly-used nanoparticles (NPs) (Ag, CuO and ZnO NPs) and their ion forms (Ag+, Cu2+ and Zn2+) at realistic concentrations within aquatic environments can significantly promote the transformation of extracellular antibiotic resistance genes in Acinetobacter baylyi ADP1 by a factor of 11.0-folds, which is comparable to the effects of antibiotics. The enhanced transformation by Ag NPs/Ag+ and CuO NPs/Cu2+ was primarily associated with the overproduction of reactive oxygen species and cell membrane damage. ZnO NPs/Zn2+ might increase the natural transformation rate by stimulating the stress response and ATP synthesis. All tested NPs/ions resulted in upregulating the competence and SOS response-associated genes. These findings highlight a new concern that nanomaterials can speed up the spread of AMR, which should not be ignored when assessing the holistic risk of nanomaterials.}, }
@article {pmid34339704, year = {2021}, author = {Torun, F and Hostins, B and De Schryver, P and Boon, N and De Vrieze, J}, title = {Molybdate effectively controls sulphide production in a shrimp pond model.}, journal = {Environmental research}, volume = {}, number = {}, pages = {111797}, doi = {10.1016/j.envres.2021.111797}, pmid = {34339704}, issn = {1096-0953}, abstract = {The production of shrimp is often performed in earthen outdoor ponds in which the high input of feed and faeces on the bottom can result in deterioration of the water quality, which negatively impacts the animals and the environment. Here, we investigate the potential of sodium molybdate (Na₂MoO₄·2H₂O), sodium nitrate (NaNO3) and sodium percarbonate (Na2CO3·1.5H2O2) to control sulphide production in a simulated shrimp pond bottom system that included the sediment, overlaying artificial seawater and organic matter input in the form of shrimp feed and shrimp faeces. Sediment depth gradient measurements of oxygen, H2S and pH were obtained during 7 days of incubation using microelectrodes. The most significant impact in terms of H2S, was observed for 50 mg/L sodium molybdate. At the water-sediment interface, there was up to 73% less H2S detected for this treatment in comparison to a control treatment, while in the deeper layers of the sediment it was up to 47% less H2S. The residual sulphate concentrations in the molybdate treated samples were 16 ± 4% higher than the control, indicating an inhibition in sulphate reduction. Nitrate and sodium percarbonate treatments also showed a limited capacity to decrease H2S entering in the water column, yet no clear difference in H2S concentrations in the sediment compared to the control were observed. Molybdate treatment appears to work through the inhibition of sulphate reducing bacteria in situ for the control of H2S production better than the chemical oxygen boosters or nitrate treatment.}, }
@article {pmid34339295, year = {2021}, author = {Göing, S and Gasperotti, AF and Yang, Q and Defoirdt, T and Jung, K}, title = {First insights into a pyruvate sensing and uptake system in Vibrio campbellii and its importance for virulence.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {JB0029621}, doi = {10.1128/JB.00296-21}, pmid = {34339295}, issn = {1098-5530}, abstract = {Pyruvate is a key metabolite in living cells and has been shown to play a crucial role in the virulence of several bacterial pathogens. The bioluminescent Vibrio campbellii, a severe infectious burden for marine aquaculture, excretes extraordinarily large amounts of pyruvate during growth and rapidly retrieves it by an as-yet unknown mechanism. We have now identified the responsible pyruvate transporter, here named BtsU, and our results show that it is the only pyruvate transporter in V. campbellii. Expression of btsU is tightly regulated by the membrane-integrated LytS-type histidine kinase BtsS, a sensor for extracellular pyruvate, and the LytTR-type response regulator BtsR. Cells lacking either the pyruvate transporter or sensing system show no chemotactic response towards pyruvate, indicating that intracellular pyruvate is required to activate the chemotaxis system. Moreover, pyruvate sensing and uptake were found to be important for the resuscitation of V. campbellii from the viable but nonculturable (VBNC) state and the bacterium's virulence against brine shrimp larvae. IMPORTANCE Bacterial infections are a serious threat to marine aquaculture, one of the fastest growing food sectors on earth. Therefore, it is extremely important to learn more about the pathogens responsible, one of which is Vibrio campbellii. This study sheds light on the importance of pyruvate sensing and uptake for V. campbellii, and reveals that the bacterium possesses only one pyruvate transporter, which is activated by a pyruvate-responsive histidine kinase/response regulator system. Without the ability to sense or take up pyruvate, the virulence of V. campbellii towards gnotobiotic brine shrimp larvae is strongly reduced.}, }
@article {pmid34338516, year = {2021}, author = {Tang, JS and Cait, A and Li, Y and Abolins-Thompson, H and Gell, K and Herst, PM and O'Sullivan, D and Gasser, O}, title = {Practical Approach To Explore the Effects of Polyphenols on Aryl Hydrocarbon Receptor Regulated Immune Function.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.1c02095}, pmid = {34338516}, issn = {1520-5118}, abstract = {The ligand-activated aryl hydrocarbon receptor (AhR) is an important molecular regulator of immune function, whose activity can be modulated by dietary glucosinolate- and tryptophan-derived metabolites. In contrast, the potential use of polyphenols as dietary regulators of AhR-dependent immunity remains unclear. In this perspective, we discuss how cellular metabolism may alter the net effect of polyphenols on AhR, thus potentially reconciling some of the conflicting observations reported in the literature. We further provide a methodological roadmap, across the fields of immunology, metabolomics, and gut microbial ecology, to explore the potential effects of polyphenol-rich diets on AhR-regulated immune function in humans.}, }
@article {pmid34335540, year = {2021}, author = {Zhang, J and Zeng, R and Labes, A}, title = {Editorial: Marine Microbial-Derived Molecules and Their Potential Medical and Cosmetic Applications.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {706152}, doi = {10.3389/fmicb.2021.706152}, pmid = {34335540}, issn = {1664-302X}, }
@article {pmid34333428, year = {2021}, author = {Boada, E and Santos-Clotas, E and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F}, title = {The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149162}, doi = {10.1016/j.scitotenv.2021.149162}, pmid = {34333428}, issn = {1879-1026}, abstract = {Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.}, }
@article {pmid34333046, year = {2021}, author = {Hunt, KA and Forbes, J and Taub, F and Elliott, N and Hardwicke, J and Petersen, R and Stopnisek, N and Beck, DAC and Stahl, DA}, title = {An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {106294}, doi = {10.1016/j.mimet.2021.106294}, pmid = {34333046}, issn = {1872-8359}, abstract = {Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.}, }
@article {pmid34331150, year = {2021}, author = {de Freitas, F and Vendruscolo, SJ and Soares, MA and Battirola, LD and de Andrade, RLT}, title = {Biomass of the macrophyte remedies and detoxifies Cd(II) and Pb(II) in aqueous solution.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {8}, pages = {537}, pmid = {34331150}, issn = {1573-2959}, abstract = {Aquatic plants are considered to be important remedial agents in aquatic environments contaminated by metals. The Salvinia biloba macrophyte was evaluated in relation to its removal kinetics, adsorption capacity, and toxicology, aiming at its application in the removal of Cd+2 and Pb+2 ions from aqueous solutions. A batch-type system was used, in which the plants were cultivated in microcosms containing nutritive solution and metallic ions, stored in a controlled environment (pH, temperature, and luminosity). The removal kinetics consisted in the analysis of efficiency, varying the concentrations of the metals, and time of cultivation of plants in solution. To describe the process, adsorption isotherms were constructed with the equilibrium data, which were later adjusted to Langmuir and Freundlich models. The toxicological trial was performed by sub-acute exposure test of Caenorhabditis elegans nematode to phytoremediated solutions. The results highlight the remedial effect of the plant in solutions contaminated with both metals. The kinetic study demonstrated that the plant responds differently to metals, and physical-chemical and biological processes can be attributed to the removal of metals from the solution by the plant. The equilibrium time obtained was 48 h for both metals, and the adsorption capacity was higher for Cd2+. The toxicological evaluation indicates that there was a reduction in toxicity after the remediation of the solutions by S. biloba, for all times and concentrations evaluated. Salvinia biloba was efficient for the removal of Cd2+ and Pb2+ metals from aqueous solution. The plant is a low-cost metal biosorbent and can be considered promising for phytoremediation strategies in liquid effluents and water bodies.}, }
@article {pmid34331071, year = {2021}, author = {Haydon, TD and Suggett, DJ and Siboni, N and Kahlke, T and Camp, EF and Seymour, JR}, title = {Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34331071}, issn = {1432-184X}, abstract = {Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.}, }
@article {pmid34330907, year = {2021}, author = {Rahlff, J and Turzynski, V and Esser, SP and Monsees, I and Bornemann, TLV and Figueroa-Gonzalez, PA and Schulz, F and Woyke, T and Klingl, A and Moraru, C and Probst, AJ}, title = {Lytic archaeal viruses infect abundant primary producers in Earth's crust.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4642}, pmid = {34330907}, issn = {2041-1723}, abstract = {The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.}, }
@article {pmid34326823, year = {2021}, author = {Gu, Q and Chen, M and Zhang, J and Guo, W and Wu, H and Sun, M and Wei, L and Wang, J and Wei, X and Zhang, Y and Ye, Q and Xue, L and Pang, R and Ding, Y and Wu, Q}, title = {Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {687511}, doi = {10.3389/fmicb.2021.687511}, pmid = {34326823}, issn = {1664-302X}, abstract = {Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the "seed" bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.}, }
@article {pmid34324834, year = {2021}, author = {Christensen, SM and Munkres, I and Vannette, RL}, title = {Nectar bacteria stimulate pollen germination and bursting to enhance microbial fitness.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2021.07.016}, pmid = {34324834}, issn = {1879-0445}, abstract = {Many organisms consume pollen, yet mechanisms of its digestion remain a fundamental enigma in pollination biology,1-3 as pollen is protected by a recalcitrant outer shell.4-8 Pollen is commonly found in floral nectar,9,10 as are nectar microbes, which are nearly ubiquitous among flowers.11-13 Nectar specialist bacteria, like Acinetobacter, can reach high densities (up to 109 cells/mL), despite the fact that floral nectar is nitrogen poor.14-17 Here, we show evidence that the genus Acinetobacter, prevalent nectar- and bee-associated bacteria,12,18-20 can induce pollen germination and bursting, gain access to protoplasm nutrients, and thereby grow to higher densities. Although induced germination had been suggested as a potential method in macroscopic pollen consumers,2,21-23 and fungal inhibition of pollen germination has been shown,24-27 direct biological induction of germination has not been empirically documented outside of plants.28-32Acinetobacter pollinis SCC47719 induced over 5× greater pollen germination and 20× greater pollen bursting than that of uninoculated pollen by 45 min. When provided with germinable pollen, A. pollinis stimulates protein release and grows to nearly twice the density compared to growth with ungerminable pollen, indicating that stimulation of germination benefits bacterial fitness. In contrast, a common nectar-inhabiting yeast (Metschnikowia)33 neither induced nor benefited from pollen germination. We conclude that Acinetobacter both specifically causes and benefits from inducing pollen germination and bursting. Further study of microbe-pollen interactions may inform many aspects of pollination ecology, including floral microbial ecology,34,35 pollinator nutrient acquisition from pollen,2,3,21,36 and cues of pollen germination for plant reproduction.37-39.}, }
@article {pmid34320736, year = {2021}, author = {Rimboud, M and Etcheverry, L and Barakat, M and Achouak, W and Bergel, A and Délia, ML}, title = {Hypersaline microbial fuel cell equipped with an oxygen-reducing microbial cathode.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125448}, doi = {10.1016/j.biortech.2021.125448}, pmid = {34320736}, issn = {1873-2976}, abstract = {Microbial anodes and oxygen reducing microbial cathodes were designed separately under constant polarization at + 0.1 V/SCE in a hypersaline medium (NaCl 45 g/L). They were then associated to design two-compartment microbial fuel cells (MFCs). These MFCs produced up to 209 ± 24 mW m-2 during a week. This was the first demonstration that hypersaline MFCs equipped with microbial cathodes can produce power density at this level. Desulfuromonas sp. were confirmed to be key species of the anodes. The efficiency of the cathodes was linked to the development of a redox system centred at + 0.2 V/SCE and to the presence of Gammaproteobacteria (Alteromonadales and Oceanospirillales), especially an unclassified order phylogenetically linked to the genus Thioalobacter. Comparing the different performance of the four MFCs with the population analyses suggested that polarization at + 0.1 V/SCE should be maintained longer to promote the growth of Thioalobacter on the cathode and thus increase the MFC performance.}, }
@article {pmid34320208, year = {2021}, author = {Minnebo, Y and De Paepe, K and Raes, J and Van de Wiele, T}, title = {Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab111}, pmid = {34320208}, issn = {1574-6941}, abstract = {A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardised feed concentrations from 100% to 33, 20 and 10% in five-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35 and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively. After the tenfold nutrient reduction, the microbial load decreased by 79.72 ± 9% and 82.96 ± 1.66% in the proximal and distal colon, respectively, while the net total short-chain fatty acid production dropped by 79.42 ± 4.42% and 84.58 ± 2.42%, respectively. The majority of microbial taxa quantitatively decreased, whereas a select group of nutritional specialists, such as Akkermansia muciniphila and Bilophila wadsworthia and a number of opportunistic pathogens remained unaffected. This shows that nutrient load is an important driver of the human gut microbiome and should be considered in future in vitro and in vivo dietary research.}, }
@article {pmid34316298, year = {2021}, author = {Wang, Q and Zhang, Y and Yang, Q and Fu, S and Qu, B and Defoirdt, T}, title = {One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming.}, journal = {Gut pathogens}, volume = {13}, number = {}, pages = {47}, doi = {10.1186/s13099-021-00442-4}, pmid = {34316298}, issn = {1757-4749}, abstract = {Background: Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp.<br><br>Results: Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella.<br><br>Conclusions: In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.<br><br>Supplementary Information: The online version contains supplementary material available at 10.1186/s13099-021-00442-4.}, }
@article {pmid34313080, year = {2021}, author = {Zou, WX and Shen, JP and Zhang, LM and Hu, A and Wang, JJ and He, JZ}, title = {Quantitative stable isotope probing technique and its applications in microbial ecology.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {32}, number = {7}, pages = {2615-2622}, doi = {10.13287/j.1001-9332.202107.032}, pmid = {34313080}, issn = {1001-9332}, mesh = {Carbon Isotopes ; DNA ; High-Throughput Nucleotide Sequencing ; Isotope Labeling ; *Microbiota ; }, abstract = {Quantitative stable isotope probing (qSIP) is a powerful tool, which links microbial taxon with functional metabolism in ecosystems and quantitatively determines the metabolic activity or growth rate of individual microbial taxa exposed to isotope tracers in the environment. qSIP technique employs quantitative PCR, high-throughput sequencing and stable isotope probing (SIP) techniques. The procedure involves adding labeled substrates to environmental samples for cultivation, separating labeled heavy fraction from unlabeled light fraction via isopycnic ultracentrifugation, making absolute quantification and sequencing analysis for microbial populations in all fractions, and then quantifying the isotope abundance of DNA involved in uptake and transformation based on the DNA density curve of unlabeled treatment and GC content. Here, we reviewed the rationale, data analysis and application of qSIP in microbial ecology, and discussed the existing problems and prospects of qSIP.}, }
@article {pmid34312710, year = {2021}, author = {Islam, MS and Sobur, MA and Rahman, S and Ballah, FM and Ievy, S and Siddique, MP and Rahman, M and Kafi, MA and Rahman, MT}, title = {Detection of blaTEM, blaCTX-M, blaCMY, and blaSHV Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Migratory Birds Travelling to Bangladesh.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34312710}, issn = {1432-184X}, support = {2019/8/BAU//Bangladesh Agricultural University Research System/ ; 2020/28/UGC//University Grants Commission/ ; }, abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli cause severe health hazards. Migratory birds are reservoirs and transmitters of many pathogens including ESBL-producing E. coli. To examine migratory birds as potential carriers of ESBL-producing E. coli and E. coli-carrying antibiotic resistance genes, 55 PCR-positive E. coli isolates were screened using the disk diffusion method, double-disk synergy test, and further polymerase chain reaction (PCR) tests. Genes encoding resistance to tetracycline [tetA, 100% (35/35); tetB, 31.43% (11/35)], fluoroquinolone [qnrA, 35.71% (10/28); qnrB, 25% (7/28)], and streptomycin [aadA1, 90.24% (37/41)] were detected in the isolated E. coli. Of the 55 E. coli isolates, 21 (38.18%) were ESBL producers, and all of them were multidrug resistant. All the ESBL-producing E. coli isolates harbored at least two or more beta-lactamase genes, of which blaTEM, blaCMY, blaCTX-M, and blaSHV were detected in 95.24%, 90.48%, 85.71%, and 42.86% of isolates, respectively. All the beta-lactamase genes were present in four of the ESBL-producing E. coli isolates. Furthermore, 95.24% of ESBL-producing E. coli isolates were positive for one or more antibiotic resistance genes. To the best of our knowledge, this is the first study to detect E. coli-carrying antibiotic resistance genes including beta-lactamase blaCMY and blaSHV originating from migratory birds in Bangladesh. These results suggest that migratory birds are potential carriers of ESBL-producing E. coli along with other clinically important antibiotic resistance genes which may have detrimental impacts on human health.}, }
@article {pmid34312709, year = {2021}, author = {de Los Ríos, A and Garrido-Benavent, I and Limón, A and Cason, ED and Maggs-Kölling, G and Cowan, D and Valverde, A}, title = {Novel lichen-dominated hypolithic communities in the Namib Desert.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34312709}, issn = {1432-184X}, support = {CTM2015-64728-C2-2-R//(MINECO/FEDER, EU)/ ; PID2019-105469RB-C22//MICINN-AEI/ ; }, abstract = {The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.}, }
@article {pmid34312335, year = {2021}, author = {Wanner, J}, title = {The development in biological wastewater treatment over the last 50 years.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {84}, number = {2}, pages = {274-283}, doi = {10.2166/wst.2021.095}, pmid = {34312335}, issn = {0273-1223}, mesh = {Bioreactors ; Nitrogen ; Phosphorus ; Sewage ; *Waste Disposal, Fluid ; Waste Water ; *Water Purification ; }, abstract = {The paper summarizes the development in the understanding and practical application of the activated sludge process over the last 50 years. Since its invention, the activated sludge process has been a big challenge to design engineers. Traditionally, the technology was covered by sanitary engineers. However, with the development in the understanding of activated sludge process principles, further progress was not possible without knowledge of reaction kinetics and reactor theory. The shift from BOD removal only to combined removal of organic pollution, nitrogen and phosphorus required a chemical engineering approach with outputs of activated sludge microbiology and microbial ecology. Molecular biology enabled more accurate identification of important activated sludge microorganisms. The development in activated sludge process also required more efficient activated sludge separation and thickening. The paper describes the development from secondary clarifiers to membrane separation. Increasing water stress around the globe has also changed the main wastewater paradigm from wastewater treatment and safe discharge to safe reuse.}, }
@article {pmid34297464, year = {2021}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Indole decreases the virulence of pathogenic vibrios belonging to the Harveyi clade.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15227}, pmid = {34297464}, issn = {1365-2672}, abstract = {AIM: Indole is a signaling molecule secreted by over 85 species of bacteria, including several Vibrio species, and it has been reported to affect different bacterial phenotypes such as biofilm formation, motility, and virulence. In this study, we aimed at investigating the inter-strain variability of the effect of indole in 12 different strains belonging to the Harveyi clade of vibrios.<br><br>METHODS AND RESULTS: Indole reduced the virulence of all strains towards gnotobiotic brine shrimp larvae. The survival rate of brine shrimp larvae challenged with vibrios pretreated with indole was increased by 1.3-fold to 1.8-fold. Additionally, indole significantly decreased the biofilm formation in all of the strains, decreased the swimming motility in eight of the strains, and decreased swarming motility in five of the strains. When cultured in the presence of exogenous indole, the mRNA level of the pirA and pirB toxin genes were down-regulated to 65% and 46%, and to 62% and 55% in the AHPND-causing strains V. parahaemolyticus M0904 and V. campbellii S01, respectively.<br><br>CONCLUSIONS: These data indicate that indole has a significant impact on the virulence of different strains belonging to the Harveyi clade of vibrios.<br><br>Our results suggest that indole signaling is a valid target for the development of novel therapeutics in order to control infections caused by Harveyi clade vibrios in aquaculture.}, }
@article {pmid34294810, year = {2021}, author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Zayed, N and Quirynen, M and Teughels, W}, title = {Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15033}, pmid = {34294810}, issn = {2045-2322}, support = {C24/17/086//KU Leuven/ ; FWO G091218N//Research Foundation Flanders (FWO)/ ; }, abstract = {Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.}, }
@article {pmid34247483, year = {2021}, author = {Jakus, N and Mellage, A and Höschen, C and Maisch, M and Byrne, JM and Mueller, CW and Grathwohl, P and Kappler, A}, title = {Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {14}, pages = {9876-9884}, doi = {10.1021/acs.est.1c02049}, pmid = {34247483}, issn = {1520-5851}, abstract = {Neutrophilic microbial pyrite (FeS2) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes (NAFe-pyrite) and 57Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO3) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S0), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the NAFe-pyrite/57Fe-siderite setups by maps of 56FeO and 32S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of 56Fe(III) (oxyhydr)oxides that could solely originate from 56FeS2. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe3+ appeared to be negligible in our experimental setup.}, }
@article {pmid34311495, year = {2021}, author = {Pascual, J and Tanner, K and Vilanova, C and Porcar, M and Delgado, A}, title = {The microbial terroir: open questions on the Nagoya protocol applied to microbial resources.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13839}, pmid = {34311495}, issn = {1751-7915}, support = {820699//European Commission/ ; }, abstract = {The Nagoya Protocol on Access and Benefit-sharing (https://www.cbd.int/abs/), primarily designed for vascular plant and animal resources, is also extended to the use of microbial resources, but its application to the microbiological realm has raised many doubts and provoked criticisms. This is because of the particularities of microbial ecology and the technical and legal difficulties encompassed in its application.}, }
@article {pmid34311349, year = {2021}, author = {Williams, MR and Stedtfeld, RD and Stedtfeld, TM and Crawford, RB and Kuwahara, T and Kaminski, NE and Tiedje, JM and Hashsham, SA}, title = {MicroRNA-based host response to toxicant exposure is influenced by the presence of gut microbial populations.}, journal = {The Science of the total environment}, volume = {797}, number = {}, pages = {149130}, doi = {10.1016/j.scitotenv.2021.149130}, pmid = {34311349}, issn = {1879-1026}, abstract = {Segmented filamentous bacteria (SFB) and Bacteroides fragilis are known to interact with the host immune response through the aryl hydrocarbon receptor (Ahr). 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and a high-affinity Ahr ligand has the potential to modify the effect of SFB and B. fragilis. MicroRNAs (miRNA) with their role in regulating gene expression post-transcriptionally, may potentially be used to observe such interactions between SFB, B. fragilis, and TCDD. However, little is known regarding the impact of gut microbial members on miRNA expression or its modulation in the presence of an environmental toxicant. This information is important in understanding toxicant-mediated dysbiosis in gut microbiome and the resulting human health impacts. In this study, C57BL/6 germ-free (GF) mice were colonized with SFB and B. fragilis and administered 30 μg/kg TCDD every 4 d for 28 d and miRNA were measured. Compared to GF mice, colonization with SFB resulted in an increase in up- and down-regulated Ileal miRNAs. TCDD treatment of this group decreased the number of upregulated miRNA and increased the number of down-regulated miRNAs. Association with SFB and B. fragilis together had a similar but less pronounced effect in response to TCDD treatment. TCDD treatment of GF mice had no miRNA expression response. Immune and inflammatory responses and T-cell differentiation were the key functions impacted by these miRNAs. Overall, these results reveal that the host response to toxicants may also depend on the presence of specific gut microbial populations.}, }
@article {pmid34309697, year = {2021}, author = {Begum, N and Wang, L and Ahmad, H and Akhtar, K and Roy, R and Khan, MI and Zhao, T}, title = {Co-inoculation of Arbuscular Mycorrhizal Fungi and the Plant Growth-Promoting Rhizobacteria Improve Growth and Photosynthesis in Tobacco Under Drought Stress by Up-Regulating Antioxidant and Mineral Nutrition Metabolism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34309697}, issn = {1432-184X}, abstract = {Drought stress is a major environmental concern that limits crop growth on a large scale around the world. Significant efforts are required to overcome this issue in order to improve crop production. Therefore, the exciting role of beneficial microorganisms under stress conditions needs to be deeply explored. In this study, the role of two biotic entities, i.e., Arbuscular mycorrhizal fungi (AMF, Glomus versiforme) and plant growth-promoting rhizobacteria (PGPR, Bacillus methylotrophicus) inoculation in drought tolerance of tobacco (Nicotiana tabacum L.), was investigated. The present results showed that drought stress considerably reduced tobacco plant's growth and their physiological attributes. However, the plants co-inoculated with AMF and PGPR showed higher drought tolerance by bringing up significant improvement in the growth and biomass of tobacco plants. Moreover, the co-inoculation of AMF and PGPR considerably increased chlorophyll a, b, total chlorophylls, carotenoids, photosynthesis, and PSII efficiency by 96.99%, 76.90%, and 67.96% and 56.88%, 53.22%, and 33.43% under drought stress conditions, respectively. Furthermore, it was observed that drought stress enhanced lipid peroxidation and electrolyte leakage. However, the co-inoculation of AMF and PGPR reduced the electrolyte leakage and lipid peroxidation and significantly enhanced the accumulation of phenols and flavonoids by 57.85% and 71.74%. Similarly, the antioxidant enzymatic activity and the plant nutrition status were also considerably improved in co-inoculated plants under drought stress. Additionally, the AMF and PGPR inoculation also enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) concentrations by 67.71% and 54.41% in the shoots of tobacco plants. The current findings depicted that inoculation of AMF and PGPR (alone or in combination) enhanced the growth and mitigated the photosynthetic alteration with the consequent up-regulation of secondary metabolism, osmolyte accumulation, and antioxidant system.}, }
@article {pmid34305833, year = {2021}, author = {Hernández, R and Jimenez, H and Vargas-Garcia, C and Caro-Quintero, A and Reyes, A}, title = {Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {664754}, pmid = {34305833}, issn = {1664-302X}, abstract = {The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.}, }
@article {pmid34305582, year = {2021}, author = {Chen, Z and Lv, Y and Xu, H and Deng, L}, title = {Herbal Medicine, Gut Microbiota, and COVID-19.}, journal = {Frontiers in pharmacology}, volume = {12}, number = {}, pages = {646560}, pmid = {34305582}, issn = {1663-9812}, abstract = {Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. The symptoms of COVID-19 range from mild flu-like symptoms, including cough and fever, to life threatening complications. There are still quite a number of patients with COVID-19 showed enteric symptoms including nausea, vomiting, and diarrhea. The gastrointestinal tract may be one of the target organs of SARS-CoV-2. Angiotensin converting enzyme 2 (ACE2) is the main receptor of SARS-CoV-2 virus, which is significantly expressed in intestinal cells. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Intestinal flora imbalance and endotoxemia may accelerate the progression of COVID-19. Many herbs have demonstrated properties relevant to the treatment of COVID-19, by supporting organs and systems of the body affected by the virus. Herbs can restore the structure of the intestinal flora, which may further modulate the immune function after SARS-CoV-2 infection. Regulation of intestinal flora by herbal medicine may be helpful for the treatment and recovery of the disease. Understanding the role of herbs that regulate intestinal flora in fighting respiratory virus infections and maintaining intestinal flora balance can provide new ideas for preventing and treating COVID-19.}, }
@article {pmid34304501, year = {2021}, author = {Liu, X and Liu, H and Li, C}, title = {[Advances in the study of chronic sinusitis microbiology using 16SrRNA gene sequencing technology].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery}, volume = {35}, number = {7}, pages = {658-661}, doi = {10.13201/j.issn.2096-7993.2021.07.019}, pmid = {34304501}, issn = {2096-7993}, mesh = {Bacteria/genetics ; Chronic Disease ; Humans ; *Rhinitis ; *Sinusitis ; Technology ; }, abstract = {Traditional conventional bacterial culture techniques can cultivate fewer types of bacteria, aiming to isolate and identify specific pathogens, guide antibiotic treatment and eradicate pathogens.Macrogenomics techniques can simultaneously identify both cultured and uncultured bacteria in the flora, providing the possibility for the study of symbiotic flora. With the vigorous development of SrRNA and application of 16 gene sequencing technology, the microbial ecology research of chronic sinusitis （chronic rhinosinusitis,CRS） has once again become a hot topic.And the CRS view of microbial community composition and microbial diversity were presented. This review describes the use of 16 SrRNA gene sequencing in recent years advances in technical studies CRS microbial ecology.}, }
@article {pmid34304356, year = {2021}, author = {Araujo, ASF and de Pereira, APA and Antunes, JEL and Oliveira, LMS and de Melo, WJ and Rocha, SMB and do Amorim, MR and Araujo, FF and Melo, VMM and Mendes, LW}, title = {Dynamics of bacterial and archaeal communities along the composting of tannery sludge.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {34304356}, issn = {1614-7499}, support = {305069/2018-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.}, }
@article {pmid34304060, year = {2021}, author = {Sepúlveda-Correa, A and Daza-Giraldo, LV and Polanía, J and Arenas, NE and Muñoz-García, A and Sandoval-Figueredo, AV and Vanegas, J}, title = {Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities.}, journal = {Marine pollution bulletin}, volume = {171}, number = {}, pages = {112740}, doi = {10.1016/j.marpolbul.2021.112740}, pmid = {34304060}, issn = {1879-3363}, abstract = {Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.}, }
@article {pmid34303166, year = {2021}, author = {Li, C and Wang, L and Ji, S and Chang, M and Wang, L and Gan, Y and Liu, J}, title = {The ecology of the plastisphere: Microbial composition, function, assembly, and network in the freshwater and seawater ecosystems.}, journal = {Water research}, volume = {202}, number = {}, pages = {117428}, doi = {10.1016/j.watres.2021.117428}, pmid = {34303166}, issn = {1879-2448}, abstract = {Microplastics provide a unique habitat for microorganisms, forming the plastisphere. Yet the ecology of the plastisphere, including the microbial composition, functions, assembly processes, and interaction networks, needs to be understood. Here, we collected microplastics and their surrounding water samples in freshwater and seawater ecosystems. The bacterial and fungal communities of the plastisphere and the aquatic environment were studied based on 16S and internal transcribed spacer (ITS) high-throughput sequencing. We found that the plastisphere had a distinct microbial community and recruited a noteworthy proportion of unique species compared to the aquatic environment community, potentially altering ecosystem microbial community and causing microbial invasion. Using a random-forest machine-learning model, we identified a group of biomarkers that could best distinguish the plastisphere from the aquatic environment. Significant differences exist in microbial functions between the plastisphere and the aquatic environment, including functions of pathogenicity, compound degradation, as well as functions related to the cycling of carbon, nitrogen, and sulfur. And these functional differences were expressed differently in freshwater and seawater ecosystems. The oxidation-reduction potential, salinity, the concentrations of nitrogen-related ions (NO3-, NO2-, and NH4+), and the concentration of dissolved organic carbon in the surrounding environment drive the variation of the plastisphere. But environmental physicochemical properties explain less of the microbial community variation in the plastisphere than that in the aquatic environment. Niche-based processes govern the assembly of the plastisphere community, while neutral-based processes dominate the community assembly of the aquatic environment. Furthermore, compared to the aquatic environment, the plastisphere has a network of less complexity, more modules, higher modularity, and more competitive links in freshwater ecosystems, but the pattern is reversed in seawater ecosystems. Altogether, the microbial ecology of the new anthropogenic ecosystem-plastisphere-is unique and exerts different effects in freshwater and seawater ecosystems.}, }
@article {pmid34302509, year = {2021}, author = {Ren, Z and Zhang, Y and Cai, T and Mao, K and Xu, Y and Li, C and He, S and Li, J and Wan, H}, title = {Dynamics of Microbial Communities across the Life Stages of Nilaparvata lugens (Stål).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34302509}, issn = {1432-184X}, support = {32072462//National Natural Science Foundation of China/ ; }, abstract = {Understanding the composition of microorganismal communities hosted by insect pests is an important prerequisite for revealing their functions and developing new pest control strategies. Although studies of the structure of the microbiome of Nilaparvata lugens have been published, little is known about the dynamic changes in this microbiome across different developmental stages, and an understanding of the core microbiota is still lacking. In this study, we investigated the dynamic changes in bacteria and fungi in different developmental stages of N. lugens using high-throughput sequencing technology. We observed that the microbial diversity in eggs and mated adults was higher than that in nymphs and unmated adults. We also observed a notable strong correlation between fungal and bacterial α-diversity, which suggests that fungi and bacteria are closely linked and may perform functions collaboratively during the whole developmental period. Arsenophonus and Hirsutella were the predominant bacterial and fungal taxa, respectively. Bacteria were more conserved than fungi during the transmission of the microbiota between developmental stages. Compared with that in the nymph and unmated adult stages of N. lugens, the correlation between bacterial and fungal communities in the mated adult and egg stages was stronger. Moreover, the core microbiota across all developmental stages in N. lugens was identified, and there were more bacterial genera than fungal genera; notably, the core microbiota of eggs, nymphs, and mated and unmated adults showed distinctive functional enrichment. These findings highlight the potential value of further exploring microbial functions during different developmental stages and developing new pest management strategies.}, }
@article {pmid34302348, year = {2021}, author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y}, title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab108}, pmid = {34302348}, issn = {1574-6941}, abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.}, }
@article {pmid34302194, year = {2021}, author = {Zhang, SK and Wang, Y and Li, ZK and Xue, HJ and Zhou, XD and Huang, JH}, title = {Two Apriona Species Sharing a Host Niche Have Different Gut Microbiome Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34302194}, issn = {1432-184X}, support = {2020SY08//Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; }, abstract = {The adaptability of herbivorous insects to toxic plant defense compounds is partly related to the structure of the gut microbiome. To overcome plant resistance, the insect gut microbiome should respond to a wide range of allelochemicals derived from dietary niches. Nevertheless, for sibling herbivorous insect species, whether the gut microbiome contributes to success in food niche competition is unclear. Based on 16S rDNA high-throughput sequencing, the gut microbiomes of two Apriona species that share the same food niche were investigated in this study to determine whether the gut microbiome contributes to insect success in food-niche competition. Our observations indicated that the gut microbiome tended to play a part in host niche competition between the two Apriona species. The gut microbiome of Apriona swainsoni had many enriched pathways that can help degrade plant toxic secondary compounds, including xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, and secondary metabolite biosynthesis. Meanwhile, A. swainsoni hosted a much greater variety of microorganisms and had more viable bacteria than A. germari. We conclude that gut microbes may influence the coevolution of herbivores and host plants. Gut bacteria may not only serve to boost nutritional relationships, but may also play an important role in insect food niche competition.}, }
@article {pmid34301298, year = {2021}, author = {Wang, Q and Zhang, Y and Yang, Q and Fu, S and Qu, B and Defoirdt, T}, title = {One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming.}, journal = {Gut pathogens}, volume = {13}, number = {1}, pages = {47}, pmid = {34301298}, issn = {1757-4749}, support = {81903372//Young Scientists Fund/ ; }, abstract = {BACKGROUND: Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp.<br><br>RESULTS: Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella.<br><br>CONCLUSIONS: In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.}, }
@article {pmid34298185, year = {2021}, author = {Zhao, L and Xu, M and Pan, X and Zhang, B and Dou, Q}, title = {Binding and detoxification ability of lactobacillus acidophilus towards di-n-butyl phthalate: Change of MAPK pathway in Caco-2 cell model.}, journal = {Journal of proteomics}, volume = {247}, number = {}, pages = {104333}, doi = {10.1016/j.jprot.2021.104333}, pmid = {34298185}, issn = {1876-7737}, abstract = {Di-n-butyl phthalate (DBP), a common compound of phthalates, can pose a risk to humans as a contaminant in the food industry. At present, the molecular mechanism of gene and protein toxicity caused by DBP in human cells is unclear. This in vitro study investigated the potential of inactivated Lactobacillus acidophilus NCFM in alleviating the damage caused by DBP in Caco-2 cells. According to the results from transcriptome and proteome analyses, the Caco-2 cells treated by DBP was resulted finally endoplasmic reticulum stress and mitochondrial oxidative damage. The most important differentially expressed genes and proteins involved in Caco-2 cells treated with NCFM to relieve DBP's cytotoxicity were TNF, NF-κB, CREB, P21, GADD45, FOS and CASP3. The molecular mechanism of DBP toxicity alleviated by strain NCFM was involved the MAPK pathway, via DBP bind to strain NCFM and avoid the activation of TNF receptor by DBP, so down-regulated the NF-κB, CREB, P21, GADD45, and CASP3, relieving the apoptosis of Caco-2 cells. Overall, our data provide new insights into detoxification of phthalate by using Lactobacillus. SIGNIFICANCE: Here we sequenced and assembled the transcriptome from Caco-2 cells which were treated with 4 groups: Control, DBP, strain NCFM, and strain NCFM+DBP groups, and combined it with proteome to characterize DBP detoxification genes/proteins through multiomics analysis. The cell viability in DBP treated groups were significantly increased by NCFM strain, indicating NCFM strain has the ability to alleviate the cytotoxicity of DBP via their binding ability with toxins. Furthermore, the results of transcriptome and proteome analysis showed that the signaling pathway of strain NCFM can alleviate DBP toxicity through MAPK pathway, and the potential biomarkers were identified too. This research may provided new information for developing new detoxification strategies for DBP.}, }
@article {pmid34290548, year = {2021}, author = {Do, H and Kim, SH and Cho, G and Kim, DR and Kwak, YS}, title = {Investigation of Fungal Strains Composition in Fruit Pollens for Artificial Pollination.}, journal = {Mycobiology}, volume = {49}, number = {3}, pages = {249-257}, doi = {10.1080/12298093.2021.1893137}, pmid = {34290548}, issn = {1229-8093}, abstract = {Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen.}, }
@article {pmid34288928, year = {2021}, author = {Harlow, BE and Flythe, MD and Klotz, JL and Harmon, DL and Aiken, GE}, title = {Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253754}, doi = {10.1371/journal.pone.0253754}, pmid = {34288928}, issn = {1932-6203}, abstract = {Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d-1), or BCA (6 g d-1). The basal diet consisted of corn silage and dried distiller's grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1-4: 40% corn; d 5-8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.}, }
@article {pmid34287300, year = {2021}, author = {Santschi, PH and Chin, WC and Quigg, A and Xu, C and Kamalanathan, M and Lin, P and Shiu, RF}, title = {Marine Gel Interactions with Hydrophilic and Hydrophobic Pollutants.}, journal = {Gels (Basel, Switzerland)}, volume = {7}, number = {3}, pages = {}, doi = {10.3390/gels7030083}, pmid = {34287300}, issn = {2310-2861}, abstract = {Microgels play critical roles in a variety of processes in the ocean, including element cycling, particle interactions, microbial ecology, food web dynamics, air-sea exchange, and pollutant distribution and transport. Exopolymeric substances (EPS) from various marine microbes are one of the major sources for marine microgels. Due to their amphiphilic nature, many types of pollutants, especially hydrophobic ones, have been found to preferentially associate with marine microgels. The interactions between pollutants and microgels can significantly impact the transport, sedimentation, distribution, and the ultimate fate of these pollutants in the ocean. This review on marine gels focuses on the discussion of the interactions between gel-forming EPS and pollutants, such as oil and other hydrophobic pollutants, nanoparticles, and metal ions.}, }
@article {pmid34287003, year = {2021}, author = {Schloss, PD}, title = {Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0019121}, doi = {10.1128/mSphere.00191-21}, pmid = {34287003}, issn = {2379-5042}, abstract = {Amplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in an rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full-length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full-length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as Escherichia coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, these risks are of less concern than artificially splitting a genome into separate ASVs and OTUs. IMPORTANCE 16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene. Furthermore, the naming of bacterial taxa reflects the biases of those who name them. One motivation for the recent push to adopt ASVs in place of OTUs in microbial community analyses is to allow researchers to perform their analyses at the finest possible level that reflects species-level taxonomy. The current research is significant because it quantifies the risk of artificially splitting bacterial genomes into separate clusters. Far from providing a better representation of bacterial taxonomy and biology, the ASV approach can lead to conflicting inferences about the ecology of different ASVs from the same genome.}, }
@article {pmid34285323, year = {2021}, author = {Mafla-Endara, PM and Arellano-Caicedo, C and Aleklett, K and Pucetaite, M and Ohlsson, P and Hammer, EC}, title = {Microfluidic chips provide visual access to in situ soil ecology.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {889}, pmid = {34285323}, issn = {2399-3642}, support = {FFL 18-0089//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; VR-621-2014-5912//Vetenskapsrådet (Swedish Research Council)/ ; 20161044//Crafoordska Stiftelsen (Crafoord Foundation)/ ; }, abstract = {Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.}, }
@article {pmid34283261, year = {2021}, author = {Xu, R and Tao, W and Lin, H and Huang, D and Su, P and Gao, P and Sun, X and Yang, Z and Sun, W}, title = {Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34283261}, issn = {1432-184X}, support = {Grant No. 42007357 and 41771301//National Natural Science Foundation of China (CN)/ ; Grant Nos. 2020T130127 and 2019M662825//postdoctoral research foundation of china/ ; Grant Nos. 202002030271//the Science and Technology Planning Project of Guangzhou/ ; Grant No. 2019A1515110351//Guangdong Basic and Applied Basic Research Foundation/ ; Grant Nos. 2020GDASYL-20200103086, 2020GDASYL-20200102015, 2020GDASYL-20200102014 and 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; Grant No. 2017GC010570//Guangdong Introducing Innovative and Entrepreneurial Talents/ ; Grant No. 2019B121205006//Guangdong Foundation for Program of Science and Technology Research/ ; }, abstract = {The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.}, }
@article {pmid34282938, year = {2021}, author = {Cruz-Loya, M and Tekin, E and Kang, TM and Cardona, N and Lozano-Huntelman, N and Rodriguez-Verdugo, A and Savage, VM and Yeh, PJ}, title = {Antibiotics Shift the Temperature Response Curve of Escherichia coli Growth.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0022821}, doi = {10.1128/mSystems.00228-21}, pmid = {34282938}, issn = {2379-5077}, abstract = {Temperature variation-through time and across climatic gradients-affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here, we quantify two key features-optimal temperature and temperature breadth-to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth of Escherichia coli under single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes. IMPORTANCE The growth of living organisms varies with temperature. This dependence is described by a temperature response curve that is described by an optimal temperature where growth is maximized and a temperature range (termed breadth) across which the organism can grow. Because an organism's temperature response evolves or acclimates to its environment, it is often assumed to change over only evolutionary or developmental timescales. Counter to this, we show here that antibiotics can quickly (over hours) change the optimal growth temperature and temperature breadth for the bacterium Escherichia coli. Moreover, our results suggest a shared-damage hypothesis: when an antibiotic damages similar cellular components as hot (or cold) temperatures do, this shared damage will combine and compound to more greatly reduce growth when that antibiotic is administered at hot (or cold) temperatures. This hypothesis could potentially also explain how temperature responses are modified by stressors other than antibiotics.}, }
@article {pmid34282310, year = {2021}, author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A}, title = {Publisher Correction: Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-021-00936-6}, pmid = {34282310}, issn = {2058-5276}, support = {P29426//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25111//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, }
@article {pmid34280807, year = {2021}, author = {De Vrieze, J and Heyer, R and Props, R and Van Meulebroek, L and Gille, K and Vanhaecke, L and Benndorf, D and Boon, N}, title = {Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles.}, journal = {Water research}, volume = {202}, number = {}, pages = {117422}, doi = {10.1016/j.watres.2021.117422}, pmid = {34280807}, issn = {1879-2448}, abstract = {The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.}, }
@article {pmid34279697, year = {2021}, author = {Zhou, D and Wang, R and Li, X and Peng, B and Yang, G and Zhang, KQ and Zhang, Y and Xu, J}, title = {Genetic Diversity and Azole Resistance Among Natural Aspergillus fumigatus Populations in Yunnan, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34279697}, issn = {1432-184X}, support = {31760010//National Natural Science Foundation of China/ ; 2020R3//McMaster University/ ; KY2018412//Department of Education of Guizhou Province/ ; }, abstract = {The emergence and spread of azole resistance alleles in clinical and environmental isolates of Aspergillus fumigatus is a global human health concern and endangers the "One Health" approach in our fight against antifungal resistance (AFR) in this pathogen. A major challenge to combat AFR in A. fumigatus is the massive aerial dispersal ability of its asexual spores. Our recent fine-scale survey of greenhouse populations of A. fumigatus near Kunming, Yunnan, China, suggested that the use of azole fungicides for plant protection was likely a major driver of the high-frequency azole-resistant A. fumigatus (ARAF) in greenhouses. Here, we investigated the potential spread of those ARAF and the structure of geographic populations of A. fumigatus by analyzing 452 isolates from 19 geographic locations across Yunnan. We found lower frequencies of ARAF in these outdoor populations than those in greenhouses near Kunming, but there were abundant new alleles and new genotypes, including those associated with azole resistance, consistent with multiple independent origins of ARAF across Yunnan. Interestingly, among the four ecological niches, the sediments of a large lake near Kunming were found to have the highest frequency of ARAF (~ 43%). While most genetic variations were observed within the 19 local populations, statistically significant genetic differentiations were found between many subpopulations within Yunnan. Furthermore, similar to greenhouse populations, these outdoor populations of A. fumigatus in Yunnan were significantly different from those in other parts of the world. Our results call for increased attention to local and regional studies of this fungal pathogen to help develop targeted control strategies against ARAF.}, }
@article {pmid34279696, year = {2021}, author = {Adomako, MO and Xue, W and Du, DL and Yu, FH}, title = {Soil Microbe-Mediated N:P Stoichiometric Effects on Solidago canadensis Performance Depend on Nutrient Levels.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34279696}, issn = {1432-184X}, abstract = {Both soil microbes and soil N:P ratios can affect plant growth, but it is unclear whether they can interact to alter plant growth and whether such an interactive effect depends on nutrient levels. Here, we tested the hypothesis that soil microbes can ameliorate the negative effects of nutrient imbalance caused by low or high N:P ratios on plant growth and that such an ameliorative effect of soil microbes depends on nutrient supply levels. We grew individuals of six populations of the clonal plant Solidago canadensis at three N:P ratios (low (1.7), intermediate (15), and high (135)), under two nutrient levels (low versus high) and in the presence versus absence of soil microbes. The presence of soil microbes significantly increased biomass of S. canadensis at all three N:P ratios and under both nutrient levels. Under the low-nutrient level, biomass, height, and leaf number of S. canadensis did not differ significantly among the three N:P ratio treatments in the absence of soil microbes, but they were higher at the high than at the low and the intermediate N:P ratio in the presence of soil microbes. Under the high-nutrient level, by contrast, biomass, height, and leaf number of S. canadensis were significantly higher at the low than at the high and the intermediate N:P ratio in the absence of soil microbes, but increased with increasing the N:P ratio in the presence of soil microbes. In the presence of soil microbes, number of ramets (asexual individuals) and the accumulation of N and P in plants were significantly higher at the high than at the low and the intermediate N:P ratio under both nutrient levels, whereas in the absence of soil microbes, they did not differ significantly among the three N:P ratio regardless of the nutrient levels. Our results provide empirical evidence that soil microbes can alter effects of N:P ratios on plant performance and that such an effect depends on nutrient availability. Soil microbes may, therefore, play a role in modulating ecosystem functions such as productivity and carbon and nutrient cycling via modulating nutrient imbalance caused by low and high N:P ratios.}, }
@article {pmid34277691, year = {2021}, author = {Calatayud, M and Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Rohs, E and Birkett, A}, title = {Comparative Effect of 22 Dietary Sources of Fiber on Gut Microbiota of Healthy Humans in vitro.}, journal = {Frontiers in nutrition}, volume = {8}, number = {}, pages = {700571}, doi = {10.3389/fnut.2021.700571}, pmid = {34277691}, issn = {2296-861X}, abstract = {Human gut microbiota has a fundamental role in human health, and diet is one of the most relevant factors modulating the gut microbial ecosystem. Fiber, fat, proteins, and micronutrients can shape microbial activity and structure. Much information is available on the role of defined prebiotic fibers on gut microbiota, but less known are the effects of intact dietary fiber sources on healthy gut ecosystems. This research investigated in vitro the short-term effect of 22 commercially available food sources of dietary fiber on gut microbiota activity [pH, gas, short-chain fatty acids (SCFA), branched fatty acids (BCFA), lactate] and specific composition of Firmicutes, Bacteroidetes, bifidobacteria, and lactobacilli populations. More than 80% (19 of 22) of the products were highly fermentable and induced SCFAs production, with specific product differences. In general, all the whole grain cereals had a similar effect on gut microbiota modulation, inducing acetate and butyrate production and increasing bifidobacteria levels. Incorporating and comparing a large variety of products, including "non-conventional" fiber sources, like konjac, bamboo fiber, or seeds fiber, about which there is little information, contributes to our knowledge on the modulatory activity of diverse food fiber sources on human gut microbiota, and therefore potential health promotion through dietary fiber diversification.}, }
@article {pmid34277527, year = {2021}, author = {Larroya, A and Pantoja, J and Codoñer-Franch, P and Cenit, MC}, title = {Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain.}, journal = {Frontiers in pediatrics}, volume = {9}, number = {}, pages = {705859}, doi = {10.3389/fped.2021.705859}, pmid = {34277527}, issn = {2296-2360}, abstract = {Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.}, }
@article {pmid34276734, year = {2021}, author = {Yoshiura, CA and Venturini, AM and Braga, LPP and da França, AG and de Lyra, MDCCP and Tsai, SM and Rodrigues, JLM}, title = {Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {683658}, doi = {10.3389/fpls.2021.683658}, pmid = {34276734}, issn = {1664-462X}, abstract = {The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.}, }
@article {pmid34276600, year = {2021}, author = {Liu, J and Su, J and Zhang, M and Luo, Z and Li, X and Chai, B}, title = {Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {669131}, doi = {10.3389/fmicb.2021.669131}, pmid = {34276600}, issn = {1664-302X}, abstract = {Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.}, }
@article {pmid34273695, year = {2021}, author = {Ntagia, E and Chatzigiannidou, I and Carvajal-Arroyo, JM and Arends, JBA and Rabaey, K}, title = {Continuous H2/CO2 fermentation for acetic acid production under transient and continuous sulfide inhibition.}, journal = {Chemosphere}, volume = {285}, number = {}, pages = {131536}, doi = {10.1016/j.chemosphere.2021.131536}, pmid = {34273695}, issn = {1879-1298}, abstract = {Waste gas fermentation powered by renewable H2 is reaching kiloton scale. The presence of sulfide, inherent to many waste gases, can cause inhibition, requiring additional gas treatment. In this work, acetogenesis and methanogenesis inhibition by sulfide were studied in a 10-L mixed-culture fermenter, supplied with CO2 and connected with a water electrolysis unit for electricity-powered H2 supply. Three cycles of inhibition (1.3 mM total dissolved sulfide (TDS)) and recovery were applied, then the fermenter was operated at 0.5 mM TDS for 35 days. During operation at 0.5 mM TDS the acetate production rate reached 7.1 ± 1.5 mmol C L-1 d-1. Furthermore, 43.7 ± 15.6% of the electrons, provided as H2, were distributed to acetate and 7.7 ± 4.1% to butyrate, the second most abundant fermentation product. Selectivity of sulfide as inhibitor was demonstrated by a 7 days lag-phase of methanogenesis recovery, compared to 48 h for acetogenesis and by the less than 1% electrons distribution to CH4, under 0.5 mM TDS. The microbial community was dominated by Eubacterium, Proteiniphilum and an unclassified member of the Eggerthellaceae family. The taxonomic diversity of the community decreased and conversely the phenotypic diversity increased, during operation. This work illustrated the scale-up potential of waste gas fermentations, by elucidating the effect of sulfide as a common gas impurity, and by demonstrating continuous, potentially renewable supply of electrons.}, }
@article {pmid34272992, year = {2021}, author = {Lu, Y and Zhang, Y and Wang, J and Zhang, M and Wu, Y and Xiao, X and Xu, J}, title = {Dynamics in Bacterial Community Affected by Mesoscale Eddies in the Northern Slope of the South China Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34272992}, issn = {1432-184X}, support = {2014CB441503//National Basic Research Program of China (973 Program)/ ; }, abstract = {Mesoscale eddies are common oceanographic processes that can enhance primary productivity by transporting nutrients to the euphotic zone. In the northern South China Sea (SCS), eddies were frequently found to promote the exchange between the nutrient-rich shelf water and the oligotrophic water at the slope area. However, the response of bacterial community to eddy perturbations remains unclear. In the present study, we examined the variation of bacterial community under the impact of eddies in early spring and summer. The results showed that both the summer cyclonic eddy and spring anticyclonic eddy enhanced the bacterial abundance in surface water. The bacterial community composition and their functional potentials of surface samples were also influenced by the summer cyclonic eddy, while no significant change was observed in the case of spring anticyclonic eddy. Salinity and nutrients, which varied between the inside and outside of the eddies, were the significant factors explaining the differentiation of the community composition and related functions. Taken together, the results of our present study reveal the effects of mesoscale eddies on the bacterial community and associated metagenomes, providing a better understanding of the dynamics of bacteria in the slope ecosystem of the SCS.}, }
@article {pmid34272991, year = {2021}, author = {Paul, P and Das, S and Chatterjee, S and Shukla, A and Chakraborty, P and Sarkar, S and Maiti, D and Das, A and Tribedi, P}, title = {1,4-Naphthoquinone disintegrates the pre-existing biofilm of Staphylococcus aureus by accumulating reactive oxygen species.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {34272991}, issn = {1432-072X}, abstract = {Staphylococcus aureus causes several nosocomial and community-acquired infections in human host involving biofilm. Thus, strategies need to be explored to curb biofilm threats by either inhibiting the formation of biofilm or disintegrating the pre-existing biofilm. Towards this direction, we had already revealed the biofilm inhibiting properties of 1,4-naphthoquinone against S. aureus. In this study, we have investigated whether this compound can act on pre-existing biofilm. Hence, biofilm of S. aureus was developed first and challenged further with 1,4-naphthoquinone. Experiments such as crystal violet assay, fluorescence microscopy, and estimation of total biofilm protein were performed to confirm the biofilm disintegration properties of 1,4-naphthoquinone. The disintegration of pre-existing biofilm could be attributed to the generation of reactive oxygen species (ROS). To investigate further, we observed that extracellular DNA (eDNA) was found to play an important role in holding the biofilm network as DNaseI treatment could cause an efficient disintegration of the same. To examine the effect of ROS on the eDNA, we exposed pre-existing biofilm to either 1,4-naphthoquinone or a combination of both 1,4-naphthoquinone and ascorbic acid for different length of time. Post-incubation, ROS generation and the amount of eDNA associated with the biofilm were determined wherein an inversely proportional relationship was observed between them. The result indicated that with the increase of ROS generation, the amount of eDNA associated with biofilm got decreased substantially. Thus, the results indicated that the generation of ROS could degrade the eDNA thereby compromising the integrity of biofilm which lead to the disintegration of pre-existing biofilm.}, }
@article {pmid34272569, year = {2021}, author = {Martínez-Reyes, CM and Rodríguez-Zaragoza, S and Cabirol, N and Alarcón, A and Mendoza-López, MR}, title = {Effect of Predation by Colpoda sp. in Nitrogen Fixation Rate of Two Free-Living Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34272569}, issn = {1432-184X}, support = {IN222618//PAPIIT/ ; }, abstract = {Biological nitrogen fixation is limited to several groups of prokaryotes, some of them reduce nitrogen as free-living nitrogen-fixing bacteria. Protozoa predation on these latter releases sequestered nitrogen that may enhance the formation of new bacterial biomass and possibly increase nitrogen fixation within soil microbial communities. We aim to evaluate the predation effect of Colpoda sp. on two nitrogen fixers: Azospirillum lipoferum and Stenotrophomonas sp. during their lag, early exponential, and exponential phases. The kinetics of bacterial population growth was determined in the predators' presence or absence and the effect of predation on the rate of N fixation was evaluated through the reduction of acetylene to ethylene technique. Colpoda sp. showed a non-significant difference in preferences between the two species offered as prey. Consequently, the abundance of A. lipoferum and Stenotrophomonas sp. decreased significantly due to predator's pressure and both species responded by increasing their specific growth rate. Likewise, predation promoted greater nitrogen fixation rate by CFU during the lag phase in A. lipoferum (0.20 nM/CFU with predation vs 0.09 nM/CFU without predation) and Stenotrophomonas sp. (0.22 nM/CFU vs 0.09 nM/CFU respectively). During early exponential phase (29 h), the rate diminished to 0.13 and 0.05 nM/CFU in A. lipoferum and to 0.09 nM/CFU and 0.05 nM/CFU in Stenotrophomonas sp. Finally, during the exponential phase (52 h), only A. lipoferum without predation produced 0.003 nM/CFU of ethylene. Thus, the nitrogenase activity was higher in the lag and the early exponential phases when predator activity was involved.}, }
@article {pmid34269959, year = {2021}, author = {Đurović, G and Van Neerbos, FAC and Bossaert, S and Herrera-Malaver, B and Steensels, J and Arnó, J and Wäckers, F and Sobhy, IS and Verstrepen, KJ and Jacquemyn, H and Lievens, B}, title = {The Pupal Parasitoid Trichopria drosophilae Is Attracted to the Same Yeast Volatiles as Its Adult Host.}, journal = {Journal of chemical ecology}, volume = {}, number = {}, pages = {}, pmid = {34269959}, issn = {1573-1561}, support = {722642 (INTERFUTURE)//Horizon 2020 Framework Programme/ ; 722642 (INTERFUTURE)//Horizon 2020 Framework Programme/ ; PID2019-107030RB-C21//CERCA Programme/ ; }, abstract = {There is increasing evidence that microorganisms, particularly fungi and bacteria, emit volatile compounds that mediate the foraging behaviour of insects and therefore have the potential to affect key ecological relationships. However, to what extent microbial volatiles affect the olfactory response of insects across different trophic levels remains unclear. Adult parasitoids use a variety of chemical stimuli to locate potential hosts, including those emitted by the host's habitat, the host itself, and microorganisms associated with the host. Given the great capacity of parasitoids to utilize and learn odours to increase foraging success, parasitoids of eggs, larvae, or pupae may respond to the same volatiles the adult stage of their hosts use when locating their resources, but compelling evidence is still scarce. In this study, using Saccharomyces cerevisiae we show that Trichopria drosophilae, a pupal parasitoid of Drosophila species, is attracted to the same yeast volatiles as their hosts in the adult stage, i.e. acetate esters. Parasitoids significantly preferred the odour of S. cerevisiae over the blank medium in a Y-tube olfactometer. Deletion of the yeast ATF1 gene, encoding a key acetate ester synthase, decreased attraction of T. drosophilae, while the addition of synthetic acetate esters to the fermentation medium restored parasitoid attraction. Bioassays with individual compounds revealed that the esters alone were not as attractive as the volatile blend of S. cerevisiae, suggesting that other volatile compounds also contribute to the attraction of T. drosophilae. Altogether, our results indicate that pupal parasitoids respond to the same volatiles as the adult stage of their hosts, which may aid them in locating oviposition sites.}, }
@article {pmid34269858, year = {2021}, author = {Lin, YC and Chin, CP and Yang, JW and Chiang, KP and Hsieh, CH and Gong, GC and Shih, CY and Chen, SY}, title = {How Communities of Marine Stramenopiles Varied with Environmental and Biological Variables in the Subtropical Northwestern Pacific Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34269858}, issn = {1432-184X}, support = {104-2811-M-019- 003//Ministry of Science and Technology, Taiwan/ ; 109-2611-M-019 -018//Ministry of Science and Technology, Taiwan/ ; 107-2611-M-019 -002 -MY3//Ministry of Science and Technology, Taiwan/ ; }, abstract = {MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables.}, }
@article {pmid34267209, year = {2021}, author = {Chen, F and Chen, Z and Chen, M and Chen, G and Huang, Q and Yang, X and Yin, H and Chen, L and Zhang, W and Lin, H and Ou, M and Wang, L and Chen, Y and Lin, C and Xu, W and Yin, G}, title = {Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {60}, pmid = {34267209}, issn = {2055-5008}, support = {81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81200619//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81900541//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.}, }
@article {pmid34263935, year = {2021}, author = {Amini, S and Arsova, B and Gobert, S and Carnol, M and Bosman, B and Motte, P and Watt, M and Hanikenne, M}, title = {Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14151}, pmid = {34263935}, issn = {1365-3040}, abstract = {The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67 Zn isotope revealed whole plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1893 zinc-responsive genes. Multiple ZIP transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots. This article is protected by copyright. All rights reserved.}, }
@article {pmid34263341, year = {2021}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Correction to: Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipis Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01811-x}, pmid = {34263341}, issn = {1432-184X}, abstract = {A Correction to this paper has been published: https://doi.org/10.1007/s00248-021-01811-x.}, }
@article {pmid34262548, year = {2021}, author = {Leinberger, J and Holste, J and Bunk, B and Freese, HM and Spröer, C and Dlugosch, L and Kück, AC and Schulz, S and Brinkhoff, T}, title = {High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {688754}, doi = {10.3389/fmicb.2021.688754}, pmid = {34262548}, issn = {1664-302X}, abstract = {Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.}, }
@article {pmid34260793, year = {2021}, author = {Yang, Q and Wang, Q and Wu, J and Zhang, Y and Wei, D and Qu, B and Liu, Y and Fu, S}, title = {Distinct dynamics of Vibrio parahaemolyticus populations in two farming models.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15217}, pmid = {34260793}, issn = {1365-2672}, abstract = {AIMS: Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of V. parahaemolyticus populations and the antibiotic resistance of this bacterium.<br><br>METHODS AND RESULTS: To this end, we conducted continuous surveillance of Vibrio parahaemolyticus on four farms over three years, two traditional shrimp farms with daily water exchange, and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing (MLST) was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harbored a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.<br><br>CONCLUSIONS: These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.<br><br>Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.}, }
@article {pmid34258685, year = {2021}, author = {Carpio, LE and Sanz, Y and Gozalbes, R and Barigye, SJ}, title = {Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review.}, journal = {Molecular diversity}, volume = {}, number = {}, pages = {}, pmid = {34258685}, issn = {1573-501X}, support = {INNTAL32/19/002//Agencia Valenciana de la Investigación/ ; 893810//H2020 Marie Skłodowska-Curie Actions/ ; }, abstract = {Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.}, }
@article {pmid34255112, year = {2021}, author = {Pavlova, ON and Izosimova, ON and Chernitsyna, SM and Ivanov, VG and Pogodaeva, TV and Khabuev, AV and Gorshkov, AG and Zemskaya, TI}, title = {Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34255112}, issn = {1432-184X}, support = {0279-2021-0006 (121032300223-1)//Ministry of Education and Science of the Russian Federation/ ; }, abstract = {This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.}, }
@article {pmid34254828, year = {2021}, author = {Harrison, JG and Randolph, GD and Buerkle, CA}, title = {Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029421}, doi = {10.1128/mSystems.00294-21}, pmid = {34254828}, issn = {2379-5077}, abstract = {New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes-from extraction to library preparation-including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.}, }
@article {pmid34253727, year = {2021}, author = {Wan, T and Liu, Z and Leitch, IJ and Xin, H and Maggs-Kölling, G and Gong, Y and Li, Z and Marais, E and Liao, Y and Dai, C and Liu, F and Wu, Q and Song, C and Zhou, Y and Huang, W and Jiang, K and Wang, Q and Yang, Y and Zhong, Z and Yang, M and Yan, X and Hu, G and Hou, C and Su, Y and Feng, S and Yang, J and Yan, J and Chu, J and Chen, F and Ran, J and Wang, X and Van de Peer, Y and Leitch, AR and Wang, Q}, title = {The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4247}, pmid = {34253727}, issn = {2041-1723}, abstract = {The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.}, }
@article {pmid34252564, year = {2021}, author = {Fournier, E and Roussel, C and Dominicis, A and Ley, D and Peyron, MA and Collado, V and Mercier-Bonin, M and Lacroix, C and Alric, M and Van de Wiele, T and Chassard, C and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {In vitro models of gut digestion across childhood: current developments, challenges and future trends.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {107796}, doi = {10.1016/j.biotechadv.2021.107796}, pmid = {34252564}, issn = {1873-1899}, abstract = {The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.}, }
@article {pmid34252020, year = {2021}, author = {Doll, EV and Staib, L and Huptas, C and Scherer, S and Wenning, M}, title = {Facklamia lactis sp. nov., isolated from raw milk.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {7}, pages = {}, doi = {10.1099/ijsem.0.004869}, pmid = {34252020}, issn = {1466-5034}, abstract = {Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842T (96.9 %), and Facklamia hominis CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10-40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l-1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.}, }
@article {pmid34251452, year = {2021}, author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Pirttilä, AM and Häggman, H}, title = {Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L., and Vaccinium vitis-idaea L.).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab097}, pmid = {34251452}, issn = {1574-6941}, abstract = {Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry V. vitis-idaea L., and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae, and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.}, }
@article {pmid34251412, year = {2021}, author = {Collins, SM and Gibson, GR and Kennedy, OB and Walton, G and Rowland, I and Commane, DM}, title = {Development of a prebiotic blend to influence in vitro fermentation effects, with a focus on propionate, in the gut.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab101}, pmid = {34251412}, issn = {1574-6941}, abstract = {Short chain fatty acids (SCFAs) derived from the human gut microbiota, and in particular propionate, may beneficially influence metabolic processes such as appetite regulation. Development of prebiotics that induce high propionate levels during fermentation is desirable. Eleven candidate prebiotics were screened to investigate their fermentation characteristics, with a focus on propionate production in mixed anaerobic batch culture of faecal bacteria. Further to this, a continuous 3-stage colonic fermentation model (simulating the human colon) was used to evaluate changes in microbial ecology, lactate and SCFA production of three 50:50 blends, comprising both slow and rapidly fermented prebiotics. In mixed batch culture: xylo-oligosaccharide, polydextrose and α-gluco-oligosaccharide were associated with the greatest increase in propionate. Polydextrose, α-gluco-oligosaccharide, β-1,4 glucan and oat fibre induced the greatest reductions in the acetate to propionate ratio. The most bifidogenic prebiotics were the oligosaccharides. Fermentation of a 50:50 blend of inulin and arabinoxylan, through the continuous 3-stage colonic fermentation model, induced a substantial and sustained release of propionate. The sustained release of propionate through the colon, if replicable in vivo, could potentially influence blood glucose, blood lipids and appetite regulation, however, dietary intervention studies are needed. Bifidogenic effects were also observed for the inulin and arabinoxylan blend and an increase synthesis of butyrate and lactate, thus indicating wider prebiotic potential.}, }
@article {pmid34249520, year = {2021}, author = {Priest, T and Orellana, LH and Huettel, B and Fuchs, BM and Amann, R}, title = {Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11721}, pmid = {34249520}, issn = {2167-8359}, abstract = {The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2-3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.}, }
@article {pmid34249034, year = {2021}, author = {Kaur, J and Sharma, J}, title = {Orchid Root Associated Bacteria: Linchpins or Accessories?.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {661966}, pmid = {34249034}, issn = {1664-462X}, abstract = {Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.}, }
@article {pmid34245330, year = {2021}, author = {Fall, F and Sanguin, H and Fall, D and Tournier, E and Bakhoum, N and Ndiaye, C and Diouf, D and Bâ, AM}, title = {Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34245330}, issn = {1432-184X}, support = {I-1-D-6153-1//International Foundation for Science/ ; }, abstract = {The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.}, }
@article {pmid34245329, year = {2021}, author = {Rosado, D and Pérez-Losada, M and Severino, R and Xavier, R}, title = {Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34245329}, issn = {1432-184X}, abstract = {The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.}, }
@article {pmid34244148, year = {2021}, author = {Delgado-Baquerizo, M and Eldridge, DJ and Liu, YR and Sokoya, B and Wang, JT and Hu, HW and He, JZ and Bastida, F and Moreno, JL and Bamigboye, AR and Blanco-Pastor, JL and Cano-Díaz, C and Illán, JG and Makhalanyane, TP and Siebe, C and Trivedi, P and Zaady, E and Verma, JP and Wang, L and Wang, J and Grebenc, T and Peñaloza-Bojacá, GF and Nahberger, TU and Teixido, AL and Zhou, XQ and Berdugo, M and Duran, J and Rodríguez, A and Zhou, X and Alfaro, F and Abades, S and Plaza, C and Rey, A and Singh, BK and Tedersoo, L and Fierer, N}, title = {Global homogenization of the structure and function in the soil microbiome of urban greenspaces.}, journal = {Science advances}, volume = {7}, number = {28}, pages = {}, doi = {10.1126/sciadv.abg5809}, pmid = {34244148}, issn = {2375-2548}, abstract = {The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations.}, }
@article {pmid34243050, year = {2021}, author = {Favere, J and Waegenaar, F and Boon, N and De Gusseme, B}, title = {Online microbial monitoring of drinking water: How do different techniques respond to contaminations in practice?.}, journal = {Water research}, volume = {202}, number = {}, pages = {117387}, doi = {10.1016/j.watres.2021.117387}, pmid = {34243050}, issn = {1879-2448}, abstract = {Safeguarding the microbial water quality remains a challenge for drinking water utilities, and because of population growth and climate change, new issues arise regularly. To overcome these problems, biostable drinking water production and water reuse will become increasingly important. In this respect, high-resolution online microbial monitoring during treatment and distribution could prove essential. Here, we present the first scientific and practical comparison of multiple online microbial monitoring techniques in which six commercially available devices were set up in a full-scale drinking water production plant. Both the devices' response towards operational changes and contaminations, as well as their detection limit for different contaminations were evaluated and compared. During normal operation, all devices were able to detect abrupt operational changes such as backwashing of activated carbon filters and interruption of the production process in a fast and sensitive way. To benchmark their response to contaminations, the calculation of a dynamic baseline for sensitive separation between noise and events is proposed. In order of sensitivity, enzymatic analysis, ATP measurement, and flow cytometric fingerprinting were the most performant for detection of rain- and groundwater contaminations (0.01 - 0.1 v%). On the other hand, optical classification and flow cytometric cell counts showed to be more robust techniques, requiring less maintenance and providing direct information about the cell concentration, even though they were still more sensitive than plate counting. The choice for a certain technology will thus depend on the type of application and is a balance between sensitivity, price and maintenance. All things considered, a combination of several devices and use of advanced data analysis such as fingerprinting may be of added value. In general, the strategic implementation of online microbial monitoring as early-warning system will allow for intensive quality control by high-frequency sampling as well as a short event response timeframe.}, }
@article {pmid34242738, year = {2021}, author = {Thompson, RS and Gaffney, M and Hopkins, S and Kelley, T and Gonzalez, A and Bowers, SJ and Hotz Vitaterna, M and Turek, FW and Foxx, CL and Lowry, CA and Vargas, F and Dorrestein, PC and Wright, KP and Knight, R and Fleshner, M}, title = {Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2021.07.006}, pmid = {34242738}, issn = {1090-2139}, abstract = {Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems, which in turn is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.}, }
@article {pmid34242413, year = {2021}, author = {Tuganbaev, T and Honda, K}, title = {Non-zero-sum microbiome immune system interactions.}, journal = {European journal of immunology}, volume = {}, number = {}, pages = {}, doi = {10.1002/eji.202049065}, pmid = {34242413}, issn = {1521-4141}, abstract = {Fundamental asymmetries between the host and its microbiome in enzymatic activities and nutrient storage capabilities have promoted mutualistic adaptations on both sides. As a result, the enteric immune system has evolved so as not to cause a zero-sum sterilization of non-self, but rather achieve a non-zero-sum self-reinforcing cooperation with its evolutionary partner the microbiome. In this review we attempt to integrate the accumulated knowledge of immune - microbiome interactions into an evolutionary framework and trace the pattern of positive immune - microbiome feedback loops across epithelial, enteric nervous system, innate and adaptive immune circuits. Indeed, the immune system requires commensal signals for its development and function, and reciprocally protects the microbiome from nutrient shortage and pathogen outgrowth. In turn, a healthy microbiome is the result of immune system curatorship as well as microbial ecology. The paradigms of host-microbiome asymmetry and the cooperative nature of their interactions identified in the gut are applicable across all tissues influenced by microbial activities. Incorporation of immune system influences into models of microbiome ecology will be a step forward towards defining what constitutes a healthy human microbiome and guide discoveries of novel host-microbiome mutualistic adaptations that may be harnessed for promotion of human health. This article is protected by copyright. All rights reserved.}, }
@article {pmid34241654, year = {2021}, author = {Ahmad, T and Farooq, S and Mirza, DN and Kumar, A and Mir, RA and Riyaz-Ul-Hassan, S}, title = {Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34241654}, issn = {1432-184X}, abstract = {The study was undertaken to unravel the culturable endophytic bacterial microbiome of Crocus sativus L. (saffron crocus) and consequently obtain potential leads to develop plant growth-promoting and biocontrol agents for increased productivity and sustainable cultivation. The endophytes formed 47 different operational taxonomic units (OTUs), spanning over 28 genera. The host was preferentially colonized by the genus Bacillus, followed by Burkholderia and Pantoea, respectively. Several endophytes possessed potential plant growth-promoting properties and inhibitory activities against the specific fungal pathogens of saffron. The endophytes, except for Microbacterium oxydans, did not cause any disease symptoms in the pot experiments. The selected cultures, Burkholderia gladioli, Streptomyces achromogenes, and three species of Bacillus, enhanced the host plant growth significantly. Based on the pot experiment results, two isolates, Bacillus mojavensis CS4EB32 and Burkholderia gladioli E39CS3, were selected for the field experiments. We obtained an increase of 67.5%, 69.8%, and 68.3% in the production of flowers with the individual and collective treatments, respectively. The treatments also enhanced the biomass of the plant and the length and weight of stigmas significantly. The endophyte treatments induced the expression of the pathway genes, resulting in a marked increase in the concentration of apocarotenoids. The study indicates that the dominant endophytes support plant growth and development in nature and present an opportunity for developing microbial formulations for the sustainability of saffron cultivation.}, }
@article {pmid34240513, year = {2021}, author = {Shi, Y and Wang, J and Ao, Y and Han, J and Guo, Z and Liu, X and Zhang, J and Mu, C and Le Roux, X}, title = {Responses of soil N2 O emissions and their abiotic and biotic drivers to altered rainfall regimes and co-occurring wet N deposition in a semi-arid grassland.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15792}, pmid = {34240513}, issn = {1365-2486}, abstract = {Global change factors such as changed rainfall regimes and nitrogen (N) deposition contribute to increases in the emission of the greenhouse gas nitrous oxide (N2 O) from the soil. In previous research, N deposition has often been simulated by using a single or a series of N addition events over the course of a year, but wet N deposition actually co-occurs with rainfall. How soil N2 O emissions respond to altered rainfall amount and frequency, wet N deposition, and their interactions is still not fully understood. We designed a three-factor fully factorial experiment with factors of rainfall amounts (ambient, -30%) rainfall frequency (ambient, ±50%) and wet N deposition (with/without) co-occurring with rainfall in semi-arid grassland mesocosms, and measured N2 O emissions and their possible biotic and abiotic drivers. Across all treatments, reduced rainfall amount and N deposition increased soil N2 O emissions by 35% and 28%, respectively. A significant interactive effect was observed between rainfall amount and N deposition, and to a lesser extent between rainfall frequency and N deposition. Without N deposition, reduced rainfall amount and altered rainfall frequency indirectly affected soil N2 O emissions by changing the abundance of nirK and soil net N mineralization, and the changes in nirK abundance were indirectly driven by soil N availability rather than directly by soil moisture. With N deposition, both the abundance of nirK and the level of soil water filled pore space contributed to changes in N2 O emissions in response to altered rainfall regimes, and the changes in the abundance of nirK were indirectly driven by plant N uptake and nitrifier (AOB) abundance. Our results imply that unlike wetter grassland ecosystems, reduced precipitation may increase N2 O emissions and N deposition may only slightly increase N2 O emissions in arid and semi-arid N-limited ecosystems that are dominated by grasses with high soil N uptake capacity.}, }
@article {pmid34238491, year = {2021}, author = {Schweyer, L and Pougnet, L}, title = {[Microbial ecology, the understanding of the invisible living].}, journal = {Revue de l'infirmiere}, volume = {70}, number = {272}, pages = {25-26}, doi = {10.1016/j.revinf.2021.04.007}, pmid = {34238491}, issn = {1293-8505}, abstract = {Microorganisms are invisible to the naked eye. Hospital hygiene practices are therefore based on the representation that caregivers have of them. This difficulty can generate irrational behavior and fear of blame. Conversely, a better knowledge of the specificities of this invisible living world favors a rationalization of care practices. To do this, caregivers will be able to appropriate the major concepts of microbiology, particularly microbial ecology.}, }
@article {pmid34238316, year = {2021}, author = {Oberman, K and Hovens, I and de Haan, J and Falcao-Salles, J and van Leeuwen, B and Schoemaker, R}, title = {Acute pre-operative ibuprofen improves cognition in a rat model for postoperative cognitive dysfunction.}, journal = {Journal of neuroinflammation}, volume = {18}, number = {1}, pages = {156}, pmid = {34238316}, issn = {1742-2094}, abstract = {BACKGROUND: Inflammation is considered a key factor in the development of postoperative cognitive dysfunction (POCD). Therefore, we hypothesized that pre-operative anti-inflammatory treatment with ibuprofen would inhibit POCD in our rat-model.<br><br>METHODS: Male Wistar rats of 3 or 23 months old received a single injection of ibuprofen (15 mg/kg i.p.) or were control handled before abdominal surgery. Timed blood and fecal samples were collected for analyses of inflammation markers and gut microbiome changes. Behavioral testing was performed from 9 to 14 days after surgery, in the open field, novel object- and novel location-recognition tests and Morris water maze. Neuroinflammation and neurogenesis were assessed by immune histochemistry after sacrifice on postoperative day 14.<br><br>RESULTS: Ibuprofen improved short-term spatial memory in the novel location recognition test, and increased hippocampal neurogenesis. However, these effects were associated with increased hippocampal microglia activity. Whereas plasma cytokine levels (IL1-β, IL6, IL10, and TNFα) were not significantly affected, VEGF levels increased and IFABP levels decreased after ibuprofen. Long-term memory in the Morris water maze was not significantly improved by ibuprofen. The gut microbiome was neither significantly affected by surgery nor by ibuprofen treatment. In general, effects in aged rats appeared similar to those in young rats, though less pronounced.<br><br>CONCLUSION: A single injection of ibuprofen before surgery improved hippocampus-associated short-term memory after surgery and increased neurogenesis. However, this favorable outcome seemed not attributable to inhibition of (neuro)inflammation. Potential contributions of intestinal and blood-brain barrier integrity need further investigation. Although less pronounced compared to young rats, effects in aged rats indicate that even elderly individuals could benefit from ibuprofen treatment.}, }
@article {pmid34235554, year = {2021}, author = {Buysse, M and Binetruy, F and Leibson, R and Gottlieb, Y and Duron, O}, title = {Ecological Contacts and Host Specificity Promote Replacement of Nutritional Endosymbionts in Ticks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34235554}, issn = {1432-184X}, support = {EVOSYM//Ministry of Science and Technology, Israel/ ; EVOSYM//centre national de la recherche scientifique (CNRS)/ ; ANR-10-LAX-25-01//Agence Nationale de la Recherche (FR)/ ; ISF No. 1074/18//Israel science foundation/ ; }, abstract = {Symbiosis with vitamin-provisioning microbes is essential for the nutrition of animals with some specialized feeding habits. While coevolution favors the interdependence between symbiotic partners, their associations are not necessarily stable: Recently acquired symbionts can replace ancestral symbionts. In this study, we demonstrate successful replacement by Francisella-like endosymbionts (-LE), a group of B-vitamin-provisioning endosymbionts, across tick communities driven by horizontal transfers. Using a broad collection of Francisella-LE-infected tick species, we determined the diversity of Francisella-LE haplotypes through a multi-locus strain typing approach and further characterized their phylogenetic relationships and their association with biological traits of their tick hosts. The patterns observed showed that Francisella-LE commonly transfer through similar ecological networks and geographic distributions shared among different tick species and, in certain cases, through preferential shuffling across congeneric tick species. Altogether, these findings reveal the importance of geographic, ecological, and phylogenetic proximity in shaping the replacement pattern in which new nutritional symbioses are initiated.}, }
@article {pmid34231344, year = {2021}, author = {Ossowicki, A and Raaijmakers, JM and Garbeva, P}, title = {Disentangling soil microbiome functions by perturbation.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12989}, pmid = {34231344}, issn = {1758-2229}, abstract = {Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes. This article is protected by copyright. All rights reserved.}, }
@article {pmid34231036, year = {2021}, author = {Viana, TA and Barbosa, WF and Jojoa, LLB and Bernardes, RC and da Silva, JS and Jacobs-Lorena, M and Martins, GF}, title = {A Genetically Modified Anti-Plasmodium Bacterium Is Harmless to the Foragers of the Stingless Bee Partamona helleri.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34231036}, issn = {1432-184X}, support = {301725/2019-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CBB-APQ-00247-14//Fundação de Apoio ao Ensino, Pesquisa e Assistência do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (BR)/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; R01AI031478/NH/NIH HHS/United States ; }, abstract = {Paratransgenesis consists of genetically engineering an insect symbiont to control vector-borne diseases. Biosafety assessments are a prerequisite for the use of genetically modified organisms (GMOs). Assessments rely on the measurement of the possible impacts of GMOs on different organisms, including beneficial organisms, such as pollinators. The bacterium Serratia AS1 has been genetically modified to express anti-Plasmodium effector proteins and does not impose a fitness cost on mosquitoes that carry it. In the present study, we assessed the impact of this bacterium on the native bee Partamona helleri (Meliponini), an ecologically important species in Brazil. Serratia eGFP AS1 (recombinant strain) or a wild strain of Serratia marcescens were suspended in a sucrose solution and fed to foragers, followed by measurements of survival, feeding rate, and behavior (walking and flying). These bacteria did not change any of the variables measured at 24, 72, and 144 h after the onset of the experiment. Recombinant and wild bacteria were detected in the homogenates of digestive tract during the 144 h period analyzed, but their numbers decreased with time. The recombinant strain was detected in the midgut at 24 h and in the hindgut at 72 h and 144 h after the onset of the experiment under the fluorescent microscope. As reported for mosquitoes, Serratia eGFP AS1 did not compromise the foragers of P. helleri, an ecologically relevant bee.}, }
@article {pmid34229570, year = {2021}, author = {Rizwan, T and Kothidar, A and Meghwani, H and Sharma, V and Shobhawat, R and Saini, R and Vaishnav, HK and Singh, V and Pratap, M and Sihag, H and Kumar, S and Dey, JK and Dey, SK}, title = {Comparative analysis of SARS-CoV-2 envelope viroporin mutations from COVID-19 deceased and surviving patients revealed implications on its ion-channel activities and correlation with patient mortality.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/07391102.2021.1944319}, pmid = {34229570}, issn = {1538-0254}, abstract = {One major obstacle in designing a successful therapeutic regimen to combat COVID-19 pandemic is the frequent occurrence of mutations in the SARS-CoV-2 resulting in patient to patient variations. Out of the four structural proteins of SARS-CoV-2 namely, spike, envelope, nucleocapsid and membrane, envelope protein governs the virus pathogenicity and induction of acute-respiratory-distress-syndrome which is the major cause of death in COVID-19 patients. These effects are facilitated by the viroporin (ion-channel) like activities of the envelope protein. Our current work reports metagenomic analysis of envelope protein at the amino acid sequence level through mining all the available SARS-CoV-2 genomes from the GISAID and coronapp servers. We found majority of mutations in envelope protein were localized at or near PDZ binding motif. Our analysis also demonstrates that the acquired mutations might have important implications on its structure and ion-channel activity. A statistical correlation between specific mutations (e.g. F4F, R69I, P71L, L73F) with patient mortalities were also observed, based on the patient data available for 18,691 SARS-CoV-2-genomes in the GISAID database till 30 April 2021. Albeit, whether these mutations exist as the cause or the effect of co-infections and/or co-morbid disorders within COVID-19 patients is still unclear. Moreover, most of the current vaccine and therapeutic interventions are revolving around spike protein. However, emphasizing on envelope protein's (1) conserved epitopes, (2) pathogenicity attenuating mutations, and (3) mutations present in the deceased patients, as reported in our present study, new directions to the ongoing efforts of therapeutic developments against COVID-19 can be achieved by targeting envelope viroporin.}, }
@article {pmid34228269, year = {2021}, author = {Agustí, A and Campillo, I and Balzano, T and Benítez-Páez, A and López-Almela, I and Romaní-Pérez, M and Forteza, J and Felipo, V and Avena, NM and Sanz, Y}, title = {Bacteroides uniformis CECT 7771 Modulates the Brain Reward Response to Reduce Binge Eating and Anxiety-Like Behavior in Rat.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {34228269}, issn = {1559-1182}, support = {AGL2014-52101-P//Ministry of Science, Innovationa and Universities (MCIU, Spain)/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU,Spain)/ ; PROMETEO/2019/015//Conselleria de Educación, Investigación, Cultura y Deporte de la Comunidad valenciana/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU, Spain)/ ; PTA//Ministry of Science, Innovation and Univesities (MCIU, Spain)/ ; }, abstract = {Food addiction (FA) is characterized by behavioral and neurochemical changes linked to loss of food intake control. Gut microbiota may influence appetite and food intake via endocrine and neural routes. The gut microbiota is known to impact homeostatic energy mechanisms, but its role in regulating the reward system is less certain. We show that the administration of Bacteroides uniformis CECT 7771 (B. uniformis) in a rat FA model impacts on the brain reward response, ameliorating binge eating and decreasing anxiety-like behavior. These effects are mediated, at least in part, by changes in the levels of dopamine, serotonin, and noradrenaline in the nucleus accumbens and in the expression of dopamine D1 and D2 receptors in the prefrontal cortex and intestine. B. uniformis reverses the fasting-induced microbiota changes and increases the abundance of species linked to healthy metabolotypes. Our data indicate that microbiota-based interventions might help to control compulsive overeating by modulating the reward response.}, }
@article {pmid34228196, year = {2021}, author = {de Menezes, GCA and Câmara, PEAS and Pinto, OHB and Convey, P and Carvalho-Silva, M and Simões, JC and Rosa, CA and Rosa, LH}, title = {Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34228196}, issn = {1432-184X}, abstract = {We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.}, }
@article {pmid34227830, year = {2021}, author = {McDaniel, EA and Moya-Flores, F and Keene Beach, N and Camejo, PY and Oyserman, BO and Kizaric, M and Khor, EH and Noguera, DR and McMahon, KD}, title = {Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0047421}, doi = {10.1128/mSystems.00474-21}, pmid = {34227830}, issn = {2379-5077}, abstract = {Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. "Candidatus Accumulibacter phosphatis" (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage. IMPORTANCE "Candidatus Accumulibacter phosphatis" is a model polyphosphate-accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the shared sequence identity of the polyphosphate kinase (ppk1) locus. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen-cycling capabilities. However, such hypotheses have largely been made based on gene content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.}, }
@article {pmid34227829, year = {2021}, author = {Trojan, D and Garcia-Robledo, E and Meier, DV and Hausmann, B and Revsbech, NP and Eichorst, SA and Woebken, D}, title = {Microaerobic Lifestyle at Nanomolar O2 Concentrations Mediated by Low-Affinity Terminal Oxidases in Abundant Soil Bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0025021}, doi = {10.1128/mSystems.00250-21}, pmid = {34227829}, issn = {2379-5077}, abstract = {High-affinity terminal oxidases (TOs) are believed to permit microbial respiration at low oxygen (O2) levels. Genes encoding such oxidases are widespread, and their existence in microbial genomes is taken as an indicator for microaerobic respiration. We combined respiratory kinetics determined via highly sensitive optical trace O2 sensors, genomics, and transcriptomics to test the hypothesis that high-affinity TOs are a prerequisite to respire micro- and nanooxic concentrations of O2 in environmentally relevant model soil organisms: acidobacteria. Members of the Acidobacteria harbor branched respiratory chains terminating in low-affinity (caa3-type cytochrome c oxidases) as well as high-affinity (cbb3-type cytochrome c oxidases and/or bd-type quinol oxidases) TOs, potentially enabling them to cope with varying O2 concentrations. The measured apparent Km (Km(app)) values for O2 of selected strains ranged from 37 to 288 nmol O2 liter-1, comparable to values previously assigned to low-affinity TOs. Surprisingly, we could not detect the expression of the conventional high-affinity TO (cbb3 type) at micro- and nanomolar O2 concentrations but detected the expression of low-affinity TOs. To the best of our knowledge, this is the first observation of microaerobic respiration imparted by low-affinity TOs at O2 concentrations as low as 1 nM. This challenges the standing hypothesis that a microaerobic lifestyle is exclusively imparted by the presence of high-affinity TOs. As low-affinity TOs are more efficient at generating ATP than high-affinity TOs, their utilization could provide a great benefit, even at low-nanomolar O2 levels. Our findings highlight energy conservation strategies that could promote the success of Acidobacteria in soil but might also be important for as-yet-unrevealed microorganisms. IMPORTANCE Low-oxygen habitats are widely distributed on Earth, ranging from the human intestine to soils. Microorganisms are assumed to have the capacity to respire low O2 concentrations via high-affinity terminal oxidases. By utilizing strains of a ubiquitous and abundant group of soil bacteria, the Acidobacteria, and combining respiration kinetics, genomics, and transcriptomics, we provide evidence that these microorganisms use the energetically more efficient low-affinity terminal oxidases to respire low-nanomolar O2 concentrations. This questions the standing hypothesis that the ability to respire traces of O2 stems solely from the activity of high-affinity terminal oxidases. We propose that this energetically efficient strategy extends into other, so-far-unrevealed microbial clades. Our findings also demonstrate that physiological predictions regarding the utilization of different O2 concentrations based solely on the presence or absence of terminal oxidases in bacterial genomes can be misleading.}, }
@article {pmid34226946, year = {2021}, author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM}, title = {Correction to: First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01807-7}, pmid = {34226946}, issn = {1432-184X}, }
@article {pmid34225812, year = {2021}, author = {Stothart, MR and Newman, AEM}, title = {Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {46}, pmid = {34225812}, issn = {2524-4671}, abstract = {BACKGROUND: Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).<br><br>RESULTS: Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.<br><br>CONCLUSIONS: Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.}, }
@article {pmid34223947, year = {2021}, author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF}, title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34223947}, issn = {1432-184X}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 000//Gillson Longenbaugh Foundation/ ; 000//Golfers Against Cancer/ ; R01CA172880//Division of Cancer Prevention, National Cancer Institute/ ; CX001430//Office of Academic Affiliations, Department of Veterans Affairs/ ; CIN13-413//Office of Academic Affiliations, Department of Veterans Affairs/ ; P30 DK56338/DK/NIDDK NIH HHS/United States ; }, abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.}, }
@article {pmid34223869, year = {2021}, author = {Smercina, DN and Bailey, VL and Hofmockel, KS}, title = {Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab091}, pmid = {34223869}, issn = {1574-6941}, abstract = {Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution, and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.}, }
@article {pmid34220760, year = {2021}, author = {Ceron-Chafla, P and Chang, YT and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {675763}, pmid = {34220760}, issn = {1664-302X}, abstract = {Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.}, }
@article {pmid34219185, year = {2021}, author = {Jani, K and Bandal, J and Shouche, Y and Shafi, S and Azhar, EI and Zumla, A and Sharma, A}, title = {Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34219185}, issn = {1432-184X}, support = {BT/Coord.II/01/03/2016//Department of Biotechnology , Ministry of Science and Technology/ ; }, abstract = {The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.}, }
@article {pmid34218293, year = {2021}, author = {Németh, JB and Knapp, DG and Kósa, A and Hegedűs, PÁ and Herczeg, G and Vági, P and Kovács, GM}, title = {Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34218293}, issn = {1432-184X}, support = {János Bolyai Research Scholarship//Magyar Tudományos Akadémia/ ; K109102//Hungarian Scientific Research Fund/ ; K105517//Hungarian Scientific Research Fund/ ; ELTE Thematic Excellence Program 2020 (TKP2020-IKA-05)//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; }, abstract = {The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.}, }
@article {pmid34218232, year = {2021}, author = {Huang, YM and Straub, D and Kappler, A and Smith, N and Blackwell, N and Kleindienst, S}, title = {A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction.}, journal = {Microbial physiology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1159/000517083}, pmid = {34218232}, issn = {2673-1673}, abstract = {Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant Gallionellaceae sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a Gallionellaceae sp., Noviherbaspirillum sp., and Thiobacillus sp., were likely involved in metal oxidation (e.g., cyc2, mtoA), denitrification (e.g., nirK/S, norBC), carbon fixation (e.g., rbcL), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the Gallionellaceae sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms in situ. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct Gallionellaceae taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance in situ). Since several of these in situ-detected Gallionellaceae taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.}, }
@article {pmid34214906, year = {2021}, author = {Desiderio, TM and Stacy, NI and Ossiboff, RJ and Iredale, M and Archer, LL and Alexander, AB and Heard, DJ and Crevasse, SE and Craft, WF and Fredholm, DVE and Donnelly, KA and Rosenberg, JF and Childress, AL and Russell, K and Wellehan, JFX}, title = {Identification of a novel mortality-associated Helicobacter species in gopher tortoises (Gopherus polyphemus), qPCR test development and validation, and correlation with mortality in a wildlife rehabilitation population.}, journal = {Veterinary microbiology}, volume = {259}, number = {}, pages = {109136}, doi = {10.1016/j.vetmic.2021.109136}, pmid = {34214906}, issn = {1873-2542}, abstract = {The genus Helicobacter includes spiral-shaped bacteria in the phylum Proteobacteria, class Epsilonproteobacteria, order Campylobacteriales, that have been associated with disease in animals, including reptiles. Three wild gopher tortoise (Gopherus polyphemus) index cases presented between 2012 and 2019 with nasal discharge, lethargy, and weight loss. Cytological examination of nasal discharge from all 3 tortoises identified marked heterophilic and mild histiocytic rhinitis with abundant extracellular and phagocytized spiral shaped bacteria that stained positive with Warthin-Starry stain. Polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene revealed this to be a novel Helicobacter species. Two tortoises died despite treatment attempts, and the third was moribund and was euthanized. Histological examination of the nasal mucosa (n = 3) showed granulocytic to lymphocytic rhinitis with variable mucosal hyperplasia, erosion, and ulceration; Warthin-Starry staining highlighted the presence of spiral bacteria in the untreated tortoise. Genus-specific primers were designed, and the gyrA and groEL genes were amplified by PCR and sequenced. Phylogenetic analysis shows that this organism and other previously characterized Helicobacter from tortoises form a clade. Development and cross-validation of two qPCR diagnostic assays for the gyrA and groEL genes showed significant correlation of the results of two assays (P < 0.0001). These assays were used to survey nasal wash samples from 31 rehabilitating gopher tortoises. Mortality of tortoises significantly correlated with higher Helicobacter loads detected by qPCR (P = 0.028). Appropriate quarantine protocols for tortoises during rehabilitation should consider this organism. Upper respiratory disease in tortoises may involve complex microbial ecology; factors beyond Mycoplasmopsis (Mycoplasma) agassizii should be taken into account.}, }
@article {pmid34214230, year = {2021}, author = {Gyeong, H and Hyun, CU and Kim, SC and Tripathi, BM and Yun, J and Kim, J and Kang, H and Kim, JH and Kim, S and Kim, M}, title = {Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16054}, pmid = {34214230}, issn = {1365-294X}, abstract = {Although microorganisms are the very first colonizers of recently deglaciated soils even prior to plant colonization, the drivers and patterns of microbial community succession at early-successional stages remain poorly understood. The successional dynamics and assembly processes of bacterial and fungal communities were compared on a glacier foreland in the maritime Antarctic across the ~10-year soil-age gradient from bare soil to sparsely vegetated area. Bacterial communities shifted more rapidly than fungal communities in response to glacial retreat; species turnover (primarily the transition from glacier- to soil-favoring taxa) contributed greatly to bacterial beta diversity, but this pattern was less clear in fungi. Bacterial communities underwent more predictable (more deterministic) changes along the soil-age gradient, with compositional changes paralleling the direction of changes in soil physicochemical properties following deglaciation. In contrast, the compositional shift in fungal communities was less associated with changes in deglaciation-induced changes in soil geochemistry and most fungal taxa displayed mosaic abundance distribution across the landscape, suggesting that the successional dynamics of fungal communities are largely governed by stochastic processes. A co-occurrence network analysis revealed that biotic interactions between bacteria and fungi are very weak in early succession. Taken together, these results collectively suggest that bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces.}, }
@article {pmid34213774, year = {2021}, author = {Kiesewetter, KN and Afkhami, ME}, title = {Microbiome-mediated effects of habitat fragmentation on native plant performance.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.17595}, pmid = {34213774}, issn = {1469-8137}, abstract = {●Habitat fragmentation is a leading cause of biodiversity and ecosystem function loss in the Anthropocene. Despite the importance of plant-microbiome interactions to ecosystem productivity, we have limited knowledge of how fragmentation affects microbiomes and even less knowledge of its consequences for microbial interactions with plants. ●Combining field surveys, microbiome sequencing, manipulative experiments, and random forest models, we (1) investigated fragmentation legacy effects on soil microbiomes in imperiled Pine Rocklands, (2) tested how compositional shifts across 14 fragmentation-altered soil microbiomes affected performance and resource allocation of three native plant species, and (3) identified fragmentation-responding microbial families underpinning plant performance. ●Legacies of habitat fragmentation were associated with significant changes in microbial diversity and composition (across three of four community axes). Experiments showed plants often strongly benefited from the microbiome's presence, but fragmentation-associated changes in microbiome composition also significantly affected plant performance and resource allocation across all seven metrics examined. Finally, random forest models identified ten fungal and six bacterial families important for plant performance that changed significantly with fragmentation. ●Our findings not only support the existence of significant fragmentation effects on natural microbiomes, but also demonstrate for the first time that fragmentation-associated changes in microbiomes can have meaningful consequences for native plant performance and investment.}, }
@article {pmid34209897, year = {2021}, author = {Hugoni, M and Galland, W and Lecomte, S and Bruto, M and Barakat, M and Piola, F and Achouak, W and Haichar, FEZ}, title = {Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/microorganisms9071406}, pmid = {34209897}, issn = {2076-2607}, support = {ANR-18-CE32-0005, DIORE//The French National Research Agency/ ; }, abstract = {Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.}, }
@article {pmid34209778, year = {2021}, author = {Vanwijnsberghe, S and Peeters, C and De Ridder, E and Dumolin, C and Wieme, AD and Boon, N and Vandamme, P}, title = {Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, doi = {10.3390/ijms22137003}, pmid = {34209778}, issn = {1422-0067}, support = {BOF15/GOA/006//Geconcerteerde Onderzoeksacties (GOA) of Ghent University/ ; }, abstract = {We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia&amp;nbsp;domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia&amp;nbsp;nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia&amp;nbsp;haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.}, }
@article {pmid34209491, year = {2021}, author = {Inui, T and Hanley, B and Tee, ES and Nishihira, J and Tontisirin, K and Van Dael, P and Eggersdorfer, M}, title = {The Role of Micronutrients in Ageing Asia: What Can Be Implemented with the Existing Insights.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/nu13072222}, pmid = {34209491}, issn = {2072-6643}, abstract = {Life expectancy as a measure of population health does not reflect years of healthy life. The average life expectancy in the Asia-Pacific region has more than doubled since 1900 and is now above 70 years. In the Asia-Pacific region, the proportion of aged people in the population is expected to double between 2017 and 2050. Increased life expectancy leads to an increase in non-communicable diseases, which consequently affects quality of life. Suboptimal nutritional status is a contributing factor to the prevalence and severity of non-communicable diseases, including cardiovascular, cognitive, musculoskeletal, immune, metabolic and ophthalmological functions. We have reviewed the published literature on nutrition and healthy ageing as it applies to the Asia-Pacific region, focusing on vitamins, minerals/trace elements and omega-3 fatty acids. Optimal nutritional status needs to start before a senior age is reached and before the consequences of the disease process are irreversible. Based on the nutritional status and health issues in the senior age in the region, micronutrients of particular importance are vitamins A, D, E, C, B-12, zinc and omega-3 fatty acids. The present paper substantiates the creation of micronutrient guidelines and proposes actions to support the achievement of optimal nutritional status as contribution to healthy ageing for Asia-Pacific populations.}, }
@article {pmid34207561, year = {2021}, author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K}, title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207561}, issn = {2076-2607}, support = {n/a (grant for a scientist//Research Foundation of Dairy Science at the Technical University of Munich (VFMF)/ ; n/a (grant for a doctorate position)//ZIEL-Institute for Food &amp; Health at the Technical University of Munich/ ; 281A105616//Federal Ministry of Food and Agriculture (BMEL)/ ; AiF 20027N//IGF Project of the FEI via AiF/ ; }, abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.}, }
@article {pmid34207412, year = {2021}, author = {Lopes, LD and Chai, YN and Marsh, EL and Rajewski, JF and Dweikat, I and Schachtman, DP}, title = {Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207412}, issn = {2076-2607}, support = {DE-SC0014395//U.S. Department of Energy/ ; }, abstract = {The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.}, }
@article {pmid34207399, year = {2021}, author = {Van Gerrewey, T and El-Nakhel, C and De Pascale, S and De Paepe, J and Clauwaert, P and Kerckhof, FM and Boon, N and Geelen, D}, title = {Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207399}, issn = {2076-2607}, support = {Not applicable//MELiSSA/ ; }, abstract = {Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3-/NH4+ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.}, }
@article {pmid34206618, year = {2021}, author = {Rilling, JI and Maruyama, F and Sadowsky, MJ and Acuña, JJ and Jorquera, MA}, title = {CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/microorganisms9071351}, pmid = {34206618}, issn = {2076-2607}, support = {1201386//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1181050//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.}, }
@article {pmid34206081, year = {2021}, author = {Lai, CC and Ko, CY and Austria, E and Shiah, FK}, title = {Extreme Weather Events Enhance DOC Consumption in a Subtropical Freshwater Ecosystem: A Multiple-Typhoon Analysis.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34206081}, issn = {2076-2607}, abstract = {Empirical evidence suggests that the frequency/intensity of extreme weather events might increase in a warming climate. It remains unclear how these events quantitatively impact dissolved organic carbon (DOC), a pool approximately equal to CO2 in the atmosphere. This study conducted a weekly-to-biweekly sampling in a deep subtropical reservoir in the typhoon-prevailing season (June to September) from 2004 to 2009, at which 33 typhoons with distinctive precipitation (<1~362 mm d-1) had passed the study site. Our analyses indicated that the phosphate (i.e., DIP; <10~181 nMP) varied positively with the intensity of the accumulated rainfall 2-weeks prior; bacteria growth rate (0.05~3.68 d-1) behaved as a positive function of DIP, and DOC concentrations (54~119 µMC) changed negatively with bacterial production (1.2~26.1 mgC m-3 d-1). These implied that the elevated DIP-loading in the hyperpycnal flow induced by typhoons could fuel bacteria growth and cause a significant decline of DOC concentrations. As the typhoon's intensity increases, many mineral-limited lentic freshwater ecosystems might become more like a CO2 source injecting more CO2 back to the atmosphere, creating a positive feedback loop that might generate severer extreme weather events.}, }
@article {pmid34204924, year = {2021}, author = {Blanchette, ML and Lund, MA}, title = {Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34204924}, issn = {2076-2607}, support = {C27043//Australian Coal Association Research Program/ ; }, abstract = {Mine pit lakes ('pit lakes') are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by 'core' taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.}, }
@article {pmid34204724, year = {2021}, author = {Clocchiatti, A and Hannula, SE and Rizaludin, MS and Hundscheid, MPJ and Klein Gunnewiek, PJA and Schilder, MT and Postma, J and de Boer, W}, title = {Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34204724}, issn = {2076-2607}, support = {14012//Stichting voor de Technische Wetenschappen/ ; }, abstract = {Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.}, }
@article {pmid34201311, year = {2021}, author = {Šulčius, S and Alzbutas, G and Juknevičiūtė, V and Šimoliūnas, E and Venckus, P and Šimoliūnienė, M and Paškauskas, R}, title = {Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34201311}, issn = {2073-4425}, support = {S-MIP-20-38//Lietuvos Mokslo Taryba/ ; }, abstract = {Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus-host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.}, }
@article {pmid34199628, year = {2021}, author = {Rizaludin, MS and Stopnisek, N and Raaijmakers, JM and Garbeva, P}, title = {The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots.}, journal = {Metabolites}, volume = {11}, number = {6}, pages = {}, pmid = {34199628}, issn = {2218-1989}, abstract = {Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved "a cry for help" response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.}, }
@article {pmid34198081, year = {2021}, author = {Yuan, H and Yuan, J and You, Y and Zhang, B and Wu, Y and Huang, S and Zhang, Y}, title = {Simultaneous ammonium and sulfate biotransformation driven by aeration: Nitrogen/sulfur metabolism and metagenome-based microbial ecology.}, journal = {The Science of the total environment}, volume = {794}, number = {}, pages = {148650}, doi = {10.1016/j.scitotenv.2021.148650}, pmid = {34198081}, issn = {1879-1026}, abstract = {The present study aimed to clarify the effect of oxygen respiration on biotransformation of alternative electron acceptors (e.g., nitrate and sulfate) underlying the simultaneous removal of ammonium and sulfate in a single aerated sequencing batch reactor. Complete nitrification was achieved in feast condition, while denitrification was carried out in both feast and famine conditions when aeration intensity (AI) was higher than 0.22 L/(L·min). Reactors R1 [0.56 L/(L·min)], R2 [0.22 L/(L·min)], and R3 [0.08 L/(L·min)] achieved 72.39% sulfate removal efficiency in feast condition, but H2S release occurred in R3. Following exogenous substrate depletion, sulfate concentration increased again and exceeded the influent value in R1, indicating that sulfate transformation was affected by oxygen intrusion. Metagenomic analysis showed that a higher AI promoted sulfate reduction by switching from dissimilatory to assimilatory pathway. Lower AI-acclimated microorganisms (R3) produced H2S and ammonium, while higher AI-acclimated microorganisms (R1) accumulated nitrite, which confirmed that biotransformation of N and S was strongly regulated by redox imbalance driven by aeration. This implied that respiration control, a microbial self-regulation mechanism, was linked to the dynamic imbalance between electron donors and electron acceptors. Aerobic nitrate (sulfate) reduction, as one of the effects of respiration control, could be used as an alternative strategy to compensate for dynamic imbalance, when supported by efficient endogenous metabolism. Moderate aeration induced microorganisms to change their energy conservation and survival strategy through respiration control and inter-genus protection of respiratory activity among keystone taxa (including Azoarcus in R1, Thauera in R2, and Thiobacillus, Ottowia, and Geoalkalibacter in R3) to form an optimal niche in response to oxygen intrusion and achieve benign biotransformation of C, N, and S without toxic intermediate accumulation. This study clarified the biotransformation mechanism of ammonium and sulfate driven by aeration and provided theoretical guidance for optimizing existing aeration-based techniques.}, }
@article {pmid34195856, year = {2021}, author = {McGirr, S and Clarke, D and Kilcoyne, J and Silke, J and Touzet, N}, title = {Co-localisation of Azaspiracid Analogs with the Dinoflagellate Species Azadinium spinosum and Amphidoma languida in the Southwest of Ireland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34195856}, issn = {1432-184X}, support = {CF/15/01//Marine Research Sub-programme by the Irish Government/ ; }, abstract = {Phytoplankton and biotoxin monitoring programmes have been implemented in many countries to protect human health and to mitigate the impacts of harmful algal blooms (HABs) on the aquaculture industry. Several amphidomatacean species have been confirmed in Irish coastal waters, including the azaspiracid-producing species Azadinium spinosum and Amphidoma languida. Biogeographic distribution studies have been hampered by the fact that these small, armoured dinoflagellates share remarkably similar morphologies when observed by light microscopy. The recent releases of species-specific molecular detection assays have, in this context, been welcome developments. A survey of the south west and west coasts of Ireland was carried out in August 2017 to investigate the late summer distribution of toxic amphidomataceans and azaspiracid toxins. Azadinium spinosum and Am. languida were detected in 83% of samples in the southwest along the Crease Line and Bantry Bay transects between 20 and 70 m depth, with maximal cell concentrations of 7000 and 470,000 cells/L, respectively. Azaspiracid concentrations were well aligned with the distributions of Az. spinosum and Am. languida, up to 1.1 ng/L and 4.9 ng/L for combined AZA-1, -2, -33, and combined AZA-38, -39, respectively. Although a snapshot in time, this survey provides new insights in the late summer prominence of AZAs and AZA-producing species in the southwest of Ireland, where major shellfish aquaculture operations are located. Results showed a substantial overlap in the distribution of amphidomatacean species in the area and provide valuable baseline information in the context of ongoing monitoring efforts of toxigenic amphidomataceans in the region.}, }
@article {pmid34192775, year = {2021}, author = {Vadaq, N and Schirmer, M and Tunjungputri, RN and Vlamakis, H and Chiriac, C and Ardiansyah, E and Gasem, MH and Joosten, L and de Groot, PG and Xavier, RJ and Netea, MG and van der Ven, AJAM and de Mast, Q}, title = {Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals.}, journal = {Thrombosis and haemostasis}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-1541-3706}, pmid = {34192775}, issn = {2567-689X}, abstract = {Background Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling. Methods We used data of a cohort of 534 healthy adult Dutch volunteers (500FG study).Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin αIIbβ3, both in unstimulated blood as well as after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples. Results Untargeted metabolomics yielded 1979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ('alanine, aspartate, and glutamate metabolism' and 'arginine biosynthesis') that were associated with platelet reactivity. Conclusions This comprehensive overview is an important resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.}, }
@article {pmid34192637, year = {2021}, author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y}, title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125450}, doi = {10.1016/j.biortech.2021.125450}, pmid = {34192637}, issn = {1873-2976}, abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4+-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.}, }
@article {pmid34191105, year = {2021}, author = {Paolinelli, M and Escoriaza, G and Cesari, C and Garcia-Lampasona, S and Hernandez-Martinez, R}, title = {Characterization of Grapevine Wood Microbiome Through a Metatranscriptomic Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34191105}, issn = {1432-184X}, support = {PRET-1251101//Instituto Nacional de Tecnología Agropecuaria/ ; }, abstract = {Grapevine trunk diseases threaten wine and table grape production worldwide, primarily by reducing yields and, in its advanced stages, causing plant death. Among those diseases, the complex etiology disease known as hoja de malvón (HDM) significantly concerns Argentinian and Uruguayan viticulture. At least four different fungi are associated with this disease, but their role and interactions with other wood microorganisms are understudied. In this sense, analyzing grapevine wood microbiome composition could help understand microbial interactions occurring in HDM onset. Hence, a metatranscriptomic study was performed for the microbiome characterization of mature field-grown Vitis vinifera cv. Malbec, leaf-symptomatic or leaf-asymptomatic. The microbiome was mainly represented by Dothideomycetes and Actinobacteria. In the plant with more marked symptoms, higher levels of the Basidiomycota Arambarria destruens and Phellinus laevigatus were detected. Despite this particular difference, discriminating symptomatic from asymptomatic plants based on the presence or abundance of HDM pathogens was not possible. Alpha diversity and rank-abundance curve analyses indicated that plants with foliar symptoms have lower microbial evenness than asymptomatic plants. The co-occurrence network modeled microbial interkingdom interactions. Molecular data generated in this study will help develop future targeted molecular quantification for specific taxa.}, }
@article {pmid34190973, year = {2021}, author = {Sadiq, FA and Wenwei, L and Heyndrickx, M and Flint, S and Wei, C and Jianxin, Z and Zhang, H}, title = {Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab096}, pmid = {34190973}, issn = {1574-6941}, abstract = {Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis, and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three, and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.}, }
@article {pmid34190389, year = {2021}, author = {Barnes, EM and Kutos, S and Naghshineh, N and Mesko, M and You, Q and Lewis, JD}, title = {Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15653}, pmid = {34190389}, issn = {1462-2920}, abstract = {A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function. This article is protected by copyright. All rights reserved.}, }
@article {pmid34190033, year = {2021}, author = {Duysburgh, C and Van den Abbeele, P and Morera, M and Marzorati, M}, title = {Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-16}, doi = {10.3920/BM2020.0180}, pmid = {34190033}, issn = {1876-2891}, abstract = {Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.}, }
@article {pmid34189610, year = {2021}, author = {Wang, X and Shang, Y and Wei, Q and Wu, X and Dou, H and Zhang, H and Zhou, S and Sha, W and Sun, G and Ma, S and Zhang, H}, title = {Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34189610}, issn = {1432-184X}, support = {31872242//the national natural science foundation of china/ ; 31672313//the national natural science foundation of china/ ; 32070405//the national natural science foundation of china/ ; 32001228//the national natural science foundation of china/ ; 32000291//the national natural science foundation of china/ ; 61902368//the national natural science foundation of china/ ; 201404420//the Special Fund for Forest Scientific Research in the Public Welfare/ ; }, abstract = {The gut microbiome is integral for the host's living and environmental adaptation and crucially important for understanding host adaptive mechanisms. The red fox (Vulpes vulpes) dominates a wider ecological niche and more complicated habitat than that of the corsac fox (V. corsac). However, the adaptive mechanisms (in particular, the gut microbiome responsible for this kind of difference) are still unclear. Therefore, we investigated the gut microbiome of these two species in the Hulunbuir grassland, China, and evaluated their microbiome composition, function, and adaptive mechanisms. We profiled the gut microbiome and metabolism function of red and corsac foxes via 16S rRNA gene and metagenome sequencing. The foxes harbored species-specific microbiomes and functions that were related to ecological niche and habitat. The red fox had abundant Bacteroides, which leads to significant enrichment of metabolic pathways (K12373 and K21572) and enzymes related to chitin and carbohydrate degradation that may help the red fox adapt to a wider niche. The corsac fox harbored large proportions of Blautia, Terrisporobacter, and ATP-binding cassette (ABC) transporters (K01990, K02003, and K06147) that can help maintain corsac fox health, allowing it to live in harsh habitats. These results indicate that the gut microbiome of the red and corsac foxes may have different abilities which may provide these species with differing capabilities to adapt to different ecological niches and habitats, thus providing important microbiome data for understanding the mechanisms of host adaptation to different niches and habitats.}, }
@article {pmid34185360, year = {2021}, author = {Jiao, S and Zhang, B and Zhang, G and Chen, W and Wei, G}, title = {Stochastic community assembly decreases soil fungal richness in arid ecosystems.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16047}, pmid = {34185360}, issn = {1365-294X}, abstract = {Uncovering the linkages between community assembly and species diversity is a fundamental issue in microbial ecology. In this study, a large-scale (transect intervals of 1257.6 km) cross-biome soil survey was conducted, which ranged over agricultural fields, forests, wetlands, grasslands and desert, in the arid regions of northwest China. The aim was to investigate the biogeographic distribution, community assembly and species co-occurrence of soil fungi. The fungal communities in agricultural soils exhibited a steeper distance-decay slope and wider niche breadths, and were more strongly affected by stochastic assembly processes, than fungi in other natural habitats. A strong relationship was revealed between soil fungal richness and community assembly in arid ecosystems, with the influence of stochastic assembly processes decreasing with increasing fungal richness. Moreover, aridity was the most important environmental factor influencing fungal richness, β-diversity and species co-occurrence patterns. Specifically, the predicted increase in arid conditions will likely reduce fungal richness and network complexity. These findings represent a considerable advance in linking fungal richness to mechanisms underlying the biogeographic patterns and assembly processes of fungal communities in arid ecosystems. These results can thus be used to forecast species co-occurrence and diversities pattern of soil fungi under climate aridity and land-use change scenarios.}, }
@article {pmid34184914, year = {2021}, author = {Savoie, ER and Lanclos, VC and Henson, MW and Cheng, C and Getz, EW and Barnes, SJ and LaRowe, DE and Rappé, MS and Thrash, JC}, title = {Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria).}, journal = {mSystems}, volume = {}, number = {}, pages = {e0027621}, doi = {10.1128/mSystems.00276-21}, pmid = {34184914}, issn = {2379-5077}, abstract = {Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.}, }
@article {pmid34182782, year = {2021}, author = {Murareanu, BM and Sukhdeo, R and Qu, R and Jiang, J and Reinke, AW}, title = {Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia.}, journal = {mBio}, volume = {}, number = {}, pages = {e0149021}, doi = {10.1128/mBio.01490-21}, pmid = {34182782}, issn = {2150-7511}, abstract = {Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.}, }
@article {pmid34180595, year = {2021}, author = {Suleiman, M and Choffat, Y and Daugaard, U and Petchey, OL}, title = {Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach.}, journal = {MicrobiologyOpen}, volume = {10}, number = {3}, pages = {e1189}, pmid = {34180595}, issn = {2045-8827}, support = {FK-20-125//Forschungskredit of the UZH/ ; Project 310030_188431/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory-based approach with small, replicated, and liquid-dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16S rRNA gene seq.) and the abiotic conditions (O2 , H2 S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.}, }
@article {pmid34179320, year = {2021}, author = {Hoogenkamp, MA and Brandt, BW and Laheij, AMGA and de Soet, JJ and Crielaard, W}, title = {16S rDNA sequencing and metadata of Dutch dental unit water.}, journal = {Data in brief}, volume = {37}, number = {}, pages = {107221}, pmid = {34179320}, issn = {2352-3409}, abstract = {Dental practices were approached to fill out a questionnaire on the infection control protocols in use to control biofilm growth in the dental unit and to send two types of water sample. Sampling of the dental units had to be performed prior to any infection control measures and on the second day of operation, to avoid residual effects of biofilm disinfection protocols performed in the weekend. Instructions were given on how to sample the units. Only samples, accompanied with a completed questionnaire and returned within two days by regular mail, were analysed. Samples were processed for heterotrophic plate counts, 16S (V4) rDNA microbiome sequencing and q-PCR for the concentration of bacterial 16S rDNA, fungal 18S rDNA, Legionella spp. and the presence of amoeba. The files contain the metadata needed to interpret and analyse the microbiome data. This dataset can be used by other scientists, members of infection control units, (trainee) bioinformaticians and policy makers. This dataset can provide leads to further unexplored parameters which could influence the microbial ecology of the dental unit.}, }
@article {pmid34177846, year = {2021}, author = {Tláskal, V and Pylro, VS and Žifčáková, L and Baldrian, P}, title = {Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {668644}, pmid = {34177846}, issn = {1664-302X}, abstract = {The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.}, }
@article {pmid34177841, year = {2021}, author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG}, title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661410}, pmid = {34177841}, issn = {1664-302X}, abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.}, }
@article {pmid34173031, year = {2021}, author = {Zhang, W and Zhang, YC and Wang, ZG and Gu, QY and Niu, JZ and Wang, JJ}, title = {The Diversity of Viral Community in Invasive Fruit Flies (Bactrocera and Zeugodacus) Revealed by Meta-transcriptomics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34173031}, issn = {1432-184X}, support = {2019YFD1002100//National Key R&amp;D Program of China/ ; 31701846//National Natural Science Foundation of China/ ; CARS-26//earmarked fund for Modern Agro-industry (Citrus) Technology Research System of China/ ; B18044//111 Project/ ; }, abstract = {RNA viruses are extremely diverse and rapidly evolving in various organisms. Our knowledge on viral evolution with interacted hosts in the manner of ecology is still limited. In the agricultural ecosystem, invasive insect species are posing a great threat to sustainable crop production. Among them, fruit flies (Diptera: Tephritidae Bactrocera and Zeugodacus) are destructive to fruits and vegetables, which are also closely related and often share similar ecological niches. Thus, they are ideal models for investigating RNA virome dynamics in host species. Using meta-transcriptomics, we found 39 viral sequences in samples from 12 fly species. These viral species represented the diversity of the viromes including Dicistroviridae, negev-like virus clades, Thika virus clades, Solemoviridae, Narnaviridae, Nodaviridae, Iflaviridae, Orthomyxoviridae, Bunyavirales, Partitiviridae, and Reoviridae. In particular, dicistrovirus, negev-like virus, orthomyxovirus, and orbivirus were common in over four of the fly species, which suggests a positive interaction between fly viromes that exist under the same ecological conditions. For most of the viruses, the virus-derived small RNAs displayed significantly high peaks in 21 nt and were symmetrically distributed throughout the viral genome. These results suggest that infection by these viruses can activate the host's RNAi immunity. Our study provides RNA virome diversity and evidence on their infection activity in ecologically associated invasive fruit fly species, which could help our understanding of interactions between complex species and viruses.}, }
@article {pmid34170682, year = {2021}, author = {Mamet, SD and Jimmo, A and Conway, A and Teymurazyan, A and Talebitaher, A and Papandreou, Z and Chang, YF and Shannon, W and Peak, D and Siciliano, SD}, title = {Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c01113}, pmid = {34170682}, issn = {1520-5851}, abstract = {Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.}, }
@article {pmid34169333, year = {2021}, author = {Cobo-Díaz, JF and Legrand, F and Le Floch, G and Picot, A}, title = {Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34169333}, issn = {1432-184X}, support = {Grant#9097 MycoRes//Région Bretagne/ ; }, abstract = {Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.}, }
@article {pmid34169332, year = {2021}, author = {Djemai, K and Drancourt, M and Tidjani Alou, M}, title = {Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34169332}, issn = {1432-184X}, support = {Méditerranée Infection 10-IAHU-03//National Research Agency/ ; }, abstract = {Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.}, }
@article {pmid34168166, year = {2021}, author = {Gan, L and Xu, WH and Xiong, Y and Lv, Z and Zheng, J and Zhang, Y and Lin, J and Liu, J and Chen, S and Chen, M and Guo, Q and Wu, J and Chen, J and Su, Z and Sun, J and He, Y and Liu, C and Wang, W and Verstraete, W and Sorgeloos, P and Defoirdt, T and Qin, Q and Liu, Y}, title = {Probiotics: their action against pathogens can be turned around.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13247}, pmid = {34168166}, issn = {2045-2322}, support = {GDOE[2019]A26//Guangdong Marine Economy Promotion Projects (MEPP) Fund/ ; 2019KJ150//Guangdong Provincial Special Fund For Modern Agriculture Industry Technology Innovation Teams, Department of Agriculture and Rural Affairs of Guangdong Province/ ; 31871323//National Natural Science Foundation of China (NSFC)/ ; 31571350//National Natural Science Foundation of China (NSFC)/ ; 2014A030306044//National Natural Science Funds of Guangdong Province for Distinguished Young Scholar/ ; CARS-47-G16//China Agriculture Research System/ ; 8000-218043//Scientific Research Startup Fund of South China Agricultural University/ ; 8000-219242//Scientific Research Startup Fund of South China Agricultural University/ ; 8000-220141//Scientific Research Startup Fund of South China Agricultural University/ ; }, abstract = {Probiotics when applied in complex evolving (micro-)ecosystems, might be selectively beneficial or detrimental to pathogens when their prophylactic efficacies are prone to ambient interactions. Here, we document a counter-intuitive phenomenon that probiotic-treated zebrafish (Danio rerio) were respectively healthy at higher but succumbed at lower level of challenge with a pathogenic Vibrio isolate. This was confirmed by prominent dissimilarities in fish survival and histology. Based upon the profiling of the zebrafish microbiome, and the probiotic and the pathogen shared gene orthogroups (genetic niche overlaps in genomes), this consequently might have modified the probiotic metabolome as well as the virulence of the pathogen. Although it did not reshuffle the architecture of the commensal microbiome of the vertebrate host, it might have altered the probiotic-pathogen inter-genus and intra-species communications. Such in-depth analyses are needed to avoid counteractive phenomena of probiotics and to optimise their efficacies to magnify human and animal well-being. Moreover, such studies will be valuable to improve the relevant guidelines published by organisations such as FAO, OIE and WHO.}, }
@article {pmid34161269, year = {2021}, author = {Qian, X and Gunturu, S and Sun, W and Cole, JR and Norby, B and Gu, J and Tiedje, JM}, title = {Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34161269}, issn = {1091-6490}, abstract = {While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.}, }
@article {pmid34160245, year = {2021}, author = {Shi, X and Oliveira, DAF and Holsten, L and Steinhauer, K and de Rezende, JR}, title = {Long-term biocide efficacy and its effect on a souring microbial community.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0084221}, doi = {10.1128/AEM.00842-21}, pmid = {34160245}, issn = {1098-5336}, abstract = {Reservoir souring, which is the production of H2S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons behind biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) dosages were individually applied to a complex sulfate-reducing microbial community, followed by one-year monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at 100 ppm dosage regardless the biocide type, and that lasting souring control for the entire one-year timespan was only achieved with ARB at 750 ppm. Microbial community analyses suggested that the high dosage biocide treatments resulted in one order of magnitude lower average total microbial abundance and average SRM abundance compared to the low dosage treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure change, thus monitoring changes in microbial community metrics may serve as early warnings of the failure of a biocide-based souring control programme in the field. Furthermore, spore-forming sulfate reducers (Desulfotomaculum and Desulfurispora) were enriched and became dominant in both GA-treated groups, which could cause challenges to the design of long-lasting remedial souring control strategies. IMPORTANCE Reservoir souring is a detrimental problem for the oil and gas industry as H2S corrodes the steel infrastructure, downgrades the oil quality and poses substantial risks to the field personnel and the environment. Biocides have been widely applied to remedy souring, yet the long-term performance of biocide treatments is hard to predict or optimise due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity and structure of the souring microbial community, thus advancing the knowledge towards a deeper understanding of the microbial ecology of biocide-treated systems, and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring and highlights the long-term consequences of the biocide treatment on the microbial communities, with relevance to both operators and regulators.}, }
@article {pmid34157595, year = {2021}, author = {Volpiano, CG and Sant'Anna, FH and da Mota, FF and Sangal, V and Sutcliffe, I and Munusamy, M and Saravanan, VS and See-Too, WS and Passaglia, LMP and Rosado, AS}, title = {Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {4}, pages = {126223}, doi = {10.1016/j.syapm.2021.126223}, pmid = {34157595}, issn = {1618-0984}, abstract = {Streptomyces thermoautotrophicus UBT1T has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether 'S. thermoautotrophicus' represents a higher taxonomic rank, 'S. thermoautotrophicus' strains UBT1T and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1T and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1T and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between 'S. thermoautotrophicus' and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1T and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the 'S. thermoautotrophicus' proteomic profiles and KEGG orthology demonstrated that UBT1T and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1T, = DSM 100163T = KCTC 49540T) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.}, }
@article {pmid34156270, year = {2021}, author = {Zhu, M and Duan, X and Guo, H and Huang, W and Quan, K and Yan, X and Ji, J and Li, Y and Li, Z}, title = {Occurrence of Powdery Mildew Caused by Erysiphe buhrii on Dianthus chinensis in Inner Mongolia, China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-21-0048-PDN}, pmid = {34156270}, issn = {0191-2917}, abstract = {Dianthus chinensis is widely cultivated for ornamental and medicinal use in China (Guo et al. 2017). The plant has been used in traditional Chinese medicine for the treatment of urinary problems such as strangury and diuresis (Han et al. 2015). In June and July 2020, powdery mildew-like signs and symptoms were seen on leaves of D. chinensis cultivated on the campus of Inner Mongolia Agricultural University, Hohhot city, Inner Mongolia Province, China. White powder-like masses occurred in irregular shaped lesions on both leaf surfaces and covered up to 50% of leaf area. Some infected leaves were deformed on their edges and some leaf senescence occurred. More than 40 % of plants (n = 180) exhibited these signs and symptoms. Conidiophores (n = 50) of the suspect fungus were unbranched and measured 70 to 140 µm long × 6 to 10 µm wide and had foot cells that were 25 to 48 µm long. Conidia (n = 50) were produced singly, elliptical to cylindrical shaped, 30 to 45 µm long × 12 to 19 µm wide, with length/width ratio of 2.0 to 3.2, and lacked fibrosin bodies. No chasmothecia were found. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Braun and Cook 2012). Fungal structures were isolated from diseased leaves and genomic DNA of the pathogen extracted utilizing the method described by Zhu et al. (2019). The internal transcribed spacer (ITS) region was amplified by PCR employing the primers PMITS1/PMITS2 (Cunnington et al. 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The sequence for the powdery mildew fungus (deposited into GenBank under Accession No. MW144997) showed 100 % identity (558/558 bp) with E. buhrii (Accession No. LC009898) that was reported on Dianthus sp. in Japan (Takamatsu et al. 2015). Pathogenicity tests were done by collecting fungal conidia from infected D. chinensis leaves and brushing them onto leaves of four healthy plants. Four uninoculated plants served as controls. Inoculated and uninoculated plants were placed in separate growth chambers maintained at 19 ℃, 65 % humidity, with a 16 h/8 h light/dark period. Nine-days post-inoculation, powdery mildew disease signs appeared on inoculated plants, whereas control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was identified and confirmed as E. buhrii based on morphological and molecular analysis. An Oidium sp. causing powdery mildew on D. chinensis previously was reported in Xinjiang Province, China (Zheng and Yu 1987). This, to the best of our knowledge, is the first report of powdery mildew caused by E. buhrii on D. chinensis in China (Farr and Rossman 2020). The sudden occurrence of this destructive powdery mildew disease on D. chinensis may adversely affect the health, ornamental value and medicinal uses of the plant in China. Identifying the cause of the disease will support efforts for its future control and management.}, }
@article {pmid34154406, year = {2021}, author = {Guo, H and Rischer, M and Westermann, M and Beemelmanns, C}, title = {Two Distinct Bacterial Biofilm Components Trigger Metamorphosis in the Colonial Hydrozoan Hydractinia echinata.}, journal = {mBio}, volume = {}, number = {}, pages = {e0040121}, doi = {10.1128/mBio.00401-21}, pmid = {34154406}, issn = {2150-7511}, abstract = {In marine environments, the bacterially induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon that is critical for the persistence of many marine invertebrates. However, the majority of inducing bacterial signals and underlying cellular mechanisms remain enigmatic. The marine hydroid Hydractinia echinata is a well-known model system for investigating bacterially stimulated larval metamorphosis, as larvae transform into the colonial adult stage within 24 h of signal detection. Although H. echinata has served as a cell biological model system for decades, the identity and influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first determined that specific bacterial (lyso)phospholipids, naturally present in bacterial membranes and vesicles, elicit metamorphosis in Hydractinia larvae in a dose-response manner. Lysophospholipids, as single compounds or in combination (50 μM), induced metamorphosis in up to 50% of all larvae within 48 h. Using fluorescence-labeled bacterial phospholipids, we demonstrated that phospholipids are incorporated into the larval membranes, where interactions with internal signaling cascades are proposed to occur. Second, we identified two structurally distinct exopolysaccharides of bacterial biofilms, the new Rha-Man polysaccharide from Pseudoalteromonas sp. strain P1-9 and curdlan from Alcaligenes faecalis, to induce metamorphosis in up to 75% of tested larvae. We also found that combinations of (lyso)phospholipids and curdlan induced transformation within 24 h, thereby exceeding the morphogenic activity observed for single compounds and bacterial biofilms. Our results demonstrate that two structurally distinct, bacterium-derived metabolites converge to induce high transformation rates of Hydractinia larvae and thus may help ensure optimal habitat selection. IMPORTANCE Bacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as the formation of coral reefs, the maintenance of marine fisheries, and the fouling of submerged surfaces. However, the complex composition of biofilms often makes the characterization of individual signals and regulatory mechanisms challenging. Developing tractable model systems to characterize these coevolved interactions is the key to understanding fundamental processes in evolutionary biology. Here, we characterized two types of bacterial signaling molecules, phospholipids and polysaccharides, that induce the morphogenic transition. We then analyzed their abundance and combinatorial activity. This study highlights the general importance of multiple bacterial signal converging activity in development-related cross-kingdom signaling and poses the question of whether complex lipids and polysaccharides are general metamorphic cues for cnidarian larvae.}, }
@article {pmid34148108, year = {2021}, author = {Rosado-Porto, D and Ratering, S and Cardinale, M and Maisinger, C and Moser, G and Deppe, M and Müller, C and Schnell, S}, title = {Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34148108}, issn = {1432-184X}, abstract = {Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.}, }
@article {pmid34148107, year = {2021}, author = {Deignan, LK and McDougald, D}, title = {Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34148107}, issn = {1432-184X}, support = {MSRDP-03//National Research Foundation Singapore/ ; }, abstract = {As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.}, }
@article {pmid34146566, year = {2021}, author = {Baumgartner, M and Lang, M and Holley, H and Crepaz, D and Hausmann, B and Pjevac, P and Moser, D and Haller, F and Hof, F and Beer, A and Orgler, E and Frick, A and Khare, V and Evstatiev, R and Strohmaier, S and Primas, C and Dolak, W and Köcher, T and Kristaps, K and Rath, T and Neurath, MF and Berry, D and Makristathis, A and Muttenthaler, M and Gasche, C}, title = {Mucosal biofilms are an endoscopic feature of irritable bowel syndrome and ulcerative colitis.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2021.06.024}, pmid = {34146566}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socio-economic impact. In IBS, diagnosis and treatment options are limited, but evidence for an involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism.<br><br>METHODS: The presence of mucosal biofilms was assessed in 1,426 patients at two European university-based endoscopy centers. One-hundred-seventeen patients were selected for in-depth molecular and microscopic analysis using 16S-rRNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics and in vitro biofilm formation assays.<br><br>RESULTS: Biofilms were present in 57% of IBS and 34% of ulcerative colitis (UC) patients, compared to 6% of controls (p<0.001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing link the presence of biofilms to a dysbiotic gut microbiome including overgrowth of Escherichia coli and Ruminococcus gnavus. R. gnavus isolates cultivated from patient biofilms also formed biofilms in vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea.<br><br>CONCLUSIONS: The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and UC with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and UC, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.}, }
@article {pmid34145482, year = {2021}, author = {González-Olalla, JM and Medina-Sánchez, JM and Carrillo, P}, title = {Fluctuation at High Temperature Combined with Nutrients Alters the Thermal Dependence of Phytoplankton.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34145482}, issn = {1432-184X}, abstract = {The Metabolic Theory of Ecology (MTE) predicts that the temperature increases exert a common effect on organisms stimulating metabolic rates, this being stronger for a heterotrophic than for an autotrophic metabolism. However, no available studies within the MTE framework have focused on organisms' response under fluctuation at high temperature interacting with factors such as nutrient availability, or how this interaction could affect the coexistence between mixotrophic and strict autotrophic phytoplankton. Hence, we assess how the phytoplankton metabolism and species composition are affected under scenarios of high temperature and fluctuation at high temperature, and how nutrients alter the direction and magnitude of such impact. For that, we use a mixed culture composed of two phytoplankton species: a strict autotrophic species and a mixotrophic species. Our results indicate that, in agreement with the MTE, only fluctuation at high temperature treatment registered a greater activation energy (Ea) value for respiration than for primary production and stimulated mixotrophic over strict autotrophic species abundance compared to control treatment. Remarkably, fluctuation at high temperature had a strong negative impact on the total abundance of the mixed-culture. The interaction between nutrient enrichment and fluctuation at high temperature increased abundance of the strict autotrophic species and overall species abundance, and led to Ea values that were higher in primary production than in respiration. Changes in community composition, enhanced by nutrient enrichment, could be behind this response, which can have implications in ecosystem functioning in a changing world.}, }
@article {pmid34143976, year = {2021}, author = {Yang, JY and Fang, W and Miranda-Sanchez, F and Brown, JM and Kauffman, KM and Acevero, CM and Bartel, DP and Polz, MF and Kelly, L}, title = {Degradation of host translational machinery drives tRNA acquisition in viruses.}, journal = {Cell systems}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cels.2021.05.019}, pmid = {34143976}, issn = {2405-4720}, abstract = {Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.}, }
@article {pmid34143648, year = {2021}, author = {Hawkes, CV and Kjøller, R and Raaijmakers, JM and Riber, L and Christensen, S and Rasmussen, S and Christensen, JH and Dahl, AB and Westergaard, JC and Nielsen, M and Brown-Guedira, G and Hestbjerg Hansen, L}, title = {Extension of Plant Phenotypes by the Foliar Microbiome.}, journal = {Annual review of plant biology}, volume = {72}, number = {}, pages = {823-846}, doi = {10.1146/annurev-arplant-080620-114342}, pmid = {34143648}, issn = {1545-2123}, mesh = {Ecology ; *Microbiota ; Phenotype ; Plant Development ; Plants ; }, abstract = {The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.}, }
@article {pmid34143451, year = {2021}, author = {Romaní-Pérez, M and López-Almela, I and Bullich-Vilarrubias, C and Rueda-Ruzafa, L and Gómez Del Pulgar, EM and Benítez-Páez, A and Liebisch, G and Lamas, JA and Sanz, Y}, title = {Holdemanella biformis improves glucose tolerance and regulates GLP-1 signaling in obese mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {7}, pages = {e21734}, doi = {10.1096/fj.202100126R}, pmid = {34143451}, issn = {1530-6860}, support = {797297//European Union Horizon 2020 research and innovation program/ ; 613979//European Union 7th Framework Program/ ; AGL2017-88801-P//Spanish Ministry of Science and Innovation/ ; }, abstract = {Impaired glucose homeostasis in obesity is mitigated by enhancing the glucoregulatory actions of glucagon-like peptide 1 (GLP-1), and thus, strategies that improve GLP-1 sensitivity and secretion have therapeutic potential for the treatment of type 2 diabetes. This study shows that Holdemanella biformis, isolated from the feces of a metabolically healthy volunteer, ameliorates hyperglycemia, improves oral glucose tolerance and restores gluconeogenesis and insulin signaling in the liver of obese mice. These effects were associated with the ability of H. biformis to restore GLP-1 levels, enhancing GLP-1 neural signaling in the proximal and distal small intestine and GLP-1 sensitivity of vagal sensory neurons, and to modify the cecal abundance of unsaturated fatty acids and the bacterial species associated with metabolic health. Our findings overall suggest the potential use of H biformis in the management of type 2 diabetes in obesity to optimize the sensitivity and function of the GLP-1 system, through direct and indirect mechanisms.}, }
@article {pmid34142402, year = {2021}, author = {Simonin, M and Rocca, JD and Gerson, JR and Moore, E and Brooks, AC and Czaplicki, L and Ross, MRV and Fierer, N and Craine, JM and Bernhardt, ES}, title = {Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {e2389}, doi = {10.1002/eap.2389}, pmid = {34142402}, issn = {1051-0761}, abstract = {The rivers of Appalachia (USA) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macro-invertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, USA) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150 to 200 µS·cm-1 that are substantially below the current EPA Aquatic Life Benchmark of 300 µS·cm-1 for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.}, }
@article {pmid34141244, year = {2021}, author = {Boynton, PJ and Wloch-Salamon, D and Landermann, D and Stukenbrock, EH}, title = {Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes.}, journal = {Ecology and evolution}, volume = {11}, number = {11}, pages = {6604-6619}, pmid = {34141244}, issn = {2045-7758}, abstract = {Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.}, }
@article {pmid34141209, year = {2021}, author = {Li, Y and Chesters, D and Wang, MQ and Wubet, T and Schuldt, A and Anttonen, P and Guo, PF and Chen, JT and Zhou, QS and Zhang, NL and Ma, KP and Bruelheide, H and Wu, CS and Zhu, CD}, title = {Tree diversity and functional leaf traits drive herbivore-associated microbiomes in subtropical China.}, journal = {Ecology and evolution}, volume = {11}, number = {11}, pages = {6153-6166}, pmid = {34141209}, issn = {2045-7758}, abstract = {Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar-associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.}, }
@article {pmid34137824, year = {2021}, author = {Abiriga, D and Jenkins, A and Alfsnes, K and Vestgarden, LS and Klempe, H}, title = {Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {7}, pages = {}, pmid = {34137824}, issn = {1574-6941}, abstract = {The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3-V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour different microbial communities compared to the groundwater samples. While Proteobacteria dominated both the recharge and groundwater samples, Acidobacteria dominated the aquifer sediment. The most abundant genera detected from the contaminated aquifer were Polynucleobacter, Rhodoferax, Pedobacter, Brevundimonas, Pseudomonas, Undibacterium, Sulfurifustis, Janthinobacterium, Rhodanobacter, Methylobacter and Aquabacterium. The result also shows that the microbial communities of the groundwater varied spatially, seasonally and interannually, although the interannual variation was significant for only one of the wells. Variation partitioning analysis indicates that water chemistry and well distance are intercorrelated and they jointly accounted for most of the variation in microbial composition. This implies that the species composition and water chemistry characteristics have a similar spatial structuring, presumably caused by the landfill leachate plume. The study improves our understanding of the dynamics in subsurface microbial communities in space and time.}, }
@article {pmid34136953, year = {2021}, author = {Nair, A and Ghugare, GS and Khairnar, K}, title = {An Appraisal of Bacteriophage Isolation Techniques from Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34136953}, issn = {1432-184X}, abstract = {Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.}, }
@article {pmid34136952, year = {2021}, author = {Jorge, F and Dheilly, NM and Froissard, C and Wainwright, E and Poulin, R}, title = {Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34136952}, issn = {1432-184X}, abstract = {Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.}, }
@article {pmid34135464, year = {2021}, author = {Ware, IM and Van Nuland, ME and Yang, ZK and Schadt, CW and Schweitzer, JA and Bailey, JK}, title = {Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {748}, pmid = {34135464}, issn = {2399-3642}, abstract = {Soil microbiomes are rapidly becoming known as an important driver of plant phenotypic variation and may mediate plant responses to environmental factors. However, integrating spatial scales relevant to climate change with plant intraspecific genetic variation and soil microbial ecology is difficult, making studies of broad inference rare. Here we hypothesize and show: 1) the degree to which tree genotypes condition their soil microbiomes varies by population across the geographic distribution of a widespread riparian tree, Populus angustifolia; 2) geographic dissimilarity in soil microbiomes among populations is influenced by both abiotic and biotic environmental variation; and 3) soil microbiomes that vary in response to abiotic and biotic factors can change plant foliar phenology. We show soil microbiomes respond to intraspecific variation at the tree genotype and population level, and geographic variation in soil characteristics and climate. Using a fully reciprocal plant population by soil location feedback experiment, we identified a climate-based soil microbiome effect that advanced and delayed bud break phenology by approximately 10 days. These results demonstrate a landscape-level feedback between tree populations and associated soil microbial communities and suggest soil microbes may play important roles in mediating and buffering bud break phenology with climate warming, with whole ecosystem implications.}, }
@article {pmid34134353, year = {2021}, author = {Guo, X and Akram, S and Stedtfeld, R and Johnson, M and Chabrelie, A and Yin, D and Mitchell, J}, title = {Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147489}, doi = {10.1016/j.scitotenv.2021.147489}, pmid = {34134353}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Farms ; Genes, Bacterial ; Manure ; Michigan ; Soil ; Soil Microbiology ; }, abstract = {The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.}, }
@article {pmid34133848, year = {2021}, author = {Stella, R and Bovo, D and Mastrorilli, E and Pezzolato, M and Bozzetta, E and Biancotto, G}, title = {Anabolic treatments in bovines: quantification of plasma protein markers of dexamethasone administration.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e2000238}, doi = {10.1002/pmic.202000238}, pmid = {34133848}, issn = {1615-9861}, support = {IZS PLV 13/18 RC//Ministero della Salute/ ; IZS VE 08/2014 RC - CUP B22I15000380001//Ministero della Salute/ ; RF IZ PLV-2006-364645//Ministero della Salute/ ; }, abstract = {The aim of this study was to profile plasma proteome responses in bulls experimentally treated with dexamethasone at anabolic dosage. Illicit use of active substances in animal husbandry remains a matter of concern in Europe. Corticosteroids are probably one of the most widespread growth promoter family illegally used in beef cattle and veal calves. Testing for corticosteroids relies on detection of drug residues or their metabolites in biological fluids or tissues. Their indirect detection by mapping altered physiological parameters may overcome limits linked to route of administration, dosage, biotransformation and elimination kinetics that can lower residual drug concentration, hampering official controls. A set of 11 proteins proposed in literature as potential markers of anabolic treatments with dexamethasone, was quantified in bovine plasma by targeted proteomics based on liquid chromatography-high resolution tandem mass spectrometry. Among investigated proteins, sex hormone-binding globulin (SHBG), histidine-rich glycoprotein (HRG) and paraoxonase-1 (PON1) were found to be biomarkers of treatment. To investigate further such biomarkers, an additional group of veal calves was experimentally treated with dexamethasone at anabolic. These animals also demonstrated a significant alteration in SHBG, HRG and PON1 concentration, suggesting that quantification of plasma markers have the potential to detect animals illegally exposed to dexamethasone.}, }
@article {pmid34133817, year = {2021}, author = {Mitiku, AA and Vandeweyer, D and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Yisehak, K and Van Campenhout, L}, title = {Microbial profile during fermentation and aerobic stability of ensiled mixtures of maize stover and banana pseudostem in South Ethiopia.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15183}, pmid = {34133817}, issn = {1365-2672}, abstract = {AIMS: This study evaluated pH reduction and microbial growth during fermentation of maize stover (MS) mixed with banana pseudostem (BPS) under South Ethiopian conditions.<br><br>MATERIALS AND RESULTS: The MS and BPS were chopped and mixed into six treatments (T): 80% BPS plus 20% DMS (T1), 70% BPS plus 30% DMS (T2), 40% BPS plus 60% FMS (fresh maize stover) (T3), 20% BPS plus 80% FMS (T4), 100% FMS (T5), and 95% BPS plus 5% molasses (T6). At 0, 7, 14, 30, 60 and 90 days, pH and dry matter were determined. Microbiological quality was assessed using plate counts and Illumina MiSeq sequencing. On day 60 and 90, aerobic stability was investigated. The results showed a significant reduction in pH in all mixtures, except in T1 and T2. Lactic acid bacteria counts reached a maximum in all treatments within 14 days. Sequencing showed marked changes in dominant bacteria, such as Buttiauxella and Acinetobacter to Lactobacillus and Bifidobacterium.<br><br>CONCLUSIONS: The fresh maize stover and banana pseudostem mixtures and fresh maize showed significant pH reduction and dominance of desirable microbial groups.<br><br>The study enables year-round livestock feed supplementation to boost milk and meat production in South Ethiopia.}, }
@article {pmid34132846, year = {2021}, author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Cole, N and Naidu, R and Megharaj, M}, title = {Extracellular Polymeric Substances Drive Symbiotic Interactions in Bacterial‒Microalgal Consortia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34132846}, issn = {1432-184X}, support = {RTP//Australian Government/ ; }, abstract = {The importance of several factors that drive the symbiotic interactions between bacteria and microalgae in consortia has been well realised. However, the implication of extracellular polymeric substances (EPS) released by the partners remains unclear. Therefore, the present study focused on the influence of EPS in developing consortia of a bacterium, Variovorax paradoxus IS1, with a microalga, Tetradesmus obliquus IS2 or Coelastrella sp. IS3, all isolated from poultry slaughterhouse wastewater. The bacterium increased the specific growth rates of microalgal species significantly in the consortia by enhancing the uptake of nitrate (88‒99%) and phosphate (92‒95%) besides accumulating higher amounts of carbohydrates and proteins. The EPS obtained from exudates, collected from the bacterial or microalgal cultures, contained numerous phytohormones, vitamins, polysaccharides and amino acids that are likely involved in interspecies interactions. The addition of EPS obtained from V. paradoxus IS1 to the culture medium doubled the growth of both the microalgal strains. The EPS collected from T. obliquus IS2 significantly increased the growth of V. paradoxus IS1, but there was no apparent change in bacterial growth when it was cultured in the presence of EPS from Coelastrella sp. IS3. These observations indicate that the interaction between V. paradoxus IS1 and T. obliquus IS2 was mutualism, while commensalism was the interaction between the bacterial strain and Coelastrella sp. IS3. Our present findings thus, for the first time, unveil the EPS-induced symbiotic interactions among the partners involved in bacterial‒microalgal consortia.}, }
@article {pmid34132589, year = {2021}, author = {Tedersoo, L and Albertsen, M and Anslan, S and Callahan, B}, title = {Perspectives and benefits of high-throughput long-read sequencing in microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0062621}, doi = {10.1128/AEM.00626-21}, pmid = {34132589}, issn = {1098-5336}, abstract = {Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities such as rapid molecular diagnostics and direct RNA sequencing, and both PacBio and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.}, }
@article {pmid34130083, year = {2021}, author = {Yan, L and Hermans, SM and Totsche, KU and Lehmann, R and Herrmann, M and Küsel, K}, title = {Groundwater bacterial communities evolve over time in response to recharge.}, journal = {Water research}, volume = {201}, number = {}, pages = {117290}, doi = {10.1016/j.watres.2021.117290}, pmid = {34130083}, issn = {1879-2448}, abstract = {Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.}, }
@article {pmid34128692, year = {2021}, author = {Zhang, ZF and Pan, J and Pan, YP and Li, M}, title = {Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0138120}, doi = {10.1128/mSystems.01381-20}, pmid = {34128692}, issn = {2379-5077}, support = {31970105//National Natural Science Foundation of China (NSFC)/ ; 91851105//National Natural Science Foundation of China (NSFC)/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; 2019FY100700//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2020KCXTD023//Innovation Team Project of Universities in Guangdong Province/ ; 2020M672779//China Postdoctoral Science Foundation/ ; }, abstract = {Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.}, }
@article {pmid34127845, year = {2021}, author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A}, title = {Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.}, journal = {Nature microbiology}, volume = {6}, number = {7}, pages = {885-898}, pmid = {34127845}, issn = {2058-5276}, support = {P29426//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25111//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.}, }
@article {pmid34126927, year = {2021}, author = {Shao, K and Yao, X and Wu, Z and Jiang, X and Hu, Y and Tang, X and Xu, Q and Gao, G}, title = {The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {179}, pmid = {34126927}, issn = {1471-2180}, support = {41930760//the National Natural Science Foundation of China/ ; 41977322//the National Natural Science Foundation of China/ ; 2017ZX07603-001//the Major Science and Technology Program for Water Pollution Control and Treatment, China/ ; QYZDJSSWDQC008//the Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; ZDRW-ZS-2017-3-4//the Key Program of the Chinese Academy of Sciences/ ; }, abstract = {BACKGROUND: Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.<br><br>RESULTS: We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6-97.30 %), Actinobacteria (0.1-17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12-80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33-49.28 %). Other dominant bacterial genera including Massilia (0.06-25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01-22.86 %), Brevundimonas (0.01-12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08-23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+)were the dominant environmental drivers affecting the bacterial community variance.<br><br>CONCLUSIONS: The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.}, }
@article {pmid34126067, year = {2021}, author = {Li, J and Morrow, C and Barnes, S and Wilson, L and Womack, ED and McLain, A and Yarar-Fisher, C}, title = {Gut microbiome composition and serum metabolome profile among individuals with spinal cord injury and normal glucose tolerance or prediabetes/type 2 diabetes.}, journal = {Archives of physical medicine and rehabilitation}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.apmr.2021.03.043}, pmid = {34126067}, issn = {1532-821X}, abstract = {OBJECTIVE: To compare the gut microbiome composition and serum metabolome profile among individuals with spinal cord injury (SCI) and normal glucose tolerance (NGT) or prediabetes/type 2 diabetes (P/DM).<br><br>DESIGN: Cross-sectional design.<br><br>SETTING: Research university.<br><br>PARTICIPANTS: A total of 25 adults with SCI were included in the analysis and categorized as NGT (n=16) or P/DM (n=9) based on their glucose concentration at minute 120 during a 75-g oral glucose tolerance test. The American Diabetes Association diagnosis guideline was used for grouping participants.<br><br>INTERVENTIONS: Not applicable.<br><br>MAIN OUTCOME MEASURE(S): A stool sample was collected and used to assess the gut microbiome composition (alpha and beta diversity, microbial abundance) via the 16s rRNA sequencing technique. A fasting serum sample was used for liquid chromatography-mass spectrometry-based untargeted metabolomics analysis, the results from which reflect the relative quantity of metabolites detected and identified. Gut microbiome and metabolomics data were analyzed by the Quantitative Insights into Microbial Ecology 2 and Metaboanalyst platforms, respectively.<br><br>RESULTS: Gut microbiome alpha diversity (Pielou's evenness index, Shannon's index) and beta diversity (weighted UniFrac distances) differed between groups. Compared with participants with NGT, participants with P/DM had less evenness in microbial communities. In particular, those with P/DM had a lower abundance of the Clostridiales order and higher abundance of the Akkermansia genus, as well as higher serum levels of gut-derived metabolites, including indoxyl sulfate and phenylacetylglutamine (P < 0.05 for all).<br><br>CONCLUSION(S): Our results provide evidence for altered gut microbiome composition and dysregulation of gut-derived metabolites in participants with SCI and P/DM. Both indoxyl sulfate and phenylacetylglutamine have been implicated in the development of cardiovascular diseases in the able-bodied population. These findings may inform future investigations in the field of SCI and cardio-metabolic health.}, }
@article {pmid34124627, year = {2021}, author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, EÁ and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ}, title = {New and Interesting Fungi. 4.}, journal = {Fungal systematics and evolution}, volume = {7}, number = {}, pages = {255-343}, pmid = {34124627}, issn = {2589-3831}, abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.}, }
@article {pmid34123319, year = {2021}, author = {Prothiwa, M and Filz, V and Oehler, S and Böttcher, T}, title = {Inhibiting quinolone biosynthesis of Burkholderia.}, journal = {Chemical science}, volume = {12}, number = {20}, pages = {6908-6912}, pmid = {34123319}, issn = {2041-6520}, abstract = {2-Alkylquinolones are important signalling molecules of Burkholderia species. We developed a substrate-based chemical probe against the central quinolone biosynthesis enzyme HmqD and applied it in competitive profiling experiments to discover the first known HmqD inhibitors. The most potent inhibitors quantitatively blocked quinolone production in Burkholderia cultures with single-digit micromolar efficacy.}, }
@article {pmid34122370, year = {2021}, author = {Cyriaque, V and Madsen, JS and Fievez, L and Leroy, B and Hansen, LH and Bureau, F and Sørensen, SJ and Wattiez, R}, title = {Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {655903}, pmid = {34122370}, issn = {1664-302X}, abstract = {Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.}, }
@article {pmid34119873, year = {2021}, author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS}, title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {5}, pages = {101768}, doi = {10.1016/j.ttbdis.2021.101768}, pmid = {34119873}, issn = {1877-9603}, abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.}, }
@article {pmid34118665, year = {2021}, author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y}, title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.}, journal = {The Science of the total environment}, volume = {791}, number = {}, pages = {148096}, doi = {10.1016/j.scitotenv.2021.148096}, pmid = {34118665}, issn = {1879-1026}, abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.}, }
@article {pmid34117524, year = {2021}, author = {Morales Medina, WR and Eramo, A and Fahrenfeld, NL}, title = {Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34117524}, issn = {1432-184X}, support = {1510461//National Science Foundation (US)/ ; }, abstract = {Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.}, }
@article {pmid34112519, year = {2021}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].}, journal = {Chemosphere}, volume = {}, number = {}, pages = {131081}, doi = {10.1016/j.chemosphere.2021.131081}, pmid = {34112519}, issn = {1879-1298}, }
@article {pmid34112387, year = {2021}, author = {Vissenaekens, H and Smagghe, G and Criel, H and Grootaert, C and Raes, K and Rajkovic, A and Goeminne, G and Boon, N and De Schutter, K and Van Camp, J}, title = {Intracellular quercetin accumulation and its impact on mitochondrial dysfunction in intestinal Caco-2 cells.}, journal = {Food research international (Ottawa, Ont.)}, volume = {145}, number = {}, pages = {110430}, doi = {10.1016/j.foodres.2021.110430}, pmid = {34112387}, issn = {1873-7145}, mesh = {Caco-2 Cells ; Humans ; Membrane Potential, Mitochondrial ; *Mitochondria/metabolism ; *Quercetin/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {PURPOSE: Flavonoid bioavailability and bioactivity is associated with interindividual variability, which is partially due to differences in health status. Previously, it was demonstrated that cellular stress, especially mitochondrial stress, increases intracellular quercetin uptake and this is associated with beneficial health effects. Here, the impact of quercetin on mitochondrial dysfunction, induced by stressors targeting different sites of the electron transport chain, is investigated. The influence of the mitochondrial stress on quercetin uptake and subcellular location is studied and the accumulated quercetin metabolites in intestinal Caco-2 cells and mitochondria are characterized.<br><br>PRINCIPAL RESULTS: It was observed that quercetin counteracted (i) the carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP)-induced decrease in maximum oxygen consumption, (ii) the valinomycin-, oligomycin- and FCCP-induced reactive oxygen species production and (iii) the valinomycin-induced disruption of mitochondrial membrane potential. Using confocal microscopy, it was found that upon mitochondrial stress, the intracellular quercetin accumulation increased and was partially located in the mitochondria. Finally, it was demonstrated that quercetin was present as O-methyl, O-methylglucuronide and O-methylsulfate conjugates in the cell lysate and mitochondria-enriched fraction.<br><br>MAJOR CONCLUSIONS: This study shows that quercetin can partially restore, especially FCCP-induced, mitochondrial dysfunction and this protective effect was linked with an intracellular quercetin accumulation in the mitochondria of intestinal cells.}, }
@article {pmid34110473, year = {2021}, author = {Rivera, AJ and Tyx, RE}, title = {Microbiology of the American Smokeless Tobacco.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {4843-4853}, pmid = {34110473}, issn = {1432-0614}, mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; Tobacco ; *Tobacco, Smokeless ; United States ; }, abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.}, }
@article {pmid34110072, year = {2021}, author = {Nir, I and Barak, H and Kramarsky-Winter, E and Kushmaro, A and de Los Ríos, A}, title = {Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15635}, pmid = {34110072}, issn = {1462-2920}, abstract = {Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.}, }
@article {pmid34108452, year = {2021}, author = {Zhao, T and Zwaenepoel, A and Xue, JY and Kao, SM and Li, Z and Schranz, ME and Van de Peer, Y}, title = {Whole-genome microsynteny-based phylogeny of angiosperms.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3498}, pmid = {34108452}, issn = {2041-1723}, mesh = {Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Magnoliopsida/classification/*genetics ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; *Synteny ; }, abstract = {Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.}, }
@article {pmid34107988, year = {2021}, author = {Flachs, A and Orkin, JD}, title = {On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {17}, number = {1}, pages = {39}, pmid = {34107988}, issn = {1746-4269}, support = {Global Synergy Grant//College of Liberal Arts, Purdue University/ ; }, abstract = {BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.<br><br>METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.<br><br>RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.<br><br>CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.}, }
@article {pmid34106771, year = {2021}, author = {Scales, BS and Cable, RN and Duhaime, MB and Gerdts, G and Fischer, F and Fischer, D and Mothes, S and Hintzki, L and Moldaenke, L and Ruwe, M and Kalinowski, J and Kreikemeyer, B and Pedrotti, ML and Gorsky, G and Elineau, A and Labrenz, M and Oberbeckmann, S}, title = {Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0085120}, doi = {10.1128/mSphere.00851-20}, pmid = {34106771}, issn = {2379-5042}, support = {//Tara Expeditions Foundation/ ; 03F0775A//BONUS/BMBF/ ; //EU-EFRE/ ; SAW-2014-IOW-2//IPF | Leibniz-Gemeinschaft (Leibniz)/ ; }, abstract = {While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems. IMPORTANCE This study represents one of the largest comparisons of biofilms from environmentally sampled plastic and nonplastic particles from aquatic environments. By including particles sampled through three separate campaigns in the Baltic, Sargasso, and Mediterranean seas, we were able to make cross-geographical comparisons and discovered common taxonomical signatures that define the plastic biofilm. For the first time, we identified plastic-specific bacteria that reoccur across marine regions. Our data reveal that plastics have selective properties that repeatedly enrich for similar bacteria regardless of location, potentially shifting aquatic microbial communities in areas with high levels of plastic pollution. Furthermore, we show that bacterial communities on plastic do not appear to be strongly influenced by polymer type, suggesting that other properties, such as the absorption and/or leaching of chemicals from the surface, are likely to be more important in the selection and enrichment of specific microorganisms.}, }
@article {pmid34106767, year = {2021}, author = {Dove, NC and Veach, AM and Muchero, W and Wahl, T and Stegen, JC and Schadt, CW and Cregger, MA}, title = {Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0131620}, doi = {10.1128/mSphere.01316-20}, pmid = {34106767}, issn = {2379-5042}, support = {DEAC05- 00OR22725//U.S. Department of Energy (DOE)/ ; }, abstract = {Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.}, }
@article {pmid34105010, year = {2021}, author = {Naidoo, Y and Valverde, A and Pierneef, RE and Cowan, DA}, title = {Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34105010}, issn = {1432-184X}, support = {Free standing//National Research Foundation/ ; }, abstract = {Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.}, }
@article {pmid34105009, year = {2021}, author = {Febinia, CA and Malik, SG and Djuwita, R and Weta, IW and Wihandani, DM and Maulida, R and Sudoyo, H and Holmes, AJ}, title = {Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34105009}, issn = {1432-184X}, abstract = {An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.}, }
@article {pmid34105008, year = {2021}, author = {Sun, Y and Huang, Y and Xu, S and Li, J and Yin, M and Tian, H}, title = {Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34105008}, issn = {1432-184X}, abstract = {Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM10 and PM2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO3- contributed the most to the formation of particulate matter in spring and winter, while SO42- contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO3- levels, NH4+ levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.}, }
@article {pmid34100639, year = {2021}, author = {Rochefort, A and Simonin, M and Marais, C and Guillerm-Erckelboudt, AY and Barret, M and Sarniguet, A}, title = {Transmission of Seed and Soil Microbiota to Seedling.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0044621}, doi = {10.1128/mSystems.00446-21}, pmid = {34100639}, issn = {2379-5077}, support = {//INRAE Metaomics and Ecosystems Metaprogram/ ; //INRAE Plant Health and Environment division/ ; //Conseil Régional de Bretagne (Brittany Council)/ ; }, abstract = {The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.}, }
@article {pmid34100635, year = {2021}, author = {Tracanna, V and Ossowicki, A and Petrus, MLC and Overduin, S and Terlouw, BR and Lund, G and Robinson, SL and Warris, S and Schijlen, EGWM and van Wezel, GP and Raaijmakers, JM and Garbeva, P and Medema, MH}, title = {Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0111620}, doi = {10.1128/mSystems.01116-20}, pmid = {34100635}, issn = {2379-5077}, support = {ALWGR. 2015.1//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, abstract = {Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.}, }
@article {pmid34099808, year = {2021}, author = {Timmers, LFSM and Peixoto, JV and Ducati, RG and Bachega, JFR and de Mattos Pereira, L and Caceres, RA and Majolo, F and da Silva, GL and Anton, DB and Dellagostin, OA and Henriques, JAP and Xavier, LL and Goettert, MI and Laufer, S}, title = {SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11998}, pmid = {34099808}, issn = {2045-2322}, mesh = {Brazil ; COVID-19/*genetics ; Genome, Viral ; Genomics ; Humans ; Mutation/*genetics ; SARS-CoV-2/*genetics/pathogenicity ; Severity of Illness Index ; Viral Proteins/*genetics ; }, abstract = {Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.}, }
@article {pmid34097120, year = {2021}, author = {Hou, D and Zhou, R and Zeng, S and Wei, D and Deng, X and Xing, C and Weng, S and He, J and Huang, Z}, title = {Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {5013-5022}, pmid = {34097120}, issn = {1432-0614}, support = {31902392//National Natural Science Foundation of China/ ; CARS-48//China Agriculture Research System/ ; 2019A1515011557//Natural Science Foundation of Guangdong Province/ ; 19lgpy103//Fundamental Research Funds for the Central Universities/ ; 2020B0202010009//Key Research and Development Projects in Guangdong Province/ ; }, mesh = {Animals ; Bacteria/genetics ; *Geologic Sediments ; *Ponds ; RNA, Ribosomal, 16S ; Stochastic Processes ; }, abstract = {Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.}, }
@article {pmid34094994, year = {2021}, author = {Kumar, S and Kumari, N and Talukdar, D and Kothidar, A and Sarkar, M and Mehta, O and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and Desiraju, BK and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B and , }, title = {The Vaginal Microbial Signatures of Preterm Birth Delivery in Indian Women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {622474}, pmid = {34094994}, issn = {2235-2988}, mesh = {Female ; Fusobacteria ; Humans ; India ; Infant, Newborn ; Lactobacillus ; Pregnancy ; *Premature Birth/epidemiology ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {Background: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.<br><br>Objective: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.<br><br>Methods: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. Lactobacillus species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.<br><br>Results: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of Lactobacillus iners (p-value All_Trimesters<0.02), Megasphaera sp (p-value1st_Trimester <0.05), Gardnerella vaginalis (p-value2nd_Trimester= 0.01) and Sneathia sanguinegens (p-value2nd_Trimester <0.0001) were identified in preterm samples whereas higher abundance of L. gasseri (p-value3rd_Trimester =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of L. iners, and Megasphaera sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of L. crispatus and L. gasseri indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of L. crispatus and L. gasseri in reducing the risk of PTB.<br><br>Conclusion: Our findings indicate that the dominance of specific Lactobacillus species and few other facultative anaerobes are associated with birth outcomes.}, }
@article {pmid34093488, year = {2021}, author = {Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Herbold, CW and Loy, A and Berry, D}, title = {An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {669776}, pmid = {34093488}, issn = {1664-302X}, abstract = {In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.}, }
@article {pmid34091718, year = {2021}, author = {Girolamini, L and Salaris, S and Pascale, MR and Mazzotta, M and Cristino, S}, title = {Dynamics of Legionella Community Interactions in Response to Temperature and Disinfection Treatment: 7 Years of Investigation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34091718}, issn = {1432-184X}, abstract = {In man-made water distribution systems, Legionella community interactions remain unknown, due to their ability to change from sessile to planktonic states or live in viable but non-culturable forms, in response to anthropic and environmental stress. During 7 years of hospital Legionella surveillance, in 191 hot water positive samples, the interactions among the Legionella species, temperature, and disinfection treatment were evaluated. Legionella was isolated following ISO 11731:2017, and identification was performed by mip gene sequencing and sequence-based typing (SBT) for L. anisa or L. rubrilucens and L. pneumophila, respectively. The species with the higher frequency of isolation was L. pneumophila serogroup 1 (78.53%; 4865.36 ± 25,479.11 cfu/L), followed by L. anisa (54.45%; 558.79 ± 2637.41 cfu/L) and L. rubrilucens (21.99%; 307.73 ± 1574.95 cfu/L), which were sometimes present together. Spearman's rho correlation test was conducted among the species with respect to temperature and disinfectant (H2O2/Ag+). The results showed a generally positive interaction among these species sharing the same environment, except for competition between L. anisa and L. rubrilucens. High temperature (48.83 ± 2.59 °C) and disinfection treatment (11.58 ± 4.99 mg/L) affected the presence of these species. An exception was observed with L. anisa, which showed disinfection treatment resistance. For the purposes of environmental surveillance, it is fundamental to better understand the interactions and dynamic of the Legionella community in man-made water systems in order to choose the proper physical or chemical treatments. The simultaneous presence of different Legionella species could result in an increased resistance to high temperature and disinfectant treatment, leading to changes in contamination level and species diversity.}, }
@article {pmid34091717, year = {2021}, author = {Jaskulska, A and Šulčius, S and Kokociński, M and Koreivienė, J and Nájera, AF and Mankiewicz-Boczek, J}, title = {Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-Based Genetic Markers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34091717}, issn = {1432-184X}, abstract = {Studies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequence analyses for each gene demonstrated low variability between them, although the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii, was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.}, }
@article {pmid34091223, year = {2021}, author = {Sun, C and Zhang, B and Ning, D and Zhang, Y and Dai, T and Wu, L and Li, T and Liu, W and Zhou, J and Wen, X}, title = {Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern.}, journal = {Water research}, volume = {200}, number = {}, pages = {117295}, doi = {10.1016/j.watres.2021.117295}, pmid = {34091223}, issn = {1879-2448}, mesh = {*Microbiota ; Phylogeny ; Seasons ; Sewage ; *Water Purification ; }, abstract = {The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.}, }
@article {pmid34089088, year = {2021}, author = {Zhao, Z and Cheng, M and Li, Y and Song, X and Wang, Y and Zhang, Y}, title = {A Novel Constructed Wetland Combined with Microbial Desalination Cells and its Application.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34089088}, issn = {1432-184X}, support = {51909157//National Natural Science Foundation of China/ ; 2019YFC0408604//National Key Research and Development Project/ ; 19QC1401100//Shanghai Rising-Star Program/ ; hklk201912//Open Foundation of Hebei Key Laboratory of Wetland Ecology and Conservation/ ; SZGXZS2020068//Research project of ecological environment protection and restoration of Yangtze River in Zhoushan/ ; }, abstract = {Wastewater recycling can alleviate the shortage of water resources. Saline water is seldom treated with biological processes, and its recycling rate is low. Constructed wetland (CW) is a safe, economical, and ecological water treatment method. However, the saline water treatment performance of CW is not good. Microbial desalination cells (MDC) utilizing a bioelectrochemical approach achieve functions of desalination and power generation. In this study, MDC was used to strengthen CW to form a composite system, MDC-CW. Through optimization of design parameters, MDC-CW was applied in the treatment of salt-containing water. The average total nitrogen removal rate in MDC-CW-P1 reached 87.33% and the average COD removal rate was 92.79%. The average desalination rate of MDC-CW-P1 was 55.78% and the average voltage of MDC-CW-P1 reached 0.40 mV. Planting Canna indica in the MDC-CW was conducive to the functions of desalination and power generation. The above results were also verified by the microbial analysis results of gravels in the substrate, plant rhizosphere, and electrodes. In addition, the decontamination of the device mainly depended on the function of the bacteria commonly used in water treatment, such as Proteobacteria and Bacteroidetes, whereas the generation of power depended on the function of Geobacter. Salt ions moved spontaneously to the cathode and anode under the influence of current generation so that the desalination function was realized under the selective isolation function of exchange membranes. The device design and laboratory applications of MDC-CW experimentally achieved the electrochemical function and broadened the treatment scale of CW.}, }
@article {pmid34086451, year = {2021}, author = {De Paepe, J and Clauwaert, P and Gritti, MC and Ganigué, R and Sas, B and Vlaeminck, SE and Rabaey, K}, title = {Electrochemical In Situ pH Control Enables Chemical-Free Full Urine Nitrification with Concomitant Nitrate Extraction.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {12}, pages = {8287-8298}, doi = {10.1021/acs.est.1c00041}, pmid = {34086451}, issn = {1520-5851}, mesh = {Ammonia ; Bioreactors ; Hydrogen-Ion Concentration ; *Nitrates ; *Nitrification ; Nitrogen ; }, abstract = {Urine is a valuable resource for nutrient recovery. Stabilization is, however, recommended to prevent urea hydrolysis and the associated risk for ammonia volatilization, uncontrolled precipitation, and malodor. This can be achieved by alkalinization and subsequent biological conversion of urea and ammonia into nitrate (nitrification) and organics into CO2. Yet, without pH control, the extent of nitrification is limited as a result of insufficient alkalinity. This study explored the feasibility of an integrated electrochemical cell to obtain on-demand hydroxide production through water reduction at the cathode, compensating for the acidification caused by nitritation, thereby enabling full nitrification. To deal with the inherent variability of the urine influent composition and bioprocess, the electrochemical cell was steered via a controller, modulating the current based on the pH in the bioreactor. This provided a reliable and innovative alternative to base addition, enabling full nitrification while avoiding the use of chemicals, the logistics associated with base storage and dosing, and the associated increase in salinity. Moreover, the electrochemical cell could be used as an in situ extraction and concentration technology, yielding an acidic concentrated nitrate-rich stream. The make-up of the end product could be tailored by tweaking the process configuration, offering versatility for applications on Earth and in space.}, }
@article {pmid34085863, year = {2021}, author = {Jakus, N and Blackwell, N and Osenbrück, K and Straub, D and Byrne, JM and Wang, Z and Glöckler, D and Elsner, M and Lueders, T and Grathwohl, P and Kleindienst, S and Kappler, A}, title = {Nitrate removal by a novel lithoautotrophic nitrate-reducing iron(II)-oxidizing culture enriched from a pyrite-rich limestone aquifer.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {AEM0046021}, doi = {10.1128/AEM.00460-21}, pmid = {34085863}, issn = {1098-5336}, abstract = {Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer and as such there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic co-substrates for growth, within 7-11 days 0.3-0.5 mM of nitrate was reduced and 1.3-2 mM of iron(II) was oxidized leading to a stoichiometric NO3-/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, microaerophilic iron(II)-oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically impacted aquifers. Importance Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment and as such there are no model cultures available to study the rate-limiting factors of this potentially important process. Here we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II)-oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.}, }
@article {pmid34083720, year = {2021}, author = {Cao, YL and Li, YL and Fan, YF and Li, Z and Yoshida, K and Wang, JY and Ma, XK and Wang, N and Mitsuda, N and Kotake, T and Ishimizu, T and Tsai, KC and Niu, SC and Zhang, D and Sun, WH and Luo, Q and Zhao, JH and Yin, Y and Zhang, B and Wang, JY and Qin, K and An, W and He, J and Dai, GL and Wang, YJ and Shi, ZG and Jiao, EN and Wu, PJ and Liu, X and Liu, B and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Xu, XY and Zou, SQ and Li, MH and Hsiao, YY and Lin, YF and Liang, CK and Chen, YY and Wu, WL and Lu, HC and Lan, SR and Wang, ZW and Zhao, X and Zhong, WY and Yeh, CM and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Wolfberry genomes and the evolution of Lycium (Solanaceae).}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {671}, pmid = {34083720}, issn = {2399-3642}, abstract = {Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.}, }
@article {pmid34083551, year = {2021}, author = {Fabersani, E and Portune, K and Campillo, I and López-Almela, I and la Paz, SM and Romaní-Pérez, M and Benítez-Páez, A and Sanz, Y}, title = {Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11788}, pmid = {34083551}, issn = {2045-2322}, support = {GRISOLIAP/2014/110//Generalitat Valenciana/ ; Grant agreement no 613979 (MyNewGut project)//The European Union's Seventh Framework Program/ ; Grant agreement no 613979 (MyNewGut project)//The European Union's Seventh Framework Program/ ; Grant agreement no 613979 (MyNewGut project)//The European Union's Seventh Framework Program/ ; Grant agreement no 613979 (MyNewGut project)//The European Union's Seventh Framework Program/ ; PTA2013-8836-I//The Spanish Ministry of Economy and Competitiveness/ ; AGL2017-88801-P//The Spanish Ministry of Economy and Competitiveness/ ; AGL2017-88801-P//The Spanish Ministry of Economy and Competitiveness/ ; BES-2015-073930//Spanish Ministry of Economy and Competitiveness/ ; }, abstract = {This study investigated the immune mechanisms whereby administration of Bacteroides uniformis CECT 7771 reduces metabolic dysfunction in obesity. C57BL/6 adult male mice were fed a standard diet or a Western diet high in fat and fructose, supplemented or not with B. uniformis CECT 7771 for 14 weeks. B. uniformis CECT 7771 reduced body weight gain, plasma cholesterol, triglyceride, glucose, and leptin levels; and improved oral glucose tolerance in obese mice. Moreover, B. uniformis CECT 7771 modulated the gut microbiota and immune alterations associated with obesity, increasing Tregs and reducing B cells, total macrophages and the M1/M2 ratio in both the gut and epididymal adipose tissue (EAT) of obese mice. B. uniformis CECT 7771 also increased the concentration of the anti-inflammatory cytokine IL-10 in the gut, EAT and peripheral blood, and protective cytokines TSLP and IL-33, involved in Treg induction and type 2 innate lymphoid cells activation, in the EAT. It also restored the obesity-reduced TLR5 expression in the ileum and EAT. The findings indicate that the administration of a human intestinal bacterium with immunoregulatory properties on the intestinal mucosa helps reverse the immuno-metabolic dysfunction caused by a Western diet acting over the gut-adipose tissue axis.}, }
@article {pmid34081148, year = {2021}, author = {Mezzasoma, A and Coleine, C and Sannino, C and Selbmann, L}, title = {Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34081148}, issn = {1432-184X}, abstract = {The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.}, }
@article {pmid34081147, year = {2021}, author = {Zhang, T and Wang, NF and Yu, LY}, title = {Geographic Distance and Habitat Type Influence Fungal Communities in the Arctic and Antarctic Sites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34081147}, issn = {1432-184X}, support = {31670025//National Natural Science Foundation of China/ ; }, abstract = {The Antarctic and Arctic regions are collectively referred to as the "Two Poles" of the earth and have extremely harsh climate conditions and fragile ecosystems. Until now, the biogeography of the fungal communities in the bipolar regions is not well known. In this study, we focused on the fungal communities in 110 samples collected from four habitat types (i.e., soil, vascular plant, freshwater, moss) in the Antarctic and Arctic sites using high-throughput sequencing. The data showed that the diversity and composition of fungal communities were both geographically patterned and habitat-patterned. ANOSIM tests revealed statistically significant differences among fungal communities in the eight sample types (R = 0.5035, p < 0.001) and those in the bipolar regions (R = 0.32859, p < 0.001). Only 396 OTUs (14.8%) were shared between the bipolar sites. Fungal communities in the four habitat types clustered together in the Arctic site but were separate from those of the Antarctic site, indicating that geographic distance was a more important determinant of fungal communities in the bipolar sites. These findings offer insights into the present-day biogeography of fungal communities in the bipolar sites.}, }
@article {pmid34080061, year = {2021}, author = {Carbonero, F and Strobel, G}, title = {Fungal Ecology Special Issue: Editorial.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34080061}, issn = {1432-184X}, }
@article {pmid34078434, year = {2021}, author = {Gresse, R and Chaucheyras-Durand, F and Denis, S and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S}, title = {Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM).}, journal = {Journal of animal science and biotechnology}, volume = {12}, number = {1}, pages = {75}, pmid = {34078434}, issn = {1674-9782}, abstract = {BACKGROUND: Risk factors for the etiology of post-weaning diarrhea, a major problem in swine industry associated with enormous economic losses, remain to be fully elucidated. In concordance with the ethical concerns raised by animal experiments, we developed a new in vitro model of the weaning piglet colon (MPigut-IVM) including a mucin bead compartment to reproduce the mucus surface from the gut to which gut microbes can adhere.<br><br>RESULTS: Our results indicated that the MPigut-IVM is able to establish a representative piglet archaeal and bacterial colon microbiota in terms of taxonomic composition and function. The MPigut-IVM was consequently used to investigate the potential effects of feed deprivation, a common consequence of weaning in piglets, on the microbiota. The lack of nutrients in the MPigut-IVM led to an increased abundance of Prevotellaceae and Escherichia-Shigella and a decrease in Bacteroidiaceae and confirms previous in vivo findings. On top of a strong increase in redox potential, the feed deprivation stress induced modifications of microbial metabolite production such as a decrease in acetate and an increase in proportional valerate, isovalerate and isobutyrate production.<br><br>CONCLUSIONS: The MPigut-IVM is able to simulate luminal and mucosal piglet microbiota and represent an innovative tool for comparative studies to investigate the impact of weaning stressors on piglet microbiota. Besides, weaning-associated feed deprivation in piglets provokes disruptions of MPigut-IVM microbiota composition and functionality and could be implicated in the onset of post-weaning dysbiosis in piglets.}, }
@article {pmid34077260, year = {2021}, author = {Cornell, CR and Zhang, Y and Van Nostrand, JD and Wagle, P and Xiao, X and Zhou, J}, title = {Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0116020}, doi = {10.1128/mSphere.01160-20}, pmid = {34077260}, issn = {2379-5042}, support = {2016-68002-24967//USDA | National Institute of Food and Agriculture (NIFA)/ ; }, abstract = {During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.}, }
@article {pmid34073029, year = {2021}, author = {Broadhead, R and Craeye, L and Callewaert, C}, title = {The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34073029}, issn = {2076-2607}, support = {F2019/IOF-STARTT/261//Ghent University/ ; }, abstract = {The skin microbiome has become a hot field of research in the last few years. The emergence of next-generation sequencing has given unprecedented insights into the impact and involvement of microbiota in skin conditions. More and more cosmetics contain probiotics or bacteria as an active ingredient, with or without scientific data. This research is also acknowledged by the textile industry. There has been a more holistic approach on how the skin and textile microbiome interacts and how they influence the pH, moisture content and odour generation. To date, most of the ingredients have a broad-spectrum antibacterial action. This manuscript covers the current research and industry developments in the field of skin and textiles. It explores the nature of antimicrobial finishing in textiles which can disrupt the skin microbiome, and the benefits of more natural and microbiome friendly therapies to combat skin conditions, malodour and skin infection.}, }
@article {pmid34072450, year = {2021}, author = {Romaní-Pérez, M and Bullich-Vilarrubias, C and López-Almela, I and Liébana-García, R and Olivares, M and Sanz, Y}, title = {The Microbiota and the Gut-Brain Axis in Controlling Food Intake and Energy Homeostasis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34072450}, issn = {1422-0067}, support = {797297//H2020 Marie Skłodowska-Curie Actions/ ; AGL2017-88801-P//Spanish Ministry of Science and Innovation/ ; }, mesh = {Brain/*physiology ; Circadian Rhythm ; Diet ; Disease Susceptibility ; Eating ; *Energy Metabolism ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*physiology ; *Homeostasis ; Humans ; Microbiota/*physiology ; Micronutrients ; Nutrients ; Obesity/etiology/metabolism ; }, abstract = {Obesity currently represents a major societal and health challenge worldwide. Its prevalence has reached epidemic proportions and trends continue to rise, reflecting the need for more effective preventive measures. Hypothalamic circuits that control energy homeostasis in response to food intake are interesting targets for body-weight management, for example, through interventions that reinforce the gut-to-brain nutrient signalling, whose malfunction contributes to obesity. Gut microbiota-diet interactions might interfere in nutrient sensing and signalling from the gut to the brain, where the information is processed to control energy homeostasis. This gut microbiota-brain crosstalk is mediated by metabolites, mainly short chain fatty acids, secondary bile acids or amino acids-derived metabolites and subcellular bacterial components. These activate gut-endocrine and/or neural-mediated pathways or pass to systemic circulation and then reach the brain. Feeding time and dietary composition are the main drivers of the gut microbiota structure and function. Therefore, aberrant feeding patterns or unhealthy diets might alter gut microbiota-diet interactions and modify nutrient availability and/or microbial ligands transmitting information from the gut to the brain in response to food intake, thus impairing energy homeostasis. Herein, we update the scientific evidence supporting that gut microbiota is a source of novel dietary and non-dietary biological products that may beneficially regulate gut-to-brain communication and, thus, improve metabolic health. Additionally, we evaluate how the feeding time and dietary composition modulate the gut microbiota and, thereby, the intraluminal availability of these biological products with potential effects on energy homeostasis. The review also identifies knowledge gaps and the advances required to clinically apply microbiome-based strategies to improve the gut-brain axis function and, thus, combat obesity.}, }
@article {pmid34068093, year = {2021}, author = {Zhu, J and Sun, X and Zhang, ZD and Tang, QY and Gu, MY and Zhang, LJ and Hou, M and Sharon, A and Yuan, HL}, title = {Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34068093}, issn = {2076-2607}, support = {31760009//National Natural Science Foundation of China/ ; 2021SKLAB6-9//Project for Extramural Scientists of State Key Laboratory of Agrobiotechnology/ ; nkypt005//Improvement Project of Agricultural Science and Capacity of Technology Innovation Platform in Xinjiang Academy of Agricultural Sciences/ ; KY2019021//Special Project for Basic Scientific Activities of Non-profit Institutes Supported the Government of Xinjiang Uyghur Autonomous Region/ ; }, abstract = {Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.}, }
@article {pmid34064714, year = {2021}, author = {Park, T and Yoon, J and Kim, A and Unno, T and Yun, Y}, title = {Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea.}, journal = {Veterinary sciences}, volume = {8}, number = {5}, pages = {}, pmid = {34064714}, issn = {2306-7381}, support = {2016R1A6A1A03012862//National Research Foundation of Korea/ ; }, abstract = {(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.}, }
@article {pmid34064045, year = {2021}, author = {Uriot, O and Kebouchi, M and Lorson, E and Galia, W and Denis, S and Chalancon, S and Hafeez, Z and Roux, E and Genay, M and Blanquet-Diot, S and Dary-Mourot, A}, title = {Identification of Streptococcus thermophilus Genes Specifically Expressed under Simulated Human Digestive Conditions Using R-IVET Technology.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34064045}, issn = {2076-2607}, abstract = {Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.}, }
@article {pmid34063014, year = {2021}, author = {Weiss, B and Souza, ACO and Constancio, MTL and Alvarenga, DO and Pylro, VS and Alves, LMC and Varani, AM}, title = {Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34063014}, issn = {2076-2607}, support = {Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/ ; [16/16624-1] and [10/17520-9]//São Paulo Research Foundation (FAPESP)/ ; [303061/2019-7] and [302085/2017-3]//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Second-generation biofuel production is in high demand, but lignocellulosic biomass' complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber's appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.}, }
@article {pmid34059942, year = {2021}, author = {Siebert, A and Hofmann, K and Staib, L and Doll, EV and Scherer, S and Wenning, M}, title = {Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {11}, pages = {4761-4773}, pmid = {34059942}, issn = {1432-0614}, support = {Projekt DEAL (German DEAL agreement)//Technische Universität München/ ; }, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics ; Female ; *Microbiota ; *Milk ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. KEY POINTS: • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.}, }
@article {pmid34059936, year = {2021}, author = {Zhao, XF and Shu, WS and Hao, YQ}, title = {Seasonal Climate Variations Promote Bacterial α-Diversity in Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34059936}, issn = {1432-184X}, support = {31901113//National Natural Science Foundation of China/ ; 31901112//National Natural Science Foundation of China/ ; 2019M662951//China Postdoctoral Science Foundation/ ; 2019A1515011879//Natural Science Foundation of Guangdong Province/ ; }, abstract = {Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria's short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation had weak but significant positive effect on soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the potential confounding factors (such as vegetation type) and the lack of sampling across seasons. As a supplement, we analyzed a previously published wheat cropland dataset with samples collected in both winter and the following summer across North China Plain. As expected, bacterial α-diversity was positively correlated with seasonal climate variations in the cropland dataset, and climate seasonality explained a larger proportion of variations in bacterial α-diversity. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.}, }
@article {pmid34058098, year = {2021}, author = {Paredes, GF and Viehboeck, T and Lee, R and Palatinszky, M and Mausz, MA and Reipert, S and Schintlmeister, A and Maier, A and Volland, JM and Hirschfeld, C and Wagner, M and Berry, D and Markert, S and Bulgheresi, S and König, L}, title = {Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0118620}, doi = {10.1128/mSystems.01186-20}, pmid = {34058098}, issn = {2379-5077}, support = {P28743//Austrian Science Fund (FWF)/ ; DK plus grant W1257: Microbial Nitrogen Cycling//Austrian Science Fund (FWF)/ ; P28953//Austrian Science Fund (FWF)/ ; }, abstract = {Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.}, }
@article {pmid34054786, year = {2021}, author = {Guerrero-Cruz, S and Vaksmaa, A and Horn, MA and Niemann, H and Pijuan, M and Ho, A}, title = {Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {678057}, pmid = {34054786}, issn = {1664-302X}, abstract = {Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.}, }
@article {pmid34054772, year = {2021}, author = {Trego, AC and McAteer, PG and Nzeteu, C and Mahony, T and Abram, F and Ijaz, UZ and O'Flaherty, V}, title = {Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {666584}, pmid = {34054772}, issn = {1664-302X}, abstract = {Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery "winners" were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out-an important consideration for process control.}, }
@article {pmid34054757, year = {2021}, author = {Rocha, FYO and Negrisoli Júnior, AS and de Matos, GF and Gitahy, PM and Rossi, CN and Vidal, MS and Baldani, JI}, title = {Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {659965}, pmid = {34054757}, issn = {1664-302X}, abstract = {Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.}, }
@article {pmid34053521, year = {2021}, author = {Jang, MJ and Kim, SY and Ricke, SC and Rhee, MS and Kim, SA}, title = {Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {144}, number = {}, pages = {110316}, doi = {10.1016/j.foodres.2021.110316}, pmid = {34053521}, issn = {1873-7145}, mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Medicago sativa ; *Microbiota ; RNA, Ribosomal, 16S ; *Raphanus ; }, abstract = {Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety.}, }
@article {pmid34052880, year = {2021}, author = {Fernández, LD and Seppey, CVW and Singer, D and Fournier, B and Tatti, D and Mitchell, EAD and Lara, E}, title = {Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34052880}, issn = {1432-184X}, abstract = {Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.}, }
@article {pmid34052601, year = {2021}, author = {Chandler, L and Harford, AJ and Hose, GC and Humphrey, CL and Chariton, A and Greenfield, P and Davis, J}, title = {Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {284}, number = {}, pages = {117318}, doi = {10.1016/j.envpol.2021.117318}, pmid = {34052601}, issn = {1873-6424}, abstract = {Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg2+) and sulfate (SO42-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO42-, Mg2+ and Na+. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.}, }
@article {pmid34049069, year = {2021}, author = {Lim, JH and Lee, CW and Bong, CW and Kudo, I}, title = {The impact of eutrophication towards selected bacterial process rates in tropical coastal waters.}, journal = {Marine pollution bulletin}, volume = {169}, number = {}, pages = {112524}, doi = {10.1016/j.marpolbul.2021.112524}, pmid = {34049069}, issn = {1879-3363}, abstract = {The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R2 ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.}, }
@article {pmid34039416, year = {2021}, author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH}, title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {112}, pmid = {34039416}, issn = {2049-2618}, support = {R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; }, mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.<br><br>RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.<br><br>CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.}, }
@article {pmid34037999, year = {2021}, author = {Petje, LM and Jensen, SA and Szikora, S and Sulzbacher, M and Bartosik, T and Pjevac, P and Hausmann, B and Hufnagl, K and Untersmayr, E and Fischer, L and Vyskocil, E and Eckl-Dorna, J and Jensen-Jarolim, E and Hofstetter, G and Afify, SM and Krenn, CG and Roth, GA and Rivelles, E and Hann, S and Roth-Walter, F}, title = {Functional iron-deficiency in women with allergic rhinitis is associated with symptoms after nasal provocation and lack of iron-sequestering microbes.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.14960}, pmid = {34037999}, issn = {1398-9995}, support = {//Bencard Allergy GmbH, Munich/ ; //Biomedical International R&amp;D GmbH, Vienna/ ; }, }
@article {pmid34031701, year = {2021}, author = {Ao, L and Zhao, M and Li, X and Sun, G}, title = {Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34031701}, issn = {1432-184X}, support = {41701289//National Natural Science Foundation of China/ ; 31870373//National Natural Science Foundation of China/ ; 2018M640287//Postdoctoral Research Foundation of China/ ; }, abstract = {The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.}, }
@article {pmid34030967, year = {2021}, author = {Yang, Y}, title = {Emerging Patterns of Microbial Functional Traits.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2021.04.004}, pmid = {34030967}, issn = {1878-4380}, abstract = {Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.}, }
@article {pmid34030400, year = {2021}, author = {Hildebrandt, L and Zimmermann, T and Primpke, S and Fischer, D and Gerdts, G and Pröfrock, D}, title = {Comparison and uncertainty evaluation of two centrifugal separators for microplastic sampling.}, journal = {Journal of hazardous materials}, volume = {414}, number = {}, pages = {125482}, doi = {10.1016/j.jhazmat.2021.125482}, pmid = {34030400}, issn = {1873-3336}, abstract = {For commonly applied microplastic sampling approaches based on filtration, high throughput and no size-discrimination are conflicting goals. Therefore, we propose two efficient centrifugal separators for small microplastic sampling, namely the utilization of a hydrocyclone as well as a continuous flow centrifuge. Thorough method optimization was followed by application in an extensive sampling study to investigate the separators' retention behavior for particulate plastics from estuarine waters. Microplastic concentrations ranged from 193 to 2072 particles m-3. The most dominant identified polymer types were polypropylene, acrylates, polyvinyl chloride and polyethylene. More than 95% of particles were < 100 µm. For the first time in microplastic research, an expanded uncertainty was calculated according to the "Guide to the expression of Uncertainty in Measurement" (JCGM 100:2008). Bottom-up uncertainty evaluation revealed the different sampling methods (~ 44%), sample replicates (~ 26%) and the different detection techniques (~ 16%) as the major sources of uncertainty. Depending on the number of particles detected in the samples, the relative expanded uncertainty (Urel (k = 2)) ranged from 24% up to > 200% underpinning tremendous importance of sound uncertainty evaluation. Our results indicate that scientist should rethink many "observed patterns" in the literature due to being insignificant and herewith not real.}, }
@article {pmid34030262, year = {2021}, author = {Glodowska, M and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Straub, D and Berg, M and Prommer, H and Bostick, BC and Nghiem, AA and Kleindienst, S and Kappler, A}, title = {Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146501}, doi = {10.1016/j.scitotenv.2021.146501}, pmid = {34030262}, issn = {1879-1026}, mesh = {*Arsenic/analysis ; Fermentation ; Ferric Compounds ; *Groundwater ; Humans ; Oxidation-Reduction ; Vietnam ; *Water Pollutants, Chemical/analysis ; }, abstract = {High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH4) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH4 oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.}, }
@article {pmid34029817, year = {2021}, author = {Zhang, Y and Chen, M and Zhao, YY and Zhang, AY and Peng, DH and Lu, F and Dai, CC}, title = {Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147794}, doi = {10.1016/j.scitotenv.2021.147794}, pmid = {34029817}, issn = {1879-1026}, mesh = {Animals ; Astacoidea ; China ; *Oryza ; *Soil ; Soil Microbiology ; }, abstract = {The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.}, }
@article {pmid34025695, year = {2021}, author = {Li, T and Wu, S and Yang, W and Selosse, MA and Gao, J}, title = {How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {647114}, pmid = {34025695}, issn = {1664-462X}, abstract = {Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.}, }
@article {pmid34025597, year = {2021}, author = {Suominen, S and van Vliet, DM and Sánchez-Andrea, I and van der Meer, MTJ and Sinninghe Damsté, JS and Villanueva, L}, title = {Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {628301}, pmid = {34025597}, issn = {1664-302X}, abstract = {Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.}, }
@article {pmid34025590, year = {2021}, author = {You, Y and Aho, K and Lohse, KA and Schwabedissen, SG and Ledbetter, RN and Magnuson, TS}, title = {Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {569791}, pmid = {34025590}, issn = {1664-302X}, abstract = {Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.}, }
@article {pmid34023922, year = {2021}, author = {Kaur, M and Kumari, A and Singh, R}, title = {The Indigenous Volatile Inhibitor 2-Methyl-2-butene Impacts Biofilm Formation and Interspecies Interaction of the Pathogenic Mucorale Rhizopus arrhizus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34023922}, issn = {1432-184X}, support = {ECR/2016/000102//Early Career Research Award, Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Govt. of India/ ; DST/INSPIRE Faculty Award/2013/DST/INSPIRE/04/2013/000925//DST-INSPIRE Faculty Scheme, Govt. of India/ ; }, abstract = {2-Methyl-2-butene has recently been reported to be a quorum-based volatile self-inhibitor of spore germination and growth in pathogenic Mucorale Rhizopus arrhizus. The present study aimed to elucidate if this compound can influence R. arrhizus biofilm formation and interspecies interaction. The compound was found to significantly decrease R. arrhizus biofilm formation (p < 0.001), with nearly 25% and 50% lesser biomass in the biofilms cultured with exposure to 4 and 32 µg/ml of 2-methyl-2-butene, respectively. The growth of pre-formed biofilms was also impacted, albeit to a lesser extent. Additionally, 2-methyl-2-butene was found to self-limit R. arrhizus growth during interspecies interaction with Staphylococcus aureus and was detected at a substantially greater concentration in the headspace of co-cultures (2338.75 µg/ml) compared with monocultures (69.52 µg/ml). Some of the C5 derivatives of this compound (3-methyl-1-butanol, 2-methyl-2-butanol, and 3-methyl-1-butyne) were also observed to partially mimic its action, such as inhibition of spore germination, but did not impact R. arrhizus biofilm formation. Finally, the treated R. arrhizus displayed changes in fungal morphology suggestive of cytoskeletal alterations, such as filopodia formation, blebs, increased longitudinal folds and/or corrugations, and finger-like and sheet-like surface protrusions, depending upon the concentration of the compound(s) and the planktonic or biofilm growth mode.}, }
@article {pmid34021563, year = {2021}, author = {Wright, ES and Gupta, R and Vetsigian, KH}, title = {Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {6}, pages = {}, doi = {10.1093/femsec/fiab073}, pmid = {34021563}, issn = {1574-6941}, abstract = {Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.}, }
@article {pmid34020935, year = {2021}, author = {Huang, YM and Straub, D and Blackwell, N and Kappler, A and Kleindienst, S}, title = {Meta-omics reveal Gallionellaceae and Rhodanobacter as interdependent key players for Fe(II) oxidation and nitrate reduction in the autotrophic enrichment culture KS.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00496-21}, pmid = {34020935}, issn = {1098-5336}, abstract = {Nitrate reduction coupled to iron(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing iron(II)-oxidizing bacteria are rare and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics and metaproteomics) to the nitrate-reducing iron(II)-oxidizing enrichment culture KS, growing under autotrophic compared to heterotrophic conditions, and originating from a freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The presence of Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in iron(II) oxidation (e.g., mtoAB, cyc2, mofA), denitrification (e.g., napGHI) and oxidative phosphorylation (e.g., respiratory chain complexes I-V), along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be done by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3 - and aa3 - type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and iron(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments.ImportanceNitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of studies is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to iron(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS, and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key iron(II)-oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to iron(II) oxidation is not performed by an individual strain but a cooperation of at least two members of the bacterial community in culture KS. These findings serve as foundation for our understanding of nitrate-reducing iron(II)-oxidizing bacteria in the environment.}, }
@article {pmid34020712, year = {2021}, author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Vega Thurber, RL and Peixoto, RS}, title = {Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {118}, pmid = {34020712}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Petroleum ; *Petroleum Pollution ; *Probiotics ; }, abstract = {BACKGROUND: Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.<br><br>RESULTS: The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.<br><br>CONCLUSIONS: Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.}, }
@article {pmid34017060, year = {2021}, author = {Kim, JH and Kim, K and Kim, W}, title = {Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy.}, journal = {Experimental &amp; molecular medicine}, volume = {53}, number = {5}, pages = {907-916}, pmid = {34017060}, issn = {2092-6413}, support = {NRF-2019R1A6A3A01093804//National Research Foundation of Korea (NRF)/ ; }, abstract = {The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.}, }
@article {pmid34016155, year = {2021}, author = {LaMartina, EL and Mohaimani, AA and Newton, RJ}, title = {Urban wastewater bacterial communities assemble into seasonal steady states.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {116}, pmid = {34016155}, issn = {2049-2618}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; R01AI091829/NH/NIH HHS/United States ; }, mesh = {Ecosystem ; Humans ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Sewage ; *Waste Water ; }, abstract = {BACKGROUND: Microorganisms in urban sanitary sewers exhibit community properties that suggest sewers are a novel ecosystem. Sewer microorganisms present both an opportunity as a control point for wastewater treatment and a risk to human health. If treatment processes are to be improved and health risks quantified, then it is necessary to understand microbial distributions and dynamics within this community. Here, we use 16S rRNA gene sequencing to characterize raw influent wastewater bacterial communities in a 5-year time series from two wastewater treatment plants in Milwaukee, WI; influent wastewater from 77 treatment plants across the USA; and wastewater in 12 Milwaukee residential sewers.<br><br>RESULTS: In Milwaukee, we find that in transit from residences to treatment plants, the human bacterial component of wastewater decreases in proportion and exhibits stochastic temporal variation. In contrast, the resident sewer community increases in abundance during transit and cycles seasonally according to changes in wastewater temperature. The result is a bacterial community that assembles into two distinct community states each year according to the extremes in wastewater temperature. Wastewater bacterial communities from other northern US cities follow temporal trends that mirror those in Milwaukee, but southern US cities have distinct community compositions and differ in their seasonal patterns.<br><br>CONCLUSIONS: Our findings provide evidence that environmental conditions associated with seasonal change and climatic differences related to geography predictably structure the bacterial communities residing in below-ground sewer pipes. Video abstract.}, }
@article {pmid34016152, year = {2021}, author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Rodo, A and Goździk, K and Behnke-Borowczyk, J and Kiewra, D and Kartawik, N and Bajer, A}, title = {Monitoring the expansion of Dermacentor reticulatus and occurrence of canine babesiosis in Poland in 2016-2018.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {267}, pmid = {34016152}, issn = {1756-3305}, abstract = {BACKGROUND: The significance of tick-borne diseases has increased considerably in recent years. Because of the unique distribution of the tick species Dermacentor reticulatus in Poland, comprising two expanding populations, Eastern and Western that are separated by a Dermacentor-free zone, it is important to conduct studies on the process of tick expansion and emergence of canine babesiosis. The main aim of the current study was to monitor the expansion of D. reticulatus populations from spring 2016 to autumn 2018 to determine (1) the actual geographical range of this tick species, and (2) and the seasonal/annual shift in range limits and changes in distance between Western and Eastern populations of ticks (the size of the non-endemic area).<br><br>METHODS: Ticks were collected in spring/autumn during a 3-year study. From each season and year at least three pairs of sites from the Western and Eastern populations were selected. Then the mean distance between paired sites was calculated for each season and year. We collected and analyzed data from veterinary clinics on the number of canine babesiosis cases treated in the clinic during a whole year (2018).<br><br>RESULTS: Accordingly, further expansion of the two D. reticulatus populations was recorded, mainly along river basins. Marked colonization of the gap zone was observed, with a mean annual shift in the range of 2.5-10 km and a steadily decreasing distance between the two tick populations. The occurrence of babesiosis in different regions revealed low numbers of cases in Western Poland (19 cases/year) and the gap area (only 7 cases/year) and high incidence (up to 250 cases/1000 dogs) and fatality (total 3.65%) in Central and Eastern Poland. Strong associations were found geographically between tick and babesiosis occurrence and temporally in the seasonal patterns of occurrence of ticks and outbreaks of babesiosis.<br><br>CONCLUSIONS: We documented the shift in range limits and continued process of colonization of the gap zone accompanied by the emergence of canine babesiosis in the Eastern expansion zone. Updated maps of the distribution of ticks and occurrence of babesiosis in different regions of Poland have allowed us to predict of the emergence of pathogens vectored by D. reticulatus. Incidence (per 1000 dogs) of canine babesiosis in veterinary clinics by current range of D. reticulatus.}, }
@article {pmid34014937, year = {2021}, author = {Tibatá, VM and Sanchez, A and Palmer-Young, E and Junca, H and Solarte, VM and Madella, S and Ariza, F and Figueroa, J and Corona, M}, title = {Africanized honey bees in Colombia exhibit high prevalence but low level of infestation of Varroa mites and low prevalence of pathogenic viruses.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0244906}, pmid = {34014937}, issn = {1932-6203}, abstract = {The global spread of the ectoparasitic mite Varroa destructor has promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees (AHBs), which are considered more resistant to Varroa compared to European honey bees. However, the relationship between Varroa levels and the spread of honey bee viruses in AHBs remains unknown. In this study, we determined Varroa prevalence and infestation levels as well as the prevalence of seven major honey bee viruses in AHBs from three regions of Colombia. We found that although Varroa exhibited high prevalence (92%), its infestation levels were low (4.5%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all colonies were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4%, ABPV 10.56%). Our findings indicate that AHBs possess a natural resistance to Varroa that does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.}, }
@article {pmid34013437, year = {2021}, author = {Romero-Olivares, AL and Morrison, EW and Pringle, A and Frey, SD}, title = {Correction to: Linking Genes to Traits in Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01776-x}, pmid = {34013437}, issn = {1432-184X}, }
@article {pmid34009446, year = {2021}, author = {Antunes, VDC and Freitag, D and Serrato, RV}, title = {Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {34009446}, issn = {1432-072X}, abstract = {Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.}, }
@article {pmid34008895, year = {2021}, author = {Ketchum, RN and Smith, EG and Vaughan, GO and McParland, D and Al-Mansoori, N and Burt, JA and Reitzel, AM}, title = {Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15990}, pmid = {34008895}, issn = {1365-294X}, support = {//ICRS Fellowship/ ; 1924498//NSF/ ; CG007//NYUAD Water Research Center/ ; //NSF GRF/ ; //Incentive Funds/ ; }, abstract = {Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.}, }
@article {pmid34006626, year = {2021}, author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ}, title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {34006626}, issn = {2379-5077}, abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.}, }
@article {pmid34003315, year = {2021}, author = {Kim, J and Heo, YM and Yun, J and Lee, H and Kim, JJ and Kang, H}, title = {Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34003315}, issn = {1432-184X}, support = {2019R1A6A3A01091184//Ministry of Education (KR)/ ; 2020R1I1A2072824//Ministry of Education (KR)/ ; 2018K2A9A1A01090455, 2019K1A3A1A74107424, 2019K1A3A1A80113041//Ministry of Science and ICT (KR)/ ; 20170318//Ministry of Oceans and Fisheries (KR)/ ; 2019H1A2A1076239//Ministry of Education/ ; }, abstract = {Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.}, }
@article {pmid33993638, year = {2021}, author = {Ng, CK and Putra, SL and Kennerley, J and Habgood, R and Roy, RA and Raymond, JL and Thompson, IP and Huang, WE}, title = {Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13823}, pmid = {33993638}, issn = {1751-7915}, support = {SGRF-2017-471//Commonwealth Scholarship Commission/ ; EP/M002403/1//Engineering and Physical Sciences Research Council/ ; EP/N009746/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10-7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm-2) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm-2). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm3 and 300 cm3 , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.}, }
@article {pmid33992330, year = {2021}, author = {Battistelli, N and Perpetuini, G and Piva, A and Pepe, A and Sidari, R and Wache, Y and Tofalo, R}, title = {Cultivable microbial ecology and aromatic profile of "mothers" for Vino cotto wine production.}, journal = {Food research international (Ottawa, Ont.)}, volume = {143}, number = {}, pages = {110311}, doi = {10.1016/j.foodres.2021.110311}, pmid = {33992330}, issn = {1873-7145}, mesh = {Fermentation ; Hanseniaspora ; Metschnikowia ; Saccharomycetales ; *Wine/analysis ; }, abstract = {The aim of the present study was to assess the cultivable microbiota of "mothers" of Vino cotto collected from production of different years 1890, 1895, 1920, 1975, 2008. A total of 73 yeasts and 81 bacteria were isolated. Starmerella lactis-condensi, Starmerella bacillaris, Hanseniaspora uvarum, Saccharomyces cerevisiae, Hanseniaspora guillermondi and Metschnikowia pulcherrima were identified. Bacteria isolates belonged to lactic acid bacteria (Lactiplantibacillus plantarum and Pediococcus pentosaceus) and acetic acid bacteria (Gluconobacter oxydans). Remarkable biodiversity was observed for Starm. bacillaris, as well as L. plantarum and G. oxydans. Organic acids and volatile compounds were also determined. Malic and succinic acids were the main ones with values ranging from 8.49 g/L to 11.76 g/L and from 4.15 g/L to 7.73 g/L respectively, while citric acid was present at low concentrations (<0.2 g/L) in all samples. Esters and higher alcohols were the main volatile compounds detected followed by alkanes. This study permits to better understand the microbial communities associated to this product and could be considered a starting point for the definition of tailored starter cultures to improve the quality of Vino cotto preserving its typical traits.}, }
@article {pmid33990304, year = {2021}, author = {Hartwick, M and Berenson, A and Whistler, CA and Naumova, EN and Jones, SH}, title = {The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast US.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02973-20}, pmid = {33990304}, issn = {1098-5336}, abstract = {Microbial ecology studies have proven to be important resources for improving infectious disease response and outbreak prevention. Vibrio parahaemolyticus is an ongoing source of shellfish-borne food illness in the Northeast, United States and there is keen interest in understanding the environmental conditions that coincide with V. parahaemolyticus disease risk to aid harvest management and prevent further illness. Zooplankton and chitinous phytoplankton associate with V. parahaemolyticus dynamics elsewhere, however, this relationship is undetermined for the Great Bay estuary (GBE), an important emerging shellfish growing region in the Northeast, US. A comprehensive evaluation of the microbial ecology of V. parahaemolyticus associated with plankton was conducted in the GBE using three years of plankton community, nutrient concentration, water quality and V. parahaemolyticus concentration in plankton data. The concentrations of V. parahaemolyticus associated with plankton were highly seasonal and the highest concentrations of V. parahaemolyticus cultured from zooplankton occurred approximately one month before the highest concentrations of V. parahaemolyticus from phytoplankton. The two V. parahaemolyticus peaks corresponded with different water quality variables and a few highly seasonal plankton taxa. Importantly, V. parahaemolyticus concentrations and plankton community dynamics were poorly associated with nutrient concentrations and chlorophyll-a, commonly applied proxy variables for assessing ecological health risks, and human health risks from harmful plankton and V. parahaemolyticus elsewhere. Together, these statistical associations (or lack thereof) provide valuable insights to characterize the plankton-V. parahaemolyticus dynamic and inform approaches for understanding the potential contribution of plankton to human health risks from V. parahaemolyticus for the Northeast US.IMPORTANCEThe Vibrio-plankton interaction is a focal relationship in Vibrio disease research; however, little is known about this dynamic in the Northeast, US where V. parahaemolyticus is an established public health issue. We integrated phototactic plankton separation with seasonality analysis to determine the dynamics of the plankton community, water quality and V. parahaemolyticus concentrations. Distinct bimodal peaks in the seasonal timing of V. parahaemolyticus abundance from phyto- vs zooplankton and differing associations with water quality variables and plankton taxa highlight that monitoring and forecasting approaches should consider the source of exposure when designing predictive methods for V. parahaemolyticus Heliotheca tamensis has not been previously reported in the GBE. Its detection during this study provides evidence of the changes occurring in the ecology of regional estuaries and potential mechanisms for changes in V. parahaemolyticus populations. The Vibrio monitoring approaches can be translated to aid other areas facing similar public health challenges.}, }
@article {pmid33990222, year = {2021}, author = {Qian, X and Gunturu, S and Guo, J and Chai, B and Cole, JR and Gu, J and Tiedje, JM}, title = {Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {108}, pmid = {33990222}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents ; Ecosystem ; Genes, Bacterial ; Grassland ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Tropical Climate ; Tundra ; }, abstract = {BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.<br><br>RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.<br><br>CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.}, }
@article {pmid33989956, year = {2021}, author = {Zhong, X and Yu, S and Xu, H}, title = {Influence of tidal events on the body-size spectrum of periphytic ciliates for marine bioassessment using artificial substrata.}, journal = {Marine pollution bulletin}, volume = {168}, number = {}, pages = {112435}, doi = {10.1016/j.marpolbul.2021.112435}, pmid = {33989956}, issn = {1879-3363}, mesh = {Body Size ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Water Quality ; }, abstract = {As an internal functional trait of a community, the body-size spectrum is a highly informative indicator for bioassessment of water/environmental quality in aquatic ecosystems. To determine the influence of tidal events on body-size spectra of protozoan periphytons, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). The body-size spectrum of the protozoans showed a clear temporal pattern during the study period using both sampling systems. However, the temporal dynamics showed significantly different trajectories in the body-size spectrum between the two sampling methods during the study period. The bootstrapped average analysis revealed that the patterns of the body-size spectrum were significantly different between the PFES and CS systems, especially in terms of frequency of occurrence. These findings suggest that the tidal events may significantly influence body-size spectrum of periphytic ciliates for bioassessment in marine ecosystems.}, }
@article {pmid33989624, year = {2021}, author = {Singh, NS and Sharma, R and Singh, SK and Singh, DK}, title = {A comprehensive review of environmental fate and degradation of fipronil and its toxic metabolites.}, journal = {Environmental research}, volume = {199}, number = {}, pages = {111316}, doi = {10.1016/j.envres.2021.111316}, pmid = {33989624}, issn = {1096-0953}, mesh = {Agriculture ; *Insecticides/toxicity ; *Pesticides ; Pyrazoles ; }, abstract = {The use of pesticides to increase crop production has become one of the inevitable components of modern agriculture. Fipronil, a phenylpyrazoles insecticide, is one of the most widely used, systemic, broad-spectrum insecticides. Owing to its unique mode of action and selective toxicity, it was once regarded as safer alternatives to more toxic and persistent organochlorine insecticides. However, with the increased use, many studies have reported the toxicity of fipronil and its metabolites in various non-target organisms during the last two decades. Currently, it is regarded as one of the most persistent and lipophilic insecticides in the market. In the environment, fipronil can undergo oxidation, reduction, hydrolysis, or photolysis to form fipronil sulfone, fipronil sulfide, fipronil amide, or fipronil desulfinyl respectively. These metabolites except fipronil amide are more or less toxic and persistent than fipronil and have been reported from diverse environmental samples. Recently many studies have focused on the degradation and removal of fipronil residues from the environment. However, a comprehensive review summarizing and combining these recent findings is lacking. In the present review, we evaluate, summarize, and combine important findings from recent degradation studies of fipronil and its metabolites. An attempt has been made to elucidate the possible mechanism and pathways of degradation of fipronil and its toxic metabolites.}, }
@article {pmid33987687, year = {2021}, author = {Figueiredo, G and Gomes, M and Covas, C and Mendo, S and Caetano, T}, title = {The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33987687}, issn = {1432-184X}, support = {SFRH/BD/98446/2013//Fundação para a Ciência e a Tecnologia/ ; CEECIND/01463/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.}, }
@article {pmid33986093, year = {2021}, author = {Girolamini, L and Salaris, S and Orsini, M and Pascale, MR and Mazzotta, M and Grottola, A and Cristino, S}, title = {Draft Genome Sequences of Legionella Presumptive Novel Species Isolated during Environmental Surveillance in Artificial Water Systems.}, journal = {Microbiology resource announcements}, volume = {10}, number = {19}, pages = {}, pmid = {33986093}, issn = {2576-098X}, abstract = {We present the draft genome sequences of three Legionella strains that were isolated from a hotel water distribution system. Legionella species identification was performed by macrophage infectivity potentiator (mip) and RNA polymerase β subunit (rpoB) gene sequencing. Whole-genome sequencing and average nucleotide identity results supported the hypothesis of new Legionella species isolation.}, }
@article {pmid33984318, year = {2021}, author = {Stevens, BR and Pepine, CJ and Richards, EM and Kim, S and Raizada, MK}, title = {Depressive hypertension: A proposed human endotype of brain/gut microbiome dysbiosis.}, journal = {American heart journal}, volume = {239}, number = {}, pages = {27-37}, doi = {10.1016/j.ahj.2021.05.002}, pmid = {33984318}, issn = {1097-6744}, abstract = {BACKGROUND: Hypertension (HTN) is frequently linked with depression (DEP) in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms," such that cardiovascular disease dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology.<br><br>METHODS: Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with HTN only (N = 18), DEP only (N = 7), DEP plus HTN (DEP-HTN) (N = 8), or reference subjects with neither HTN nor DEP (N = 21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (false discovery rate (FDR)-adjusted P ≤ .05); data clustering within 95% confidence interval).<br><br>RESULTS: Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurrence of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis, and Lachnospiraceae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction.<br><br>CONCLUSIONS: These data suggest a new putative endotype of hypertension, which we denote "depressive-hypertension" (DEP-HTN), for which we posit a model that is distinctive from either HTN alone or DEP alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of blood pressure and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of HTN-coupled mood disorders.}, }
@article {pmid33981000, year = {2021}, author = {Flieder, M and Buongiorno, J and Herbold, CW and Hausmann, B and Rattei, T and Lloyd, KG and Loy, A and Wasmund, K}, title = {Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33981000}, issn = {1751-7370}, support = {P29426//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25111//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.}, }
@article {pmid33980683, year = {2021}, author = {De Leόn, KB}, title = {mSphere of Influence: Surface Sensing in Biofilm Formation.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33980683}, issn = {2379-5042}, abstract = {Kara B. De Leόn works in the field of microbial ecology, environmental biofilms, and microbial genetics. In this mSphere of Influence article, she reflects on how the paper "Multigenerational memory and adaptive adhesion in early bacterial biofilm communities" by C. K. Lee et al. (C. K. Lee, J. de Anda, A. E. Baker, R. R. Bennett, et al., Proc Natl Acad Sci U S A 115:4471-4476, 2018, https://dx.doi.org/10.1073/pnas.1720071115) made an impact on her by changing the way she thinks about initial cell attachment to a surface in an environment.}, }
@article {pmid33980476, year = {2021}, author = {Liébana-García, R and Olivares, M and Bullich-Vilarrubias, C and López-Almela, I and Romaní-Pérez, M and Sanz, Y}, title = {The gut microbiota as a versatile immunomodulator in obesity and associated metabolic disorders.}, journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism}, volume = {35}, number = {3}, pages = {101542}, doi = {10.1016/j.beem.2021.101542}, pmid = {33980476}, issn = {1878-1594}, abstract = {Obesity has reached epidemic proportions and is associated with chronic-low-grade inflammation and metabolic morbidities. Energy-dense diets and a sedentary lifestyle are determinants of obesity. The gut microbiome is a novel biological factor involved in obesity via interactions with the host and the diet. The gut microbiome act as a synergistic force protecting or aggravating the effects of the diet on the metabolic phenotype. The role of the microbiome in the regulation of intestinal and systemic immunity is one of the mechanisms by which it contributes to the host's response to the diet and to the pathophysiology of diet-induced obesity. Here, we review the mechanisms whereby "obesogenic" diets and the microbiome impact immunity, locally and systemically, focusing on the consequences in the gut-adipose tissue axis. We also review the structural and microbial metabolites that influence immunity and how advances in this field could help design microbiome-informed strategies to tackle obesity-related disorders more effectively.}, }
@article {pmid33978602, year = {2021}, author = {Jung, CE and Estaki, M and Chopyk, J and Taylor, BC and Gonzalez, A and McDonald, D and Shin, J and Ferrante, K and Wasenda, E and Lippmann, Q and Knight, R and Pride, D and Lukacz, ES}, title = {Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection.}, journal = {Female pelvic medicine &amp; reconstructive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/SPV.0000000000001051}, pmid = {33978602}, issn = {2154-4212}, abstract = {OBJECTIVE: The aim of this study was to describe effects of vaginal estrogen (VE) on the urogenital microbiome in postmenopausal women with recurrent urinary tract infections (rUTIs).<br><br>METHODS: This is a secondary analysis of 17 participants enrolled in a randomized controlled trial of VE versus placebo on urinary tract infection recurrence in postmenopausal women with rUTIs. Paired clean-catch urine samples were collected at baseline and after 6 months of VE and sequenced using 16S rRNA gene sequencing. Sequence reads were analyzed using Quantitative Insights Into Microbial Ecology 2. Changes in α diversity, β diversity, and differentially abundant genera were measured between paired baseline and 6-month samples and between those with a urinary tract infection at 6 months (failures) and those without (successes).<br><br>RESULTS: Of the 17 women, 11 were successes and 6 were failures after 6 months of VE treatment. There was a significant change in α diversity from baseline to month 6 in samples overall (Kruskal-Wallis χ2 = 3.47, P = 0.037) and in the treatment success group (Yuen T = -2.53, P = 0.035). The increase in relative abundance of Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners AB-1 was correlated with month 6. A relative bloom of L. crispatus compared with L. gasseri was associated with treatment success (Kruskal-Wallis χ2 = 4.9, P = 0.0014).<br><br>CONCLUSIONS: Lactobacillus increases in the urogenital microbiome of postmenopausal women with rUTI after 6 months of VE. However, only the relative increase in L. crispatus specifically may be associated with treatment success.}, }
@article {pmid33976843, year = {2021}, author = {Eliades, SJ and Brown, JC and Colston, TJ and Fisher, RN and Niukula, JB and Gray, K and Vadada, J and Rasalato, S and Siler, CD}, title = {Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes.}, journal = {Ecology and evolution}, volume = {11}, number = {9}, pages = {4731-4743}, pmid = {33976843}, issn = {2045-7758}, abstract = {Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.}, }
@article {pmid33975968, year = {2021}, author = {Sieradzki, ET and Morando, M and Fuhrman, JA}, title = {Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33975968}, issn = {2379-5077}, abstract = {Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.}, }
@article {pmid33975966, year = {2021}, author = {Chuckran, PF and Fofanov, V and Hungate, BA and Morrissey, EM and Schwartz, E and Walkup, J and Dijkstra, P}, title = {Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33975966}, issn = {2379-5077}, abstract = {Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.}, }
@article {pmid33975908, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {21}, pages = {}, pmid = {33975908}, issn = {1091-6490}, }
@article {pmid33974954, year = {2021}, author = {Lima, J and Manning, T and Rutherford, KM and Baima, ET and Dewhurst, RJ and Walsh, P and Roehe, R}, title = {Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.}, journal = {Journal of microbiological methods}, volume = {186}, number = {}, pages = {106235}, doi = {10.1016/j.mimet.2021.106235}, pmid = {33974954}, issn = {1872-8359}, abstract = {Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.}, }
@article {pmid33973345, year = {2021}, author = {Clocchiatti, A and Hannula, SE and Hundscheid, MPJ and Klein Gunnewiek, PJA and de Boer, W}, title = {Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15563}, pmid = {33973345}, issn = {1462-2920}, support = {STW 14012//Stichting voor de Technische Wetenschappen/ ; }, abstract = {Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13 CO2 -pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.}, }
@article {pmid33973200, year = {2021}, author = {Moossavi, S and Fehr, K and Maleki, H and Seyedpour, S and Keshavarz-Fathi, M and Tabasi, F and Heravi, M and Sharifian, R and Shafiei, G and Badihian, N and Kelishadi, R and Nematollahi, S and Almasi, M and Popescu, S and Keshavarz-Fathi, M and Rezaei, N}, title = {Prevention of COVID-19: Preventive Strategies for General Population, Healthcare Setting, and Various Professions.}, journal = {Advances in experimental medicine and biology}, volume = {1318}, number = {}, pages = {575-604}, pmid = {33973200}, issn = {0065-2598}, mesh = {*COVID-19 ; *Cancer Vaccines ; Delivery of Health Care ; Humans ; Immunotherapy ; SARS-CoV-2 ; }, abstract = {The disease 2019 (COVID-19) made a public health emergency in early 2020. Despite attempts for the development of therapeutic modalities, there is no effective treatment yet. Therefore, preventive measures in various settings could help reduce the burden of disease. In this chapter, the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19, non-pharmaceutical approaches at individual and population level, chemoprevention, immunoprevention, preventive measures in different healthcare settings and other professions, special considerations in high-risk groups, and the role of organizations to hamper the psychosocial effects will be discussed.}, }
@article {pmid33973059, year = {2021}, author = {Castelli, L and Branchiccela, B and Romero, H and Zunino, P and Antúnez, K}, title = {Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate : Seasonal Dynamics of Honey Bee Gut Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33973059}, issn = {1432-184X}, abstract = {Honey bees (Apis mellifera) provide invaluable benefits for food production and maintenance of biodiversity of natural environments through pollination. They are widely spread across the world, being adapted to different climatic conditions. To survive the winter in cold temperate regions, honey bees developed different strategies including storage of honey and pollen, confinement of individuals during the winter, and an annual cycle of colony growth and reproduction. Under these conditions, winter honey bees experience physiological changes, including changes in immunity and the composition of honey bee gut microbiota. However, under tropical or subtropical climates, the life cycle can experience alterations, i.e., queens lay eggs during almost all the year and new honey bees emerge constantly. In the present study, we characterized nurses' honey bee gut microbiota in colonies under subtropical region through a year, combining qPCR, PCR-DGGE, and 16S rDNA high-throughput sequencing. We also identified environmental variables involved in those changes. Our results showed that under the mentioned conditions, the number of bacteria is stable throughout the year. Diversity of gut microbiota is higher in spring and lower in summer and winter. Gradual changes in compositions occur between seasons: Lactobacillus spp. predominate in spring while Gilliamella apicola and Snodgrasella alvi predominate in summer and winter. Environmental variables (mainly precipitations) affected the composition of the honey bee gut microbiota. Our findings provide new insights into the dynamics of honey bee gut microbiota and may be useful to understand the adaptation of bees to different environmental conditions.}, }
@article {pmid33970854, year = {2021}, author = {Alvarez-Perez, S and Baker, LJ and Morris, MM and Tsuji, K and Sanchez, VA and Fukami, T and Vannette, RL and Lievens, B and Hendry, TA}, title = {Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov., isolated from floral nectar and honey bees.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.004783}, pmid = {33970854}, issn = {1466-5034}, mesh = {Acinetobacter/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; Bees/*microbiology ; California ; DNA, Bacterial/genetics ; Flowers ; Nucleic Acid Hybridization ; *Phylogeny ; *Plant Nectar ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter. Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis, Acinetobacter boissieri and Acinetobacter nectaris, previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477T (=TSD-214T=LMG 31655T), B10AT (=TSD-213T=LMG 31702T) and EC24T (=TSD-215T=LMG 31703T=DSM 111781T).}, }
@article {pmid33970312, year = {2021}, author = {Zhao, J and Wang, B and Zhou, X and Alam, MS and Fan, J and Guo, Z and Zhang, H and Gubry-Rangin, C and Zhongjun, J}, title = {Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33970312}, issn = {1432-184X}, support = {41530857//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 41977056//National Natural Science Foundation of China/ ; URF150571//The Royal Society/ ; NE/ K016342/1//Natural Environment Research Council/ ; }, abstract = {Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.}, }
@article {pmid33969432, year = {2021}, author = {Nasehi, SF and Fathipour, Y and Asgari, S and Mehrabadi, M}, title = {Environmental Temperature, but Not Male Age, Affects Wolbachia and Prophage WO Thereby Modulating Cytoplasmic Incompatibility in the Parasitoid Wasp, Habrobracon Hebetor.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33969432}, issn = {1432-184X}, support = {98008582//Iran National Science Foundation/ ; }, abstract = {Wolbachia is an endosymbiotic bacterium found in many species of arthropods and manipulates its host reproduction. Cytoplasmic incompatibility (CI) is one of the most common manipulations that is induced when an uninfected female mates with a Wolbachia-infected male. The CI factors (cifA and cifB genes) are encoded by phage WO that naturally infects Wolbachia. Here, we questioned whether an environmental factor (temperature) or host factor (male age) affected the strength of the CI phenotype in the ectoparasitoid wasp, Habrobracon hebetor. We found that temperature, but not male age, results in reduced CI penetrance. Consistent with these results, we also found that the expression of the cif CI factors decreased in temperature-exposed males but was consistent across aging male wasps. Similar to studies of other insect systems, cifA showed a higher expression level than cifB, and male hosts showed increased cif expression relative to females. Our results suggest that prophage WO is present in the Wolbachia-infected wasps and expression of cif genes contributes to the induction of CI in this insect. It seems that male aging has no effect on the intensity of CI; however, temperature affects Wolbachia and prophage WO titers as well as expression levels of cif genes, which modulate the CI level.}, }
@article {pmid33968313, year = {2021}, author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Masters, JG and Zayed, N and Quirynen, M and Teughels, W}, title = {Potential prebiotic substrates modulate composition, metabolism, virulence and inflammatory potential of an in vitro multi-species oral biofilm.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1910462}, pmid = {33968313}, issn = {2000-2297}, abstract = {Background: Modulation of the commensal oral microbiota constitutes a promising preventive/therapeutic approach in oral healthcare. The use of prebiotics for maintaining/restoring the health-associated homeostasis of the oral microbiota has become an important research topic. Aims: This study hypothesised that in vitro 14-species oral biofilms can be modulated by (in)direct stimulation of beneficial/commensal bacteria with new potential prebiotic substrates tested at 1 M and 1%(w/v), resulting in more host-compatible biofilms with fewer pathogens, decreased virulence and less inflammatory potential. Methods: Established biofilms were repeatedly rinsed with N-acetyl-D-glucosamine, α-D-lactose, D-(+)-trehalose or D-(+)-raffinose at 1 M or 1%(w/v). Biofilm composition, metabolic profile, virulence and inflammatory potential were eventually determined. Results: Repeated rinsing caused a shift towards a more health-associated microbiological composition, an altered metabolic profile, often downregulated virulence gene expression and decreased the inflammatory potential on oral keratinocytes. At 1 M, the substrates had pronounced effects on all biofilm aspects, whereas at 1%(w/v) they had a pronounced effect on virulence gene expression and a limited effect on inflammatory potential. Conclusion: Overall, this study identified four new potential prebiotic substrates that exhibit different modulatory effects at two different concentrations that cause in vitro multi-species oral biofilms to become more host-compatible.}, }
@article {pmid33966095, year = {2021}, author = {Frare, R and Pascuan, C and Galindo-Sotomonte, L and McCormick, W and Soto, G and Ayub, N}, title = {Exploring the Role of the NO-Detoxifying Enzyme HmpA in the Evolution of Domesticated Alfalfa Rhizobia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33966095}, issn = {1432-184X}, abstract = {We have previously shown the extensive loss of genes during the domestication of alfalfa rhizobia and the high nitrous oxide emission associated with the extreme genomic instability of commercial inoculants. In the present note, we describe the molecular mechanism involved in the evolution of alfalfa rhizobia. Genomic analysis showed that most of the gene losses in inoculants are due to large genomic deletions rather than to small deletions or point mutations, a fact consistent with recurrent DNA double-strand breaks (DSBs) at numerous locations throughout the microbial genome. Genetic analysis showed that the loss of the NO-detoxifying enzyme HmpA in inoculants results in growth inhibition and high DSB levels under nitrosative stress, and large genomic deletions in planta but not in the soil. Therefore, besides its known function in the effective establishment of the symbiosis, HmpA can play a critical role in the preservation of the genomic integrity of alfalfa rhizobia under host-derived nitrosative stress.}, }
@article {pmid33959106, year = {2021}, author = {Parks, DH and Rigato, F and Vera-Wolf, P and Krause, L and Hugenholtz, P and Tyson, GW and Wood, DLA}, title = {Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {643682}, pmid = {33959106}, issn = {1664-302X}, abstract = {A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.}, }
@article {pmid33958420, year = {2021}, author = {McDaniel, EA and Wever, R and Oyserman, BO and Noguera, DR and McMahon, KD}, title = {Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal.}, journal = {Microbiology resource announcements}, volume = {10}, number = {18}, pages = {}, pmid = {33958420}, issn = {2576-098X}, abstract = {Enhanced biological phosphorus removal (EBPR) is an economically and environmentally significant wastewater treatment process for removing excess phosphorus by harnessing the metabolic physiologies of enriched microbial communities. We present a genome-resolved metagenomic data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.}, }
@article {pmid33957514, year = {2021}, author = {Zhao, Z and Li, H and Sun, Y and Yang, Q and Fan, J}, title = {Contrasting the assembly of phytoplankton and zooplankton communities in a polluted semi-closed sea: Effects of marine compartments and environmental selection.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {285}, number = {}, pages = {117256}, doi = {10.1016/j.envpol.2021.117256}, pmid = {33957514}, issn = {1873-6424}, abstract = {Understanding the underlying mechanisms of community assembly is a major challenge in microbial ecology, particularly in communities composed of diverse organisms with different ecological characteristics. However, very little is known about the effects of marine compartments in shaping marine planktonic communities; primarily, how they are related to organism types and environmental variables. In this study, we used multiple statistical methods to explore the mechanisms driving phytoplankton and zooplankton metacommunity dynamics at the regional scale in the Bohai Sea, China. Clear geographic patterns were observed in both phytoplankton and zooplankton communities. Zooplankton showed a stronger distance-decay of similarity than phytoplankton, which had greater community differences between locations with further distances. Our analyses indicated that the zooplankton communities were primarily governed by species sorting versus dispersal limitation than the phytoplankton communities. Furthermore, we detected that zooplankton exhibited wider habitat niche breadths and dispersal abilities than phytoplankton. Our findings also showed that environmental pollution affected high trophic organisms via food webs; the presence of heavy metals in the Bohai Sea altered the abundance of some phytoplankton, and thus modified the zooplankton that feed on them.}, }
@article {pmid33956174, year = {2021}, author = {Zhou, Q and He, R and Zhao, D and Zeng, J and Yu, Z and Wu, QL}, title = {Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33956174}, issn = {1432-184X}, support = {32022050 and 31971478//National Natural Science Foundation of China/ ; U2040201//National Natural Science Foundation of China/ ; 41871096//National Natural Science Foundation of China/ ; 2021NIGLAS-CJH01//the Project of Young Scientist Group of NIGLAS/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; BK20181311//Natural Science Foundation of Jiangsu Province/ ; }, abstract = {Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.}, }
@article {pmid33955463, year = {2021}, author = {d'Enfert, C and Kaune, AK and Alaban, LR and Chakraborty, S and Cole, N and Delavy, M and Kosmala, D and Marsaux, B and Fróis-Martins, R and Morelli, M and Rosati, D and Valentine, M and Xie, Z and Emritloll, Y and Warn, PA and Bequet, F and Bougnoux, ME and Bornes, S and Gresnigt, MS and Hube, B and Jacobsen, ID and Legrand, M and Leibundgut-Landmann, S and Manichanh, C and Munro, CA and Netea, MG and Queiroz, K and Roget, K and Thomas, V and Thoral, C and Van den Abbeele, P and Walker, AW and Brown, AJP}, title = {The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {3}, pages = {}, doi = {10.1093/femsre/fuaa060}, pmid = {33955463}, issn = {1574-6976}, abstract = {Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.}, }
@article {pmid33954842, year = {2021}, author = {Fernández-Juárez, V and Jaén-Luchoro, D and Brito-Echeverría, J and Agawin, NSR and Bennasar-Figueras, A and Echeveste, P}, title = {Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33954842}, issn = {1432-184X}, support = {11170837//Fondecyt Iniciación/ ; EQM120137//FONDEQUIP/ ; 170403//REDI/ ; CTM2016-75457-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.}, }
@article {pmid33953314, year = {2021}, author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM}, title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {530}, pmid = {33953314}, issn = {2399-3642}, abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.}, }
@article {pmid33952668, year = {2021}, author = {Lesniak, NA and Schubert, AM and Sinani, H and Schloss, PD}, title = {Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33952668}, issn = {2379-5042}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, abstract = {The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. difficile colonization. To elucidate the changes necessary to clear colonization, we compared differences in bacterial abundance between communities able and unable to clear C. difficile colonization. We treated mice with titrated doses of antibiotics prior to C. difficile challenge, resulting in no colonization, colonization and clearance, or persistent colonization. Previously, we observed that clindamycin-treated mice were susceptible to colonization but spontaneously cleared C. difficile Therefore, we investigated whether other antibiotics would show the same result. We found that reduced doses of cefoperazone and streptomycin permitted colonization and clearance of C. difficile Mice that cleared colonization had antibiotic-specific community changes and predicted interactions with C. difficile Clindamycin treatment led to a bloom in populations related to Enterobacteriaceae Clearance of C. difficile was concurrent with the reduction of those blooming populations and the restoration of community members related to the Porphyromonadaceae and Bacteroides Cefoperazone created a susceptible community characterized by drastic reductions in the community diversity and interactions and a sustained increase in the abundance of many facultative anaerobes. Lastly, clearance in streptomycin-treated mice was associated with the recovery of multiple members of the Porphyromonadaceae, with little overlap in the specific Porphyromonadaceae observed in the clindamycin treatment. Further elucidation of how C. difficile colonization is cleared from different gut bacterial communities will improve C. difficile infection treatments.IMPORTANCE The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The recurrent infection cycle often ends when the fecal microbiota from a presumed resistant person is transplanted into the susceptible person. Although this treatment is highly effective, we do not understand the mechanism. We hope to improve the treatment of CDI through elucidating how the bacterial community eliminates CDI. We found that C. difficile colonized susceptible mice but was spontaneously eliminated in an antibiotic treatment-specific manner. These data indicate that each community had different requirements for clearing colonization. Understanding how different communities clear colonization will reveal targets to improve CDI treatments.}, }
@article {pmid33952552, year = {2021}, author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE}, title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.}, journal = {BMJ open}, volume = {11}, number = {5}, pages = {e047069}, pmid = {33952552}, issn = {2044-6055}, support = {R03 AG064260/AG/NIA NIH HHS/United States ; }, mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; }, abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.<br><br>METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (≤7 days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.<br><br>ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04399252.}, }
@article {pmid33952355, year = {2021}, author = {Baker, JM and Hinkle, KJ and McDonald, RA and Brown, CA and Falkowski, NR and Huffnagle, GB and Dickson, RP}, title = {Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {99}, pmid = {33952355}, issn = {2049-2618}, support = {R01 AI138348/AI/NIAID NIH HHS/United States ; R01 HL121774/HL/NHLBI NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; DNA, Bacterial/genetics ; Female ; Lung ; Mice ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice.<br><br>RESULTS: Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls.<br><br>CONCLUSIONS: An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.}, }
@article {pmid33948706, year = {2021}, author = {Stabili, L and Di Salvo, M and Alifano, P and Talà, A}, title = {An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33948706}, issn = {1432-184X}, support = {LIFE16 ENV/IT/000343//LIFE Environment and Resource Efficiency 2016/ ; }, abstract = {As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.}, }
@article {pmid33947808, year = {2021}, author = {Boysen, AK and Carlson, LT and Durham, BP and Groussman, RD and Aylward, FO and Ribalet, F and Heal, KR and White, AE and DeLong, EF and Armbrust, EV and Ingalls, AE}, title = {Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947808}, issn = {2379-5077}, abstract = {Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community-level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2% of total particulate organic carbon (POC). The concentrations of 55/79 (70%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscriptome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that trehalose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabolites and transcripts resolve strategies that microbes use to manage daily energy and redox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems.IMPORTANCE Fueled by light, phytoplankton produce the organic matter that supports ocean ecosystems and carbon sequestration. Ocean change impacts microbial metabolism with repercussions for biogeochemical cycling. As the small molecule products of cellular metabolism, metabolites often change rapidly in response to environmental conditions and form the basis of energy and nutrient management and storage within cells. By pairing measurements of metabolites and gene expression in the stratified surface ocean, we reveal strategies of microbial energy management over the day-night cycle and hypothesize that oscillating metabolites are important substrates for dark respiration by phytoplankton. These high-resolution diel measurements of in situ metabolite concentrations form the basis for future work into the specific roles these compounds play in marine microbial communities.}, }
@article {pmid33947800, year = {2021}, author = {Heal, KR and Durham, BP and Boysen, AK and Carlson, LT and Qin, W and Ribalet, F and White, AE and Bundy, RM and Armbrust, EV and Ingalls, AE}, title = {Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947800}, issn = {2379-5077}, abstract = {Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus, and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition.IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure.}, }
@article {pmid33940748, year = {2021}, author = {Guarin, TC and Pagilla, KR}, title = {Microbial community in biofilters for water reuse applications: A critical review.}, journal = {The Science of the total environment}, volume = {773}, number = {}, pages = {145655}, doi = {10.1016/j.scitotenv.2021.145655}, pmid = {33940748}, issn = {1879-1026}, mesh = {*Drinking Water ; Filtration ; *Microbiota ; Reproducibility of Results ; *Water Purification ; }, abstract = {The combination of ozonation (O3) and biofiltration processes has become practical and desirable in advanced water reclamation for water reuse applications. However, the role of microbial community and its characteristics (source, abundance, composition, viability, structure) on treatment performance has not received the same attention in water reclamation biofilters as in other applications, such as in drinking water biofilters. Microbial community characterization of biofilters used in water reuse applications will add evidence to better understand the potential microorganisms, consequent risks, and mechanisms that will populate drinking water sources and ultimately influence public health and the environment. This critical review provides insights into O3-biofiltration as a treatment barrier with a focus on development, structure, and composition of the microbial community characteristics involved in the process. The effect of microorganism seeding by the influent before and after the biofilter and ozone oxidation effects are explored to capture the microbial ecology interactions and environmental factors affecting the media ecosystem. The findings of reviewed studies concurred in identifying Proteobacteria as the most dominant phylum. However, Proteobacteria and other phyla relative abundance differ substantially depending upon environmental factors (e.g., pH, temperature, nutrients availability, among others) gradients. In general, we found significant gaps to relate and explain the biodegradation performance and metabolic processes within the biofilter, and hence deserve future attention. We highlighted and identified key challenges and future research ideas to assure O3-biofiltration reliability as a promising barrier in advanced water treatment applications.}, }
@article {pmid33935412, year = {2021}, author = {Sergaliev, NK and Kakishev, MG and Ginayatov, NS and Nurzhanova, FK and Andronov, EE}, title = {Microbiome structure in a recirculating aquaculture system and its connection to infections in sturgeon fish.}, journal = {Veterinary world}, volume = {14}, number = {3}, pages = {661-668}, pmid = {33935412}, issn = {0972-8988}, abstract = {Aim: This study aimed to determine the bacterial composition at various stages of the temperature regime in a recirculating aquaculture system (RAS) to assess the pathological risk of a group of opportunistic pathogenic microflora.<br><br>Materials and Methods: Water temperature, incidences of illnesses, and fish mortality were monitored, during the research period to identify the causes of pathogens in sturgeons. Analysis of the nucleotide sequences was performed using the quantitative insights into microbial ecology module. Sequence alignment in the analysis of the distribution of gene libraries was performed using the Unclust method. The RDP database was used for the taxonomic identification of operational taxonomic units.<br><br>Results: The pattern of the contraction of infection among sturgeons bred in the RAS was established. A detailed analysis of the microbiome structure's taxonomic features showed dominant taxa during the "artificial wintering" period and at a temperature optimum in industrial aquaculture. It was found that the main outbreaks of pseudomonosis occurred during this period in the RAS. With a decrease in temperature of the aquatic environment, the incidence of illness increased by 75% compared with the optimum temperature period. Pseudomonas, Cetobacterium, and Lactococcus were specific taxa characteristic for the "artificial wintering" period. Xanthomonadaceae and Flavobacterium were specific taxa characteristic for the optimum temperature.<br><br>Conclusion: Consequently, the microbial structure was determined at different temperature regimes in a RAS, and the dominant communities were identified. The pattern of the contraction of infection caused by an opportunistic microflora (pseudomonosis) among sturgeons was established, allowing for the development and correction of treatment and preventive measures.}, }
@article {pmid33933764, year = {2021}, author = {Vermeire, ML and Thoresen, J and Lennard, K and Vikram, S and Kirkman, K and Swemmer, AM and Te Beest, M and Siebert, F and Gordijn, P and Venter, Z and Brunel, C and Wolfaard, G and Krumins, JA and Cramer, MD and Hawkins, HJ}, title = {Fire and herbivory drive fungal and bacterial communities through distinct above- and belowground mechanisms.}, journal = {The Science of the total environment}, volume = {785}, number = {}, pages = {147189}, doi = {10.1016/j.scitotenv.2021.147189}, pmid = {33933764}, issn = {1879-1026}, mesh = {Bacteria ; Biomass ; Ecosystem ; *Fires ; Fungi ; Grassland ; *Herbivory ; Soil ; Soil Microbiology ; }, abstract = {Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition and diversity (using 16S and ITS rRNA amplicon sequencing, respectively) in six long-term (18 to 70 years) ecological research sites in South African savanna and grassland ecosystems. We found that fire and herbivory regimes profoundly modified soil physico-chemical properties, plant species richness and standing biomass. In all sites, an increase in woody biomass (ranging from 12 to 50%) was observed when natural disturbances were excluded. The intensity and direction of changes in soil properties were highly dependent on the topo-pedo-climatic context. Overall, fire and herbivory shaped bacterial and fungal communities through distinct driving forces: edaphic properties (including Mg, pH, Ca) for bacteria, and vegetation (herbaceous biomass and woody cover) for fungi. Fire and herbivory explained on average 7.5 and 9.8% of the fungal community variability, respectively, compared to 6.0 and 5.6% for bacteria. The relatively small changes in microbial communities due to natural disturbance is in stark contrast to dramatic vegetation and edaphic changes and suggests that soil microbial communities, having evolved with disturbance, are resistant to change. This represents both a buffer to short-term anthropogenic-induced changes and a restoration challenge in the face of long-term changes.}, }
@article {pmid33931358, year = {2021}, author = {Lucas, SK and Feddema, E and Boyer, HC and Hunter, RC}, title = {Diversity of cystic fibrosis chronic rhinosinusitis microbiota correlates with different pathogen dominance.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2021.03.022}, pmid = {33931358}, issn = {1873-5010}, abstract = {Chronic rhinosinusitis (CRS) affects nearly all individuals with cystic fibrosis (CF) and is thought to serve as a reservoir for microbiota that subsequently colonize the lung. To better understand the microbial ecology of CRS, we generated a 16S rRNA gene sequencing profile of sinus mucus from CF-CRS patients. We show that CF-CRS sinuses harbor bacterial diversity not entirely captured by clinical culture. Culture data consistently identified the dominant organism in most patients, though lower abundance bacteria were not always identified. We also demonstrate that bacterial communities dominated by Staphylococcus spp. were significantly more diverse compared to those dominated by Pseudomonas spp. Diversity was not significantly associated with clinical factors or patient age, however, younger subjects yielded a much wider range of bacterial diversity. These data mirror bacterial community dynamics in the lung and provide additional insight into the role of sinus microbiota in chronic airway disease progression.}, }
@article {pmid33930130, year = {2021}, author = {Co, R and Hug, LA}, title = {Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {5}, pages = {}, doi = {10.1093/femsec/fiab065}, pmid = {33930130}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Waste Disposal Facilities ; }, abstract = {Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.}, }
@article {pmid33928761, year = {2021}, author = {Wilson, JM and Chamberlain, EJ and Erazo, N and Carter, ML and Bowman, JS}, title = {Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {3225-3239}, doi = {10.1111/1462-2920.15548}, pmid = {33928761}, issn = {1462-2920}, support = {NA11NOS120029//National Oceanic and Atmospheric Administration/ ; NA16NOS0120022//National Oceanic and Atmospheric Administration/ ; NA17RJ1231//National Oceanic and Atmospheric Administration/ ; //Simons Foundation Early Career Marine Microbial Ecology &amp; Evolution/ ; }, abstract = {A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.}, }
@article {pmid33928415, year = {2021}, author = {Solans, M and Pelliza, YI and Tadey, M}, title = {Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33928415}, issn = {1432-184X}, support = {PIP 0235.//Conicet/ ; PICT 3478//FONCYT/ ; }, abstract = {Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.}, }
@article {pmid33927711, year = {2021}, author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA}, title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {673810}, pmid = {33927711}, issn = {1664-302X}, abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.}, }
@article {pmid33927707, year = {2021}, author = {Orevi, T and Kashtan, N}, title = {Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {655459}, pmid = {33927707}, issn = {1664-302X}, abstract = {While many natural and artificial surfaces may appear dry, they are in fact covered by thin liquid films and microdroplets invisible to the naked eye known as microscopic surface wetness (MSW). Central to the formation and the retention of MSW are the deliquescent properties of hygroscopic salts that prevent complete drying of wet surfaces or that drive the absorption of water until dissolution when the relative humidity is above a salt-specific level. As salts are ubiquitous, MSW occurs in many microbial habitats, such as soil, rocks, plant leaf, and root surfaces, the built environment, and human and animal skin. While key properties of MSW, including very high salinity and segregation into droplets, greatly affect microbial life therein, it has been scarcely studied, and systematic studies are only in their beginnings. Based on recent findings, we propose that the harsh micro-environment that MSW imposes, which is very different from bulk liquid, affects key aspects of bacterial ecology including survival traits, antibiotic response, competition, motility, communication, and exchange of genetic material. Further research is required to uncover the fundamental principles that govern microbial life and ecology in MSW. Such research will require multidisciplinary science cutting across biology, physics, and chemistry, while incorporating approaches from microbiology, genomics, microscopy, and computational modeling. The results of such research will be critical to understand microbial ecology in vast terrestrial habitats, affecting global biogeochemical cycles, as well as plant, animal, and human health.}, }
@article {pmid33925970, year = {2021}, author = {Saw, NMMT and Suwanchaikasem, P and Zuniga-Montanez, R and Qiu, G and Marzinelli, EM and Wuertz, S and Williams, RBH}, title = {Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR).}, journal = {Metabolites}, volume = {11}, number = {5}, pages = {}, pmid = {33925970}, issn = {2218-1989}, support = {1102-IRIS-10-02//National Research Foundation, Republic of Singapore/ ; }, abstract = {Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study.}, }
@article {pmid33923841, year = {2021}, author = {van der Linde, C and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Swann, JR and Costabile, A}, title = {An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {33923841}, issn = {1420-3049}, mesh = {*Chlorella ; Enterobacteriaceae/classification/genetics ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; RNA, Ribosomal, 16S ; }, abstract = {The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by1H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.}, }
@article {pmid33922357, year = {2021}, author = {Oh, RM and Bollati, E and Maithani, P and Huang, D and Wainwright, BJ}, title = {The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {33922357}, issn = {2076-2607}, abstract = {The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.}, }
@article {pmid33920240, year = {2021}, author = {Skliros, D and Kalatzis, PG and Kalloniati, C and Komaitis, F and Papathanasiou, S and Kouri, ED and Udvardi, MK and Kokkari, C and Katharios, P and Flemetakis, E}, title = {The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy.}, journal = {Viruses}, volume = {13}, number = {4}, pages = {}, pmid = {33920240}, issn = {1999-4915}, abstract = {Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.}, }
@article {pmid33919845, year = {2021}, author = {Thompson, HJ and Levitt, JO and McGinley, JN and Chandler, P and Guenther, PM and Huybrechts, I and Playdon, MC}, title = {Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure.}, journal = {Nutrients}, volume = {13}, number = {4}, pages = {}, pmid = {33919845}, issn = {2072-6643}, support = {5R00CA218694-03/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Algorithms ; Chronic Disease/prevention &amp; control ; Diet Surveys/*methods/statistics &amp; numerical data ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; *Phytochemicals ; Plants, Edible/*chemistry ; }, abstract = {The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.}, }
@article {pmid33918726, year = {2021}, author = {Khomutovska, N and de Los Ríos, A and Syczewski, MD and Jasser, I}, title = {Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan).}, journal = {Biology}, volume = {10}, number = {4}, pages = {}, pmid = {33918726}, issn = {2079-7737}, support = {DSM501-D114-86-0117600-16//Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw/ ; PID2019-105469RB-C22//Ministerio de Ciencia e Innovación/ ; 2015/19/B/NZ9/00473//Narodowe Centrum Nauki/ ; }, abstract = {Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria-Proteobacteria-Bacteroidetes-Chloroflexi-Cyanobacteria, while the BSCs' can be described as Proteobacteria-Actinobacteria-Bacteroidetes-Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches' specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.}, }
@article {pmid33911260, year = {2021}, author = {Kremer, JM and Sohrabi, R and Paasch, BC and Rhodes, D and Thireault, C and Schulze-Lefert, P and Tiedje, JM and He, SY}, title = {Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research.}, journal = {Nature protocols}, volume = {16}, number = {5}, pages = {2450-2470}, pmid = {33911260}, issn = {1750-2799}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Arabidopsis/*growth &amp; development/*microbiology ; Culture Techniques/*methods ; Germ-Free Life ; Industry ; *Microbiota ; Soil/*chemistry ; }, abstract = {The complex structure and function of a plant microbiome are driven by many variables, including the environment, microbe-microbe interactions and host factors. Likewise, resident microbiota can influence many host phenotypes. Gnotobiotic growth systems and controlled environments empower researchers to isolate these variables, and standardized methods equip a global research community to harmonize protocols, replicate experiments and collaborate broadly. We developed two easily constructed peat-based gnotobiotic growth platforms: the FlowPot system and the GnotoPot system. Sterile peat is amenable to colonization by microbiota and supports growth of the model plant Arabidopsis thaliana in the presence or absence of microorganisms. The FlowPot system uniquely allows one to flush the substrate with water, nutrients and/or suspensions of microbiota via an irrigation port, and a mesh retainer allows for the inversion of plants for dip or vacuum infiltration protocols. The irrigation port also facilitates passive drainage, preventing root anoxia. In contrast, the GnotoPot system utilizes a compressed peat pellet, widely used in the horticultural industry. GnotoPot construction has fewer steps and requires less user handling, thereby reducing the risk of contamination. Both protocols take up to 4 d to complete with 4-5 h of hands-on time, including substrate and seed sterilization. In this protocol, we provide detailed assembly and inoculation procedures for the two systems. Both systems are modular, do not require a sterile growth chamber, and cost less than US$2 per vessel.}, }
@article {pmid33906488, year = {2021}, author = {García-González, I and Corona-Cervantes, K and Hernández-Quiroz, F and Villalobos-Flores, LE and Galván-Rodríguez, F and Romano, MC and Miranda-Brito, C and Piña-Escobedo, A and Borquez-Arreortúa, FG and Rangel-Calvillo, MN and García-Mena, J}, title = {The Effect of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing.}, journal = {Journal of human lactation : official journal of International Lactation Consultant Association}, volume = {}, number = {}, pages = {8903344211011946}, doi = {10.1177/08903344211011946}, pmid = {33906488}, issn = {1552-5732}, abstract = {BACKGROUND: Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization.<br><br>RESEARCH AIM: To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process.<br><br>METHODS: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors (N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment.<br><br>RESULTS: A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples.<br><br>CONCLUSION: The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.}, }
@article {pmid33903927, year = {2021}, author = {Kajan, K and Cukrov, N and Cukrov, N and Bishop-Pierce, R and Orlić, S}, title = {Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33903927}, issn = {1432-184X}, support = {KK.01.1.1.01//European Regional Development Fund/ ; }, abstract = {Anchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.}, }
@article {pmid33902741, year = {2021}, author = {Zhou, X and Leite, MFA and Zhang, Z and Tian, L and Chang, J and Ma, L and Li, X and van Veen, JA and Tian, C and Kuramae, EE}, title = {Facilitation in the soil microbiome does not necessarily lead to niche expansion.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {4}, pmid = {33902741}, issn = {2524-6372}, support = {XDA23070501, XDB15030103//Science Foundation of the Chinese Academy of Sciences/ ; 2016YFC0501202//National Key Research and Development Program of China/ ; KFZD-SW-112//Key Research Project of the Chinese Academy of Sciences/ ; 41571255//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown.<br><br>RESULTS: Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent.<br><br>CONCLUSIONS: Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.}, }
@article {pmid33902740, year = {2020}, author = {Chopyk, J and Nasko, DJ and Allard, S and Bui, A and Pop, M and Mongodin, EF and Sapkota, AR}, title = {Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {18}, pmid = {33902740}, issn = {2524-6372}, support = {2016-68007-25064//United States Department of Agriculture-National Institute of Food and Agriculture/ ; 1632976//National Science Foundation/ ; }, abstract = {BACKGROUND: Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.<br><br>RESULTS: Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.<br><br>CONCLUSIONS: Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.}, }
@article {pmid33902721, year = {2020}, author = {Tang, X and Xie, G and Shao, K and Hu, Y and Cai, J and Bai, C and Gong, Y and Gao, G}, title = {Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {10}, pmid = {33902721}, issn = {2524-6372}, support = {NIGLAS2017GH05//"One-Three-Five" Strategic Planning of NGLAS, CAS/ ; 41971062//National Natural Science Foundation of China/ ; 41790423//National Natural Science Foundation of China/ ; 41621002//National Natural Science Foundation of China/ ; QYZDJ-SSW-DQC008//Key Research Program of Frontier Sciences, CAS/ ; }, abstract = {BACKGROUND: Microorganisms in rivers and lakes are essential for nutrient recycling in aquatic ecosystems. Understanding the ecological processes shaping microbial communities is of crucial importance for aquatic microbial ecology and biogeography. However, the diversity of microorganisms and the forces that control this diversity are poorly understood. This is particularly true within the framework of the river-lake continuum in arid regions.<br><br>RESULTS: Using a whole catchment-sampling effort, we explored biogeographical patterns and mechanisms of microbial community (bacteria and archaea) assembly within the catchment of the largest inland once freshwater lake (Lake Bosten) in China. Water samples from headstream tributaries, the mainstream of the River Kaidu to downstream Lake Bosten were characterized using amplicon sequencing of 16S rRNA genes. Higher α-diversity was found in mainstream of River Kaidu and in the tributaries compared with Lake Bosten. And the microbial community composition was also significantly different between the lake and its connected river habitats. Canonical correspondence analysis demonstrated that salinity and total suspended solids were the most important environmental factors shaping the community variations. Overall, pure environmental and pure spatial factors explained 13.7 and 5.6% of the community variation, respectively, while 32.0% of the variation was explained by combined environmental and spatial variables. These observations suggested that spatially structured environmental variations mainly shaped the microbial biogeography in this region. Both deterministic and stochastic processes influenced the microbial community assembly in river and lake habitats, and the stochastic pattern was particularly pronounced for microbiome in river habitat. Co-occurrence network analysis revealed more abundant and complicated correlations among frequently occurred taxa in lake habitat compared with the river habitat, implying that ecological multispecies interactions (e.g., competition) shaped lake microbial community structures.<br><br>CONCLUSIONS: Our findings demonstrate an ecological succession along the river-lake continuum of microbial communities across the largest inland once freshwater lake basin in China, and highlight the effects of spatially structured environmental factors on regional microbial β-diversity and species interactions on local community assembly.}, }
@article {pmid33902717, year = {2020}, author = {Bagnaro, A and Baltar, F and Brownstein, G and Lee, WG and Morales, SE and Pritchard, DW and Hepburn, CD}, title = {Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {16}, pmid = {33902717}, issn = {2524-6372}, abstract = {BACKGROUND: One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries.<br><br>RESULTS: We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time.<br><br>CONCLUSION: We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.}, }
@article {pmid33901904, year = {2021}, author = {Rahman, MS and Kazmi, SSUH and Uroosa,  and Xu, H}, title = {Insights into seasonal shift in the homogeneity of periphytic protozoan fauna in coastal waters of the Yellow Sea, northern China.}, journal = {Marine pollution bulletin}, volume = {168}, number = {}, pages = {112367}, doi = {10.1016/j.marpolbul.2021.112367}, pmid = {33901904}, issn = {1879-3363}, mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Seasons ; }, abstract = {The seasonal shift in the homogeneity of the periphytic protozoan fauna was studied based on a four-season baseline survey in the coastal waters of the Yellow Sea, northern China. Samples were collected using glass microscope slides as an artificial substratum at a depth of 2 m after the immersion time of 14 days during each of the four seasons (winter, spring, summer, and autumn, 2017). The protozoan fauna showed a clear seasonal shift in species composition and a significant variation in homogeneity in terms of both compositional and community structure during four seasons. The dispersion measures and β-diversity index represented an increase in the trend from spring to winter. These findings suggest that the homogeneity of the periphytic protozoan fauna was subject to a significant variability shaped mainly by species composition during a four-season cycle in marine ecosystems.}, }
@article {pmid33900007, year = {2021}, author = {Pham, VHT and Ahn, JY and Ro, YH and Ravindran, B and Kim, JS and Chang, SW and Shim, JH and Chung, WJ}, title = {The efficiency of potential food waste-degrading bacteria under harsh conditions.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15119}, pmid = {33900007}, issn = {1365-2672}, abstract = {AIMS: Investigate the impact of highly adapted bacterial strains and their ability in waste degradation under a wide range of temperatures.<br><br>METHODS AND RESULTS: Bacteria isolated from soil and food waste were grown in various media under fluctuated temperatures. After screening for organic compound degradation, the seven strongest bacterial strains have been selected for further experiments. Their enzyme activities were expressed in terms of the size of the hydrolysis zone in a wide temperature range of 2.5-70 ºC. The enzyme production assay was carried out for each protease, cellulase, and amylase. The waste degradation was determined with a maximum 80% decrease in the volume of food waste in 21 days compared to the control in lab-scale with enriched bacterial cultures and soil bacteria as additives at room temperature around 18 ºC-20 ºC.<br><br>CONCLUSION: These seven bacteria are promising candidates for food waste biodegradation in composting especially in the winter without heating expense for maintaining ambient temperature.<br><br>It is necessary to coax the uncultured bacteria from the various environments into the laboratory for investigating their valuable functions. Herein, using enrichment culture of consortium and additive of soil have illustrated the significant mean in food waste degradation.}, }
@article {pmid33899919, year = {2021}, author = {Lin, Q and Dini-Andreote, F and Li, L and Umari, R and Novotny, V and Kukla, J and Heděnec, P and Frouz, J}, title = {Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {5}, pages = {}, doi = {10.1093/femsec/fiab063}, pmid = {33899919}, issn = {1574-6941}, mesh = {Agriculture ; Basidiomycota ; *Burns ; Ecosystem ; Forests ; Fungi/genetics ; Humans ; Papua New Guinea ; *Soil ; Soil Microbiology ; }, abstract = {Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.}, }
@article {pmid33897672, year = {2021}, author = {Estrela, S and Sánchez, Á and Rebolleda-Gómez, M}, title = {Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {657467}, pmid = {33897672}, issn = {1664-302X}, abstract = {Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.}, }
@article {pmid33893533, year = {2021}, author = {Ding, L and Zhou, J and Li, Q and Tang, J and Chen, X}, title = {Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33893533}, issn = {1432-184X}, support = {2016YFC0502703//the National Key Research and Development Program of China/ ; 31470483//National Natural Science Foundation of China/ ; 31570411//National Natural Science Foundation of China/ ; }, abstract = {Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.}, }
@article {pmid33893532, year = {2021}, author = {Maltsev, Y and Maltseva, S and Maltseva, I}, title = {Diversity of Cyanobacteria and Algae During Primary Succession in Iron Ore Tailing Dumps.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33893532}, issn = {1432-184X}, abstract = {The extraction of commercial minerals is often accompanied by the formation of large areas of quarry and dump technogenic ecosystems. This stimulates the search for measures to reduce their negative impact on the environment, as well as a detailed study of all the constituent elements of ecosystems that spontaneously or after reclamation form on them. Primary stages of syngenesis on the tailing dumps of iron ore mines in Kryvorizhzhia took place involving cyanobacteria and eukaryotic algae. The dynamics of the community structures of algae and cyanobacteria depends on the mineralogical composition of tailings, salinity conditions, pH, and content of particles of physical clay and humus. The assessment of the features of the dynamics of algae communities was carried out based on the ordination procedure because of the method of non-metric multidimensional scaling. The considered environmental variables were statistically significant predictors of community structure and could explain 47-90% of the variation in measurements. Diagnostic signs of the species composition of communities of algae and cyanobacteria tailing dumps were established by physical and chemical parameters. An increase in the content of physical clay particles in the substrate and a pH shift towards the alkaline side increased the species richness of cyanobacteria, while an increase in the humus content increased the total species diversity. Based on the specificity of the type of growth and the species composition of algae communities, when describing the primary successions, it is proposed to allocate the following stages of development of algae and cyanobacteria communities: dispersal aerophyton, stratose epilitophyton, algal crust, mixed moss and algal crust, and edaphone.}, }
@article {pmid33892834, year = {2021}, author = {Delikan, E and Caliskan, S and Cankilic, MY and Aksu, S and Kesim, B and Ulger, ST}, title = {Microbiota of Endodontically Infected Primary and Permanent Teeth.}, journal = {Pediatric dentistry}, volume = {43}, number = {2}, pages = {102-110}, pmid = {33892834}, issn = {1942-5473}, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Tooth, Deciduous ; }, abstract = {Purpose: Differences in the endodontic microbiome of permanent and primary teeth during the mixed dentition period are still unknown. The purpose of this study was to examine bacterial diversity in endodontically infected primary and permanent teeth using 16S rRNA gene sequencing and the QIIME 2 (Quantitative Insights Into Microbial Ecology 2) bioinformatics pipeline. Methods: Microbial samples from endodontically infected primary (n equals 15) and permanent (n equals 15) maxillary or mandibular molar teeth were subjected to next-generation sequencing analysis based on examination of the hypervariable V3 to V4 region of the 16S rRNA gene. Statistical analysis was performed using R software. Results: Of 1,664,926 reads and 2,237 operational taxonomic units, 14 phyla, 89 families, and 236 genera were identified. Firmicutes were the most commonly detected phyla in both endodontically infected primary and permanent root canals. Bacteroides and Proteobacteria were more common in primary teeth, whereas Actinobacteria and Verrucomicrobia were more common in permanent teeth. The overall canal microbiota composition was similar in endodontically infected primary and permanent teeth (P=0.338). Conclusions: This study provides a comprehensive assessment of microbiota composition in endodontically infected primary and permanent teeth and gives a deeper insight into the origin of the root canal infections.}, }
@article {pmid33891367, year = {2021}, author = {Wang, T and Persson, P and Tunlid, A}, title = {A widespread mechanism in ectomycorrhizal fungi to access nitrogen from mineral-associated proteins.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15539}, pmid = {33891367}, issn = {1462-2920}, support = {2013.0073//Knut och Alice Wallenbergs Stiftelse/ ; 2016-04561//The Swedish Research Council (VR)/ ; 2017-04261//The Swedish Research Council (VR)/ ; }, abstract = {A large fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and minerals limits microbial accessibility to this source, which is a relatively stable reservoir of soil N. We have shown that the ectomycorrhizal (ECM) fungus Paxillus involutus can acquire N from iron oxide-associated proteins. Using tightly controlled isotopic, spectroscopic and chromatographic experiments, we demonstrated that the capacity to access N from iron oxide-associated bovine serum albumin (BSA) is shared with the ECM fungi Hebeloma cylindrosporum and Piloderma olivaceum. Despite differences in evolutionary history, growth rates, exploration types and the decomposition mechanisms of organic matter, their N acquisition mechanisms were similar to those described for P. involutus. The fungi released N from mineral-associated BSA by direct action of extracellular aspartic proteases on the mineral-associated BSA, without initial desorption of the protein. Hydrolysis was suppressed by the adsorption of proteases to minerals, but this adverse effect was counteracted by the secretion of compounds that conditioned the mineral surface. These data suggest that the enzymatic exudate-driven mechanism to access N from mineral-associated proteins is found in ECM fungi of multiple lineages and exploration types.}, }
@article {pmid33890146, year = {2021}, author = {Kanjanapruthipong, T and Sukphopetch, P and Reamtong, O and Isarangkul, D and Muangkaew, W and Thiangtrongjit, T and Sansurin, N and Fongsodsri, K and Ampawong, S}, title = {Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33890146}, issn = {1432-184X}, support = {CU_FRB640001_01_33_1//TSRI Fund/ ; }, abstract = {Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.}, }
@article {pmid33890145, year = {2021}, author = {Fisol, AFBC and Saidi, NB and Al-Obaidi, JR and Lamasudin, DU and Atan, S and Razali, N and Sajari, R and Rahmad, N and Hussin, SNIS and Mr, NH}, title = {Differential Analysis of Mycelial Proteins and Metabolites From Rigidoporus Microporus During In Vitro Interaction With Hevea Brasiliensis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33890145}, issn = {1432-184X}, support = {S16IPDM0533//Malaysian Rubber Board/ ; }, abstract = {Rigidoporus microporus is the fungus accountable for the white root rot disease that is detrimental to the rubber tree, Hevea brasiliensis. The pathogenicity mechanism of R. microporus and the identity of the fungal proteins and metabolites involved during the infection process remain unclear. In this study, the protein and metabolite profiles of two R. microporus isolates, Segamat (SEG) and Ayer Molek (AM), were investigated during an in vitro interaction with H. brasiliensis. The isolates were used to inoculate H. brasiliensis clone RRIM 2025, and mycelia adhering to the roots of the plant were collected for analysis. Transmission electron microscope (TEM) images acquired confirms the hyphae attachment and colonization of the mycelia on the root of the H. brasiliensis clones after 4 days of inoculation. The protein samples were subjected to 2-DE analysis and analyzed using MALDI-ToF MS/MS, while the metabolites were extracted using methanol and analyzed using LC/MS-QTOF. Based on the differential analyses, upregulation of proteins that are essential for fungal evolution such as malate dehydrogenase, fructose 1,6-biphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase hints an indirect role in fungal pathogenicity, while metabolomic analysis suggests an increase in acidic compounds which may lead to increased cell wall degrading enzyme activity. Bioinformatics analyses revealed that the carbohydrate and amino acid metabolisms were prominently affected in response to the fungal pathogenicity. In addition to that, other pathways that were significantly affected include "Protein Ubiquitination Pathway," Unfolded Protein Response," "HIFα Signaling," and "Sirtuin Signaling Pathway." The identification of responsive proteins and metabolites from this study promotes a better understanding of mechanisms underlying R. microporus pathogenesis and provides a list of potential biological markers for early recognition of the white root rot disease.}, }
@article {pmid33886659, year = {2021}, author = {Han, XY}, title = {Effects of climate changes and road exposure on the rapidly rising legionellosis incidence rates in the United States.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250364}, pmid = {33886659}, issn = {1932-6203}, abstract = {Legionellosis is an infection acquired through inhalation of aerosols that are contaminated with environmental bacteria Legionella spp. The bacteria require warm temperature for proliferation in bodies of water and moist soil. The legionellosis incidence in the United States has been rising rapidly in the past two decades without a clear explanation. In the meantime, the US has recorded consecutive years of above-norm temperature since 1997 and precipitation surplus since 2008. The present study analyzed the legionellosis incidence in the US during the 20-year period of 1999 to 2018 and correlated with concurrent temperature, precipitation, solar ultraviolet B (UVB) radiation, and vehicle mileage data. The age-adjusted legionellosis incidence rates rose exponentially from 0.40/100,000 in 1999 (with 1108 cases) to 2.69/100,000 in 2018 (with 9933 cases) at a calculated annual increase of 110%. In regression analyses, the rise correlated with an increase in vehicle miles driven and with temperature and precipitation levels that have been above the 1901-2000 mean since 1997 and 2008, respectively, suggesting more road exposure to traffic-generated aerosols and promotive effects of anomalous climate. Remarkably, the regressions with cumulative anomalies of temperature and precipitation were robust (R2 ≥ 0.9145, P ≤ 4.7E-11), implying possible changes to microbial ecology in the terrestrial and aquatic environments. An interactive synergy between annual precipitation and vehicle miles was also found in multiple regressions. Meanwhile, the bactericidal UVB radiation has been decreasing, which also contributed to the rising incidence in an inverse correlation. The 2018 legionellosis incidence peak corresponded to cumulative effects of the climate anomalies, vast vehicle miles (3,240 billion miles, 15904 km per capita), record high precipitation (880.1 mm), near record low UVB radiation (7488 kJ/m2), and continued above-norm temperature (11.96°C). These effects were examined and demonstrated in California, Florida, New Jersey, Ohio, and Wisconsin, states that represent diverse incidence rates and climates. The incidence and above-norm temperature both rose most in cold Wisconsin. These results suggest that warming temperature and precipitation surplus have likely elevated the density of Legionella bacteria in the environment, and together with road exposure explain the rapidly rising incidence of legionellosis in the United States. These trends are expected to continue, warranting further research and efforts to prevent infection.}, }
@article {pmid33886638, year = {2021}, author = {Colda, A and Bossaert, S and Verreth, C and Vanhoutte, B and Honnay, O and Keulemans, W and Lievens, B}, title = {Inoculation of pear flowers with Metschnikowia reukaufii and Acinetobacter nectaris enhances attraction of honeybees and hoverflies, but does not increase fruit and seed set.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250203}, pmid = {33886638}, issn = {1932-6203}, abstract = {Currently, one of the most important challenges is to provide sufficient and affordable food and energy for a fast-growing world population, alongside preserving natural habitats and maintaining biodiversity. About 35% of the global food production depends on animals for pollination. In recent years, an alarming worldwide decline in pollinators has been reported, putting our food production under additional pressure. Therefore, there is an urgent need to find sustainable ways to ensure this crucial ecosystem service. Recent studies have shown that floral nectar is generally colonized by microorganisms, specifically yeasts and bacteria, which may alter nectar chemistry and enhance attraction of pollinators. In this study, we investigated changes in pollinator foraging behavior and pollination success in European pear (Pyrus communis L.) cultivars 'Regal Red' and 'Sweet Sensation' (red sports of 'Doyenné de Comice') after flower inoculation with the typical nectar-inhabiting microorganisms Metschnikowia reukaufii and Acinetobacter nectaris, and a combination of both. Pollination success was monitored by measuring the number of flower visits, fruit set and seed set in two consecutive years, 2019 and 2020. Results revealed that application of a mixture of M. reukaufii and A. nectaris resulted in significantly higher visitation rates of honeybees and hoverflies. By contrast, no effects on flower visits were found when yeasts and bacteria were applied separately. Fruit set and seed set were not significantly affected by any of the inoculation treatments. The only factors affecting fruit set were initial number of flower clusters on the trees and the year. The absence of treatment effects can most likely be attributed to the fact that pollination was not a limiting factor for fruit set in our experiments. Altogether, our results show that inoculation of flowers with nectar microbes can modify pollinator foraging patterns, but did not lead to increased pollination success under the conditions tested.}, }
@article {pmid33886557, year = {2021}, author = {Hewson, I and Sewell, MA}, title = {Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0241026}, pmid = {33886557}, issn = {1932-6203}, abstract = {Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.}, }
@article {pmid33885917, year = {2021}, author = {Wallenborn, JT and Gunier, RB and Pappas, DJ and Chevrier, J and Eskenazi, B}, title = {Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33885917}, issn = {1432-184X}, support = {1R01ES020360-01//Foundation for the National Institutes of Health/ ; }, abstract = {Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4-V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray-Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads.}, }
@article {pmid33880762, year = {2021}, author = {Zeng, T and Yu, X and Chen, Z}, title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {832-840}, doi = {10.1111/jgh.15503}, pmid = {33880762}, issn = {1440-1746}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.}, }
@article {pmid33880565, year = {2021}, author = {Golob, JL and Rao, K}, title = {Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {Supplement_3}, pages = {S214-S221}, pmid = {33880565}, issn = {1537-6613}, support = {R01 HS027431/HS/AHRQ HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; }, abstract = {Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.}, }
@article {pmid33879498, year = {2021}, author = {Taylor, M and Vega, NM}, title = {Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33879498}, issn = {2379-5077}, abstract = {A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation-and the consequences for the ecology of these communities-remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology.IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.}, }
@article {pmid33876556, year = {2021}, author = {Mihajlovic, J and Leutner, M and Hausmann, B and Kohl, G and Schwarz, J and Röver, H and Stimakovits, N and Wolf, P and Maruszczak, K and Bastian, M and Kautzky-Willer, A and Berry, D}, title = {Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {3037-3047}, doi = {10.1111/1462-2920.15517}, pmid = {33876556}, issn = {1462-2920}, support = {741623/ERC_/European Research Council/International ; }, abstract = {Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of seven healthy pre-menopausal women using the CHC pill, compared to the control group of nine age-matched healthy women that have not used hormonal contraceptives in the 6 months prior to the start of the study. By analysing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health.}, }
@article {pmid33870123, year = {2021}, author = {Ciobanu, D and Clum, A and Ahrendt, S and Andreopoulos, WB and Salamov, A and Chan, S and Quandt, CA and Foster, B and Meier-Kolthoff, JP and Tang, YT and Schwientek, P and Benny, GL and Smith, ME and Bauer, D and Deshpande, S and Barry, K and Copeland, A and Singer, SW and Woyke, T and Grigoriev, IV and James, TY and Cheng, JF}, title = {A single-cell genomics pipeline for environmental microbial eukaryotes.}, journal = {iScience}, volume = {24}, number = {4}, pages = {102290}, pmid = {33870123}, issn = {2589-0042}, abstract = {Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.}, }
@article {pmid33868801, year = {2021}, author = {Vikram, S and Arneodo, JD and Calcagno, J and Ortiz, M and Mon, ML and Etcheverry, C and Cowan, DA and Talia, P}, title = {Diversity structure of the microbial communities in the guts of four neotropical termite species.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10959}, pmid = {33868801}, issn = {2167-8359}, abstract = {The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.}, }
@article {pmid33866059, year = {2021}, author = {Hu, R and Zhao, H and Xu, X and Wang, Z and Yu, K and Shu, L and Yan, Q and Wu, B and Mo, C and He, Z and Wang, C}, title = {Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities.}, journal = {Environment international}, volume = {154}, number = {}, pages = {106560}, doi = {10.1016/j.envint.2021.106560}, pmid = {33866059}, issn = {1873-6750}, mesh = {Bacteria ; Biodegradation, Environmental ; *Esters ; Humans ; *Phthalic Acids ; Prospective Studies ; }, abstract = {The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.}, }
@article {pmid33864491, year = {2021}, author = {Rojas-Gätjens, D and Fuentes-Schweizer, P and Rojas-Jiménez, K and Pérez-Pantoja, D and Avendaño, R and Alpízar, R and Coronado-Ruíz, C and Chavarría, M}, title = {Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33864491}, issn = {1432-184X}, support = {809-B8-518//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; ANID PIA/Anillo ACT172128, ANID PIA/BASAL FB0002 and FONDECYT 1201741.//Chilean government/ ; }, abstract = {In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.}, }
@article {pmid33864130, year = {2021}, author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B}, title = {Correction to: Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-021-01755-2}, pmid = {33864130}, issn = {1432-184X}, }
@article {pmid33864129, year = {2021}, author = {Pereira, A and Figueiredo, A and Ferreira, V}, title = {Invasive Acacia Tree Species Affect Instream Litter Decomposition Through Changes in Water Nitrogen Concentration and Litter Characteristics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33864129}, issn = {1432-184X}, support = {SFRH/BD/118069/2016//Fundação para a Ciência e a Tecnologia/ ; IF/00129/2014//Fundação para a Ciência e a Tecnologia/ ; UIDP/04292/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Non-native nitrogen-fixing Acacia species have been invading riparian ecosystems worldwide, potentially threatening stream communities that strongly depend on allochthonous litter. We examined the effects of the invasion of native deciduous temperate forests by Acacia species on litter decomposition and associated fungal decomposers in streams. Litter of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon) species were enclosed in fine-mesh bags and immersed in three native and three invaded streams, for 14-98 days. Litter decomposition rates, fungal biomass, and aquatic hyphomycete sporulation rates were higher in invaded than in native streams, likely due to the higher water nitrogen concentration found in invaded streams. Alnus glutinosa litter had higher aquatic hyphomycete sporulation rates and species richness, and higher decomposition rates, probably because they were soft and nitrogen rich. Quercus robur litter also had high aquatic hyphomycete sporulation rates but lower decomposition rates than Al. glutinosa, probably due to high polyphenol concentration and carbon:nitrogen ratio. Acacia melanoxylon litter had lower aquatic hyphomycete sporulation rates and species richness, and lower decomposition rates, most likely because it was very tough. Thus, litter decomposition rates varied in the order: Al. glutinosa > Q. robur > Ac. melanoxylon. The aquatic hyphomycete community structure strongly differed between native and invaded streams, and among litter species, suggesting that microbes were sensitive to water nitrogen concentration and litter characteristics. Overall, increases in water nitrogen concentration and alterations in litter characteristics promoted by the invasion of native riparian forests by Acacia species may affect the activity and community structure of microbial decomposers, and instream litter decomposition, thus altering the functioning of stream ecosystems.}, }
@article {pmid33863892, year = {2021}, author = {Luhung, I and Uchida, A and Lim, SBY and Gaultier, NE and Kee, C and Lau, KJX and Gusareva, ES and Heinle, CE and Wong, A and Premkrishnan, BNV and Purbojati, RW and Acerbi, E and Kim, HL and Junqueira, ACM and Longford, S and Lohar, SR and Yap, ZH and Panicker, D and Koh, Y and Kushwaha, KK and Ang, PN and Putra, A and Drautz-Moses, DI and Schuster, SC}, title = {Experimental parameters defining ultra-low biomass bioaerosol analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {37}, pmid = {33863892}, issn = {2055-5008}, abstract = {Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.}, }
@article {pmid33860847, year = {2021}, author = {Caragata, EP and Otero, LM and Tikhe, CV and Barrera, R and Dimopoulos, G}, title = {Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33860847}, issn = {1432-184X}, support = {BAA 2017-N-18041/CC/CDC HHS/United States ; R21AI136456/NH/NIH HHS/United States ; }, abstract = {Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.}, }
@article {pmid33859339, year = {2021}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8299}, pmid = {33859339}, issn = {2045-2322}, abstract = {In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).}, }
@article {pmid33858359, year = {2021}, author = {Xue, H and Kurokawa, M and Ying, BW}, title = {Correlation between the spatial distribution and colony size was common for monogenetic bacteria in laboratory conditions.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {114}, pmid = {33858359}, issn = {1471-2180}, abstract = {BACKGROUND: Geographically separated population growth of microbes is a common phenomenon in microbial ecology. Colonies are representative of the morphological characteristics of this structured population growth. Pattern formation by single colonies has been intensively studied, whereas the spatial distribution of colonies is poorly investigated.<br><br>RESULTS: The present study describes a first trial to address the questions of whether and how the spatial distribution of colonies determines the final colony size using the model microorganism Escherichia coli, colonies of which can be grown under well-controlled laboratory conditions. A computational tool for image processing was developed to evaluate colony density, colony size and size variation, and the Voronoi diagram was applied for spatial analysis of colonies with identical space resources. A positive correlation between the final colony size and the Voronoi area was commonly identified, independent of genomic and nutritional differences, which disturbed the colony size and size variation.<br><br>CONCLUSIONS: This novel finding of a universal correlation between the spatial distribution and colony size not only indicated the fair distribution of spatial resources for monogenetic colonies growing with identical space resources but also indicated that the initial localization of the microbial colonies decided by chance determined the fate of the subsequent population growth. This study provides a valuable example for quantitative analysis of the complex microbial ecosystems by means of experimental ecology.}, }
@article {pmid33857526, year = {2021}, author = {Diego, D and Hannisdal, B and Dahle, H}, title = {On how the power supply shapes microbial survival.}, journal = {Mathematical biosciences}, volume = {338}, number = {}, pages = {108615}, doi = {10.1016/j.mbs.2021.108615}, pmid = {33857526}, issn = {1879-3134}, abstract = {Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.}, }
@article {pmid33854112, year = {2021}, author = {Mahjoubi, M and Aliyu, H and Neifar, M and Cappello, S and Chouchane, H and Souissi, Y and Masmoudi, AS and Cowan, DA and Cherif, A}, title = {Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8124}, pmid = {33854112}, issn = {2045-2322}, abstract = {Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.}, }
@article {pmid33851256, year = {2021}, author = {Birhane, E and Gebregergs, T and Hailemariam, M and Norgrove, L and Aynekulu, E}, title = {Root Colonization and Spore Abundance of Arbuscular Mycorrhizal Fungi Along Altitudinal Gradients in Fragmented Church Natural Forest Remnants in Northern Ethiopia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33851256}, issn = {1432-184X}, support = {ETH 13/0018//NORAD/NORHED/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) spore density and root colonization are considered sensitive to host species and abiotic factors such as climate and soil. However, there is a knowledge gap about how fragmented native forest remnants might contribute to AMF conservation, what is the AMF spore density and root colonization, and to what extent climate change, particularly warming, might impact AMF. The aim of the study was to quantify the AMF spore density and root colonization along altitudinal gradients in three agro-ecological zones of nine church forests in northern Ethiopia. Data were collected from 45 plots. All the surveyed church forest species were colonized by AMF. However, we found a significant (p < 0.05) decrease in root colonization and AMF abundance in forests at high elevation. The topsoil had significantly (p < 0.05) higher root colonization and AMF abundance than subsurface soil. We found strong negative correlations between altitude and both spore density and root colonization and soil fertility. While we cannot separate whether spore density was temperature or soil limited, we can demonstrate the importance of conserving certain tree species, particularly Ficus species, which harbor high spore densities, in both lowland and midland church forests. In the highland, no Ficus species were found. However, Hagenia abyssinica, another Rosales, had the highest spore density in the highland ecoregion.}, }
@article {pmid33850046, year = {2021}, author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG}, title = {Correction for Altamia et al., "Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes".}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, doi = {10.1128/mSystems.00288-21}, pmid = {33850046}, issn = {2379-5077}, }
@article {pmid33848236, year = {2021}, author = {Perez-Mon, C and Qi, W and Vikram, S and Frossard, A and Makhalanyane, T and Cowan, D and Frey, B}, title = {Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps).}, journal = {Microbial genomics}, volume = {7}, number = {4}, pages = {}, pmid = {33848236}, issn = {2057-5858}, abstract = {The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.}, }
@article {pmid33846820, year = {2021}, author = {Valencia, EY and Barros, JP and Ferenci, T and Spira, B}, title = {A Broad Continuum of E. coli Traits in Nature Associated with the Trade-off Between Self-preservation and Nutritional Competence.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33846820}, issn = {1432-184X}, support = {2016/11547-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {A trade-off between reproduction and survival is a characteristic of many organisms. In bacteria, growth is constrained when cellular resources are channelled towards environmental stress protection. At the core of this trade-off in Escherichia coli is RpoS, a sigma factor that diverts transcriptional resources towards general stress resistance. The constancy of RpoS levels in natural isolates is unknown. A uniform RpoS content in E. coli would impart a narrow range of resistance properties to the species, whereas a diverse set of RpoS levels in nature should result in a diverse range of stress susceptibilities. We explore the diversity of trade-off settings and phenotypes by measuring the level of RpoS protein in strains of E. coli cohabiting in a natural environment. Strains from a stream polluted with domestic waste were investigated in monthly samples. Analyses included E. coli phylogroup classification, RpoS protein level, RpoS-dependent stress phenotypes and the sequencing of rpoS mutations. The most striking finding was the continuum of RpoS levels, with a 100-fold range of RpoS amounts consistently found in individuals in the stream. Approximately 1.8% of the sampled strains carried null or non-synonymous mutations in rpoS. The natural isolates also exhibited a broad (>100-fold) range of stress resistance responses. Our results are consistent with the view that a multiplicity of survival-multiplication trade-off settings is a feature of the species E. coli. The phenotypic diversity resulting from the trade-off permits bet-hedging and the adaptation of E. coli strains to a very broad range of environments.}, }
@article {pmid33846334, year = {2021}, author = {Deng, X and Zhang, N and Shen, Z and Zhu, C and Liu, H and Xu, Z and Li, R and Shen, Q and Salles, JF}, title = {Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {33}, pmid = {33846334}, issn = {2055-5008}, abstract = {Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio-organic and organic amendments reshapes the taxonomic and functional potential of the soil microbiome to suppress the pathogens Ralstonia solanacearum and Fusarium oxysporum in tomato monocultures. The use of organic amendment alone generated smaller shifts in bacterial and fungal community composition and no suppressiveness. Fumigation directly decreased F. oxysporum and induced drastic changes in the soil microbiome. This was further converted from a disease conducive to a suppressive soil microbiome due to the application of organic amendment, which affected the way the bacterial and fungal communities were reassembled. These direct and possibly indirect effects resulted in a highly efficient disease control rate, providing a promising strategy for the control of the diseases caused by multiple pathogens.}, }
@article {pmid33841364, year = {2021}, author = {Lui, LM and Majumder, EL and Smith, HJ and Carlson, HK and von Netzer, F and Fields, MW and Stahl, DA and Zhou, J and Hazen, TC and Baliga, NS and Adams, PD and Arkin, AP}, title = {Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {642422}, pmid = {33841364}, issn = {1664-302X}, abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.}, }
@article {pmid33834428, year = {2021}, author = {Iturbe-Espinoza, P and Brandt, BW and Braster, M and Bonte, M and Brown, DM and van Spanning, RJM}, title = {Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {33834428}, issn = {1874-9356}, support = {216-2015-FONDECYT//FONDECYT-CONCYTEC/ ; }, abstract = {Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.}, }
@article {pmid33834254, year = {2021}, author = {Conacher, CG and Luyt, NA and Naidoo-Blassoples, RK and Rossouw, D and Setati, ME and Bauer, FF}, title = {The ecology of wine fermentation: a model for the study of complex microbial ecosystems.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {8}, pages = {3027-3043}, pmid = {33834254}, issn = {1432-0614}, support = {83471//South African National Research Foundation/ ; 118505//South African National Research Foundation/ ; FLAIR//The Royal Society/ ; }, mesh = {Ecosystem ; Fermentation ; *Microbiota ; Models, Biological ; *Wine ; }, abstract = {The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.}, }
@article {pmid33830034, year = {2021}, author = {Zama, D and Gori, D and Muratore, E and Leardini, D and Rallo, F and Turroni, S and Prete, A and Brigidi, P and Pession, A and Masetti, R}, title = {Enteral versus Parenteral Nutrition as Nutritional Support after Allogeneic Hematopoietic Stem Cell Transplantation: a Systematic Review and Meta-Analysis.}, journal = {Transplantation and cellular therapy}, volume = {27}, number = {2}, pages = {180.e1-180.e8}, doi = {10.1016/j.jtct.2020.11.006}, pmid = {33830034}, issn = {2666-6367}, mesh = {Enteral Nutrition ; *Graft vs Host Disease/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Nutritional Support ; Parenteral Nutrition ; }, abstract = {Nutritional support for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been widely debated. Enteral nutrition (EN) is recommended as first-line nutritional support by the main international guidelines. However, these recommendations are based on weak evidence, and there is wide variability in the types of nutritional support among transplantation centers, with the majority providing parenteral nutrition (PN) instead of EN. Here we provide an up-to-date systematic review and meta-analysis of studies comparing EN and PN for nutritional support during the neutropenic period after allo-HSCT. The literature search strategy identified 13 papers, of which 10 compared clinical transplantation outcomes, 2 compared gut microbiota (GM) compositions, and 1 compared systemic metabolic profiles. For the meta-analysis, among the 10 clinical studies, 8 studies in which 2 groups were compared were selected: in 1 group, EN was provided as primary nutritional support in the neutropenic phase after allo-HSCT with or without the addition of PN (EN group), whereas in the other group, only PN was provided as nutritional support. The incidence rates of acute graft-versus-host disease (aGVHD) (relative risk [RR], 0.69; 95% confidence interval [CI], 0.56 to 0.86; P = .0007), aGVHD grade III-IV (RR, 0.44; 95% CI, 0.30 to 0.64; P < .0001), and gut aGVHD (RR, 0.44; 95% CI, 0.30 to 0.66; P < .0001) were lower in the EN group than in the PN group. No differences were found between the 2 groups with regard to the incidence of severe oral mucositis (RR, 0.95; 95% CI, 0.83 to 1.09; P = .46) or overall survival at day +100 (RR, 1.07; 95% CI, 0.95 to 1.21; P = .29). Other variables were too heterogeneous to perform quantitative analyses. The results of the meta-analysis showed that EN reduced the incidence of aGVHD, specifically grade III-IV and gut aGVHD. This result should prompt improved efforts to implement EN as first-line nutritional support in patients undergoing allo-HSCT. Considering the emerging evidence regarding the association between GM dysbiosis and aGVHD onset, we speculate that this protective effect could be attributed to the improved gut eubiosis observed in enterally fed patients. Further studies are warranted to better address the relationship between the GM composition, aGVHD, and the nutritional administration route during HSCT.}, }
@article {pmid33827912, year = {2021}, author = {Gauthier, J and Derome, N}, title = {Evenness-Richness Scatter Plots: a Visual and Insightful Representation of Shannon Entropy Measurements for Ecological Community Analysis.}, journal = {mSphere}, volume = {6}, number = {2}, pages = {}, pmid = {33827912}, issn = {2379-5042}, abstract = {Shannon's entropy is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent on both those parameters, there is theoretically an infinite number of richness/evenness value combinations translating into the same index score. By decoupling both components measured by Shannon's entropy, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as permutational multivariate analysis of variance (PERMANOVA) can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise. Therefore, plotting richness and evenness on two-dimensional (2D) graphs gives a more thorough understanding of how alpha diversity differs between groups of samples.}, }
@article {pmid33827413, year = {2021}, author = {Shanmugam, G and Lee, SH and Jeon, J}, title = {EzMAP: Easy Microbiome Analysis Platform.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {179}, pmid = {33827413}, issn = {1471-2105}, support = {918017-04//Ministry of Agriculture, Food, and Rural Affairs/ ; PJ013178//Rural Development Administration , Korea/ ; NRF-2018R1A5A1023599//National Research Foundation of Korea/ ; }, mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Programming Languages ; *Software ; }, abstract = {BACKGROUND: The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills.<br><br>RESULTS: Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP.<br><br>CONCLUSIONS: This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.}, }
@article {pmid33824198, year = {2021}, author = {Cooper, RO and Vavra, JM and Cressler, CE}, title = {Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33824198}, issn = {2379-5077}, abstract = {Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that mi