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Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-27 DOI: 10.1111/1462-2920.70054
Dina Castillo Boukhchtaber, F. A. Bastiaan von Meijenfeldt, Diana X. Sahonero Canavesi, Denise Dorhout, Nicole J. Bale, Ellen C. Hopmans, Laura Villanueva

Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea are characterised by ether-linked isoprenoids forming bilayers or monolayers of membrane-spanning lipids known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification of branched GDGTs (brGDGTs), which are membrane-spanning ether-bound branched alkyl fatty acids of bacterial origin, though their producers are often unidentified. The limited availability of microbial cultures constrains the understanding of the biological sources of these membrane lipids, thus limiting their use as biomarkers. To address this issue, we identified membrane lipids in the Black Sea using high-resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also identified brGDGTs and highly branched GDGTs in the suboxic and euxinic waters, potentially attributed to Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota—based on their lipid biosynthetic genomic potential. These findings introduce new possibilities for using specific brGDGTs as biomarkers of anoxic conditions in marine environments and highlight the role of these membrane lipids in microbial adaptation.

{"title":"Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System","authors":"Dina Castillo Boukhchtaber,&nbsp;F. A. Bastiaan von Meijenfeldt,&nbsp;Diana X. Sahonero Canavesi,&nbsp;Denise Dorhout,&nbsp;Nicole J. Bale,&nbsp;Ellen C. Hopmans,&nbsp;Laura Villanueva","doi":"10.1111/1462-2920.70054","DOIUrl":"https://doi.org/10.1111/1462-2920.70054","url":null,"abstract":"<p>Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea are characterised by ether-linked isoprenoids forming bilayers or monolayers of membrane-spanning lipids known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification of branched GDGTs (brGDGTs), which are membrane-spanning ether-bound branched alkyl fatty acids of bacterial origin, though their producers are often unidentified. The limited availability of microbial cultures constrains the understanding of the biological sources of these membrane lipids, thus limiting their use as biomarkers. To address this issue, we identified membrane lipids in the Black Sea using high-resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also identified brGDGTs and highly branched GDGTs in the suboxic and euxinic waters, potentially attributed to Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota—based on their lipid biosynthetic genomic potential. These findings introduce new possibilities for using specific brGDGTs as biomarkers of anoxic conditions in marine environments and highlight the role of these membrane lipids in microbial adaptation.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 3","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Seasonal Cycles in a Seaweed Holobiont: A Multiyear Time Series Reveals Repetitive Microbial Shifts and Core Taxa
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-27 DOI: 10.1111/1462-2920.70062
Chantal Marie Mudlaff, Florian Weinberger, Luisa Düsedau, Marjan Ghotbi, Sven Künzel, Guido Bonthond

Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known about the influence of seasonality on their microbial communities. In this study, we conducted a three-year time series, sampling at two-month intervals, to assess the seasonality of microbial epibiota in the seaweed holobiont Gracilaria vermiculophylla. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, this research offers important insights into the temporal dynamics of seaweed-associated microbiota and demonstrates that the relationship between seaweed host and its epibiota is not static but naturally subject to an ongoing seasonal succession process.

{"title":"Seasonal Cycles in a Seaweed Holobiont: A Multiyear Time Series Reveals Repetitive Microbial Shifts and Core Taxa","authors":"Chantal Marie Mudlaff,&nbsp;Florian Weinberger,&nbsp;Luisa Düsedau,&nbsp;Marjan Ghotbi,&nbsp;Sven Künzel,&nbsp;Guido Bonthond","doi":"10.1111/1462-2920.70062","DOIUrl":"https://doi.org/10.1111/1462-2920.70062","url":null,"abstract":"<p>Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known about the influence of seasonality on their microbial communities. In this study, we conducted a three-year time series, sampling at two-month intervals, to assess the seasonality of microbial epibiota in the seaweed holobiont <i>Gracilaria vermiculophylla</i>. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, this research offers important insights into the temporal dynamics of seaweed-associated microbiota and demonstrates that the relationship between seaweed host and its epibiota is not static but naturally subject to an ongoing seasonal succession process.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 3","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pseudomonas Species Isolated From Lotus Nodules Are Genetically Diverse and Promote Plant Growth
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-27 DOI: 10.1111/1462-2920.70066
Yu-Hsiang Yu, Julian Kurtenbach, Duncan Crosbie, Andreas Brachmann, Macarena Marín Arancibia

Nodules harbour microbial communities composed of rhizobia and other lower-abundance bacteria. These non-rhizobial bacteria can promote plant growth. However, their genomic diversity and how this relates to their plant growth-promoting traits remain poorly investigated. Here, we isolated 14 Pseudomonas strains from the nodules of Lotus plants, sequenced their genomes, analysed their genomic and phylogenetic diversity, and assessed their ability to promote plant growth. We identified five distinct species, including a novel species named Pseudomonas monachiensis sp. nov., with strain PLb12AT, as the type strain. Genome analysis of these nodule-isolated Pseudomonas revealed an abundance of genes associated to plant growth-promoting traits, especially auxin-related genes, compared to closely related type strains. In accordance, most nodule-isolated Pseudomonas strains enhanced shoot growth of Lotus burttii, while only some promoted root growth or early onset of root hair proliferation. However, none of the strains significantly affected the ability to form nodules. Overall, our findings highlight the genotypic diversity and the plant growth-promoting potential of nodule-isolated Pseudomonas and underscore their possible applications in mixed inocula with rhizobia.

{"title":"Pseudomonas Species Isolated From Lotus Nodules Are Genetically Diverse and Promote Plant Growth","authors":"Yu-Hsiang Yu,&nbsp;Julian Kurtenbach,&nbsp;Duncan Crosbie,&nbsp;Andreas Brachmann,&nbsp;Macarena Marín Arancibia","doi":"10.1111/1462-2920.70066","DOIUrl":"https://doi.org/10.1111/1462-2920.70066","url":null,"abstract":"<p>Nodules harbour microbial communities composed of rhizobia and other lower-abundance bacteria. These non-rhizobial bacteria can promote plant growth. However, their genomic diversity and how this relates to their plant growth-promoting traits remain poorly investigated. Here, we isolated 14 <i>Pseudomonas</i> strains from the nodules of <i>Lotus</i> plants, sequenced their genomes, analysed their genomic and phylogenetic diversity, and assessed their ability to promote plant growth. We identified five distinct species, including a novel species named <i>Pseudomonas monachiensis</i> sp. nov., with strain PLb12A<sup>T</sup>, as the type strain. Genome analysis of these nodule-isolated <i>Pseudomonas</i> revealed an abundance of genes associated to plant growth-promoting traits, especially auxin-related genes, compared to closely related type strains. In accordance, most nodule-isolated <i>Pseudomonas</i> strains enhanced shoot growth of <i>Lotus burttii</i>, while only some promoted root growth or early onset of root hair proliferation. However, none of the strains significantly affected the ability to form nodules. Overall, our findings highlight the genotypic diversity and the plant growth-promoting potential of nodule-isolated <i>Pseudomonas</i> and underscore their possible applications in mixed inocula with rhizobia.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 3","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Bacterial Antimonite Oxidase AnoA: Unexpected Diversity and Environmental Widespread Occurrence
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-26 DOI: 10.1111/1462-2920.70069
Claire Da Costa, Thierry Berthe, Titouan Dehaies, Sophie Ayrault, Yannick Colin

The growing contamination of urban areas by antimony (Sb) has sparked interest in microbial processes that modulate Sb speciation in ecosystems. The bacterial antimonite oxidase AnoA is the only oxidase known so far whose gene expression is specifically induced by Sb(III), but its annotation in public databases is currently lacking. Here, the computational search for AnoA orthologs predicted an unexpected phylogenetic distribution across the Pseudomonadota and Actinomycetota. Putative orthologs were identified in both known Sb(III)-oxidisers (e.g., Shinella, Hydrogenophaga, Bosea, Cupriavidus and Pseudomonas) and taxa not previously linked to the Sb cycle (e.g., Bradyrhizobium, Mesorhizobium, Methylobacterium and Paraburkholderia). The anoA gene is single-copy in most Proteobacterial genomes, but is often detected in multiple copies in the Actinomycetota. Furthermore, sequence evolutionary distances suggest that it is mainly inherited vertically, with horizontal transfer events, in particular towards the Gammaproteobacteria. Using the constructed database, new PCR primers were designed and outperformed existing strain-specific primers in amplifying the anoA gene from samples with varying Sb levels and microbial profiles. Sequencing and quantification of PCR amplicons revealed a diverse range of sequences in sediments and natural biofilms, indicating that the oxidase is more environmentally diverse and widespread than previously thought and may play a significant role in Sb(III) detoxification.

{"title":"The Bacterial Antimonite Oxidase AnoA: Unexpected Diversity and Environmental Widespread Occurrence","authors":"Claire Da Costa,&nbsp;Thierry Berthe,&nbsp;Titouan Dehaies,&nbsp;Sophie Ayrault,&nbsp;Yannick Colin","doi":"10.1111/1462-2920.70069","DOIUrl":"https://doi.org/10.1111/1462-2920.70069","url":null,"abstract":"<div>\u0000 \u0000 <p>The growing contamination of urban areas by antimony (Sb) has sparked interest in microbial processes that modulate Sb speciation in ecosystems. The bacterial antimonite oxidase AnoA is the only oxidase known so far whose gene expression is specifically induced by Sb(III), but its annotation in public databases is currently lacking. Here, the computational search for AnoA orthologs predicted an unexpected phylogenetic distribution across the <i>Pseudomonadota</i> and <i>Actinomycetota</i>. Putative orthologs were identified in both known Sb(III)-oxidisers (e.g., <i>Shinella</i>, <i>Hydrogenophaga</i>, <i>Bosea</i>, <i>Cupriavidus</i> and <i>Pseudomonas</i>) and taxa not previously linked to the Sb cycle (e.g., <i>Bradyrhizobium</i>, <i>Mesorhizobium</i>, <i>Methylobacterium</i> and <i>Paraburkholderia</i>). The <i>anoA</i> gene is single-copy in most Proteobacterial genomes, but is often detected in multiple copies in the <i>Actinomycetota</i>. Furthermore, sequence evolutionary distances suggest that it is mainly inherited vertically, with horizontal transfer events, in particular towards the <i>Gammaproteobacteria</i>. Using the constructed database, new PCR primers were designed and outperformed existing strain-specific primers in amplifying the <i>anoA</i> gene from samples with varying Sb levels and microbial profiles. Sequencing and quantification of PCR amplicons revealed a diverse range of sequences in sediments and natural biofilms, indicating that the oxidase is more environmentally diverse and widespread than previously thought and may play a significant role in Sb(III) detoxification.</p>\u0000 </div>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 3","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-23 DOI: 10.1111/1462-2920.70061
Gareth Howells, Aysha L. Sezmis, Christopher Blake, Michael J. McDonald

Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co-culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.

{"title":"Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens","authors":"Gareth Howells,&nbsp;Aysha L. Sezmis,&nbsp;Christopher Blake,&nbsp;Michael J. McDonald","doi":"10.1111/1462-2920.70061","DOIUrl":"https://doi.org/10.1111/1462-2920.70061","url":null,"abstract":"<p>Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the <i>Pseudomonas fluorescens</i> SBW25 adaptive radiation, <i>Escherichia coli</i> and <i>P. fluorescens</i> were cultured in monoculture and co-culture for 8 weeks. In <i>P. fluorescens</i> monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while <i>E. coli</i> monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, <i>E. coli</i> did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both <i>E. coli</i> and <i>P. fluorescens.</i> Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 2","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143475568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-23 DOI: 10.1111/1462-2920.70059
Gilles De Luca, Mohamed Barakat, André Verméglio, Wafa Achouak, Thierry Heulin

Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.

{"title":"The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits","authors":"Gilles De Luca,&nbsp;Mohamed Barakat,&nbsp;André Verméglio,&nbsp;Wafa Achouak,&nbsp;Thierry Heulin","doi":"10.1111/1462-2920.70059","DOIUrl":"https://doi.org/10.1111/1462-2920.70059","url":null,"abstract":"<p><i>Ramlibacter tataouinensis</i>, the type species of the genus <i>Ramlibacter</i>, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described <i>Ramlibacter</i> species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus <i>Ramlibacter</i>. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of <i>Ramlibacter</i> in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of <i>Ramlibacter</i> species but also extends our understanding of microbial ecology in oligotrophic environments.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 2","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143475567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-16 DOI: 10.1111/1462-2920.70056
Maider J. Echeveste Medrano, Garrett J. Smith, Irene Sánchez-Andrea, Mike S. M. Jetten, Cornelia U. Welte

Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.

{"title":"Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago","authors":"Maider J. Echeveste Medrano,&nbsp;Garrett J. Smith,&nbsp;Irene Sánchez-Andrea,&nbsp;Mike S. M. Jetten,&nbsp;Cornelia U. Welte","doi":"10.1111/1462-2920.70056","DOIUrl":"https://doi.org/10.1111/1462-2920.70056","url":null,"abstract":"<p>Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by <i>Methylobacter</i> and <i>Methylomonas</i> in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched <i>Rugosibacter</i> genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 2","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Thermodynamics Underpinning the Microbial Community-Level Nitrogen Energy Metabolism
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-16 DOI: 10.1111/1462-2920.70055
Mayumi Seto, Risa Sasaki, Hideshi Ooka, Ryuhei Nakamura

Nitrogen compounds often serve as crucial electron donors and acceptors in microbial energy metabolism, playing a key role in biogeochemical cycles. The energetic favorability of nitrogen oxidation–reduction (redox) reactions, driven by the thermodynamic properties of these compounds, may have shaped the evolution of microbial energy metabolism, though the extent of their influence remains unclear. This study quantitatively evaluated the similarity between energetically superior nitrogen reactions, identified from 988 theoretically plausible reactions, and the nitrogen community-level network, reconstructed as a combination of enzymatic reactions representing intracellular to interspecies-level reaction interactions. Our analysis revealed significant link overlap rates between these networks. Notably, composite enzymatic reactions aligned more closely with energetically superior reactions than individual enzymatic reactions. These findings suggest that selective pressure from the energetic favorability of redox reactions can operate primarily at the species or community level, underscoring the critical role of thermodynamics in shaping microbial metabolic networks and ecosystem functioning.

{"title":"Thermodynamics Underpinning the Microbial Community-Level Nitrogen Energy Metabolism","authors":"Mayumi Seto,&nbsp;Risa Sasaki,&nbsp;Hideshi Ooka,&nbsp;Ryuhei Nakamura","doi":"10.1111/1462-2920.70055","DOIUrl":"https://doi.org/10.1111/1462-2920.70055","url":null,"abstract":"<p>Nitrogen compounds often serve as crucial electron donors and acceptors in microbial energy metabolism, playing a key role in biogeochemical cycles. The energetic favorability of nitrogen oxidation–reduction (redox) reactions, driven by the thermodynamic properties of these compounds, may have shaped the evolution of microbial energy metabolism, though the extent of their influence remains unclear. This study quantitatively evaluated the similarity between energetically superior nitrogen reactions, identified from 988 theoretically plausible reactions, and the nitrogen community-level network, reconstructed as a combination of enzymatic reactions representing intracellular to interspecies-level reaction interactions. Our analysis revealed significant link overlap rates between these networks. Notably, composite enzymatic reactions aligned more closely with energetically superior reactions than individual enzymatic reactions. These findings suggest that selective pressure from the energetic favorability of redox reactions can operate primarily at the species or community level, underscoring the critical role of thermodynamics in shaping microbial metabolic networks and ecosystem functioning.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 2","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143423752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Insects as Natural Hosts, Vectors and Reservoirs of Botulinum Neurotoxin-Producing Clostridia and Their Non-Toxinogenic Counterparts: Preliminary Evidence
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-13 DOI: 10.1111/1462-2920.70053
François P. Douillard, Olivia Lanzoni, Anne Duplouy, Miia Lindström

Insects play a significant role in the transmission and spread of bacterial pathogens that cause various diseases in humans and animals. The relationship among insects, bacterial pathogens and diseases is complex and depends on the specificity of the pathogens. Some clostridial species produce botulinum neurotoxin (BoNT), which is responsible for paralytic botulism. However, the ecology of these bacterial species and their non-toxinogenic phylogenetic counterparts remains unclear. This study specifically explored in silico evidence of the interconnection between BoNT-producing Clostridia and their non-toxinogenic counterparts with insects. Based on literature meta-analysis, the mining of 16S rRNA amplicon and metagenomic sequencing datasets and a pilot feeding experiment in the Glanville fritillary butterfly, Melitaea cinxia, we propose that BoNT-producing Clostridia and their non-toxinogenic phylogenetic counterparts are carried internally and/or externally in different insect orders. While previous case studies have indicated associations between Clostridia and insects, this work provides a more comprehensive view of their occurrence. It also highlights the need for further multidisciplinary investigations to characterise the natural ecology of BoNT-producing Clostridia and their non-toxinogenic counterparts in insects.

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引用次数: 0
Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases
IF 4.3 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2025-02-13 DOI: 10.1111/1462-2920.70050
Sui Nin Nicholas Yang, Michael A. Kertesz, Nicholas V. Coleman

Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.

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引用次数: 0
期刊
Environmental microbiology
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