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, F. A. Bastiaan von Meijenfeldt, Diana X. Sahonero Canavesi, Denise Dorhout, Nicole J. Bale, Ellen C. Hopmans, 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}
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, Florian Weinberger, Luisa Düsedau, Marjan Ghotbi, Sven Künzel, 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}
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, Julian Kurtenbach, Duncan Crosbie, Andreas Brachmann, 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}