mSystems最新文献

{"title":"Microbial diversity and nitrogen cycling across oxygen gradients in the eastern tropical Pacific during two La Niña years.","authors":"Peihang Xu, Damian L Arévalo-Martínez, Mathias Middelboe, Marei Pohlmann, Hermann W Bange, Carolin R Löscher","doi":"10.1128/msystems.00893-26","DOIUrl":"10.1128/msystems.00893-26","url":null,"abstract":"<p><p>The rapid expansion of ocean oxygen minimum zones (OMZs) may significantly affect the microbial processes that regulate marine nitrogen cycling. The eastern tropical Pacific (ETP) bears one of the largest perennial OMZs, which is strongly influenced by the recurring El Niño Southern Oscillation (ENSO). However, how microbial diversity and nitrogen cycling respond to oxygen variability under comparable ENSO conditions remains unclear. Here, we applied metagenomics to analyze changes in microbial communities across a dissolved oxygen (DO) gradient from oxic to suboxic conditions in the ETP during the 2022 La Niña event and compared our findings to the <i>Tara Oceans</i> data set from the same region during the 2011 La Niña. In 2022, we observed a decline in microbial alpha diversity and abundance, coupled with an increase in nitrogen metabolism genes as DO decreases. The relative abundance of many dominant microbes shifted at a DO threshold of 80 μmol kg^-1, while dominant nitrogen cycle genes varied under different DO thresholds (120, 20, 5 μmol kg^-1). Despite the 11-year interval between sampling efforts, microbial alpha diversity was similar between 2011 and 2022. We observed a significant reduction of SAR11 and an increase of Poseidoniia in 2022 compared with 2011. While certain nitrogen cycling genes differed in relative abundance in a depth-dependent manner, overall functional group composition was largely consistent, with spatial variation exceeding interannual differences. Overall, our study presents a comprehensive examination of possible shifts of microbial diversity, community, and their potential for nitrogen cycling under deoxygenation during two La Niña years.IMPORTANCEThe eastern tropical Pacific oxygen minimum zones (OMZs), largely impacted by the natural climate cycle-El Niño-Southern Oscillation, are predicted to continually expand while their core may shrink. While deoxygenation is known to profoundly influence microbial ecosystems, how microbial diversity, composition, and nitrogen cycling would shift across oxic/hypoxic/suboxic gradients, and its association with ENSO dynamics remains poorly understood. We surveyed microbial communities under two La Niña years with an 11-year gap and found that vertical variability is more critical than temporal variations for both microbial diversity and microbe-mediated nitrogen pathways, as only slight differences in microbial diversity and nitrogen cycles were detected between the two studied years despite ENSO dynamics, which might have disrupted the system among the 11 years. Moreover, we identified oxygen thresholds causing dominant microbes and potential nitrogen pathways to shift, thus helping to improve prediction on how various microbes and nitrogen pathways might respond to further deoxygenation.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0089326"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012719","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}

{"title":"Functional unknomics of the SAR11 clade reveal hidden genetic potential underlying adaptation to bottom-up and top-down pressures.","authors":"Satoshi Nishino, Kento Tominaga, Kimiho Omae, Teppei Deguchi, Koji Hamasaki, Susumu Yoshizawa, Yuki Nishimura","doi":"10.1128/msystems.01026-26","DOIUrl":"10.1128/msystems.01026-26","url":null,"abstract":"<p><p>A substantial fraction of the genes in bacteria lack detectable sequence similarity to genes with known functions. These functionally uncharacterized genes-collectively referred to as the \"unknome\"-represent a largely unexplored genetic repertoire harboring insights into marine bacterial ecology. In this study, we explored the function of the unknome of the SAR11 clade, the most abundant bacterial lineage in the ocean, with a particular focus on genes that provide insight into its ecology. Based on the Clusters of Orthologous Genes and Kyoto Encyclopedia of Genes and Genomes classifications, approximately 56% of SAR11 ortholog groups were classified as members of the unknome. Among the SAR11 unknome, we successfully inferred the functions of 57 ortholog groups that are conserved in the SAR11 clade by protein structure similarity searches and genomic context analyses. These ortholog groups include putative transporter components, supporting the current ecological understanding that the SAR11 clade is specialized in substrate uptake to adapt to oligotrophic marine environments. Furthermore, structural analysis indicated that the DUF2237-containing protein, enriched in marine environments, may interact with purine nucleotide-containing compounds. This may suggest the existence of unique nucleotide utilization mechanisms in marine bacteria. In addition, we identified candidate viral defense systems within the unknome, indicating that diverse defense systems are present in at least one-third of cultured SAR11 strains. The presence of these defense systems, even within streamlined SAR11 genomes, suggests that they confer significant ecological advantages. Our analyses provide insights into the genetic basis of bottom-up processes (adaptation to oligotrophic environments) and top-down processes (antiviral defense strategy) contributing to ecological success.</p><p><strong>Importance: </strong>Many microbial genes have no experimentally established function, limiting our ability to explain how microorganisms adapt to their environments. We examined this uncharacterized gene space, or \"unknome\" in SAR11, the most abundant bacterial clade in the ocean, by integrating evolutionary conservation, genomic context, predicted protein structure, and environmental distribution. This approach enabled us to prioritize components of the SAR11 unknome, including a core unknome conserved across the clade and genes enriched in specific lineages, and to identify several candidates with possible ecological roles in nutrient acquisition and defense against viruses. Our results suggest that the SAR11 unknome contains important clues to the ecological success of SAR11 rather than merely reflecting incomplete annotation or gene-prediction artifacts. Our study highlights the potential value of unknome analysis for identifying ecologically relevant genes in environmental microorganisms.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0102626"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990651","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}

{"title":"Fungi as a model for expanding the understanding of dormancy across microbial life.","authors":"Danae Bregnard, Saskia Bindschedler, Simona Regenspurg, Pilar Junier","doi":"10.1128/msystems.01014-26","DOIUrl":"10.1128/msystems.01014-26","url":null,"abstract":"<p><p>Dormancy is a widespread strategy that enables microorganisms to survive unfavorable environmental conditions. While bacterial dormancy has been extensively studied, a comprehensive overview of fungal dormancy is missing, despite its ecological, medical, and industrial relevance. In this minireview, we summarize the diversity of structures in fungi that could play a role in dormancy and highlight their morphophysiological complexity, emphasizing their distinct developmental pathways and resistance mechanisms. Whenever possible, these structures are presented alongside a brief description of dormant bacterial cells to illustrate potential parallels between both groups and to highlight commonalities. We also explore the challenges of detecting and identifying fungal dormant structures in environmental samples, with a focus on our own research in deep geothermal environments. Despite recent advances, significant methodological gaps remain, particularly in the detection of structures like sclerotia. Recognizing the diversity of dormant structures and integrating multiple microbial models is essential to develop a unified framework for dormancy research. Such integration will enhance our understanding of microbial survival strategies and their roles in ecosystem resilience, biogeochemical cycling, and applied contexts ranging from food safety to human health. By identifying both shared and unique features of dormancy across microbial domains, the ecological significance of this fundamental strategy can be better explained and explored.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0101426"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970059","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}

{"title":"Reading immune restoration through <i>Mycobacterium tuberculosis</i> intrahost evolution.","authors":"Lin Teng, Guangzhi Zhang","doi":"10.1128/msystems.00953-26","DOIUrl":"10.1128/msystems.00953-26","url":null,"abstract":"<p><p>Antiretroviral therapy (ART) suppresses human immunodeficiency virus replication, but does not fully restore protection against tuberculosis. The relevant mechanisms are still poorly understood. M. C. Chao, M. R. Chase, S. Wakabayashi, A. J. Vickers, et al. (mSystems 11:e00329-26, 2026, https://doi.org/10.1128/msystems.00329-26) use population-level <i>Mycobacterium tuberculosis</i> genome sequencing in macaques to show that similar bacterial burdens can conceal different evolutionary trajectories: simian immunodeficiency virus coinfection primarily increases opportunities for mutation through replication, whereas ART-treated animals show a distinct enrichment of oxidative damage-associated variants. We argue that the principal value of this work is conceptual. Pathogen genomes may provide a time-integrated, but indirect, readout of local immune ecology. To translate these genomic signatures into a framework for evaluating immune restoration, future studies should pair host and pathogen measurements, experimentally validate the mechanisms generating these mutations, and longitudinally link tissue-level selection to persistence, reactivation, and transmission.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0095326"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017403","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}

{"title":"Carbon starvation of <i>Mycobacterium abscessus</i> induces a non-replicating state with extensive proteomic remodeling.","authors":"Kaylyn L Devlin, Gyanu Lamichhane, William C Nelson, Vivian S Lin, Kimberly E Beatty","doi":"10.1128/msystems.00564-26","DOIUrl":"10.1128/msystems.00564-26","url":null,"abstract":"<p><p><i>Mycobacterium abscessus</i> (<i>Mab</i>) is an opportunistic pathogen that can cause chronic, debilitating lung disease. <i>Mab</i> is intrinsically resistant to most antibiotics, making <i>Mab</i> infections challenging to manage and frequently incurable. During infection, <i>Mab</i> adapts to survive various stresses, including hypoxia and nutrient starvation. <i>In vitro</i>, these conditions drive <i>Mab</i> into a drug-tolerant, non-replicating state. Changes in the <i>Mab</i> proteome that result from entering a non-replicating state have been minimally described despite the clinical importance of this physiological state. Using <i>Mab</i> reference strain ATCC 19977, we collected proteomic data comparing replicating to non-replicating states using a carbon starvation (CS) model of persistence. We identified 2,251 proteins overall (45% proteome coverage), and 17% of these proteins were found in only one of the two conditions. A third of identified proteins were significantly changed in abundance, indicating an extensive proteomic response to CS. The response regulator DosR and many DosRS-responsive proteins were significantly more abundant under CS, suggesting that this response regulator plays a key role in CS-induced <i>Mab</i> persistence. Many aspects of cell wall biosynthesis were altered, including changes in glycolipid abundance under CS. Proteins involved in other key cellular processes such as secretion, oxidative phosphorylation, and nutrient metabolism were altered under CS. This proteomic analysis provides new insights and clarity into how the <i>Mab</i> proteome is regulated during non-replicating persistence, a key consideration for understanding <i>Mab</i> pathophysiology.IMPORTANCE<i>Mycobacterium abscessus</i> (<i>Mab</i>) is a highly drug-resistant species of non-tuberculous mycobacteria (NTM). People most susceptible to pulmonary NTM infections are immunocompromised or have an existing lung disease, such as chronic obstructive pulmonary disease or cystic fibrosis. Infections with <i>Mab</i> cause chronic lung disease that is challenging to manage. Patients typically must take multiple antibiotics daily for at least a year. Despite aggressive treatment regimens, cure rates remain low. One reason for this is <i>Mab</i>'s ability to enter dormancy during chronic infections. The authors provide a first description of the proteomic remodeling that occurs in <i>Mab</i> in response to carbon starvation, which induces a non-replicating state. They report that a third of the proteome changes in response to carbon starvation, including pathways involved in cell envelope biosynthesis, energy production, and nutrient acquisition. The detailed description of these changes provides insights into the adaptations likely used by <i>Mab</i> to survive during infection.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0056426"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025444","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}

{"title":"Synthesis-driven reverse metabolomics reveals 3-hydroxy <i>N</i>-acyl amides as gut microbial molecules.","authors":"Victoria Deleray, Vincent Charron-Lamoureux, Kyle Vittali, Helena Mannochio-Russo, Crystal X Wang, Corinn Walker, Karsten Zengler, Dionicio Siegel, Pieter C Dorrestein","doi":"10.1128/msystems.00839-26","DOIUrl":"10.1128/msystems.00839-26","url":null,"abstract":"<p><p>3-Hydroxy <i>N</i>-acyl amides are bioactive lipids with reported anti-obesity and glucose-regulating effects, yet they are rarely detected in untargeted metabolomics studies because they are largely absent from existing spectral reference libraries. To address this gap, we synthesized an MS/MS spectral resource comprising 436 structurally diverse 3-hydroxy <i>N</i>-acyl amides, spanning 3- to 18-carbon chains with a wide range of amine headgroups, such as ornithine, valine, and dopamine. Using a synthesis-driven reverse metabolomics approach, we found 161,626 spectral matches across 54,744 publicly available files in untargeted metabolomics data sets, revealing widespread occurrences in biological samples, including human-derived specimens. Of these molecules detected through MS/MS spectral matching, 334 represent newly reported biological entities. We further confirmed their presence in human saliva, stool, and skin using retention time and ion mobility measurements. Frequent detection in microbial data sets and validation in communities of human-derived gut bacteria support microbial production. Several metabolites also showed altered abundance in individuals with diabetes mellitus, showing that this lipid class is modulated in human metabolic disease. Together, these findings establish 3-hydroxy <i>N</i>-acyl amides as a distinct and biologically relevant lipid class, and the accompanying MS/MS spectral resource will enable their broader recognition and study in untargeted metabolomics data.</p><p><strong>Importance: </strong>Microbe-host interactions lead to the production of metabolites that play an important role in human health and disease, though the annotation of such metabolites remains scarce. We created a re-usable MS/MS spectral library of an underrepresented class of compounds-3-hydroxy <i>N</i>-acyl amides. Our study characterized the presence of over 400 3-hydroxy <i>N</i>-acyl amides among thousands of public untargeted metabolomics datasets. We found over 100,000 instances of these metabolites within microbial, plant, and animal data, and used orthogonal validation methods to confirm nine previously unreported molecules within human feces, saliva, and skin samples. We cultured communities of human-derived gut bacteria and found evidence of bacterial production of four 3-hydroxy <i>N</i>-acyl amides. Our results suggest that these metabolites play important roles in human metabolism and disease, and sharing this curated resource enables the detection of these metabolites in future studies.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0083926"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149039806","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}

{"title":"Shifts in vegetation impact estuary microbiomes.","authors":"Georgina L Aitolo, Ian M Rambo, Rachel E Weisend, Megan M Mullis, Susannah Tringe, James C Kosmopoulos, Karthik Anantharaman, Brandi Kiel Reese, Brett J Baker, Valerie De Anda","doi":"10.1128/msystems.01071-26","DOIUrl":"10.1128/msystems.01071-26","url":null,"abstract":"<p><p>Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth's most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe-virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by <i>Sporobolus alterniflorus</i>), black mangrove (<i>Avicennia germinans</i>), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus-host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.IMPORTANCECoastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0107126"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081361","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}

{"title":"Resolving host-episymbiont interaction dynamics through continuous cultivation.","authors":"Alex S Grossman, Jacey Weng, Adam D Silverman, Batbileg Bor","doi":"10.1128/msystems.00592-26","DOIUrl":"10.1128/msystems.00592-26","url":null,"abstract":"<p><p>Minisyncoccota are an elusive lineage of \"microbial dark matter\" predicted to compose ~25% of total bacterial diversity. Despite near ubiquity, these organisms are challenging to cultivate, resulting from their specialized episymbiotic lifestyle. All cultivated representatives, predominantly Nanosynbacteria, depend on cognate prokaryotic hosts for growth. Studying the growth dynamics of episymbiotic bacteria and their hosts in batch cultures suggests that episymbionts typically reduce host populations and that hosts eventually adapt to episymbiont stress after serial passaging. However, discontinuous batch cultures do not reflect natural interactions between these organisms due to their drastically different growth rates, which complicates the investigation of host inhibition and adaptation. To describe these dynamics, we utilized continuous culture via small-scale bioreactors. Within a bioreactor, host bacteria can be cultivated at a consistent growth rate, providing the perfect substrate for cultivation of model Nanosynbacteria. Quantification of time until host crash, crash severity, host adaptation, and stable co-culture population provides mechanistic ways to describe episymbiont-host interactions. We used these techniques to compare infection by three episymbionts, revealing distinct infection patterns ranging from mild inhibition with rapid host adaptation to rapid host collapse followed by \"arms-race\" oscillation dynamics. Then, bioreactors were used to quantify the episymbiotic role played by a known host-binding type 4 pili (T4P-2), demonstrating that loss of pilus-range host binding (approximately 100-800 nm) significantly delayed the host crash without altering general crash dynamics. These experiments reveal that episymbionts can have drastically different effects on bacterial communities and provide the tools necessary to describe strain/species differences and molecular interactions.IMPORTANCEEpisymbiotic Minisyncoccota represent one of the largest branches of life on Earth, as well as one of the least understood. Furthermore, because Minisyncoccota can manipulate their hosts' growth and morphology, they have immense ecological potential to shape the communities they occupy, both environmental and microbiome-associated. Our study highlights, for the first time, the potential of small-scale continuous cultivation for studying episymbiotic interactions that cannot be captured in discontinuous cultures. Herein, we used these techniques to interrogate interspecies variation in host inhibition potential and to determine how loss of a pilus-dependent binding factor mechanistically alters the cycle of episymbiont infection; however, this cultivation platform will enable researchers to answer many new questions about these ubiquitous host-episymbiont interactions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0059226"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070014","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}

{"title":"Cold-water gut isolate from threespine stickleback (<i>Gasterosteus aculeatus</i>) reveals polypropylene surface oxidation and co-culture inhibition.","authors":"Sarah M Pasqualetti, Jolie Atwood, Abiodun Aderibigbe, Edward Russell, Kayleigh O'Keefe, Victoria Rosario, Kelly Ireland, Kenneth Sparks, Koral Campbell, Ruth Y Isenberg, Ryan Lucas, Kathryn Milligan-McClellan","doi":"10.1128/msystems.00599-26","DOIUrl":"10.1128/msystems.00599-26","url":null,"abstract":"<p><p>Polyethylene terephthalate (PET) and polypropylene (PP), two of the most widely produced plastics in the United States, persist in diverse environments worldwide and may persist longer in cold-water environments where plastic-degrading microbial taxa have been poorly characterized. Understanding how gut microbes interact and contribute to plastic degradation is essential for developing potential microbiome-based bioremediation strategies. We isolated 184 microbes from wild Alaskan threespine stickleback (<i>Gasterosteus aculeatus</i>) guts across six bodies of water and screened them for their plastic-degrading potential using lipase/esterase assays and biofilm formation on PET and PP. We discovered that while some members of the stickleback gut microbiota have high lipase, esterase, and biofilm activity, that activity is enhanced or suppressed by other microbes. Isolates with the highest plastic-degrading potential were incubated in minimal media with PET or PP as the primary carbon source to determine whether plastic degradation occurs. While no detectable changes were observed on PET, surface analysis identified a <i>Pseudomonas trivialis</i> strain that exhibited evidence of PP surface oxidation in monoculture; however, this activity was suppressed in the presence of another gut isolate, <i>Pseudomonas germanica</i>. These results demonstrate that microbes associated with the gut microbiome of a cold-water fish possess plastic-degrading potential and provide insights into how microbial interactions can inhibit bioremediation of plastic pollution in cold-water environments.IMPORTANCEPlastic pollution persists in cold, freshwater environments and presents a significant challenge to the ecosystem, where low temperatures slow abiotic degradation, and microbial contributions remain poorly understood and understudied. Here, we isolated 184 microbes from adult Alaskan threespine stickleback guts across six bodies of water and screened for plastic-degradation potential using plate-based assays under both monoculture and co-culture conditions. We identified a stickleback gut-associated microbe that can oxidize polypropylene and identified a second microbe, isolated from the same environment, that can significantly suppress polymer oxidation when in co-culture. Together, these findings demonstrate that microbial interactions influence plastic-degradation abilities and support efforts to identify ecologically relevant microbes or enzymes for bioremediation efforts.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0059926"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081146","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}

{"title":"Genomic and biochemical contexts determine the physiological role of a horizontally acquired gene.","authors":"Roberto E Bruna, Alagu Lakshmi Selvaraj, Somok Bhowmik, Christopher G Kendra, Ryan Heister, Mauricio H Pontes","doi":"10.1128/msystems.00845-26","DOIUrl":"10.1128/msystems.00845-26","url":null,"abstract":"<p><p>The horizontally acquired <i>mgtC</i> gene from <i>Salmonella enterica</i> confers on this bacterium the abilities to survive episodes of magnesium (Mg²⁺) starvation and to replicate in mammalian macrophages. The former property allows bacteria to persist in the environment during Mg²⁺ depletion, whereas the latter allows <i>S. enterica</i> to overcome self-limiting intestinal colonization and cause invasive systemic infection in susceptible mammalian hosts. Even though the biochemical function of MgtC is not completely understood, this protein is thought to function primarily by preventing the production of toxic levels of Mg²⁺-chelating adenosine triphosphate. In the current work, we investigated the physiological roles of <i>mgtC</i> homologs from an array of bacterial species by probing the processes controlled by this gene during replication in low-Mg²⁺ medium and in macrophages. We determined that MgtC homologs that do not participate in Pi homeostasis during Mg²⁺ starvation and do not promote intramacrophage replication in their resident species can partake in these processes when expressed in <i>S. enterica</i>. This indicates that the function of this protein is context dependent. Accordingly, we show that the physiological processes affected by <i>S. enterica</i> MgtC vary depending on whether the bacteria replicate in low-Mg²⁺ medium or inside macrophages. While these results suggest that MgtC is a regulator, they also demonstrate that horizontally acquired genes can assume different roles, depending on the genome and the biochemical context into which they are inserted.IMPORTANCEThe <i>mgtC</i> gene encodes an inner membrane protein that has been horizontally acquired by multiple bacterial species, including several mammalian pathogens. In <i>Salmonella enterica</i>, MgtC promotes replication in mammalian macrophages and allows this bacterium to survive cytoplasmic magnesium (Mg²⁺) starvation. These phenotypes are thought to result from MgtC's inhibition of Pi metabolism and adenosine triphosphate (ATP) production, which prevents the accumulation of toxic levels of Mg²⁺-chelating ATP and disrupts other physiological processes that depend strictly on Mg²⁺, such as ribosome assembly and translation. In the current study, we show that processes that are controlled by MgtC vary with the genetic and biochemical contexts in which this protein is expressed. While establishing a broader role for MgtC as a regulator, our findings illustrate how horizontally acquired regulatory genes can potentiate regulatory interactions, facilitating the evolution of new traits.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0084526"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081299","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}