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Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates. 依赖氢的异化硝酸还原成铵使弯曲杆菌分离物生长。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-05-14 DOI: 10.1093/ismejo/wraf092
Hokwan Heo, Thanh Nguyen-Dinh, Man-Young Jung, Chris Greening, Sukhwan Yoon
{"title":"Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.","authors":"Hokwan Heo, Thanh Nguyen-Dinh, Man-Young Jung, Chris Greening, Sukhwan Yoon","doi":"10.1093/ismejo/wraf092","DOIUrl":"https://doi.org/10.1093/ismejo/wraf092","url":null,"abstract":"<p><p>Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterotastrains, Aliarcobacter butzlerihDNRA1 and Sulfurospirillumsp. hDNRA2, which grow using H2as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto(i.e. NO3-reduction that includes stoichiometric NO2--to-NH4+reduction) was strictly dependent on the presence of H2and exhibited stoichiometric coupling with H2oxidation, indicating that electrons required for NO2-reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3-limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. Additionally, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes. 珊瑚组织内内生单胞菌的不同聚集模式。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-03-28 DOI: 10.1093/ismejo/wraf059
Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen
{"title":"Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes.","authors":"Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen","doi":"10.1093/ismejo/wraf059","DOIUrl":"https://doi.org/10.1093/ismejo/wraf059","url":null,"abstract":"<p><p>Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building coral, Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribed Endozoicomonas strains isolated from A. loripes. Subsequent 16S rRNA gene amplicon sequencing revealed their classification into two distinct phylogenetic clades. To resolve their spatial distribution in hospite, clade-specific fluorescence in situ hybridization probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed by Endozoicomonas from both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These morphological differences highlight the importance of further investigations into the mechanisms governing bacterial aggregate formation in corals.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean. 远洋钙化原生生物的不确定命运:变化中的海洋的细胞视角。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-02-21 DOI: 10.1093/ismejo/wraf007
Adva Shemi, Assaf Gal, Assaf Vardi
{"title":"Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean.","authors":"Adva Shemi, Assaf Gal, Assaf Vardi","doi":"10.1093/ismejo/wraf007","DOIUrl":"https://doi.org/10.1093/ismejo/wraf007","url":null,"abstract":"<p><p>Pelagic calcifying protists such as coccolithophores and foraminifera represent an important microbial component of the marine carbon cycle. Although their calcitic shells are preserved in oceanic sediments over millennia, their resilience in the future decades is uncertain. We review current literature describing the response of calcifying protists to ocean acidification and temperature warming. We examine these key ecological and biogeochemical processes through the cellular perspective, exploring the physiological, metabolic, and molecular responses of calcifying protists. Ocean acidification is a chemical process that takes place in the seawater outside the cell, whereas protists calcify inside a modified cellular microenvironment. The function of these calcification compartments depends on cellular response to ocean acidification, such as maintaining pH homeostasis. The response of calcifying protists to ocean acidification and temperature warming is species-specific, with no unifying trends but rather a range of sensitivity levels. Coccolithophores and foraminifera display physiological sensitivity that may hamper their ecological success in comparison to non-calcifying species. Yet, certain species may be more adaptable, especially when comparing to highly vulnerable calcifying molluscs as pteropods. As the molecular machinery mediating cellular calcification is not fully resolved, as well as the functional role of the calcitic shell, our ability to predict the fate of calcifying microorganisms in a warmer, more acidic ocean is limited. We propose the urgent need to expand the study of these model systems by advancing cell biology approaches, to better understand the impact of climate change on microbial food webs in the ocean.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Surfactin facilitates establishment of Bacillus subtilis in synthetic communities. 表面素促进枯草芽孢杆菌在合成群落中的建立。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf013
Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács
{"title":"Surfactin facilitates establishment of Bacillus subtilis in synthetic communities.","authors":"Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács","doi":"10.1093/ismejo/wraf013","DOIUrl":"10.1093/ismejo/wraf013","url":null,"abstract":"<p><p>Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11833321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Selection for toxin production in spatially structured environments increases with growth rate. 在空间结构环境中产生毒素的选择随着生长速度的增加而增加。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf061
Ave T Bisesi, Jeremy M Chacón, Michael J Smanski, Linda Kinkel, William R Harcombe
{"title":"Selection for toxin production in spatially structured environments increases with growth rate.","authors":"Ave T Bisesi, Jeremy M Chacón, Michael J Smanski, Linda Kinkel, William R Harcombe","doi":"10.1093/ismejo/wraf061","DOIUrl":"10.1093/ismejo/wraf061","url":null,"abstract":"<p><p>Microbes adopt diverse strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy vary depending on the environment. Existing theoretical and experimental evidence suggests that growth in spatially structured environments makes toxin production more beneficial because competitive interactions are localized. Because higher growth rates reduce the length scale of interactions in structured environments, theory predicts that toxin production should be especially beneficial under these conditions. We tested this hypothesis by developing a genome-scale metabolic modeling approach and complementing it with comparative genomics to investigate the impact of growth rate on selection for costly toxin production. Our modeling approach expands the current abilities of the dynamic flux balance analysis platform Computation Of Microbial Ecosystems in Time and Space (COMETS) to incorporate signaling and toxin production. Using this capability, we find that our modeling framework predicts that the strength of selection for toxin production increases as growth rate increases. This finding is supported by comparative genomics analyses that include diverse microbial species. Our work emphasizes that toxin production is more likely to be maintained in rapidly growing, spatially structured communities, thus improving our ability to manage microbial communities and informing natural product discovery.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dietary protein source alters gut microbiota composition and function. 膳食蛋白质来源改变肠道菌群组成和功能。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf048
J Alfredo Blakeley-Ruiz, Alexandria Bartlett, Arthur S McMillan, Ayesha Awan, Molly Vanhoy Walsh, Alissa K Meyerhoffer, Simina Vintila, Jessie L Maier, Tanner G Richie, Casey M Theriot, Manuel Kleiner
{"title":"Dietary protein source alters gut microbiota composition and function.","authors":"J Alfredo Blakeley-Ruiz, Alexandria Bartlett, Arthur S McMillan, Ayesha Awan, Molly Vanhoy Walsh, Alissa K Meyerhoffer, Simina Vintila, Jessie L Maier, Tanner G Richie, Casey M Theriot, Manuel Kleiner","doi":"10.1093/ismejo/wraf048","DOIUrl":"10.1093/ismejo/wraf048","url":null,"abstract":"<p><p>The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans. 质粒编码并能调动洋葱在泛菌凝聚体中的致病性。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf019
Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L Derie, Lindsey J du Toit, Stephen Stresow-Cortez, Jean M Bonasera, Paul Stodghill, Brian Kvitko
{"title":"Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.","authors":"Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L Derie, Lindsey J du Toit, Stephen Stresow-Cortez, Jean M Bonasera, Paul Stodghill, Brian Kvitko","doi":"10.1093/ismejo/wraf019","DOIUrl":"10.1093/ismejo/wraf019","url":null,"abstract":"<p><p>Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phylogenomic resolution of marine to freshwater dinoflagellate transitions. 海洋到淡水鞭毛虫转变的系统发育分析。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf031
Mahara Mtawali, Elizabeth C Cooney, Jayd Adams, Joshua Jin, Corey C Holt, Patrick J Keeling
{"title":"Phylogenomic resolution of marine to freshwater dinoflagellate transitions.","authors":"Mahara Mtawali, Elizabeth C Cooney, Jayd Adams, Joshua Jin, Corey C Holt, Patrick J Keeling","doi":"10.1093/ismejo/wraf031","DOIUrl":"10.1093/ismejo/wraf031","url":null,"abstract":"<p><p>Dinoflagellates are an abundant and diverse group of protists that inhabit aquatic environments worldwide. They are characterized by numerous unique cellular and molecular traits, and have adapted to an unusually broad range of life strategies, including phototrophy, heterotrophy, parasitism, and all combinations of these. For most microbial groups, transitions from marine to freshwater environments are relatively rare, as changes in salinity are thought to lead to significant osmotic challenges that are difficult for the cell to overcome. Recent work has shown that dinoflagellates have overcome these challenges relatively often in evolutionary time, but because this is mostly based on single gene trees with low overall support, many of the relationships between freshwater and marine groups remain unresolved. Normally, phylogenomics could clarify such conclusions, but despite the recent surge in data, virtually no freshwater dinoflagellates have been characterized at the genome-wide level. Here, we generated 30 transcriptomes from cultures and single cells collected from freshwater environments to infer a robustly supported phylogenomic tree from 217 conserved genes, resolving at least seven transitions to freshwater in dinoflagellates. Mapping the distribution of ASVs from freshwater environmental samples onto this tree confirms these groups and identifies additional lineages where freshwater dinoflagellates likely remain unsampled. We also sampled two species of Durinskia, a genus of \"dinotoms\" with both marine and freshwater lineages containing Nitzschia-derived tertiary plastids. Ribosomal RNA phylogenies show that the host cells are closely related, but their endosymbionts are likely descended from two distantly-related freshwater Nitzschia species that were acquired in parallel and relatively recently.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera. 甲基营养化甲基藻在地下水中产生好氧甲烷的蛋白质组学证据。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf024
Shengjie Li, Xiaoli Dong, Pauline Humez, Joanna Borecki, Jean Birks, Cynthia McClain, Bernhard Mayer, Marc Strous, Muhe Diao
{"title":"Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.","authors":"Shengjie Li, Xiaoli Dong, Pauline Humez, Joanna Borecki, Jean Birks, Cynthia McClain, Bernhard Mayer, Marc Strous, Muhe Diao","doi":"10.1093/ismejo/wraf024","DOIUrl":"10.1093/ismejo/wraf024","url":null,"abstract":"<p><p>Members of Methylotenera are signature denitrifiers and methylotrophs commonly found together with methanotrophic bacteria in lakes and freshwater sediments. Here, we show that three distinct Methylotenera ecotypes were abundant in methane-rich groundwaters recharged during the Pleistocene. Just like in surface water biomes, groundwater Methylotenera often co-occurred with methane-oxidizing bacteria, even though they were generally unable to denitrify. One abundant Methylotenera ecotype expressed a pathway for aerobic methane production from methylphosphonate. This phosphate-acquisition strategy was recently found to contribute to methane production in the oligotrophic, oxic upper ocean. Gene organization, phylogeny, and 3D protein structure of the key enzyme, carbon-phosphorus lyase subunit PhnJ, were consistent with a role in phosphate uptake. We conclude that phosphate may be a limiting nutrient in productive, methane-rich aquifers, and that methylphosphonate degradation might contribute to groundwater methane production.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks. 靶向益生元应用含葡萄糖酸寡糖通过微生物交叉取食网络促进粪杆菌的生长。
IF 10.8 1区 环境科学与生态学
ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf027
Hiroki Negishi, Ayumi Ichikawa, Saori Takahashi, Hiroshi Kano, Seiya Makino
{"title":"Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks.","authors":"Hiroki Negishi, Ayumi Ichikawa, Saori Takahashi, Hiroshi Kano, Seiya Makino","doi":"10.1093/ismejo/wraf027","DOIUrl":"10.1093/ismejo/wraf027","url":null,"abstract":"<p><p>The gut microbiome plays a crucial role in human health, and certain bacterial species, such as Faecalibacterium prausnitzii, are particularly beneficial. This study conducted a comprehensive investigation of prebiotic compounds that showed potential for specifically promoting beneficial gut bacteria. Using in vitro fecal cultures and a human intervention study, we identified maltobionic acid and lactobionic acid as compounds that specifically promoted Faecalibacterium growth both in vitro and in vivo without significantly affecting Bifidobacterium, which is typically increased by traditional prebiotics. In a human intervention study (n = 27), a significant increase was observed in Faecalibacterium abundance following maltobionic acid supplementation, with effectiveness correlating with the initial Parabacteroides abundance. Mechanistic investigations revealed a cross-feeding pathway between gut bacteria. In this pathway, Parabacteroides species converted the gluconic acid moiety of maltobionic and lactobionic acids to glucuronic acid, which was then preferentially utilized by Faecalibacterium. These findings suggest that gluconic acid-containing oligosaccharides are promising prebiotics for the targeted enhancement of beneficial Faecalibacterium and underscore the importance of microbial interactions in prebiotic research, offering new avenues for personalized microbiome modulation strategies.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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