ISME communications最新文献_第10页

Predicting bacterial interaction outcomes from monoculture growth and supernatant assays. 通过单培养基生长和上清液检测预测细菌相互作用结果

IF 5.1

ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae045

Désirée A Schmitz, Tobias Wechsler, Ingrid Mignot, Rolf Kümmerli

{"title":"Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.","authors":"Désirée A Schmitz, Tobias Wechsler, Ingrid Mignot, Rolf Kümmerli","doi":"10.1093/ismeco/ycae045","DOIUrl":"10.1093/ismeco/ycae045","url":null,"abstract":"How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae045"},"PeriodicalIF":5.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying microbial guilds. 量化微生物行会。

IF 5.1

ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae042

Juan Rivas-Santisteban, Pablo Yubero, Semidán Robaina-Estévez, José M González, Javier Tamames, Carlos Pedrós-Alió

{"title":"Quantifying microbial guilds.","authors":"Juan Rivas-Santisteban, Pablo Yubero, Semidán Robaina-Estévez, José M González, Javier Tamames, Carlos Pedrós-Alió","doi":"10.1093/ismeco/ycae042","DOIUrl":"10.1093/ismeco/ycae042","url":null,"abstract":"The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae042"},"PeriodicalIF":5.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11069341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140856076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances. 半乳糖胺和甘露胺是细菌和真菌胞外聚合物物质的组成部分。

ISME communications Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae038

Rebeca Leme Oliva, Carla Vogt, Tábata Aline Bublitz, Tessa Camenzind, Jens Dyckmans, Rainer Georg Joergensen

{"title":"Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances.","authors":"Rebeca Leme Oliva, Carla Vogt, Tábata Aline Bublitz, Tessa Camenzind, Jens Dyckmans, Rainer Georg Joergensen","doi":"10.1093/ismeco/ycae038","DOIUrl":"https://doi.org/10.1093/ismeco/ycae038","url":null,"abstract":"Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae038"},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum. 噬菌体驱动的共同进化揭示了锐毒沙门氏菌抗生素和噬菌体抗药性之间的权衡。

ISME communications Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae039

Yuanyang Zhao, Mei Shu, Ling Zhang, Chan Zhong, Ningbo Liao, Guoping Wu

{"title":"Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum.","authors":"Yuanyang Zhao, Mei Shu, Ling Zhang, Chan Zhong, Ningbo Liao, Guoping Wu","doi":"10.1093/ismeco/ycae039","DOIUrl":"https://doi.org/10.1093/ismeco/ycae039","url":null,"abstract":"Phage therapy faces challenges against multidrug-resistant (MDR) Salmonella due to rapid phage-resistant mutant emergence. Understanding the intricate interplay between antibiotics and phages is essential for shaping Salmonella evolution and advancing phage therapy. In this study, MDR Salmonella anatum (S. anatum) 2089b coevolved with phage JNwz02 for 30 passages (60 days), then the effect of coevolution on the trade-off between phage and antibiotic resistance in bacteria was investigated. Our results demonstrated antagonistic coevolution between bacteria and phages, transitioning from arms race dynamics (ARD) to fluctuating selection dynamics (FSD). The fitness cost of phage resistance, manifested as reduced competitiveness, was observed. Bacteria evolved phage resistance while simultaneously regaining sensitivity to amoxicillin, ampicillin, and gentamicin, influenced by phage selection pressure and bacterial competitiveness. Moreover, the impact of phage selection pressure on the trade-off between antibiotic and phage resistance was more pronounced in the ARD stage than in the FSD stage. Whole genome analysis revealed mutations in the btuB gene in evolved S. anatum strains, with a notably higher mutation frequency in the ARD stage compared to the FSD stage. Subsequent knockout experiments confirmed BtuB as a receptor for phage JNwz02, and the deletion of btuB resulted in reduced bacterial competitiveness. Additionally, the mutations identified in the phage-resistant strains were linked to multiple single nucleotide polymorphisms (SNPs) associated with membrane components. This correlation implies a potential role of these SNPs in reinstating antibiotic susceptibility. These findings significantly advance our understanding of phage-host interactions and the impact of bacterial adaptations on antibiotic resistance.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae039"},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140861023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors. 灵活的高通量培养方案，用于评估个体肠道微生物群对饮食、药物和宿主相关因素的反应。

IF 5.1

ISME communications Pub Date : 2024-03-12 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae035

Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin

{"title":"A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.","authors":"Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin","doi":"10.1093/ismeco/ycae035","DOIUrl":"10.1093/ismeco/ycae035","url":null,"abstract":"The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae035"},"PeriodicalIF":5.1,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria. 植物相关细菌不同 16S rRNA 可变区的分类分辨率差异很大。

ISME communications Pub Date : 2024-03-08 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae034

Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian

{"title":"Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.","authors":"Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian","doi":"10.1093/ismeco/ycae034","DOIUrl":"10.1093/ismeco/ycae034","url":null,"abstract":"Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our in silico analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae034"},"PeriodicalIF":0.0,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10980831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. 跨降水梯度的外生菌根真菌群落功能分化的潜力。

ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae031

Peter T Pellitier, Michael Van Nuland, Asaf Salamov, Igor V Grigoriev, Kabir G Peay

{"title":"Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient.","authors":"Peter T Pellitier, Michael Van Nuland, Asaf Salamov, Igor V Grigoriev, Kabir G Peay","doi":"10.1093/ismeco/ycae031","DOIUrl":"10.1093/ismeco/ycae031","url":null,"abstract":"Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae031"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia. 缺氧条件下水稻田土壤中铁酸盐介导的甲烷固氮作用

ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae030

Linpeng Yu, Rong Jia, Shiqi Liu, Shuan Li, Sining Zhong, Guohong Liu, Raymond Jianxiong Zeng, Christopher Rensing, Shungui Zhou

{"title":"Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia.","authors":"Linpeng Yu, Rong Jia, Shiqi Liu, Shuan Li, Sining Zhong, Guohong Liu, Raymond Jianxiong Zeng, Christopher Rensing, Shungui Zhou","doi":"10.1093/ismeco/ycae030","DOIUrl":"10.1093/ismeco/ycae030","url":null,"abstract":"Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 μmol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae030"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment. 大盐湖沉积物中产生天然产物的细菌多样性和化学生态学。

ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae029

Elijah R Bring Horvath, William J Brazelton, Min Cheol Kim, Reiko Cullum, Matthew A Mulvey, William Fenical, Jaclyn M Winter

{"title":"Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment.","authors":"Elijah R Bring Horvath, William J Brazelton, Min Cheol Kim, Reiko Cullum, Matthew A Mulvey, William Fenical, Jaclyn M Winter","doi":"10.1093/ismeco/ycae029","DOIUrl":"10.1093/ismeco/ycae029","url":null,"abstract":"Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae029"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments. 甲单胞菌是西藏湖泊沉积物中活跃的优势甲烷营养体。

ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae032

Yongcui Deng, Chulin Liang, Xiaomeng Zhu, Xinshu Zhu, Lei Chen, Hongan Pan, Fan Xun, Ye Tao, Peng Xing

{"title":"Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments.","authors":"Yongcui Deng, Chulin Liang, Xiaomeng Zhu, Xinshu Zhu, Lei Chen, Hongan Pan, Fan Xun, Ye Tao, Peng Xing","doi":"10.1093/ismeco/ycae032","DOIUrl":"10.1093/ismeco/ycae032","url":null,"abstract":"Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with 13CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the 13C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe3+), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae032"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0