Globally distributed marine Gemmatimonadota have unique genomic potentials.

IF 13.8 1区生物学 Q1 MICROBIOLOGY

Microbiome Pub Date : 2024-08-10 DOI:10.1186/s40168-024-01871-4

Xianzhe Gong, Le Xu, Marguerite V Langwig, Zhiyi Chen, Shujie Huang, Duo Zhao, Lei Su, Yan Zhang, Christopher A Francis, Jihua Liu, Jiangtao Li, Brett J Baker

{"title":"Globally distributed marine Gemmatimonadota have unique genomic potentials.","authors":"Xianzhe Gong, Le Xu, Marguerite V Langwig, Zhiyi Chen, Shujie Huang, Duo Zhao, Lei Su, Yan Zhang, Christopher A Francis, Jihua Liu, Jiangtao Li, Brett J Baker","doi":"10.1186/s40168-024-01871-4","DOIUrl":null,"url":null,"abstract":"Background: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.Results: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to \"hijack\" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.Conclusions: This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"149"},"PeriodicalIF":13.8000,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316326/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbiome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s40168-024-01871-4","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.

Results: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.

Conclusions: This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.

查看原文本刊更多论文

全球分布的海洋 Gemmatimonadota 具有独特的基因组潜力。

背景：Gemmatimonadota细菌广泛分布于自然界，但人们对它们在海洋环境中的代谢潜力和生态作用知之甚少：在这里，我们从世界各地的沿海到深海沉积物中获得了 495 个元基因组组装基因组（MAGs）和相关病毒。我们利用这一扩大的基因组目录来比较这些细菌的蛋白质组成并更新其系统发育。海洋 Gemmatimonadota 在系统发育上不同于之前报道的陆地环境中的细菌。对这些基因组的功能分析显示，这些海洋基因型能够降解复杂的有机碳、反硝化、还原硫酸盐以及氧化硫化物和亚硫酸盐。有趣的是，在 Gemmatimonadota 中广泛存在次生代谢物生物合成的遗传潜力，这可能是一种尚未开发的新型天然产品来源。此外，与Gemmatimonadota相关的病毒有可能 "劫持 "和操纵宿主的新陈代谢，包括在宿主体内组装脂多糖：结论：基因组多样性的扩大加深了我们对这些分布在全球各种生态系统中的细菌的了解，并揭示了陆地和海洋生物群落中细菌之间的遗传差异。视频摘要

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Microbiome MICROBIOLOGY-

CiteScore

21.90

自引率

2.60%

发文量

198

审稿时长

4 weeks

期刊介绍： Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.