Correction to: Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
Correction to: Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
复制标题
更正：Deltaproteobacteria 的大规模蛋白质水平比较揭示了内聚的代谢群体
DOI：
10.1038/s41396-021-01091-w
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Baker, Brett J.
中科院分区：
文献类型：
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作者：
Langwig, Marguerite V.;De Anda, Valerie;Dombrowski, Nina;Seitz, Kiley W.;Rambo, Ian M.;Greening, Chris;Teske, Andreas P.;Baker, Brett J.
δ变形菌，现在被认为是脱硫菌门，粘球菌门和SAR 324，在海洋环境中无处不在，在全球碳，硫和营养循环中发挥着重要作用。尽管它们很重要，但我们对这些细菌的理解偏向于培养的生物体。在这里，我们通过编译1 792个基因组的基因组目录，包括402个新的重建和表征的宏基因组组装的基因组（MAG）从沿海和深海沉积物来解决这个差距。系统基因组学分析表明，许多这些新的MAG是未培养的代表粘球菌和脱硫杆菌的研究不足。为了更好地表征Deltaproteobacteria的多样性，代谢和生态，我们根据其蛋白质家族的存在/不存在模式对约1500个基因组进行了聚类。蛋白质含量分析加上大规模的代谢重建分离八个具有独特代谢谱的Deltaproteobacteria的基因组簇。虽然这八个集群在很大程度上对应于同源性，但也有例外，即亲缘关系较远的生物似乎具有相似的生态作用，而亲缘关系较近的生物具有不同的蛋白质含量。我们的分析已经确定了以前未被认识到的作用，在未培养的Deltaproteobacteria之间的甲胺和反硝化循环。这种新的观点Deltaproteobacteria多样性扩展了我们对这些优势细菌的理解，并强调了不同类群的代谢能力。
Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.