Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
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DOI：
10.1038/s41396-021-01057-y
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发表时间：
2021-07-30
期刊：
影响因子：
11
通讯作者：
Baker, Brett J.
中科院分区：
文献类型：
--
作者：
Langwig, Marguerite V.;De Anda, Valerie;Baker, Brett J.
Deltaproteobacteria，现在被认为是 Desulfobacterota、Myxococcota 和 SAR324 门，在海洋环境中普遍存在，在全球碳、硫和养分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生物。在这里，我们通过编译 1 792 个基因组的基因组目录来解决这一空白，其中包括 402 个来自沿海和深海沉积物的新重建和表征的宏基因组组装基因组 (MAG)。系统基因组分析表明，许多新的 MAG 是未经培养的粘球菌门和脱硫杆菌门的代表，目前尚未得到充分研究。为了更好地描述 Deltaproteobacteria 的多样性、代谢和生态学特征，我们根据其蛋白质家族的存在/不存在模式对 1500 个基因组进行了聚类。蛋白质含量分析与大规模代谢重建相结合，分离出具有独特代谢特征的 Deltaproteobacteria 的八个基因组簇。虽然这八个簇在很大程度上与系统发育相对应，但也有例外，即关系较远的生物体似乎具有相似的生态作用，而密切相关的生物体则具有不同的蛋白质含量。我们的分析发现了未培养的 Deltaproteobacteria 中甲胺循环和反硝化作用中以前未被认识的作用。这种关于 Deltaproteobacteria 多样性的新观点扩大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 similar to 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.