Data_Sheet_1_Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake.PDF

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

众多微生物类群潜在的代谢功能和生态作用尚属未知，究其原因，在于评估其功能潜力的基因组数据不足。其中，两种微生物的“暗物质”类群——拟杆菌门Cloacimonadota和泛营养门Omnitrophota，均已在全球缺氧环境中被发现，包括但不限于富含有机碳的湖泊。通过从南极湖（阿斯湖，弗斯弗尔德丘陵）获取的24个宏基因组组装基因组（MAGs），我们为这两个门识别出了新的谱系和代谢特征。Cloacimonadota的MAGs展现出利用氢和硫的氧化驱动的逆向三羧酸循环进行碳固定的能力。某些Cloacimonadota的MAGs编码具有dockerin和cohesin结构域的蛋白质，这与组装类似胞外纤维素酶复合体的结构相一致，该结构用于降解多肽和多糖。Omnitrophota的MAGs代表了在系统发育上多样化的类群，预计它们具有合成氨基酸、核苷酸、脂肪酸和必需辅因子的强大生物合成能力。所有Omnitrophota都被推断为必需发酵异养生物，它们利用相对狭窄的有机化合物范围，拥有不完整的三羧酸循环，并拥有一个重要的氢酶基因，该基因对于在细胞中实现氧化还原平衡至关重要。我们认为，Cloacimonadota和Omnitrophota分别与消耗氢的合作伙伴（产甲烷菌和脱硫杆菌门）形成代谢相互作用，因此，在阿斯湖中占据特定的生态位。