State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China.
ISME J. 2021 Oct;15(10):3005-3018. doi: 10.1038/s41396-021-00935-9. Epub 2021 May 5.
Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.
化能自养微生物（如同型产乙酸菌）的碳固定作用对从无机世界向有机世界的转变产生了重大影响。最近的报告表明，放线菌门中存在与 Wood-Ljungdahl 途径（WLP）相关的关键酶基因，这增加了潜在自养生物的多样性。在这里，我们从新的和现有的宏基因组数据集汇编了 42 个放线菌宏基因组组装基因组（MAG），并提出了三个新的类群，Ca. Aquicultoria、Ca. Geothermincolia 和 Ca. Humimicrobiia。这些类群的大多数成员都含有通过 WLP 进行乙酰生成的基因，以及各种氢化酶（NiFe 组 1a 和 3b-3d；FeFe 组 C；NiFe 组 4 相关氢化酶）。我们表明，这三个类群独立获得了氢化酶，但一氧化碳脱氢酶/乙酰辅酶 A 合酶复合物（CODH/ACS）显然存在于它们的最后共同祖先中，并通过垂直遗传继承。此外，放线菌可能通过多次水平基因转移事件将 CODH/ACS 的基因捐赠给了硝化螺旋菌、δ变形菌门（脱硫杆菌门）和热脱硫杆菌门的多个谱系。最后，我们表明在有或没有甲烷生成抑制剂 2-溴乙烷磺酸盐的温泉富集培养物中，Ca. Geothermincolia 和 H 依赖性乙酸盐的生长明显，这与拟议的同型产乙酸代谢一致。
