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, 510275, People's Republic of China.
Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China.
Microbiome. 2024 Jul 6;12(1):123. doi: 10.1186/s40168-024-01836-7.
The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.
We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11 and Phoenicimicrobium oleiphilum HX-OS.bin.34 ferment sugars and n-alkanes, respectively, producing H, CO and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments.
Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.
Atribacterota 广泛分布于地下生物圈中。最近，人们首次描述了 Atribacterota 的分离株，并且从环境样本中检索到的 Atribacterota 基因组序列数量显著增加；然而，它们的多样性、生理学、生态学和进化仍然知之甚少。
我们报告了 Atribacterota 第二成员Thermatribacter velox gen. nov.，sp. nov.的分离，隶属于新的Thermatribacteraceae 科，并对 JS1 谱系的成员Phoenicimicrobium oleiphilum HX-OS.bin.34 进行了短期实验室培养，两者均来自陆地油藏。生理和代谢组学分析表明，Thermatribacter velox B11 发酵糖和正构烷烃，分别产生 H、CO 和乙酸作为共同产物。比较基因组学表明，所有 Atribacterota 成员均缺乏完整的 Wood-Ljungdahl 途径（WLP），但广泛存在还原甘氨酸途径（RGP），这表明 RGP 而不是 WLP 是 Atribacterota 代谢的中心枢纽。祖先特征状态重建和系统发育分析表明，编码 RGP（fdhA、fhs、folD、glyA、gcvT、gcvPAB、pdhD）和其他核心功能的关键基因在两个纲（Atribacteria（OP9）和 Phoenicimicrobiia（JS1）中独立获得，此后它们被垂直继承；这些基因包括延胡索酸添加酶（faeA；仅 Phoenicimicrobiia）、CODH/ACS 复合物（acsABCDE）和多种氢化酶（NiFe 组 3b、4b 和 FeFe 组 A3、C）。最后，我们提出了基因组解析的群落代谢模型，展示了 Atribacteria（OP9）和 Phoenicimicrobiia（JS1）在富含乙酸和烃的环境中的核心作用。
我们的发现扩展了 Atribacterota 门的多样性、生理学、生态学和进化的知识。本研究为促进对其共生生物学的更深入研究奠定了基础，并可能为在实验室中培养它们的策略提供指导。
