背景:在地下生物圈中广泛分布。最近,描述了第一个阿三杆菌分离株,从环境样品中检索到的阿三杆菌基因组序列数量显着增加;然而,他们的多样性,生理学,生态学,和进化仍然知之甚少。
结果:我们报告了阿三杆菌的第二个成员的分离,热杆菌veloxgen。11月。,sp.11月。,在一个新的热杆菌科家族中。11月。,以及JS1谱系成员的短期实验室培养,菲尼菌HX-OS。bin.34TS,都来自陆地油藏。生理和代谢组学分析显示,热杆菌veloxB11T和菲尼氏微生物HX-OS。BIN.34TS发酵糖和正烷烃,分别,生产H2、CO2和乙酸盐作为常见产品。比较基因组学表明,Atribacterota的所有成员都缺乏完整的Wood-Ljungdahl途径(WLP),但是还原性甘氨酸途径(RGP)很普遍,表示RGP,而不是WLP,是三杆菌代谢的中心枢纽。祖先特征状态重建和系统发育分析表明,编码RGP的关键基因(fdhA,fhs,Fold,glyA,gcvT,gcvPAB,pdhD)和其他中心功能在两个类中独立获得,曲菌属(OP9)和菲尼菌属(JS1),之后,它们被垂直遗传;这些基因包括富马酸添加酶(faeA;仅有Phoenicicmicrobiia),CODH/ACS复合体(ACSABCDE),和不同的氢化酶(NiFe组3b,4b和FeFe组A3、C)。最后,我们提供了基因组解析的群落代谢模型,显示了Atribacterium(OP9)和Phoenicimicbiia(JS1)在富含乙酸和碳氢化合物的环境中的中心作用。
结论:我们的发现扩展了多样性的知识,生理学,生态学,和四叶草门的进化。这项研究是促进对它们的互养生物学进行更深入的研究的起点,并可能指导在实验室中合理设计培养它们的策略。视频摘要。
BACKGROUND: 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.
RESULTS: 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.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-
alkanes, respectively, producing H2, CO2, 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.
CONCLUSIONS: 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.