A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

A nearly complete genome sequence of Candidatus ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO2 fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H2-dependent acetogens and methanogenes living in hydrothermal environments.

通过对地下嗜热微生物垫群落的宏基因组分析，研究人员解析出候选分类群OP1中目前尚未培养的细菌——候选属‘自热产乙酸菌（Candidatus ‘Acetothermum autotrophicum’）’的近乎完整基因组序列。基于367种原核生物共有的蛋白质串联序列开展的系统发育分析表明，Ca. ‘A. autotrophicum’属于分化最早的细菌谱系之一。该菌具备叶酸依赖型伍德-隆德哈尔（乙酰辅酶A）CO₂固定途径，被推测具有产乙酸生活方式，同时拥有新发现的古菌自养型双功能果糖1,6-二磷酸醛缩酶/磷酸酶。针对产乙酸菌、产甲烷古菌、部分硫还原菌、铁还原菌及脱氯菌共有的乙酰辅酶A途径核心基因簇开展的系统发育分析，支持了"Ca. ‘A. autotrophicum’的核心基因簇属于尤为古老的细菌途径"这一假说。Ca. ‘A. autotrophicum’的生境、生理特性及系统发育位置，佐证了"首个细菌与古菌谱系为依赖氢的产乙酸菌和产甲烷古菌，栖息于热液环境"这一观点。