Data_Sheet_5_Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis.PDF

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO2 via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C1 carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.

高等白蚁后肠内木质纤维素的共生消化，由多样的细菌与古菌群落介导。在一项大规模宏基因组研究中，我们重建了15个宏基因组组装基因组（metagenome-assembled genomes），这些基因组隶属于白蚁肠道特有的第6亚群（原MCG-6）中的两个不同演化支。其中一个演化支（TB2；候选属Candidatus Termitimicrobium）编码了通过古菌型Wood-Ljungdahl途径（Wood–Ljungdahl pathway）从CO₂还原产乙酸所需的全部酶，该途径以四氢甲烷蝶呤（tetrahydromethanopterin）作为C1载体，并包含一种ADP依赖型乙酰辅酶A合酶。该演化支还编码一种新型11亚基氢化酶，该酶具有其他古菌呼吸Fpo复合物（Fpo-complex）的基因组结构，但其催化亚基在系统发育上与第4g亚群的[NiFe]氢化酶（[NiFe] hydrogenases）亲缘相关，且共享保守的[NiFe]辅因子结合基序。我们推测，这种新型类Fpo氢化酶可为CO₂还原提供部分所需的还原型铁氧还蛋白（ferredoxin），其能量由底物水平磷酸化（substrate-level phosphorylation）产生ATP所维持的电化学膜电位驱动；其余还原力则可能来自有机电子供体的氧化，这表明TB2演化支成员属于兼养型产乙酸菌。另一个演化支（TB1；候选属Candidatus Termiticorpusculum）的成员则为专性有机营养型，因为它们均缺失氢化酶以及古菌Wood-Ljungdahl途径的关键酶——亚甲基四氢甲烷蝶呤还原酶（methylene-tetrahydromethanopterin reductase）。两个演化支均具备通过氧化氨基酸还原铁氧还蛋白的基因组潜能，且可能利用未鉴定的甲基化化合物开展甲基营养型产乙酸。本研究结果表明，第6亚群的深古菌门（Bathyarchaeia）成员参与高等白蚁肠道内乙酸盐的形成，同时为该门其他未培养类群通过有机底物（可能包括甲基化化合物）还原产乙酸提供了基因组学证据。