The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)

Abstract

Summary The Wood–Ljungdahl (WL) pathway is an important component of the metabolic machinery in multiple anaerobic prokaryotes, including numerous yet‐uncultured bacterial phyla. The pathway can operate in the reductive and oxidative directions, enabling a wide range of metabolic processes. Here, we present a detailed analysis of 14 newly acquired, previously analysed, and publicly available genomic assemblies belonging to the candidate phylum Bipolaricaulota (candidate division OP1, and candidatus Acetothermia), where the occurrence of WL pathway appears to be universal. In silico analysis of predicted metabolic capabilities indicates that the pathway enables homoacetogenic fermentation of sugars and amino acids in all three Bipolaricaulota orders (RBG‐16‐55‐9, UBA7950 and Bipolaricaulales). In addition, members of RBG‐16‐55‐9 appear to possess the additional capacity for syntrophic acetate oxidation using the WL pathway; as well as for respiratory growth using oxygen or nitrate. Anabolically, all UBA7950, and the majority of the Bipolaricaulales genomes possess the capacity for autotrophic growth using the WL pathway. Our results highlight the WL‐enabled metabolic versatility in the Bipolaricaulota, emphasize the need for examining the WL pathway in context of the overall metabolic circuitry in uncultured taxa, and demonstrate the value of comparative genomic analysis for providing a detailed overview of metabolic potential in a target microbial lineage and its potential functional niche in an ecosystem.

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum

“…Alternatively, or concomitantly, a proton-motive force could possibly be generated during the operation of Wood Ljungdahl (WL) pathway, encoded by all Class “Anaeroferrophillalia” genomes, in the homoacetogenic direction. In that case, a membrane-­-bound mechanism that achieves redox balance between heterotrophic substrate oxidation and the WL function as the electron sink (54, 55) is needed. Candidates for this membrane-bound electron bifurcation mechanism are the membrane-­-bound [Ni Fe] hydrogenase (Mbh) (HydDB group 4d), which couples reduced ferredoxin (produced via the action of pyruvate ferredoxin oxidoreductase [EC: 1.2.7.1]) oxidation to the reduction of protons to H 2 , with the concomitant export of protons to the periplasm (54, 55).…”

“…In that case, a membrane-­-bound mechanism that achieves redox balance between heterotrophic substrate oxidation and the WL function as the electron sink (54, 55) is needed. Candidates for this membrane-bound electron bifurcation mechanism are the membrane-­-bound [Ni Fe] hydrogenase (Mbh) (HydDB group 4d), which couples reduced ferredoxin (produced via the action of pyruvate ferredoxin oxidoreductase [EC: 1.2.7.1]) oxidation to the reduction of protons to H 2 , with the concomitant export of protons to the periplasm (54, 55). Recycling of electron carriers would further be achieved by the cytoplasmic [NiFe]-­-hydrogenase (MvhAGD) plus the heterodisulfide reductase HdrABC, both of which encoded in the genomes (HydDB group [Ni Fe] 3c) (Figure 2A).…”

“…ferrous ions or H 2 , serve as electron donors, we expect autotrophic capacities to be fulfilled also via the WL pathway. In that case, the proton gradient-­-driven phosphorylation (through the ATPase complex) will be the only means for ATP production (56) as no net ATP gain by substrate level phosphorylation (SLP) is achieved via the WL pathway (55). All genomes encode mechanisms for acetyl-­-CoA (produced from WL pathway) conversion to pyruvate (Pyruvate:ferrodoxin oxidoreductase [EC:1.2.7.1]), reversal of pyruvate kinase (including pyruvate-­-orthophosphate dikinase (EC 2.7.9.1), pyruvate-­-water dikinase [EC 2.7.9.2], as well as pyruvate carboxylase [EC:6.4.1.1] and PEP carboxykinase (ATP) [EC:4.1.1.49]), and the bifunctional fructose-­-1,6-­-bisphosphate aldolase/phosphatase to reverse phosphofructokinase.…”

“…Additional ATP production via oxidative phosphorylation following the generation of a proton-motive force during the operation of WL pathway, is therefore also predicted. In that case, the RNF complex encoded in the majority of genomes would re--oxidize reduced ferredoxin at the expense of NAD, with the concomitant export of protons to the periplasm, thus achieving redox balance between heterotrophic substrate oxidation and the WL function as the electron sink(54,55). Recycling of electron carriers would further be achieved by the cytoplasmic electron bifurcating mechanism (HydABC) plus MvhAGD--HdrABC, both of which are encoded in the genomes (HydDB groups [Fe Fe] A3, and [Ni Fe] 3c).Specialized cofactor biosynthesis:Interestingly, the complete pathway encoding the phosphoenol pyruvate-dependent coenzyme M (CoM) biosynthesis was identified in all genomes of Class "Anaeropigmentia" (Figure 3A,Table S3).…”

Genomic analysis of family UBA6911 (Group 18 Acidobacteria) expands the metabolic capacities of the phylum and highlights adaptations to terrestrial habitats

“…When operating in the oxidative direction, the pathway is used for acetate catabolism (81)(82)(83). Syntrophic acetate oxidizers employing the oxidative WLP usually possess high affinity acetate transporters to allow for the uptake of small concentrations of acetate, a competitive advantage in the presence of acetoclastic methanogens (84). The absence of genes encoding high affinity acetate transporters in any of the genomes argues against the involvement of WLP in syntrophic acetate catabolism.…”