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

Abstract

An overwhelming majority of bacterial life remains uncharacterized. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured bacterial lineages. We report on the characterization of 30 genomes belonging to three novel classes within the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by the capacity for heterotrophic growth, either fermentatively or utilizing polysulfide, tetrathionate and thiosulfate as electron acceptors. Autotrophic growth using the Wood Ljungdahl pathway and hydrogen or Fe(II) as an electron donor could also occur in absence of organic carbon sources. The second class (proposed name Candidatus “Anaeropigmentia”) was characterized by its capacity for fermentative or aerobic growth at low oxygen thresholds using a broad range of sugars and amino acids, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoids (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by the capacity for heterotrophic growth fermentatively using broad sugars and amino acids as carbon sources, and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater, and marine environments, over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' to hypersaline environments, e.g. hypersaline microbial mats and lagoons was observed.

Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation

“…These include fermentative processes for acetate, ethanol, and 21 lactate production from pyruvate (Table 3, Figure S1a). As well, the genomes encoded a full Wood Ljungdahl pathway (WLP), most probably acting as an electron sink mechanism for reoxidizing reduced ferredoxin, as previously noted in Candidatus Bipolaricaulota and Desulfobacterota genomes (35,78). Finally, a possible additional mechanism for ATP production in Zodletone Myxococcota is the utilization of the RNF complex for re-oxidizing reduced ferredoxin at the expense of NAD, with the concomitant export of protons to the periplasm, generating a proton motive force that can drive ATP production via oxidative phosphorylation via the encoded F-type ATP synthase.…”

“…Sampling and nucleic acid extraction. The sampling and DNA extraction processes have been previously described in detail (34,35). Briefly, ten different sediment samples (≈50 grams each) were collected at 5-cm depth, as well as from the standing overlaid water in sterile containers.…”

Gastrointestinal symbiont diversity in wild gorilla: A comparison of bacterial and strongylid communities across multiple localities

“…Numerous drivers of bacterial microbiome composition differences were identified at both the genus and the phylum level, including both dominant (Firmicutes, Actinobacteria, Bacteroidetes) and rarer phyla. Many of these probably reflect dietary differences between localities, with numerous taxa identified for their roles in digestion of various dietary compounds, such as pectin, sugars and fats (Fujio‐Vejar et al, 2017; Gharechahi et al, 2020; Gomez, Rothman, et al, 2016, Gomez, Petrzelkova, et al, 2016; Méndez‐Salazar et al, 2018; Murphy et al, 2021; Ransom‐Jones et al, 2012). As such, we speculate the community composition of the gut bacterial microbiome is more sensitive to variation of environmental factors compared with strongylid communities.…”

Biofilms for Turbidity Mitigation in Oil Sands End Pit Lakes

“…The presence of thermophilic bacteria within the microbial community is not surprising given that tailings are exposed to high temperatures (historically up to 60°C) during processing [ 54 ], and Chloroflexi (Anaerolineae ) have previously been reported in Syncrude tailings ponds [ 55 , 56 ]. Desulfobulbia is part of Desulfobacterota, which contribute to sulfate reduction, iron oxidation, and aromatic hydrocarbon degradation [ 57 ]. In nearly all samples, Desulfobulbia was present at an abundance of up to 6%, except in Biofilm10a and Biofilm20a.…”