Acidobacteria in Fens: Phylogenetic Diversity and Genome Analysis of the Key Representatives

• Published in: Microbiology (New York) 2022-12, Vol.91 (6), p.662-670
• Main Authors: Dedysh, S. N., Ivanova, A. A., Begmatov, Sh. A., Beletsky, A. V., Rakitin, A. L., Mardanov, A. V., Philippov, D. A., Ravin, N. V.
• Format: Article
• Language: English
• Subjects: Aerobic microorganisms; Aerobic respiration; Anaerobic conditions; Biomedical and Life Sciences; Biopolymers; Bogs; Carbohydrates; Cytochrome c; Electron transport chain; Experimental Articles; Fatty acids; Fens; Genomes; Gluconeogenesis; Glycosyl hydrolase; Heterotrophic microorganisms; L-Rhamnose; Life Sciences; Medical Microbiology; Metabolism; Microbiology; Molybdopterin; Peat; Peatlands; Pentose phosphate pathway; Phylogeny; Polysaccharides; Pyrinomonadaceae; Rhamnose; rRNA 16S; Sulfur; Tricarboxylic acid cycle
• ISSN: 0026-2617; 1608-3237
• DOI: 10.1134/S0026261722601440

— Acidobacteriota are one of the major prokaryotic groups in soils and peatlands. They are especially abundant in acidic peat bogs, where representatives of the well-characterized class Acidobacteriia predominate. The diversity and metabolic potential of Acidobacteriota inhabiting fens with neutral pH have been studied less thoroughly. We analyzed the composition of acidobacterial communities in four peat bogs and six fens of the Vologda region. The Acidobacteriota -affiliated 16S rRNA gene sequences comprised 30–42 and 7–22% of all reads retrieved from the peat bogs and fens, respectively. The acidobacteria of peat bogs were represented by the orders Acidobacteriales and Bryobacterales of the class Acidobacteriia , while the classes Vicinamibacteria and Blastocat•ellia predominated in fens. Genomes of four uncultured bacteria of Blastocatellia (family Pyrinomonadaceae , two genomes), Vicinamibacteria (family UBA2999), and Thermoanaerobaculia (order UBA5066) were assembled from the metagenomes of peat fens. Genome analysis revealed key pathways of aerobic heterotrophic metabolism in all four microorganisms, including the Embden–Meyerhof pathway, gluconeogenesis, the non-oxidative stage of the pentose phosphate pathway, the tricarboxylic acid cycle, and the electron transport chain of aerobic respiration, including terminal cytochrome c oxidases. All genomes encoded molybdopterin oxidoreductases of the CISM family and multiheme cytochromes c , indicating the possibility of dissimilatory reduction of sulfur compounds and Fe(III) under anaerobic conditions. Probable growth substrates may be amino acids, peptides, and fatty acids. Members of the Pyrinomonadaceae can also use various carbohydrates, including polysaccharides, and are likely involved in the degradation of various biopolymers in peat bogs. Members of Thermoanaerobaculia and Vicinamibacteria lacked the genes for secreted glycosyl hydrolases and probably could only use a limited range of simple sugars. The genome of a bacterium of the class Vicinamibacteria contained a set of genes encoding bacterial microcompartments (metabolosomes) that have not previously been described in acidobacteria and are probably involved in the metabolism of L-rhamnose.