Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Issue 10 (21st October 2022)

• Record Type: Journal Article
• Authors: , Timsy; Behrendt, Undine; Ulrich, Andreas; Foesel, Bärbel U.; Spanner, Tobias; Neumann-Schaal, Meina; Wolf, Jacqueline; Schloter, Michael; Horn, Marcus A.; Kolb, Steffen
• Is Part Of: International journal of systematic and evolutionary microbiology. Volume 72:Issue 10(2022)
• Publication Date: 2022-10-21
• Subjects: Paracoccus methylovorus sp. nov. -- phylogenomic analysis -- phenotypic characterization -- denitrification -- methylotrophy -- glutathione-dependent formaldehyde oxidation pathway -- tetrahydrofolate-dependent formaldehyde oxidation; Microbiology -- Periodicals; Microbiology -- Classification -- Periodicals; 579
• DOI: 10.1099/ijsem.0.005581
• Languages: English
• ISSNs: 1466-5026

Abstract

Abstract : Three strains (H4-D09 T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09 T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09 T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate–formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase ( mxaFI ) and methylamine dehydrogenase ( mau ) genes. Apart from dissimilatory denitrification genes ( narA, nirS, norBC and nosZ ), genes for assimilatory nitrate ( nasA ) and nitrite reductases ( nirBD ) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus . Core genome phylogeny of the type strain H4-D09 T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1 ω7 c, C19 : 0 cyclo ω7 c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L). On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09 T =LMG 31941 T = DSM 111585 T ) is proposed.