Microaceticoccus formicicus gen. nov., sp. nov., an ammonia-tolerant formate-utilizing bacterium originating from a biogas process

Abstract

A strictly anaerobic bacterial strain, designated as AMB_02^T, was isolated from a propionate enrichment culture obtained from a high-ammonia biogas digester. The cells were anaerobic and coccoid (0.5 µm), often appearing as diplococci or in a short chain of three to four cells. Growth was observed between 20 and 45 °C (optimum at 37-39 °C), with an initial pH of 6.5-9.0 (optimum pH 8.0-8.5), and the species tolerated up to 0.8 M NH₄Cl and 0.5 M NaCl. The major cellular fatty acids were C_{16 : 0} (31.6%), C_{14 : 0} (14.6%) and C_{18 : 0} (13.3%). AMB_02^T grew with formate, carbohydrates and aa, including asparagine, histidine, tryptone and tryptophan. Acetate was the major product formed. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AMB_02^T was most closely related to the species Citroniella saccharovorans (92.5%). The genome of strain AMB_02^T was 2.5 Mb in length with a G+C content of 34.8 mol%, and 2,354 protein-coding genes were predicted. Furthermore, genes coding for the reductive glycine pathway potentially used for formate metabolism were identified. Comparative genomic analysis of AMB_02^T revealed the closest similarity to C. saccharovorans [21.2% digital DNA-DNA hybridization (dDDH) and 77.4% average nt identity (ANI)] and to Parvimonas micra (24.4% dDDH and 76.9% ANI). Based on the phenotypic characteristics and phylogenetic analyses, AMB_02^T is regarded as a novel genus, Microaceticoccus, within the family Peptoniphilaceae for which the species name Microaceticoccus formicicus is proposed. The type strain is AMB_02^T=DSM 110248^T=JCM 39108^T.

Keywords: Microaceticoccus; Peptoniphilaceae; ammonia tolerant; anaerobic digestion; formate metabolism.

Fig. 1.. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences of strain AMB_02T and closely related species. Black diamonds indicate branches that were conserved and recovered in maximum-likelihood and maximum-parsimony trees (Fig. S1). Bootstrap values (based on 1,000 iterations) are shown at the nodes, and only values >70% are shown. Scale bar represents 0.05 substitutions per nt position.

Fig. 2.. Reconstructed species tree generated using OrthoFinder2, based on whole-genome sequences and 199 single-copy orthologous genes. The tree includes the closest known relatives of strain AMB_02T within the family Peptoniphilaceae. Bootstrap values from 1,000 replicates are indicated at branch nodes. Scale bar represents 0.1 substitutions per nt position.