Asticcacaulis carbonis sp. nov., isolated from sediment within coal mine drainage treatment system

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, motile with a polar flagellum, rod-shaped bacterium designated as strain EMRT-3^T was isolated from sediment collected in a coal mine drainage treatment system in the Republic of Korea. Growth of strain EMRT-3^T was observed in Reasoner's 2A medium at 10-35 °C (optimum, 25-30 °C) and pH 4.5-8.0 (optimum, pH 6.5-7.5) and in the presence of 0-0.5% NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain EMRT-3^T belongs to the genus Asticcacaulis and was closely related to Asticcacaulis solisilvae CGM1-3EN^T, Asticcacaulis biprosthecium DSM 4723^T, Asticcacaulis benevestitus DSM 16100^T and Asticcacaulis taihuensis CGMCC 1.3431^T with 97.0, 96.3, 96.2 and 95.9% sequence similarities, respectively. A phylogenomic tree also showed that strain EMRT-3^T formed a distinct clade within genus Asticcacaulis and clustered with the four type species (CGM1-3EN^T, DSM 4723^T, DSM 16100^T and CGMCC 1.3431^T). The average nucleotide identity and digital DNA-DNA hybridization values between strain EMRT-3^T and closely related type strains were 72.8-75.6% and 20.0-20.7%, respectively. The genomic DNA G+C content of EMRT-3^T was 60.0 mol%. Genome annotation for strain EMRT-3^T indicated broad metabolic capacity, encompassing complete pathways for central carbohydrate and amino acid metabolism as well as the biosynthesis of essential cofactors and vitamins. Importantly, the detection of genes associated with copper, nickel/cobalt and iron homeostasis, along with acid tolerance, highlights its adaptation to metal-rich and acidic environments. The major fatty acids of EMRT-3^T were C_12:0, C_16:0, C_12:0 3-OH, C_15:0 2-OH, C_16:0 2-OH, C_16:1 2-OH, summed feature 3 (C_16:1  ω7c and/or C_16:1  ω6c) and summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c). The major polar lipids were phosphatidylglycerol, aminophospholipids and glycolipids. Based on the polyphasic taxonomic evidence, strain EMRT-3^T represents a novel species within the genus Asticcacaulis, for which the name Asticcacaulis carbonis sp. nov. is proposed. The type strain is EMRT-3^T (=KACC 22206^T=JCM 34539^T=FBCC-B5258^T).