Afipia dichlorophenoxyacetatis sp. nov., isolated from field soil in Japan, degrades 2,4-dichlorophenoxyacetic acid

Bacterial strains, designated DD3^T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C_{18 : 1} <i> ω7c</i> and/or C_{18 : 1} <i> ω6c</i>), C_{18 : 0} and C_{17 : 0} cyclo. Phylogenetic analyses based on <i>gyrB</i> gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus <i>Afipia</i>; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA-DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95-96 and 70%, respectively), with the highest values observed for <i>Afipia broomeae</i> ATCC 49717^T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3^T/DDX28 constitute a novel <i>Afipia</i> species, for which we propose the name <i>Afipia dichlorophenoxyacetatis</i> sp. nov., with DD3^T (MAFF 311804^T=ICMP 25015^T) as the type strain.