Variovorax atrisoli sp. nov., a novel species isolated from black soil applied with herbicide atrazine in Northeast China.

Abstract

The strain tm^T was isolated from black soil applied with the herbicide atrazine in Northeast China. Phylogenetic analyses based on 16S rRNA gene sequences and phylogenomic analysis revealed that the strain tm^T is classified to the genus Variovorax. The DNA G+C content of strain tm^T was 67.5 mol%. The major fatty acids were C_16 : 0, C_10 : 0 3-OH, C_17 : 0 cyclo, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) in strain tm^T. Strain tm^T contained Q-8 as the major respiratory quinone. Polar lipids in strain tm^T were mainly comprised of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Initial selection of phylogenetically related taxa was performed through whole-genome phylogenomic analysis encompassing strain tm^T and all validly published members of the genus Variovorax. The calculation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain tm^T and phylogenetically proximal strains demonstrated that the values of ANI and dDDH with Variovorax sp. 1140, Variovorax sp. 1133, Variovorax sp. 369, Variovorax sp. 1128, Variovorax sp. 1126, Variovorax paradoxus SMAGNO29, V. paradoxus 110B, Variovorax sp. BK613 and V. paradoxus DS996 were well over thresholds (95-96%, 70%), of which strains SMAGNO29, 110B and DS996 were classified as V. paradoxus in previous publications. However, the ANI and dDDH values between these strains and the type strain V. paradoxus were significantly lower than the established taxonomic thresholds for species delineation. Thus, we deduced that these nine strains belong to a novel species with strain tm^T, Variovorax atrisoli sp. nov. We further performed phenotypic and chemotaxonomic tests which revealed that there were high levels of intraspecies variation. Based on these results, strain tm^T (=GDMCC 1.4848^T=KCTC 8741^T) was designated as the type strain of the novel species for which we propose the name V. atrisoli sp. nov.