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

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 <i>Variovorax</i>. 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 <i>ω</i>7<i>c</i> and/or C16 : 1 <i>ω</i>6<i>c</i>) and summed feature 8 (C18 : 1 <i>ω</i>7<i>c</i> and/or C18 : 1 <i>ω</i>6<i>c</i>) 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 <i>Variovorax</i>. 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 <i>Variovorax</i> sp. 1140, <i>Variovorax</i> sp. 1133, <i>Variovorax</i> sp. 369, <i>Variovorax</i> sp. 1128, <i>Variovorax</i> sp. 1126, <i>Variovorax paradoxus</i> SMAGNO29, <i>V. paradoxus</i> 110B, <i>Variovorax</i> sp. BK613 and <i>V. paradoxus</i> DS996 were well over thresholds (95-96%, 70%), of which strains SMAGNO29, 110B and DS996 were classified as <i>V. paradoxus</i> in previous publications. However, the ANI and dDDH values between these strains and the type strain <i>V. paradoxus</i> 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, <i>Variovorax atrisoli</i> 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 <i>V. atrisoli</i> sp. nov.