New insights into the species boundaries for the genus Kribbella and taxonomic description of Kribbella polygonati sp. nov., and Kribbella eucommiae sp. nov., from rhizosphere soil of different plants, with proposal of Kribbella ginsengisoli as a later heterotypic synonym of Kribbella koreensis.

Abstract

Now, 95-96% average nucleotide identity (ANI) and 70% digital DNA-DNA hybridization (dDDH) are regarded as the gold standards for delineating prokaryotic species. However, during the process of identifying Kribbella strains, we found that the contradictory phenomena may sometimes occur using 95-96% ANI and 70% dDDH as the standards, respectively; the gyrB or concatenated gyrB-rpoB-recA-relA-atpD genetic distances currently used to replace ANI or dDDH are insufficient to serve as thresholds for delineating Kribbella species. Contraposing these problems, we re-evaluated the correlations between ANI and dDDH, between gyrB genetic distance and dDDH and between gyrB-rpoB-recA-relA-atpD genetic distance and dDDH from 33 Kribbella species. Based on our analysis results, a 96.4% ANIm value or a 96.3% ANIb value can be considered as the boundary value for delineating Kribbella species; a 0.009 gyrB or 0.010 gyrB-rpoB-recA-relA-atpD genetic-distance value can also serve as a reliable threshold for species delineation within the genus Kribbella. Meanwhile, two novel actinobacterial strains, GL6^T and HUAS MG21^T, isolated from the rhizosphere soil of different plants, respectively, were characterized using a polyphasic approach. Based on phenotypic and chemotaxonomic characteristics, as well as phylogeny and genomic correlation, strains GL6^T and HUAS MG21^T represent two novel Kribbella species, for which the names Kribbella polygonati sp. nov. and Kribbella eucommiae sp. nov. are proposed, respectively. Furthermore, the comparative genomic analysis suggested that Kribbella ginsengisoli and Kribbella koreensis should be considered the same species. According to the principle of priority, it is proposed that K. ginsengisoli Cui et al. 2010 is a later heterotypic synonym of K. koreensis (Lee et al. 2000) Sohn et al. 2003.