Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

Abstract

Previous phylogenetic analysis of species of the genus Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100 % bootstrap value) containing eight species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains of spiny- to hairysurfaced, dark green spores on their aerial mycelium. The type strains of the species in this clade, specifically Streptomyces bambergiensis, Streptomyces cyanoalbus, Streptomyces emeiensis, Streptomyces hirsutus, Streptomyces prasinopilosus and Streptomyces prasinus, were subjected to multi-locus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB to clarify their taxonomic status. The type strains of several recently described species with similar gross morphology, including Streptomyces chlorus, Streptomyces herbaceus, Streptomyces incanus, Streptomyces pratens and Streptomyces viridis, were also studied along with six unidentified green-spored Streptomyces strains from the ARS Culture Collection. The MLSAs suggest that three of the species under study (S. bambergiensis, S. cyanoalbus and S. emeiensis) represent synonyms of other previously described species (S. prasinus, S. hirsutus and S. prasinopilosus, respectively). These relationships were confirmed through determination of in silico DNA-DNA hybridization estimates based on draft genome sequences. The five recently described species appear to be phylogenetically distinct but the unidentified strains from the ARS Culture Collection could be identified as representatives of S. hirsutus, S. prasinopilosus or S. prasinus.

Fig. 1.

Subtree showing the phylogenetic relationship of green-spored Streptomyces strains within the 16S rRNA phylogenetic Clade 6 (Labeda et al., 2012) based on evolutionary history inferred with the maximum-likelihood method based on the General Time Reversible model (Nei & Kumar, 2000). The tree with the highest log likelihood (-−61 149.8014) is shown. The tree is drawn to scale, with branch lengths measured in number of substitutions per site. The analysis involved 167 nucleotide sequences and a total of 2593 positions in the final dataset. The branch labels indicate the percentage of trees in which the associated taxa clustered together and asterisks indicate branches conserved in maximum-likelihood, neighbour-joining and maximum-parsimony trees. Evolutionary analyses were conducted in mega6 (Tamura et al., 2013). Bar, 0.005 substitutions per site.