Comparative genomics and ecological insights into Nonomuraea turcica sp. nov., an actinomycete from Black Sea island soil.

Abstract

A polyphasic study was undertaken to characterize strain G32^T, an actinomycete isolated from soil collected on Giresun Island (Black Sea, Turkey). 16S rRNA phylogeny placed the strain within the genus Nonomuraea, but ≤99.1% similarity to its nearest type strains, Nonomuraea turkmeniaca DSM 43926^T, Nonomuraea aridisoli KC333^T, Nonomuraea candida NRRL B-24552^T, Nonomuraea polychroma DSM 43925^T and Nonomuraea endophytica DSM 45385^T, suggested that it potentially represents a novel taxon. The total genome size is about 12.66 Mb, and the digital G+C content is 69.6 mol%. The high-quality draft genome shared ≤92.16% average nucleotide identity and ≤47.0% digital DNA-DNA hybridization with the closest related type strains, corroborating species-level distinctness. Comparative genomics against four type strains, N. turkmeniaca DSM 43926^T, N. polychrom DSM 43925^T, N. aridisoli KC333^T and N. endophytica DSM 45385^T, revealed an open pangenome of 24,056 orthologous families, of which G32^T contributed 2,785 singletons. Copy-number expansion of aqpZ with four paralogues and efeB with three paralogues, together with the sole genome-wide occurrence of ACC-deaminase and an additional fhuDBC siderophore transporter, highlights adaptations to periodic salinity, iron limitation and rhizosphere contact in island soil. Chemotaxonomic markers (meso-diaminopimelic, madurose, MK-9(H₄), iso-C_16 : 0, iso-C_16 : 0 2OH and C_17 : 0 10-methyl) of the strain were consistent with the genus Nonomuraea, but phenotypic traits further differentiated the isolate from its relatives. Based on the evidence presented here, strain G32^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea turcica sp. nov. is proposed. The type strain of the species is G32^T (=KCTC 49887^T=CGMCC 4.7873^T).