Streptomyces chodovensis sp. nov.: a novel candidate for plant growth-promoting actinomycete from bare soil developing on Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic.

A novel actinomycete, designated as BCCO 10_0861T, was isolated from overburden Miocene clay sediments undergoing primary succession in Northwest Czechia and characterized by the polyphasic approach. According to 16S rRNA gene sequence similarity, the strain was closely related to Streptomyces turgidiscabies DSM 41838T (99.00%), Streptomyces reticuliscabiei DSM 41804T (98.93%), Streptomyces lacrimifluminis DSM 111125T (98.15%), and Streptomyces geranii JCM 32177T (98.08%). Morphological and chemotaxonomic characteristics supported the assignment to the genus Streptomyces. Diagnostic diamino acid in the cell-wall peptidoglycan was LL-diaminopimelic acid and the dominant menaquinone was MK-9(H6). The major cellular fatty acids (> 10%) were anteiso-C15:0, iso-C16:0, C16:1 ω7c, and C16:0. The polar lipid profile comprised of aminophospholipids, diphosphatidylglycerol, glycophospholipids, phosphatidylethanolamine, phosphatidylinositol, and three unidentified phospholipids. The whole cell sugars were galactose, glucose, mannose, ribose, and traces of rhamnose. The genome size of the strain BCCO 10_0861T was 10.6 Mb with G+C content of 70.05%. Bioinformatic analysis suggested several biosynthetic gene clusters (BGCs) with medium-to-high similarity confidence to already known BGCs, having ethylenediaminesuccinic acid hydroxyarginine (EDHA), humidimycin, inthomycin B, and triascin C unique to BCCO 10_0861T. Similarly, predicted plant-growth promoting trait (PGPT) genes differed between genomes, when the one of BCCO 10_0861T showed the highest number of unique PGPT genes (2,255). In addition, no association with potato pathogenicity was predicted in the genome of BCCO 10_0861T. The digital DNA-DNA hybridization (ranged from 34.7 to 37.5%), average nucleotide identity values (ranged from 86.26 to 87.24%) and phenotype distinguish strain BCCO 10_0861T from closely related strains. Based on the polyphasic approach and genomic content, the strain represents a novel species of the genus Streptomyces, for which we propose the name Streptomyces chodovensis sp. nov. for BCCO 10_0861T (= DSM 117345T).