Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic

Abstract

The taxonomic position of three actinobacterial strains, BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T, recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10_0061T in the same cluster as Lentzea waywayandensis, strain BCCO 10_0798T in the same cluster as Lentzea flaviverrucosa, Lentzea californiensis, Lentzea violacea, and Lentzea albidocapillata, and strain BCCO 10_0856T clustered together with Lentzea kentuckyensis and Lentzea alba. Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea. In all three strains, MK-9(H4) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10_0061T, 69.2 for BCCO 10_0798T, and 68.5 for BCCO 10_0856T. The combination of digital DNA–DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea, for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10_0061T (=DSM 116175T), Lentzea kristufekii sp. nov. for BCCO 10_0798T (=DSM 116176T), and Lentzea miocenica sp. nov. for BCCO 10_0856T (=DSM 116177T).