Amycolatopsis nalaikhensis sp. nov. and Amycolatopsis carbonis sp. nov., two novel actinobacteria with antimicrobial activity isolated from a coal mining site in Mongolia.

Abstract

Two-novel filamentous actinobacteria designated strains 2-2^T and 2-15^T were isolated from soil of a coal mining site in Mongolia, and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that each of the strains formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity analysis showed that both strains were mostly related to Amycolatopsis rhabdoformis NCIMB 14900^T with 99.0 and 99.4% sequence similarity, respectively. The genome-based comparison indicated that strain 2-2^T shared the highest digital DNA-DNA hybridization value of 35.6% and average nucleotide identity value of 86.9% with Amycolatopsis pretoriensis DSM 44654^T, and strain 2-15^T shared the corresponding values of 36.5 and 87.9% with A. rhabdoformis NCIMB 14900^T, all of which being well below the thresholds for species delineation. The chemotaxonomic properties of both strains were typical of the genus Amycolatopsis. In silico prediction of chemotaxonomic markers was also carried out, and the results were consistent with the chemotaxonomic profiles of the genus. Genome mining for secondary metabolite production in strains 2-2^T and 2-15^T revealed the presence of 29 and 24 biosynthetic gene clusters involved in the production of polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides, lanthipeptide, terpenes, siderophore, and a number of other unknown type compounds. Both strains showed broad antifungal activity against several filamentous fungi and also antibacterial activity against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii. The phenotypic, biochemical, and chemotaxonomic properties indicated that both strains could be clearly distinguished from other species of Amycolatopsis, and thus the names Amycolatopsis nalaikhensis sp. nov. (type strain, 2-2^T=KCTC 29695^T=JCM 30462^T) and Amycolatopsis carbonis (type strain, 2-15^T=KCTC 39525^T=JCM 30563^T) are proposed accordingly.