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

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 <i>Amycolatopsis</i>. The 16S rRNA gene sequence similarity analysis showed that both strains were mostly related to <i>Amycolatopsis rhabdoformis</i> 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 <i>Amycolatopsis pretoriensis</i> DSM 44654^T, and strain 2-15^T shared the corresponding values of 36.5 and 87.9% with <i>A. rhabdoformis</i> 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 <i>Amycolatopsis</i>. <i>In silico</i> 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 <i>Staphylococcus aureus</i> and <i>Acinetobacter baumannii</i>. The phenotypic, biochemical, and chemotaxonomic properties indicated that both strains could be clearly distinguished from other species of <i>Amycolatopsis</i>, and thus the names <i>Amycolatopsis nalaikhensis</i> sp. nov. (type strain, 2-2^T=KCTC 29695^T=JCM 30462^T) and <i>Amycolatopsis carbonis</i> (type strain, 2-15^T=KCTC 39525^T=JCM 30563^T) are proposed accordingly.