Nocardia nepalensis sp. nov., a novel actinobacterium isolated from forest soil in Pokhara, Nepal

Abstract

An aerobic, non-motile, Gram-positive novel actinobacterium strain ACa13097^T was isolated from a soil sample collected from the forest of Pokhara, Nepal. Strain ACa13097^T showed morphological and growth characteristics typical for the members of the genus Nocardia. Strain ACa13097^T grew at 18–37° C (optimum 30° C), pH 4–9 (optimum 7), 0–7 % NaCl (optimum 0–1 %) and 1.80–3.60 % sea salt (optimum 1.80 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ACa13097^T was closely related to Nocardia pseudovaccinii NBRC 100343 ^T (98.86 %), Nocardia vinacea NBRC 16497 ^T (98.79 %), and Nocardia anaemiae NBRC 100462 ^T (98.64 %). Genome analysis revealed a genome size of 9609,226 bp long, composed of 46 contigs with an N50 value of 613,208 bp and annotated with 9316 protein-coding genes. The DNA G+C content was 66.20 mol%. The digital DNA-DNA hybridization between the genome of strain ACa13097^T and its closely related species N. pseudovaccinii NBRC 100343 ^T, N. vinacea NBRC 16497 ^T, and N. anaemiae NBRC 100462 ^T were 39 %, 39.10 %, and 43.40 %, respectively from GGDC formula 1 (d0) and the average nucleotide identity (ANI) value were 87.33 %, 87.52 %, and 87.33 %, respectively. The genome mining analysis using antiSMASH version 7.1.0 identified 47 putative gene clusters that may be responsible for producing numerous secondary metabolites and bioactive compounds. Genome analysis of strain ACa13097^T indicated 190 diverse families of Carbohydrate-active enzymes (CAZyme), 6575 orthologous gene clusters, and 15 sequences with CRISPR. Based on phenotypic and genotypic data and phylogenetic position as well as digital DNA-DNA hybridization and average nucleotide identity (ANI) value, the novel strain ACa13097^T is considered to represent a novel species of the genus Nocardia, for which the name Nocardia nepalensis sp. nov. (=NCCB 101050 ^T, DSM 118930 ^T) is proposed. The type strain is ACa13097^T.