Biodiversity and secondary metabolites of rare actinomycetes from soils

Abstract

Isolation of 49 strains of rare actinomycetes from 19 soil samples collected from Loei, Chonburi, Phayao, Chaiyaphum and Samutsakhon provinces was carried out using humic vitamin agar and starch casein nitrate agar. On the basis of their phenotypic and chemotaxonomic properties including the phylogenetic analysis using 16S rRNA gene sequence similarity and level of DNA-DNA relatedness of the representative strains, the isolated actinomycetes were classified into six genera, including Micromonospora (38 strains), Microbispora (2 strains), Actinomadura (4 strains), Nocardia (3 strains), Nonomuraea (1 strain) and Pseudonocardia (1 strain). All Micromonospora strains were divided into 12 groups. Groups III, IV, V, IX, XI and XII were identified as M. marina, M. aurantiaca, M. chalcea, M. chokoriensis, M. tulbaghiae and M. chersina, respectively while Groups I, II, VI, VII, VIII and X as new species. Micromonospora humi sp. nov. was proposed for the new species of Group VIII. Furthermore, Actinomadura strains were divided into 4 groups and Groups B and D were identified as A. glauciflava and A. nitritigenes, respectively. Nocardia strains were divided into 2 groups and Group 2 was N. cyriacigeorgica. The strain of Pseudonocardia was identified as P. carboxydivorans. The remaining strains of the genera Microbispora, Nonomuraea, Actinomadura and Nocardia were identified as new species. In the course of secondary metabolites screening from selected rare actinomycetes using HPLC-UV and comparing the UV spectra with in-house database, compounds rakicidin and BU-4664L were detected from Micromono-spora sp. AL7-5 of Group V. Isolation of secondary metabolites from cultured broths and chemical structure elucidation by comparison of NMR and MS spectral data revealed that Micromonospora sp. D10-9-5 of Group II produced compounds SEK34 and SEK34B in A11M culture medium and Actinomadura sp. CYP1-5 of Group A produced compounds decatromicin B and BE-45722C in A3M culture medium. Decatromicin B and BE-45722C exhibited anti-Bacillus subtilis with MICs 0.78 and 0.39 µg/ml, antimalarial activity against Plasmodium falciparum K1 with IC₅₀s 2.07 and 4.76 µg/ml and cytotoxicity against Vero cell line with IC₅₀s 47.07 and 32.71µg/ml, respectively while SEK34 and SEK34B were inactive.