Isolation and identification of rare actinomycete-like bacteria from soil-based on 16S ribosomal RNA gene sequences

Abstract

The rare actinomycete-like bacteria are mycelium-forming bacteria other than phylum Actinobacteria that difficult to isolate and cultivate. This group of bacteria was recently speculated by many scientists as a potential new microbial resource for the discovery of novel compounds, as a substitute for actinomycetes. In this study, we isolate and identify rare actinomycete-like bacteria from forest soil collected under bamboo trees, near the CisolokGeysers, Sukabumi, Indonesia. The isolation of bacteria was performed using Reasoner’s 2A (1:10 dilution) medium with 2% gellan gum instead of agar and incubated at 30 °C for three weeks. The 16S rRNA gene sequences of the isolates were examined to determine their taxonomic position. Four isolates designated K17-1, K17-2, K42, and K44 showed pale oranges colonies and formed mycelia were obtained. The results of 16S rRNA gene sequences of these isolates showed high similarity to members of the genus Dictyobacter in the family Dictyobacteraceae of the class Ktedonobacteria of the phylum Chlorofexi, with values 97.16-98.02%, and most closely related to the species Dictyobacteraurantiacus S-27T (97.16-98.02% similarities). This result suggested that the member of the class Ktedonobacteria, which considered as rare actinomycete-like bacteria, such as Dictyobacter could be found in the forest soil of the geothermal area.