Culturable and unculturable actinomycetes associated with the sponge Neofibularia from Bira Island, Indonesia

ABSTRACT

Aims: The diversity of the actinomycete community associated with Neofibularia sp. from Bira Island, Indonesia, has been largely unstudied. This study was undertaken to address the paucity of information in this respect. Methodology and results: Culturable actinomycetes were isolated and cultured on HV medium. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) targeting the metagenomic 16S rRNA was used to analyse the structure of the actinomycete community. Five culturable actinomycetes that were isolated belonged to the genus Streptomyces. They showed various degrees of similarity to the reference strains Streptomyces sampsonii (97- 99%), Streptomyces resistomycificus (97-99%), Streptomyces gougerotii (97-99%), Streptomyces erringtonii (97-99%), and Streptomyces albus (97-99%). The culturable actinomycetes isolates also showed differences in morphological characteristics as compared with the reference strains. The metagenomic analysis suggested that the actinomycete community was dominated by rare actinomycetes. Eight DGGE DNA bands that were obtained had sequences that showed similarities to Ferrithrix thermotolerans (88-94%), Lamia majanohamensis (87-92%), Aciditerrimonas ferrireducens (87-92%), and Thermobispora bispora (85-92%), while 4 bands had sequences similar to Propionibacterium acnes (97-100%) and another band matched sequences belonging to an uncultured bacterium clone (86-87%). The actinomycetes detected by the metagenomic approach were assigned identities that were mostly under 97.5% as compared with reference strains available in Genbank. Conclusion, significance and impact of study Observations from both culture and DGGE analysis give a better understanding of the diversity and community structure of actinomycetes associated with Neofibularia sp. The culturable actinomycetes were Streptomyces spp., while rare actinomycetes were dominant when the metagenomic approach was adopted. Several of these actinomycetes showed identities below 97% when matched to reference strains, indicating possible novel species associated with the sponge Neofibularia.