Malaysian Journal of Microbiology, Vol 12(3) 2016, pp. 211-220 http://dx.doi.org/10.21161/mjm.77015 Malaysian Journal of Microbiology Published by Malaysian Society for Microbiology (In since 2011) 211 ISSN (print): 1823-8262, ISSN (online): 2231-7538 Culturable and unculturable actinomycetes associated with the sponge Neofibularia from Bira Island, Indonesia Cico Jhon Karunia Simamora 1 , Dedy Duryadi Solihin 2 and Yulin Lestari 2,3* 1 Graduate School, Bogor Agricultural University, IPB Dramaga, Bogor 16680 Indonesia. 2 Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, IPB Dramaga, Bogor 16680 Indonesia. 3 Biopharmaca Research Center, Bogor Agricultural University, Campus IPB Taman Kencana, Bogor 16151 Indonesia. Email: yulinlestari@gmail.com or yulinl@ipb.ac.id Received 23 September 2015; Received in revised form 24 December 2015; Accepted 16 February 2016 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. Keywords: Actinomycetes, culturable, DGGE, Neofibularia sp., unculturable INTRODUCTION Sea sponges are ancient sessile organisms that have existed since 600 million years ago and are important members in the coral reef ecosystem. Owing to its geographical location between the Indian and Pacific Oceans, Indonesia has a high diversity of sponges belonging to 830 species across various families (Hutomo and Moosa, 2005). Neofibularia sp. has been reported as a producer of antileishmanial, antimalarial, and antibacterial compounds (Thompson and Gallimore, 2013). Such bioactive compounds produced by sponges may have arisen from their associated microbes (Peraud, 2006). Microbe density in sponges can reach up to 10 9 cells per cm 3 , covering 35% of the total biomass of sponge tissue (Hentschel et al., 2012). Close association between sponges and microbes (Hentschel et al., 2003) may also contribute to the high diversity of sponge-associated bacteria, including actinomycetes (Sun et al., 2010). Actinomycetes play an important role in the growth and development of sponges they are associated with, such as by providing nutrients, UV protection, defence against toxic compounds, and by stabilizing their skeletons, and decomposing residual metabolites (Shick and Dunlap, 2002). Various compounds are produced by different actinomycetes (Pathirana et al., 1992), and the structures of bioactive compounds produced by marine sponge- associated actinomycetes can be different from those produced by their terrestrial counterparts (Drummond, 2006). *Corresponding author