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.
Subject(s)
ActinobacteriaABSTRACT
Aims: Cricula trifenestrata is one of natural insects which has not been domesticated yet, thus called as the wild silkworm. C. trifenestrata is known as a silk producer which has high economic and market value. However, the fungi attack on C. trifenestrata cocoon decreased quality and quantity of silk yarn. Chitinolytic bacteria have a high potential as biological control against pathogenic fungi. This research aimed to isolate, select, characterize, and identify chitinolytic bacteria as pathogenic fungi growth inhibitors on C. trifenestrata cocoon. Methodology and results: Chitinolytic bacteria was isolated from the uninfected and infected cocoon while fungi was isolated from the uninfected cocoon. Inhibition test was conducted by Fokkema method and chitinase activity was measured by Spindler method. A total of 36 chitinolytic bacteria and 10 suspected pathogenic fungi isolates have been isolated. Fungal pathogenicity test showed that isolate CSAJ.2 was suspected as fungal pathogen. In vitro inhibition test indicated that chitinolytic bacteria isolate BSEP.3 could inhibit the growth of pathogenic fungi CSAJ.2 with percentage of inhibition 50%. Isolate BSEP.3 showed highest chitinase activity (5.11 U/mL) at the 15th h. It able to inhibit the growth of pathogenic fungi with percentage of inhibition of 47.5% and 46.25%, respectively. Conclusion, significance and impact of study: Identification of bacteria targeted on 16S rRNA gene showed that isolate BSEP.3 had 98% identity with Bacillus amyloliquefaciens B5 while identification of fungi using ITS region of the rDNA showed that isolate CSAJ.2 had 100% identity with Trichoderma virens TV242. Chitinase crude extract was effective to be used as a biological control agent of T. virens CSAJ.2.