Microbiology of Indonesian extremobiospheres : from unexplored actinobacteria diversity to novel antimicrobial discovery

Abstract

This present study addresses the need to extend bioprospecting campaigns to neglected and untapped biomes with the expectation that they will contain novel actinobacteria able to synthesise new bioactive compounds. Culture-dependent and culture-independent methods were used to establish the extent and biotechnological potential of actinobacteria in environmental samples drawn from thirteen extreme biomes located in the Indonesian archipelago. Nearly all of the environmental samples contained small numbers of actinobacteria which formed varying fractions of bacteria growing on the selective media. Over one hundred representative isolates were assigned to 8 orders, 15 families and 21 genera based on 16S rRNA gene sequence data. Almost 74% of these isolates inhibited the growth of wild type strains in standard plug assays., 19 filamentous isolates from the primary screens inhibited cell envelope, cell wall, DNA, fatty acid and RNA synthesis in secondary screens based on Bacillus subtilis reporter strains. Nineteen isolates with interesting bioactivity profiles or representing rare taxa were assigned to one new genus, 10 novel species and 2 new subspecies following extensive genome-based polyphasic studies. Several of these “key” isolates belonged to novel amycelial and filamentous actinobacteria rarely isolated from extremobiospheres. The metagenomic analyses of composite environmental samples from the extreme habitats contained an extraordinary degree of previously unknown actinobacterial diversity. The richest source of uncultivated actinobacterial taxa accounted for 4 new orders, 10 novel families, 30 new genera and 5790 undiscovered species was from the Parangkusumo sand-dune sample. Rank abundancy curves showed that nearly all of the actinobacterial diversity detected in this and the other composite samples from extreme habitats represented low abundancy taxa. These results demonstrate that extreme Indonesian habitats are an enormous untapped source of novel actinobacteria that present unique opportunities for bioprospecting of potential drug leads at a time when multidrug resistant pathogens are an ever-increasing threat to global health.