Identification of secondary metabolite gene clusters of bacteria from south pacific gyre subseafloor sediment

Abstract

Secondary metabolites are organic compounds that are not directly involved in the key processes (growth, reproduction and development) of an organism. They are commonly targeted in pharmaceutical science for drug discovery. Secondary metabolites that have been used in drug discovery have been derived from plants, invertebrates and microbes. Microbes, bacteria in particular, have contributed greatly and will continue to play an important role in new drug discovery. Among the bacteria from all environments, marine bacteria are a vast reservoir for many potential useful bioactive compounds. Recent studies using marine bacteria for pharmaceutical use mainly focused on the bacteria collected from near-shore sediments. However, bacteria from deep-sea sediments remain unexplored. The South Pacific Gyre (SPG) is the most oligotrophic region of the world ocean. Due to the low surface productivity and distance from land, sediments below the gyre accumulate very slowly and are characterized by very low organic carbon content and relatively high dissolved oxygen concentrations. Sediments from South Pacific Gyre were found to host a living microbial community that, compared to other marine sediments, contains very low microbial biomass and very low metabolic activity. Thus, the goal of this study is to: (1) document the cultivatable bacterial diversity; and (2) explore the pharmaceutical potential of deep-sea bacteria from South Pacific Gyre sediment. To address this, bacteria were isolated in pure culture from sediments from seven sites of the Integrated Ocean Drilling Program (IODP) Expedition 329 in the South Pacific Gyre. 16S rRNA genes from 81 bacterial isolates throughout six SPG sites (U1366, U1367, U1368, U1369, U1370 and U1371) were sequenced for phylogenetic analysis using the RDP (Ribosomal Database Project). 16S rRNA genes were amplified with bacterial primers that have been proven to amplify bacterial sequences well (27F, 1392R). Whole genomes from nine Rhodococcus isolates (with two duplicates) throughout four SPG sites (U1366, U1367, U1370 and U1371) were sequenced for secondary metabolites gene clusters discovery. By using antiSMASH (antibiotics & Secondary Metabolite Analysis SHell), secondary metabolite biosynthesis gene clusters in the bacterial genome were identified, annotated and analyzed. Of the 81 16S rRNA gene clone libraries constructed, most of the clones (63%) affiliated with the genus Bacillus, 35.8% were affiliated with the genus Rhodococcus and one clone was identified as a Corynebacterium. The phylogenetic tree further indicated that all the Rhodococci were identified as Rhodococcus erythropolis. By using antiSMASH to look for the secondary metabolites gene clusters from the Rhodococcus genomes, many gene clusters, most of which were NPRS and PKS, were found in the genomes. This study suggests that deep-sea sediments harbor bacteria with the potential to produce pharmaceutically important secondary metabolites.