Mangrove mud metagenome : the source of new gene involving in bioactive compound biosynthesis and microcial diversity access

Abstract

In this study, the polyketide synthases (PKS) genes involving in biosynthesis of polyketides, the groups of prolific and various structural and functional bioactive compounds were searched on metagenome of soil microbial community from Klongkone mangrove forest, Samut Songkhram Province, Thailand. Detection of ketosynthase (KS) domain gene of type I polyketide synthase (PKS) in the mangrove mud metagenome by polymerase chain reaction (PCR) using degenerate primers specific for the conserved motif VDPQQR and the histidine active site motif HGTGT resulted in 12 diverse KS domain genes. Deduced amino acid sequences of these novel domains were 34-70% homology. Most of the discovered KSs were phylogenetically related to cis-AT type I PKS, one was related to trans-AT and the others were related to NRPS preceding hybrid PKS/NRPS, which groups of hybrid PKS/NRPS I-II and III were newly proposed in this study. A variety of novel 16S rRNA gene phylotypes were also found by analysis of PCR-product clones. They were phylogenetically related to bacteria in phyla Proteobacteria, Acidobacteria, Deferribacteres, Chloroflexi, Verrucomicrobia, and Lentisphaerae. One phylotype was related to unclassified bacteria. In searching for PKS gene in the mangrove soil metagenomic library constructed with fosmid vector, novel PKS and NRPS modules were found in clone KKFOS_KSI_pool37_088 with the 29 kb DNA insert. These revealed that Klongkone mangrove soil harbored various novel diverse PKS genes and bacteria which could be accessed through metagenomics.