California Sea Grant College Program
Phylogenetic Diversity of Gram-positive Bacteria and Their Secondary Metabolite Genes
- Author(s): Gontang, Erin A
- et al.
To assess the bacterial diversity of marine sediments, a culture-dependent approach was employed to assess the diversity of Gram-positive bacteria in marine sediments collected around the islands of Palau. The survey of the total, aerobic Gram-positive bacterial diversity present in tropical marine sediments resulted in the isolation of a diverse assemblage of Gram-positive isolates. Of the 78 operational taxonomic units cultured (OTUs based on ≥ 98% 16S rRNA gene sequence identity), 52 were determined to be members of the order Actinomycetales and 26 were determined to be members of the order Bacillales.
Bacterial genome sequencing has provided opportunities to assess the secondary metabolite biosynthetic potential of individual strains. By elucidating entire biosynthetic pathways in the context of all other genes and pathways present, it is also possible to address questions related to the evolution of gene clusters or individual genes within a cluster. The complete genome sequence of Salinispora arenicola strain CNS-205, an actinomycete isolated during the research expedition to Palau, provided an opportunity to investigate the evolution of type I modular polyketide synthase (PKS) gene clusters.
While a tremendous amount can be learned from analyzing the entire genetic blueprint of a microorganism, additional natural product discovery approaches are necessary to gain insight into the biosynthetic potential of unsequenced organisms prior to fermentation, extraction and chemical analyses. A PCR based approach has been used successfully to suggest which representative isolates from the 52 Actinomycetales OTUs harbor type I PKS, enediyne PKS and nonribosomal peptide synthetase (NRPS) pathways. Over half of the cultured Actinomycetales OTUs were found to possess genes associated with at least one PKS or NRPS biosynthetic pathway and although some of these actinomycetes represent families well known to produce secondary metabolites, the results suggest that novel secondary metabolites can be isolated from both filamentous and unicellular actinomycete families. In addition to determining if these pathways are present, a phylogenetic approach was used successfully to suggest the number and novelty of type I PKS pathways present. By using the phylogenetic approach, the diversity, novelty and identity of type I PKS metabolites can be predicted.