Metagenomic tools to assess the diversity of polyketide synthases in the underground river of the Yucatan peninsula

The underground river in Yucatan is the largest of its kind in the world, yet its microbial community has been barely studied. As part of a collaborative effort to describe the potential of this important water resource for biotechnological applications, we explored the diversity of keto synthases (KS) present in the microbial community from an aquifer water sample. Rapid analysis of the metagenomic sequences using MG-RAST showed that Firmicutes, Proteobacteria and Actinobacteria are the dominant phyla. Regarding functionality, carbohydrate and amino acids were the dominant metabolisms, while plant hormones and aromatic amino acid derivatives dominated secondary metabolisms. In order to assess the biotechnological potential of our metagenome, further bioinformatic analyses were performed: 1) the metagenomic sequences were compared to the NaPDoS database to match our metagenome to KS domain sequences from known natural products, 2) seven sequences of known actinomycete KS were used to “probe” the metagenome using the platform prfectBlast. A total of 120 sequences were obtained with both methods. From these, 23 contigs of 600 – 1200 bp were created. Verification of function using the NCBI database resulted in 28 sequences with high similarity to KS enzymes. Phylogenetic analysis of the sequences confirmed their evolutionary relationship with KS enzymes and, a comparison against NaPDoS suggests that they may belong to novel KS from polyunsaturated fatty acids and polyketides. Further work using an existing metagenomic fosmid library will allow to probe for these 28 sequences and continue the exploration of PKS pathways in the metagenome.