Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS

Abstract

Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel's Beach) surface water-Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample.

Keywords: NRPS; PKS; coastal environment; environmental genomics; metagenomics; upwelling.

Figure 1

Classification of KS domain by NapDos. The sequences wereobtained with pHMM KS modular and pHMM KS iterative, from both samples.

Figure 2

Phylogenetic tree of environmental KS domains (larger than 200 amino acids) obtained from both sample (by KS modular and iterative pHMMs) with reference NapDoS sequences. The tree was generated by NapDos pipeline (using FASTTREE and Maximum Likelihood algorithm). Confidence values are showed on nodes. The shadows show the different groups (Modular, KS1, Trans, Hybrid, iterative and PUFA).

Figure 3

Phylogenetic tree of environmental C domains (larger than 200 amino acids) obtained from both sample (by C domain pHMM) with reference NapDoS sequences. The tree was generated by NapDos pipeline (using FASTTREE and Maximum Likelihood algorithm). Confidence values are shown on nodes. The shadows show the different groups of C domains.