Improving Natural Product Discovery Efforts Through Analysis of Biosynthetic Gene Populations in Sediment

Since the discovery of penicillin in 1928, microorganisms have served as both a significant source of biologically active natural products (NPs) and an inspiration for NP-derived small molecule scaffolds. Their remarkable biosynthetic capacity allows them to produce NPs with high structural diversity and a wide range of biological activities. In this study, the NP biosynthetic gene cluster (BGC) diversity in Lake Huron sediment was examined through biogeographic analysis of BGC domain architecture. High-throughput amplicon sequencing was employed to document geographic occurrences of NP biosynthetic domains from 59 surface sediment samples across a 59,590 square kilometer geographic area. In addition, quantifying these genes in both sediment and cultivatable bacterial populations is critical to guiding the trajectory of future NP discovery platforms. We thus employed the same sequencing method to assess the NP biosynthetic gene populations present in two of these Lake Huron sediment samples, and compared these with populations from their corresponding cultivatable bacteria. From these data, the occurrence of several classes of NPs were mapped, including antibiotics, siderophores, and other bioactive compounds across lake sediment. These maps provided evidence that some NP classes exhibit sparse occurrence, while others exhibit more cosmopolitan distribution throughout the lake. These results present some of the first preliminary evidence to support the notion that extensive sample collection efforts are required to more fully capture the NP capacity that exists in sediment. In addition, we highlight three findings, 1) after cultivation, we recovered between 7.7% and 23% of three common types of NP biosynthetic genes from the original sediment population; 2) between 76.3% and 91.5% of measured NP biosynthetic genes from nutrient agar have yet to be characterized in known BGC databases, indicating that readily cultivatable bacteria harbor potential to produce new NPs; 3) even though the predominant taxa present on nutrient media represented some of the major producers of bacterial NPs, the sediment harbored a significantly greater pool of NP biosynthetic genes that could be mined for structural novelty, and these likely belong to taxa that typically have not been represented in microbial drug discovery libraries. These results provide context for a discussion of the limitations that researchers face when employing next generation sequencing techniques to the discovery of natural products in the environment.