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Abstract Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs) that are disseminated into the environment via effluent. However, few studies have compared abundance, mobilization and selective pressures for ARGs in WWTPs as a function of variations in secondary treatment bioprocesses. We used shotgun metagenomics to provide a comprehensive analysis of ARG composition, relationship to mobile genetic elements and co-occurrences with antibiotic production genes (APGs) throughout two full-scale municipal WWTPs, one of which employs biofilm-based secondary treatment and another that uses a suspended growth system. Results showed that abundances of ARGs declined by over 90% per genome equivalent in both types of wastewater treatment processes. However, the fractions of ARGs associated with mobile genetic elements increased substantially between influent and effluent in each plant, indicating significant mobilization of ARGs throughout both treatment processes. Strong positive correlations between ARGs and APGs were found for the aminoglycoside antibiotic class in the suspended growth system and for the streptogramin antibiotic class in the biofilm system. The biofilm and suspended growth WWTPs exhibited similarities in ARG abundances, composition and mobilization trends. However, clear differences were observed for within-plant ARG persistence. These findings suggest that both biofilm and suspended growth-based WWTPs may promote genetic mobilization of persistent ARGs that are then disseminated in effluent to receiving water bodies. Wastewater treatment plants may promote genetic mobilization of antibiotic resistance determinants that are then disseminated in effluent to receiving water bodies.

GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of deposited 'living' data sets. The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu ), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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.

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data.