Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

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

Molecular Signatures of Microbial Metabolism in the Marine Water Column

Lipid biomarkers are valuable tools in studies of microbial metabolic diversity and function in both past and present marine ecosystems, but the distribution and biological sources of many of these biomarkers in the modern ocean have yet to be sufficiently defined. This dissertation examines two major classes of lipid biomarker compounds that are widely distributed in marine environments: hopanoids, biomarkers for bacteria, and intact polar diacylglycerols (IP-DAGs), potential biological tracers of recent carbon and nutrient cycling. The distribution and structural diversity of these lipid compounds is analyzed in tandem with genetic and metagenomic data, both expanding the knowledge related to the structural distribution of these lipids in the marine environment, and illuminating key aspects of the ecology of the producing organisms. This work is detailed in six chapters, consisting of an introduction, four research-oriented chapters, and concluding remarks. Chapters 2, 3, and 4 focus on the bacterial hopanoids. First, analysis of hopanoid structural diversity and abundance across oxygen gradients in the Santa Barbara Basin was complemented by a genetic survey, identifying a potential connection between hopanoid production and metabolic strategies associated with low oxygen environments. Next, this connection was further investigated using qPCR and surveys of existing metagenomes to quantify the relative abundance of groups of hopanoid producers in low oxygen regions of the Eastern North Pacific and Eastern Tropical Pacific oxygen minimum zones. Results revealed that dominant hopanoid producers in these regions are not Proteobacteria as previously hypothesized but instead are nitrite-utilizing organisms such as nitrite-oxidizing and anaerobic ammonia-oxidizing bacteria. Finally, a survey of an extensive metagenomic dataset from the Red Sea illuminated the distribution of hopanoid producers in a biogeochemically-distinct environment relative to those previously analyzed, and confirming that hopanoid producers may also play roles in marine nitrogen cycling. Chapter 5 details an exploratory investigation of the structural distribution of various classes of IP-DAGs, in the oligotrophic Tonga Trench. Results provide new insight into potential biological sources of IP-DAGs, and identify structures that may be useful as indicators of the contribution of groups of picophytoplankton to export production, or of in situ heterotrophic production at depth

Molecular Signatures of Microbial Metabolism in the Marine Water Column

Lipid biomarkers are valuable tools in studies of microbial metabolic diversity and function in both past and present marine ecosystems, but the distribution and biological sources of many of these biomarkers in the modern ocean have yet to be sufficiently defined. This dissertation examines two major classes of lipid biomarker compounds that are widely distributed in marine environments: hopanoids, biomarkers for bacteria, and intact polar diacylglycerols (IP-DAGs), potential biological tracers of recent carbon and nutrient cycling. The distribution and structural diversity of these lipid compounds is analyzed in tandem with genetic and metagenomic data, both expanding the knowledge related to the structural distribution of these lipids in the marine environment, and illuminating key aspects of the ecology of the producing organisms. This work is detailed in six chapters, consisting of an introduction, four research-oriented chapters, and concluding remarks. Chapters 2, 3, and 4 focus on the bacterial hopanoids. First, analysis of hopanoid structural diversity and abundance across oxygen gradients in the Santa Barbara Basin was complemented by a genetic survey, identifying a potential connection between hopanoid production and metabolic strategies associated with low oxygen environments. Next, this connection was further investigated using qPCR and surveys of existing metagenomes to quantify the relative abundance of groups of hopanoid producers in low oxygen regions of the Eastern North Pacific and Eastern Tropical Pacific oxygen minimum zones. Results revealed that dominant hopanoid producers in these regions are not Proteobacteria as previously hypothesized but instead are nitrite-utilizing organisms such as nitrite-oxidizing and anaerobic ammonia-oxidizing bacteria. Finally, a survey of an extensive metagenomic dataset from the Red Sea illuminated the distribution of hopanoid producers in a biogeochemically-distinct environment relative to those previously analyzed, and confirming that hopanoid producers may also play roles in marine nitrogen cycling. Chapter 5 details an exploratory investigation of the structural distribution of various classes of IP-DAGs, in the oligotrophic Tonga Trench. Results provide new insight into potential biological sources of IP-DAGs, and identify structures that may be useful as indicators of the contribution of groups of picophytoplankton to export production, or of in situ heterotrophic production at depth

Chlorophyll d15N in Lake Erie collected on NOAA GLERL weekly monitoring cruises from June to October 2017

Dataset: Chlorophyll d15N in Lake ErieChlorophyll d15N in Lake Erie collected on NOAA GLERL weekly monitoring cruises from June to October 2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/793501NSF Division of Ocean Sciences (NSF OCE) OCE-173662

Patterns in sources and forms of nitrogen in a large eutrophic lake during a cyanobacterial harmful algal bloom

Western Lake Erie experiences an annual, toxic cyanobacterial harmful algal bloom (cyanoHAB), primarily caused by excess anthropogenic inputs of nitrogen (N) and phosphorous (P). Because the non-N fixing cyanobacteria species Microcystis dominates these blooms, N availability is hypothesized to play a central role in cyanoHAB progression, as well as production of the N-rich toxin microcystin. Many previous studies focused on nitrate because it is the most abundant N substrate during bloom initiation. However, recent work implicated reduced N substrates like ammonium and dissolved organic N (DON) in promoting greater bloom biomass and longevity. To examine the relative importance of oxidized and reduced N substrates to phytoplankton during different bloom stages, we measured concentrations and natural abundance δ15N isotope values of dissolved N substrates and phytoplankton biomass throughout the entirety of the 2020 cyanoHAB in Western Lake Erie. The results provide the first data on DON dynamics and composition in Western Lake Erie, and suggest that phytoplankton, including Microcystis, likely relied on N regenerated from the DON pool in later bloom stages. In addition, the stable isotope data confirm the importance of nitrate delivered via the Maumee River to cyanobacterial growth and toxin production

Table S4, Content and stable isotopic composition of total organic carbon (TOC) and total nitrogen (TN) for ODP cores at sites 964 and 967

Bulk organic carbon (OC) and nitrogen content and stable isotope compositions for ODP cores at sites 964 and 967, including: event name, sapropel layer, core, depth (top), depth (bottom), OC content (mean), OC content (std. dev.), OC d13C (mean), OC d13C (std. dev.), nitrogen content (mean), nitrogen content (std. dev.), d15N (mean), d15N (std. dev.), and C/N ratio. All content and isotope data were generated using a Thermo Scientific Delta V isotope ratio mass spectrometer run in continuous flow mode. Samples were acidified by fumigation prior to OC content and d13C analysis; samples were run without acidification for N content and d15N analysis. This work was supported by the Gordon and Betty Moore Foundation

Table S1, Composite depths and age models for ODP coring sites 964 and 967

This dataset contains composite depths and age models for ODP sites 964 and 967, including: event name, sapropel layer, sample ID, site, hole, core, section, section position, depth (raw), depth (composite, revised), age, comment, and reference. All data were compiled from the literature. This work was supported by the Gordon and Betty Moore Foundation

Mediterranean sapropel bulk organic matter and biomarker concentrations and carbon isotope compositions

This dataset contains bulk organic matter and biomarker data for two Mediterranean Sea sites: ODP Leg 160 site 964 (including sapropels S5, S7, and i-282) and ODP Leg 160 site 967 (including sapropels S4, S5, and S74). This dataset includes: (i) compiled age model data from the literature; (ii) diagnostic mass spectrometry selective reaction monitoring m/z ratios for bacteriohopanepolyol (BHP) and heterocyst glycol (HG) analysis; (iii) bulk sediment % organic carbon (OC), % total nitrogen (TN), OC-d13C, and TN-d15N; (iv) OC-normalized abundances of various BHPs, HGs, and crenarchaeol; (v) d13C values for BHPs and crenarchaeol; and (vi) literature compilation of Eastern Mediterranean Sea diatom frustule preservation observations. Samples were analyzed at Harvard University in 2017-2018 from samples collected in 1995 during ODP Leg 160; sample ages range from 101 to 3004 kilo years before present. Samples were collected from the Eastern Mediterranean Sea and cover the Ionian and Levantine Seas. These data were generated to study the microbial ecological and biogeochemical responses to ocean anoxia in an enclosed basin; samples were analyzed using mass spectrometric and isotope-ratio mass spectrometric methods (coupled to liquid- and gas-chromatography and elemental analysis). This work was supported by the Gordon and Betty Moore Foundation

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current.

Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record