Dissolved Organic Matter in the Upwelling System off Peru: Imprints of Bacterial Activity and Water Mass Characteristics

Microbial degradation of dissolved organic matter (DOM) contributes to the formation and preservation of oxygen minimum zones (OMZs) in the ocean, but information on the spatial distribution and molecular composition of DOM in OMZ regions is scarce. We quantified molecular components of DOM that is, dissolved amino acids (DAA) and dissolved combined carbohydrates (DCCHO), in the upwelling region off Peru. We found the highest concentrations of DCCHO in fully oxygenated surface waters steeply declining at shallow depth. The highest DAA concentrations were observed close to the surface also, but attenuation of DAA concentration over depth was less pronounced. Compositional changes of DCCHO were strongest within more oxygenated waters. Compositional changes of DAA were also evident under suboxic conditions (<5 µmol O2 kg−1) and indicated bacterial peptide degradation. Moreover, specific free amino acids (alanine and threonine) were enhanced within suboxic waters, pointing to a potential production of dissolved organic nitrogen under suboxic conditions. Our results therewith suggest that deoxygenation supports a spatial decoupling of DCCHO and DAA production and degradation dynamics and give new insights to carbon and nitrogen cycling in the OMZ off Peru

Anaerobic ammonium-oxidising bacteria: A biological source of the bacteriohopanetetrol stereoisomer in marine sediments

Bacterially-derived bacteriohopanepolyols (BHPs) are abundant, well preserved lipids in modern and paleo-environments. Bacteriohopanetetrol (BHT) is a ubiquitously produced BHP while its less common stereoisomer (BHT isomer) has previously been associated with anoxic environments; however, its biological source remained unknown. We investigated the occurrence of BHPs in Golfo Dulce, an anoxic marine fjord-like enclosure located in Costa Rica. The distribution of BHT isomer in four sediment cores and a surface sediment transect closely followed the distribution of ladderane fatty acids, unique biomarkers for bacteria performing anaerobic ammonium oxidation (anammox). This suggests that BHT isomer and ladderane lipids likely shared the same biological source in Golfo Dulce. This was supported by examining the BHP lipid compositions of two enrichment cultures of a marine anammox species ('. Candidatus Scalindua profunda'), which were found to contain both BHT and BHT isomer. Remarkably, the BHT isomer was present in higher relative abundance than BHT. However, a non-marine anammox enrichment contained only BHT, which explains the infrequence of BHT isomer observations in terrestrial settings, and indicates that marine anammox bacteria are likely responsible for at least part of the environmentally-observed marine BHT isomer occurrences. Given the substantially greater residence time of BHPs in sediments, compared to ladderanes, BHT isomer is a potential biomarker for past anammox activity

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

Data for: Chlorophyll nitrogen isotope values track shifts between cyanobacteria and eukaryotic algae in a natural phytoplankton community in Lake Erie

Dataset for 15N isotopes of chlorophyll and cellular biomass measured over the course of the annual cyanobacteria harmful algal bloom in Lake Erie, along with data on phytoplankton community composition obtained via a submersible Fluoroprobe

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

Data for: Chlorophyll nitrogen isotope values track shifts between cyanobacteria and eukaryotic algae in a natural phytoplankton community in Lake Erie

Dataset for 15N isotopes of chlorophyll and cellular biomass measured over the course of the annual cyanobacteria harmful algal bloom in Lake Erie, along with data on phytoplankton community composition obtained via a submersible Fluoroprobe.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

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