Project description:This project presents field metaproteomics data from Trichodesmium colonies collected from the surface ocean. Most were collected from the tropical and subtropical Atlantic ocean, but there is also data from the long term Bermuda Atlantic Time Series and Hawaii Ocean Time Series. Trichodesmium is a globally important marine microbe and its growth and nitrogen fixation activity is limited by nutrient availability in the surface ocean. This dataset was generated to answer questions about limitations on Trichodesmium's growth and activity in the nature.
Project description:The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.
Project description:Marine dissolved organic matter from the Atlantic Ocean. Samples were analyzed by LC-MS/MS in positive and negative electrospray ionization mode using DDA (Orbitrap Eclipse).
Project description:The diazotroph Trichodesmium is an important contributor to marine dinitrogen (N2) fixation, supplying so-called new N to phytoplankton in typically N-limited ocean regions. Identifying how iron (Fe) and phosphorus (P) influence Trichodesmium activity and biogeography is an ongoing area of study, where predicting patterns of resource stress is complicated in part by the uncertain bioavailability of organically complexed Fe and P. Here, a comparison of 26 metaproteomes from picked Trichodesmium colonies identified significantly different patterns between three ocean regions: the western tropical South Pacific, the western North Atlantic, and the North Pacific Subtropical Gyre. Trichodesmium metaproteomes across these regions significantly differed in KEGG submodule signals, and vector fitting showed that dissolved Fe, phosphate, and temperature significantly correlated with regional proteome patterns. Populations in the western tropical South Pacific appeared to modulate their proteomes in response to both Fe and P stress, including a comparatively low relative abundance of the N2 fixation marker protein, NifH. Significant increases in the relative abundance of both Fe and P stress marker proteins previously validated in culture studies suggested that Trichodesmium populations in the western North Atlantic and North Pacific were P-stressed and Fe-stressed, respectively. These patterns recapitulate established regional serial and co-limitation patterns of resource stress on phytoplankton communities. Evaluating community stress patterns may therefore predict resource controls on diazotroph biogeography. These data highlight how Trichodesmium modulates its metabolism in the field and provide an opportunity to more accurately constrain controls on Trichodesmium biogeography and N2 fixation.
Project description:An Autonomous Underwater Vehicle (AUV) and large volume underwater pumps were used to collect microbial biomass from offshore waters of the Sargasso Sea, from surface waters and into the deep ocean. Seawater collection was performed along a transect in the western North Atlantic Ocean beginning near Bermuda and ending off the coast of Massachusetts, capturing metabolic signatures from oligotrophic, continental margin, and productive coastal ecosystems.
Project description:This dataset consists of 20 metaproteomic analyses of the Western Atlantic Ocean aboard the R/V Knorr KN210-04 DeepDOM expedition in 2013. Samples were collected by McLane pumps on GFF or GF75 filters, split, and frozen until analyses. Expedition metadata and co-sampled datasets are available at: https://www.bco-dmo.org/deployment/59057
Project description:The European clam, Ruditapes decussatus (Linnaeus, 1758) is a bivalve mollusc of the family Veneridae native to the European Atlantic and Mediterranean coastal waters. Its production is exclusively based on natural recruitment, which is subject to high annual fluctuations due to adversely affected by pollution and other environmental factors. A microarray-based analysis was performed with the objectives of describe genomic feature of oocytes and identify potential markers of oocyte quality in the economically important European clam, Ruditapes decussatus. The oocytes of a total of 25 females from Ria de Aveiro, Western coast of Portugal, were selected for this study and their quality was estimated by early developmental success until D-larval rate, under controlled conditions.
Project description:Transcriptional profiling of populations in the clam Ruditapes decussatus determined differentiation in gene-expression along parallel temperature gradients and between races of the Atlantic Ocean and West Mediterranean sea.
Project description:Surface waters of the vast subtropical ocean gyres are poor in nutrients such as nitrogen (N), phosphorus (P), iron (Fe) and zinc (Zn). Ocean warming is predicted to intensify and expand these low nutrient gyres, but we have limited knowledge on how natural assemblages of marine microbes acquire nutrients. While detecting regions where the lack of N and/or Fe limits biological activity appears straightforward, it is problematic for P due to divergent results from different approaches used. Using natural zonal gradients in nutrient resources and biological activity, we investigated the nutrient acquisition strategies of Prochlorococcus and Synechococcus, with a specific focus on phosphorus since Fe and Zn may constrain the activity of the metalloenzyme, alkaline phosphatase, used by microbes to access dissolved organic phosphorus (DOP) when phosphate is scarce. Analyses of proteins indicative of nutrient acquisition and stress, termed ‘biomarkers’ alongside high-resolution biogeochemical measurements and nutrient bioassays concur on more intense phosphorus limitation in the western compared to the eastern subtropical Atlantic. However, we found sparse evidence of trace metal control of alkaline phosphatase by Fe or Zn or cobalt. Instead, zonal gradients as well as the bioassays involving the addition of Fe, Zn and DOP stimulated different responses in protein production in Prochlorococcus and Synechococcus, implying these picocyanobacteria may have different biomarkers indicative of nutrient stress, which has implications for the interpretation of trends in protein, as well as different strategies to acquire essential nutrients. The divergence in acquisition strategies alongside the asynchronous zonal gradients in Prochlorococcus and Synechococcus in the subtropical North Atlantic are likely driven by other processes such as nitrogen fixation, atmospheric and upwelled delivery of nutrients and competition for resources.
Project description:In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).