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Proteomic approaches to assess the oceanic nitrogen biogeochemistry

Final Report Summary - PROTEON (Proteomic approaches to assess the oceanic nitrogen biogeochemistry)

The project “Proteomic approaches to assess the oceanic Nitrogen biogeochemistry – ProteoN” had three major objectives. In summary, these were the development of a novel, high-throughput proteomic approach by combining state-of-the-art mass spectrometric and molecular biological techniques. This unique approach links the metabolic activity of organisms to their identity by assessing the proteins in a given sample, through both their protein identity as well as the natural carbon and nitrogen stable isotope ratios. The developed approach will be established using two bacterial cultures and a characterized, environmental model system. The novel approach will then be applied to a contemporary research issue of international interest. Specifically, this second objective will compare the nitrogen (N) biogeochemistry of two ocean basins and aims at evidence for or against the hypothesis (published in 2007 by peer scientists) that the Pacific Ocean is a site of high N2 fixation with higher rates than in the Atlantic Ocean. N2 fixation is the main source of fixed N in the open ocean and is a crucial player in primary production and hence the air-sea exchange of atmospheric CO2. The skills and knowledge acquired at a prestigious research institution in the USA will be transferred to an excellent research institution in the ERA and implemented into a study on the short-term effect of dust deposition in the North Atlantic Ocean (objective 3). Atmospheric dust is the main source of iron to the open ocean, a potentially limiting nutrient for N2 fixation. Dust deposition might be subject to global change through increased desertification and changing land use and is thus of international interest.
Within the first two years of the project, the proposed method development consumed more time than originally planned but has been successfully established for the measurements of carbon stable isotopes in proteins. However, it was not possible until to date to establish the proposed method for nitrogen isotopes due to current methodological limitations. A manuscript describing the developed method (i.e. Protein stable isotope fingerprinting – P-SIF) has been published in the peer-reviewed research journal “Analytical Chemistry” (Mohr et al. 2014).
Following the method development, it was attempted to characterize a model system (sulfidic microbial mat sample from a meromictic lake) using the novel method (based on carbon stable isotopes); however, sample properties so far prevented the extraction of sufficient amounts of protein necessary for the entire method to work optimally. Final results from this experiment are still in process; however, it is unclear at this point whether part of the results will be suitable for publication. Since metagenomic data had already been processed for the meromictic lake (Mahoney Lake, B.C. Canada), a manuscript describing the microbial community with respect to the sulfur cycle has been published in the peer-reviewed journal research journal “Geobiology” (Hamilton et al. 2014).
After processing the environmental model system, it was attempted to extract proteins from one of the Atlantic Ocean samples (collected on a cruise in 2013) in order to target the second objective, i.e. the comparison of the Atlantic and Pacific Ocean in terms of carbon stable isotope distribution as nitrogen stable isotope measurements are currently not feasible. Unfortunately, until now, protein extractions from the seawater samples have shown to be challenging and the extractions did not reveal sufficient amounts of protein for processing this sample with the newly developed method.
The researcher, advisor, and co-workers believe that the development of the new method (P-SIF) will be a valuable tool to evaluate the link between the identity of marine microbial organisms and their function/identity in their respective ecosystems. This new tool will allow for a high throughput analysis and will also allow the biogeochemical characterization of unknown microbial organisms which might play significant roles in the environment.
In the final year of the ProteoN project, samples collected on a 2013 cruise between Guadeloupe (French West Indies) and the Cape Verde Islands (West Africa) were analyzed with respect to bulk primary production and N2 fixation rates and the prevailing diazotroph community. These experiments were done with concurrent measurements of dust/aerosol thickness by other scientists on the same cruise; this will allow for an indirect comparison of N2 fixation rates with projected dust input into the tropical North Atlantic. The bulk analysis was followed by single-cell N2 fixation rate measurements of the dominating diazotrophs and the estimate of their relative contribution to the bulk rates. The final analysis of these data is ongoing, and it is expected that this study will lead to one publication in a peer-reviewed research journal.
Through the combination of research in a third country with the transfer of skills and knowledge to the ERA, present-day, globally-relevant issues could (partially) be assessed at the international level in addition to strengthening the individual researchers’ as well as the institutional network. The implementation of novel, state-of-the-art assessments of the environment will enhance the European research excellence and increase the competitiveness of European research.