Physical Sciences and Mathematics | Open Access Articles

A Critical Review Of The 15N2 Tracer Method To Measure Diazotrophic Production In Pelagic Ecosystems, Angelicque E. White, Julie Granger, Corday Seldon, Mary R. Gradoville, Lindsey Potts, Annie Bourbonnais, Robinson W. Fulweiler, Angela N. Knapp, Wiebke Mohr, Pia H. Moisander, Craig R. Tobias, Mathieu Caffin, Samuel T. Wilson, Mar Benavides, Sophie Bonnet, Margaret R. Mulholland, Bonnie X. Chang

OES Faculty Publications

Dinitrogen (N₂) fixation is an important source of biologically reactive nitrogen (N) to the global ocean. The magnitude of this flux, however, remains uncertain, in part because N₂ fixation rates have been estimated following divergent protocols and because associated levels of uncertainty are seldom reported—confounding comparison and extrapolation of rate measurements. A growing number of reports of relatively low but potentially significant rates of N₂ fixation in regions such as oxygen minimum zones, the mesopelagic water column of the tropical and subtropical oceans, and polar waters further highlights the need for standardized methodological protocols for measurements …

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Abiotic Formation Of Dissolved Organic Sulfur In Anoxic Sediments Of Santa Barbara Basin, Hussain A. Abdulla, David J. Burdige, Tomoko Komada

OES Faculty Publications

Sulfurization has been found to enhance organic matter preservation and petroleum formation in marine sediments. However, we do not yet have a comprehensive understanding of sulfurization mechanisms. In this study, we investigated several possible mechanisms of dissolved organic sulfur (DOS) formation in the top 4.5 m of anoxic sediments of Santa Barbara Basin (SBB), California Borderland. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), we identified chemical formulas of potential dissolved organic matter (DOM) precursors to these DOS compounds. We also examined how the formulas of abiotically formed DOS changed as a function of depth across a major redox …

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Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data, Michael Riffle, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, Daniel Jaschob, William S. Noble, Brook L. Nunn

OES Faculty Publications

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the …

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An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble

OES Faculty Publications

In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …

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The Path To Preservation: Using Proteomics To Decipher The Fate Of Diatom Proteins During Microbial Degradation, Brook L. Nunn, Ying S. Ting, Lars Malmström, Yihsuan S. Tsai, Angela Aquier, David R. Goodlett, H. Rodger Harvey

OES Faculty Publications

We drew upon recent advances in tandem mass spectrometry-based proteomic analyses in order to examine the proteins that remain after a diatom bloom enters the stationary phase, precipitates out of the photic zone, and is subjected to microbial degradation over a 23-d period within a controlled laboratory environment. Proteins were identified from tandem mass spectra searched against three different protein databases in order to track proteins from Thalassiosira pseudonana and any potential bacterial contributions. A rapid loss of diatom protein was observed over the incubation period; 75% of the proteins initially identified were not detected after 72 h of exposure …

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Anthropogenic Osmium In Rain And Snow Reveals Global-Scale Atmospheric Contamination, Cynthia Chen, Peter N. Sedwick, Mukul Sharma

OES Faculty Publications

Osmium is one of the rarer elements in seawater, with typical concentration of ≈10 x 10^-15 g g^-1 ( 5.3 x 10^-14 mol kg^-1. The osmium isotope composition (¹⁸⁷Os/¹⁸⁸Os ratio) of deep oceans is 1.05, reflecting a balance between inputs from continental crust (≈ 1.3) and mantle/cosmic dust (≈ 0.13). Here, we show that the ¹⁸⁷Os/¹⁸⁸Os ratios measured in rain and snow collected around the world range from 0.16 to 0.48, much lower than expected (>1), but similar to the isotope composition of ores (approximate to 0.2) …

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Radiocarbon Evidence For The Importance Of Surface Vegetation On Fermentation And Methanogenesis In Contrasting Types Of Boreal Peatlands, J. P. Chanton, P. H. Glaser, L. S. Chasar, David J. Burdige, M. E. Hines, D. I. Seigel, L. B. Tremblay, W. T. Cooper

OES Faculty Publications

We found a consistent distribution pattern for radiocarbon in dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and methane replicated across spatial and temporal scales in northern peatlands from Minnesota to Alaska. The ¹⁴C content of DOC is relatively modern throughout the peat column, to depths of 3 m. In sedge-dominated peatlands, the ¹⁴C contents of the products of respiration, CH₄ and DIC, are essentially the same and are similar to that of DOC. In Sphagnum- and woody plant-dominated peatlands with few sedges, however, the respiration products are similar but intermediate between the ¹⁴C contents of …

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Full-Text Articles in Physical Sciences and Mathematics

OES Faculty Publications

Abiotic Formation Of Dissolved Organic Sulfur In Anoxic Sediments Of Santa Barbara Basin, Hussain A. Abdulla, David J. Burdige, Tomoko Komada

OES Faculty Publications

Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data, Michael Riffle, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, Daniel Jaschob, William S. Noble, Brook L. Nunn

OES Faculty Publications

An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble

OES Faculty Publications

The Path To Preservation: Using Proteomics To Decipher The Fate Of Diatom Proteins During Microbial Degradation, Brook L. Nunn, Ying S. Ting, Lars Malmström, Yihsuan S. Tsai, Angela Aquier, David R. Goodlett, H. Rodger Harvey

OES Faculty Publications

Anthropogenic Osmium In Rain And Snow Reveals Global-Scale Atmospheric Contamination, Cynthia Chen, Peter N. Sedwick, Mukul Sharma

OES Faculty Publications

Radiocarbon Evidence For The Importance Of Surface Vegetation On Fermentation And Methanogenesis In Contrasting Types Of Boreal Peatlands, J. P. Chanton, P. H. Glaser, L. S. Chasar, David J. Burdige, M. E. Hines, D. I. Seigel, L. B. Tremblay, W. T. Cooper

OES Faculty Publications