Biogeochemistry Commons^™

Biogeochemical Controls Of Surface Ocean Phosphate, Adam C. Martiny, Michael W. Lomas, Weiwei Fu, Philip W. Boyd, Yuh-Ling L. Chen, Gregory A. Cutter, Michael J. Ellwood, Ken Furuya, Fuminori Hasshihama, Jota Kanda, David M. Karl, Taketoshi Kodama, Qian P. Li, Jian Ma, Thierry Moutin, E. Malcolm S. Woodward, J. Keith Moore

OES Faculty Publications

Surface ocean phosphate is commonly below the standard analytical detection limits, leading to an incomplete picture of the global variation and biogeochemical role of phosphate. A global compilation of phosphate measured using high-sensitivity methods revealed several previously unrecognized low-phosphate areas and clear regional differences. Both observational climatologies and Earth system models (ESMs) systematically overestimated surface phosphate. Furthermore, ESMs misrepresented the relationships between phosphate, phytoplankton biomass, and primary productivity. Atmospheric iron input and nitrogen fixation are known important controls on surface phosphate, but model simulations showed that differences in the iron-to-macronutrient ratio in the vertical nutrient supply and surface lateral transport …

Lipid Biomarkers Of Bering And Chukchi Sea Euphausiids And Their Application To Diet History, Rachel L. Pleuthner

OES Theses and Dissertations

In the eastern Bering Sea, Thysanoessa raschii are the most abundant krill species and a keystone trophic member that serve as both an important grazer and link to upper level consumers. In this system krill experience large annual variation in food resources, especially during ice advance and retreat; multiple lipid classes are used to temper the effects of those fluctuations, as well as to fuel reproduction and growth. Two shipboard feeding experiments that occurred during late spring and early summer of 2010, respectively, monitored the lipid retention in adult T. raschii and examined the fluctuation of specific lipid biomarkers under …

Coupling Metaproteomics With Taxonomy To Determine Responses Of Bacterioplankton To Organic Perturbations In The Western Arctic Ocean, Molly P. Mikan

OES Theses and Dissertations

Understanding how the functionality of marine microbial communities change over time and space, and which taxonomic groups dominate distinct metabolic pathways, are essential to understanding the ecology of these microbiomes and the factors contributing to their regulation of elemental cycles in the oceans. The primary goal of this dissertation was to investigate the community metabolic and taxonomic responses and the degradation potential of two compositionally distinct marine microbiomes within the shallow shelf ecosystem of the Chukchi Sea after rapid fluctuations in algal organic matter availability. Novel bioinformatics tools were collaboratively developed and used together with community proteomics (metaproteomics) to characterize …

Compositions And Structures Of Particulate And Colloidal Organic Matter In Aquatic Environment By Advanced Analytical Techniques, Yong Ran, Dainan Zhang, Shujie Hu, Yu Yang, Jingdong Mao

Chemistry & Biochemistry Faculty Publications

Dissolved, colloidal and particulate organic matter (DOM, COM and POM) is important in the global carbon cycle and knowledge of their sources and structures can be critical to understanding their roles in biogeochemical cycles. This study explored the sources and chemical structures of COM and POM samples from the Pearl River Basin, China by elemental, chlorophyll a (Chl a), radiocarbon and stable carbon isotopic analyses, NMR techniques, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. The chemical and nano-sclae structures of two ultrafiltered dissolved organic matter (UDOM) samples from surface seawater of the Pacific and Atlantic Ocean …

Assessing Phytoplankton Nutritional Status And Potential Impact Of Wet Deposition In Seasonally Oligotrophic Waters Of The Mid-Atlantic Bight, P. N. Sedwick, P. W. Bernhardt, M. R. Mulholland, R. G. Najjar, L. M. Blumen, B. M. Sohst, C. Sookhdeo, Brittany Widner

OES Faculty Publications

To assess phytoplankton nutritional status in seasonally oligotrophic waters of the southern Mid-Atlantic Bight, and the potential for rain to stimulate primary production in this region during summer, shipboard bioassay experiments were performed using natural seawater and phytoplankton collected north and south of the Gulf Stream. Bioassay treatments comprised iron, nitrate, iron + nitrate, iron + nitrate + phosphate, and rainwater. Phytoplankton growth was inferred from changes in chlorophyll a, inorganic nitrogen, and carbon-13 uptake, relative to unamended control treatments. Results indicated the greatest growth stimulation by iron + nitrate + phosphate, intermediate growth stimulation by rainwater, modest growth …

Biogeochemical Cycling Of Selenium In The Arctic Ocean, Kyle M. Mcquiggan

OES Theses and Dissertations

Changes in the global climate may have a pronounced effect on the biogeochemical cycling of trace elements like selenium (Se) in the Arctic Ocean. This study described the first quantitative examination of the biogeochemical cycle of selenium in the Amerasian Basin, providing the baseline from which future changes can be identified. Aerosol, dissolved and particulate water samples were collected for Se determinations during the U.S. GEOTRACES GN01 Arctic expedition that sampled the two parts of the Amerasian Basin in 2015: The Makarov Basin on the way to the North Pole and the Canada Basin on the return trip to Dutch …

Carbon Budget Of Tidal Wetlands, Estuaries, And Shelf Waters Of Eastern North America, R. G. Najjar, M. Herrmann, R. Alexander, D. J. Burdige, D. Butman, W.-J. Cai, E. A. Canuel, R. F. Chen, M. A. M. Friedrichs, M. R. Mulholland

OES Faculty Publications

Carbon cycling in the coastal zone affects global carbon budgets and is critical for understanding the urgent issues of hypoxia, acidification, and tidal wetland loss. However, there are no regional carbon budgets spanning the three main ecosystems in coastal waters: tidal wetlands, estuaries, and shelf waters. Here we construct such a budget for eastern North America using historical data, empirical models, remote sensing algorithms, and process‐based models. Considering the net fluxes of total carbon at the domain boundaries, 59 ± 12% (± 2 standard errors) of the carbon entering is from rivers and 41 ± 12% is from the atmosphere, …

Composition Of Dissolved Organic Matter In Pore Waters Of Anoxic Marine Sediments Analyzed By 1h Nuclear Magnetic Resonance Spectroscopy, Christina A. Fox, Hussain A. Abdulla, David J. Burdige, James P. Lewicki, Tomoko Komada

OES Faculty Publications

Marine sediments are globally significant sources of dissolved organic matter (DOM) to the oceans, but the biogeochemical role of pore-water DOM in the benthic and marine carbon cycles remains unclear due to a lack of understanding about the molecular composition of DOM. To help fill this knowledge gap, we used 1H nuclear magnetic resonance (NMR) spectroscopy to examine depth variability in the composition of pore-water DOM in anoxic sediments of Santa Barbara Basin, California Borderland. Proton detected spectra were acquired on whole samples without pre-concentration to avoid preclusion of any DOM components from the analytical window. Broad unresolved resonance (operationally …

Interpreting Mosaics Of Ocean Biogeochemistry, Andrea Fassbender, A. Bourbonnais, Sophie Clayton, P. Gaube, M. Ormand, P.J.S. Franks, M. A. Altabet, D.J. Mcgillicuddy Jr.

OES Faculty Publications

Advances in technology and modeling capabilities are driving a surge in progress in our understanding of how ocean ecosystems mix and mingle on medium to small scales.

Multiple Metabolisms Constrain The Anaerobic Nitrite Budget In The Eastern Tropical South Pacific, Andrew R. Babbin, Brian D. Peters, Calvin W. Mordy, Brittany Widner, Karen L. Casciotti, Bess B. Ward

OES Faculty Publications

The Eastern Tropical South Pacific is one of the three major oxygen deficient zones (ODZs) in the global ocean and is responsible for approximately one third of marine water column nitrogen loss. It is the best studied of the ODZs and, like the others, features a broad nitrite maximum across the low oxygen layer. How the microbial processes that produce and consume nitrite in anoxic waters interact to sustain this feature is unknown. Here we used ¹⁵N-tracer experiments to disentangle five of the biologically mediated processes that control the nitrite pool, including a high-resolution profile of nitrogen loss rates. …

Using Rare Earth Elements To Constrain Particulate Organic Carbon Flux In The East China Sea, Chin-Chang Hung, Ya-Feng Chen, Shih-Chieh Hsu, Kui Wang, Jianfang Chen, David J. Burdige

OES Faculty Publications

Fluxes of particulate organic carbon (POC) in the East China Sea (ECS) have been reported to decrease from the inner continental shelf towards the outer continental shelf. Recent research has shown that POC fluxes in the ECS may be overestimated due to active sediment resuspension. To better characterize the effect of sediment resuspension on particle fluxes in the ECS, rare earth elements (REEs) and organic carbon (OC) were used in separate two-member mixing models to evaluate trap-collected POC fluxes. The ratio of resuspended particles from sediments to total trap-collected particles in the ECS ranged from 82-94% using the OC mixing …

Coastal Ocean And Shelf-Sea Biogeochemical Cycling Of Trace Elements And Isotopes: Lessons Learned From Geotraces, Matthew A. Charette, Phoebe J. Lam, Maeve C. Lohan, Eun Young Kwon, Vanessa Hatje, Catherine Jeandel, Alan M. Shiller, Gregory A. Cutter, Alex Thomas, Philip W. Boyd

OES Faculty Publications

Continental shelves and shelf seas play a central role in the global carbon cycle. However, their importance with respect to trace element and isotope (TEI) inputs to ocean basins is less well understood. Here, we present major findings on shelf TEI biogeochemistry from the GEOTRACES programme as well as a proof of concept for a new method to estimate shelf TEI fluxes. The case studies focus on advances in our understanding of TEI cycling in the Arctic, transformations within a major river estuary (Amazon), shelf sediment micronutrient fluxes and basin-scale estimates of submarine groundwater discharge. The proposed shelf flux tracer …

The Marine Cyanate Cycle, Brittany Widner

OES Theses and Dissertations

Cyanate (OCN-) is a reduced nitrogen compound with the potential to serve as a nitrogen and carbon source for marine microbes. Evidence from genomes and culture studies indicated that several marine cyanobacterial groups, including representatives of the globally important genera Synechococcus and Prochlorococcus, might be capable of cyanate assimilation. However, prior to this study, the distribution, bioavailability, and production pathways of cyanate were unknown in natural systems due to the absence of a sensitive cyanate assay; and the ability of organisms to assimilate cyanate on relevant timescales was unknown because we lacked a suitable tracer for measuring uptake. I developed …

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 …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

A Survey Of Aquatic Organisms For The Cyanotoxin Beta-Methylamino-L-Alanine (Bmaa), Ian M. Sammler

OES Theses and Dissertations

Cyanobacteria blooms are increasing globally as a result of eutrophication. Many cyanobacteria are potentially harmful, not only because of the oxygen depleted zones created when they decay, but also because of the toxins they produce. β- Methylamino-L-alanine (BMAA), reportedly produced by many species of cyanobacteria, is a non-proteinogenic amino acid that has been linked to the development of neurodegenerative diseases (amyotrophic lateral sclerosis (ALS) and Alzheimer's) in humans. This study presents results from an assessment of BMAA in cyanobacteria and their grazers from the lower Chesapeake Bay and Lake Erie regions. BMAA was analyzed in samples prepared with the EZ:Faast™ …

Divergent Responses Of Atlantic Coastal And Oceanic Synechococcus To Iron Limitation, Katherine R. M. Mackey, Anton F. Post, Matthew R. Mcilvin, Gregory A. Cutter, Seth G. John, Mak A. Saito

OES Faculty Publications

Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet used few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multitiered, hierarchical cascade …

The Relative Importance Of Methanogenesis In The Decomposition Of Organic Matter In Northern Peatlands, J. Elizabeth Corbett, Malak M. Tfaily, David J. Burdige, Paul H. Glaser, Jeffrey P. Chanton

OES Faculty Publications

Using an isotope-mass balance approach and assuming the equimolar production of CO₂ and CH₄ from methanogenesis (e.g., anaerobic decomposition of cellulose), we calculate that the proportion of total CO₂ production from methanogenesis varies from 37 to 83% across a variety of northern peatlands. In a relative sense, methanogenesis was a more important pathway for decomposition in bogs (80 ± 13% of CO₂ production) than in fens (64 ± 5.7% of CO₂ production), but because fens contain more labile substrates they may support higher CH4 production overall. The concentration of CO₂ produced from methanogenesis (CO …

Iron Supply And Demand In Antarctic Shelf Ecosystem, D. J. Mcgillicuddy Jr., Peter N. Sedwick, Michael S. Dinniman, K. R. Arrigo, T. S. Bibby, B. J. W. Greenan, Eileen E. Hofmann, John M. Klinck, W. O. Smith Jr., S. L. Mack, C. M. Marsay, B. M. Sohst, G. L. Van Dijken

OES Faculty Publications

The Ross Sea sustains a rich ecosystem and is the most productive sector of the Southern Ocean. Most of this production occurs within a polynya during the November-February period, when the availability of dissolved iron (dFe) is thought to exert the major control on phytoplankton growth. Here we combine new data on the distribution of dFe, high-resolution model simulations of ice melt and regional circulation, and satellite-based estimates of primary production to quantify iron supply and demand over the Ross Sea continental shelf. Our analysis suggests that the largest sources of dFe to the euphotic zone are wintertime mixing and …

Heterotrophic And Autotrophic Contribution To Dinitrogen Fixation In The Gulf Of Aqaba, Eyal Rahav, Barak Herut, Margaret R. Mulholland, Natalia Belkin, Hila Elifantz, Ilana Berman-Frank

OES Faculty Publications

We evaluated the seasonal contribution of heterotrophic and autotrophic diazotrophy to the total dinitrogen (N₂) fixation in the photic zone of a pelagic station in the northern Gulf of Aqaba, Red Sea. N₂ fixation rates were highest during a Trichodesmium bloom in winter (0.7 nmol N l^-1 d^-1), decreased 7-fold 1 wk later throughout the upper 200 m (~0.1 nmol N l^-1) d^-1), and were significantly coupled with both primary and bacterial productivity. N₂ fixation rates were generally higher in the upper 200 m (~0.4 nmol N l^{-1 …}

Dissolved Oxygen Dynamics During A Phytoplankton Bloom In The Ross Sea Polyna, Bastien Y. Queste, Karen J. Heywood, Walker O. Smith Jr., Daniel E. Kaufman, Timothy D. Jickells, Michael S. Dinniman

CCPO Publications

The Ross Sea polynya is one of the most productive regions in the Southern Ocean. However, limited access and high spatio-temporal variability of physical and biological processes limit the use of conventional oceanographic methods to measure early season primary productivity. High-resolution observations from two Seagliders provide insights into the timing of a bloom in the southern Ross Sea polynya in December 2010. Changes in chlorophyll and oxygen concentrations are used to assess bloom dynamics. Using a ratio of dissolved oxygen to carbon, net primary production is estimated over the duration of the bloom showing a sensitive balance between net autotrophy …

Chesapeake Bay Nitrogen Fluxes Derived From A Land-Estuarine Ocean Biogeochemical Modeling System: Model Description, Evaluation, And Nitrogen Bonds, Yang Feng, Marjorie A.M. Friedrichs, John Wilkin, Hanqin Tian, Qichun Yang, Eileen E. Hofmann

CCPO Publications

The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001-2005 was conducted to quantify the Chesapeake Bay nitrogen …

Spectroscopic Characterization Of Oceanic Dissolved Organic Matter Isolated By Reverse Osmosis Coupled With Electrodialysis, John R. Helms, Jingdong Mao, Hongmei Chen, E. Michael Perdue, Nelson W. Green, Patrick G. Hatcher, Kenneth Mopper, Aron Stubbins

Chemistry & Biochemistry Faculty Publications

Oceanic dissolved organic matter (DOM) is one of the largest pools of reduced carbon on Earth, yet DOM remains poorly chemically characterized. Studies to determine the chemical nature of oceanic DOM have been impeded by the lack of efficient and non-fractioning methods to recover oceanic DOM. Here, a DOM fraction (~40 to 86% recovery) was isolated using reverse osmosis/electrodialysis (RO/ED) and analyzed by solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy. Samples were obtained from biogeochemically distinct environments: photobleached surface gyre, productive coastal upwelling zone, oxygen minimum, North Atlantic Deep Water, and North Pacific Deep Water. A ubiquitous ‘background’ refractory …

Long-Term Litter Decomposition Controlled By Manganese Redox Cycling, Marco Keiluweit, Peter Nico, Mark E. Harmon, Jingdong Mao, Jennifer Pett-Ridge, Markus Kleber

Chemistry & Biochemistry Faculty Publications

Litter decomposition is a keystone ecosystem process impacting nutrient cycling and productivity, soil properties, and the terrestrial carbon (C) balance, but the factors regulating decomposition rate are still poorly understood. Traditional models assume that the rate is controlled by litter quality, relying on parameters such as lignin content as predictors. However, a strong correlation has been observed between the manganese (Mn) content of litter and decomposition rates across a variety of forest ecosystems. Here, we show that long-term litter decomposition in forest ecosystems is tightly coupled to Mn redox cycling. Over 7 years of litter decomposition, microbial transformation of litter …

Organic Copper Binding Ligands And Thiol Compounds Produced By Bacteria And In The Elizabeth River, Virginia, Christina Louise Dryden

OES Theses and Dissertations

This dissertation presents work focusing on copper and organic copper binding ligands in laboratory cultures and the Elizabeth River, Virginia. Laboratory cultures of the marine bacterium Vibrio parahaemolyticus were used to demonstrate the influence of elevated copper concentrations on copper-complexing ligand and thiol production. Copper-complexing ligands similar in binding strength to the strongest natural ligands were detected in V. parahaemolyticus cultures (log K′_CuL = 11.8–13.2). A strong correlation (r² = 0.973) was found between total thiol and copper-complexing ligand concentrations at all copper concentrations examined.

A yearlong seasonal study was undertaken in a heavily polluted estuary to ascertain …

A Comprehensive Evaluation Of C25 Highly Branched Isoprenoid Alkenes Of Marine Diatoms As Proxies For Sea Ice Extent In The Arctic Ocean, Tetiana Muniak

OES Theses and Dissertations

Sea Ice extent is one of the major factors regulating carbon cycling and ecosystem function in the modern Arctic Ocean. It is an essential component of climate models and is crucial for the evaluation of various oceanographic processes that influence a particular region. Yet it is also one of the most difficult attributes of the ocean with respect to our ability for its accurate reconstruction from paleo records. The lack of the detailed records prior to satellite information has encouraged the development of new proxy records for the reconstruction of past

sea ice conditions. In recent years, a new monounsaturated …

Implications Of Climate Change For Cyanobacteria Over The Western Florida Shelf In The Gulf Of Mexico, Ivy Mara Ozmon

OES Theses and Dissertations

Concentrations of atmospheric CO₂ are expected to double by year 2100 as a result of anthropogenic activities. Under elevated CO₂ conditions, cyanobacteria may reallocate energy from active accumulation and transport of dissolved inorganic carbon (C) required for photosynthesis to other growth processes. Stimulation of cyanobacterial production on the Western Florida Shelf in the Gulf of Mexico (GOM) could lead to improved nutritional status for the toxic, mixotrophic dinoflagellate Karenia brevis that utilizes newly fixed N₂ from co-occurring diazotrophic cyanobacteria and consumes unicellular cyanobacteria via grazing for growth. Culture studies performed by other researchers on the climate induced …

Geotraces: Changing The Way We Explore Ocean Chemistry, Robert F. Anderson, Edward Mawji, Gregory A. Cutter, Christopher I. Measures, Catherine Jeandel

OES Faculty Publications

GEOTRACES is an international study of the marine biogeochemical cycles of trace elements and their isotopes (TEIs), designed by marine geochemists to accelerate TEI research under a global program. Combining ocean sections, process studies, data synthesis, and modeling, GEOTRACES will identify and quantify the processes that supply TEIs at ocean boundaries as well as the physical and biological processes that redistribute TEIs within and between ocean basins. Constraining processes that remove TEIs from the ocean will enable complete mass budgets to be generated. Anticipated beneficiaries of GEOTRACES products include scientists studying the sustained health of marine ecosystems and their sensitivity …

Molecular Characterization And Photochemical Transformation Of Dissolved Organic Matter From Land To Ocean, Hongmei Chen

Chemistry & Biochemistry Theses & Dissertations

Molecular characterization and photochemical transformation of dissolved organic matter (DOM) in both rivers and the ocean is the main research focus of this dissertation. Chemical characterization of DOM is hampered by the limited application of advanced techniques to desalt, concentrate, isolate and then molecularly characterize DOM. An affordable, commercially available mini-electrodialysis (mini-ED) system has been evaluated and recommended for the efficient desalting of small volume samples of seawater prior to analysis by electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR-MS).

A high-recovery technique of DOM isolation – reverse osmosis coupled with electrodialysis (RO/ED) – was used to isolate …

Spectroscopic Characterization Of Dissolved Organic Matter: Insights Into The Linkage Between Sources And Chemical Composition, Xiaoyan Cao

Chemistry & Biochemistry Theses & Dissertations

This dissertation investigated the chemical structure of DOM by advanced solid-state nuclear magnetic resonance (NMR) spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) techniques, as well as isotopic measurements and UV-visible spectroscopy, to shed light on the linkages between DOM sources and DOM composition. Unique and extensive sets of DOM samples studied here were isolated from various aquatic systems, covering end-member environments in which DOM is considered either microbially derived or terrestrially derived, and areas in which DOM has characteristics intermediate between the two end members. Important insights into specific site-related questions were also gained such as …