Bess B. Ward

Impacts of Atmospheric Anthropogenic Nitrogen on the Open Ocean

Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the oceans external (nonrecycled) nitrogen supply and up to ∼3% of the annual new marine biological production, ∼0.3 petagram of carbon per year. This input could account for the production of up to ∼1.6 teragrams of nitrous oxide (N2O) per year. Although ∼10% of the oceans drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions. The effects of increasing atmospheric nitrogen deposition are expected to continue to grow in the future.

Nitrogen Uptake, Dissolved Organic Nitrogen Release, and New Production

In oceanic, coastal, and estuarine environments, an average of 25 to 41 percent of the dissolved inorganic nitrogen (NH4 + and NO3 –) taken up by phytoplankton is released as dissolved organic nitrogen (DON). Release rates for DON in oceanic systems range from 4 to 26 nanogram-atoms of nitrogen per liter per hour. Failure to account for the production of DON during nitrogen-15 uptake experiments results in an underestimate of gross nitrogen uptake rates and thus an underestimate of new and regenerated production. In these studies, traditional nitrogen-15 techniques were found to underestimate new and regenerated production by up to 74 and 50 percent, respectively. Total DON turnover times, estimated from DON release resulting from both NH4 + and NO3 – uptake, were 10 � 1, 18 � 14, and 4 days for oceanic, coastal, and estuarine sites, respectively.

Nitrogen cycling in the ocean: new perspectives on processes and paradigms.

The nitrogen (N) cycle is composed of multiple transformations of nitrogenous compounds, catalyzed primarily by microbes. The N cycle controls the availability of nitrogenous nutrients and biological productivity in marine systems ([84][1]) and thus is linked to the fixation of atmospheric carbon

Denitrification as the dominant nitrogen loss process in the Arabian Sea

Primary production in over half of the world’s oceans is limited by fixed nitrogen availability. The main loss term from the fixed nitrogen inventory is the production of dinitrogen gas (N2) by heterotrophic denitrification or the more recently discovered autotrophic process, anaerobic ammonia oxidation (anammox). Oceanic oxygen minimum zones (OMZ) are responsible for about 35% of oceanic N2 production and up to half of that occurs in the Arabian Sea. Although denitrification was long thought to be the only loss term, it has recently been argued that anammox alone is responsible for fixed nitrogen loss in the OMZs. Here we measure denitrification and anammox rates and quantify the abundance of denitrifying and anammox bacteria in the OMZ regions of the Eastern Tropical South Pacific and the Arabian Sea. We find that denitrification rather than anammox dominates the N2 loss term in the Arabian Sea, the largest and most intense OMZ in the world ocean. In seven of eight experiments in the Arabian Sea denitrification is responsible for 87–99% of the total N2 production. The dominance of denitrification is reproducible using two independent isotope incubation methods. In contrast, anammox is dominant in the Eastern Tropical South Pacific OMZ, as detected using one of the isotope incubation methods, as previously reported. The abundance of denitrifying bacteria always exceeded that of anammox bacteria by up to 7- and 19-fold in the Eastern Tropical South Pacific and Arabian Sea, respectively. Geographic and temporal variability in carbon supply may be responsible for the different contributions of denitrification and anammox in these two OMZs. The large contribution of denitrification to N2 loss in the Arabian Sea indicates the global significance of denitrification to the oceanic nitrogen budget.

Elucidation of Functional Groups on Gram-Positive and Gram-Negative Bacterial Surfaces Using Infrared Spectroscopy

Surface functional group chemistry of intact Gram-positive and Gram-negative bacterial cells and their isolated cell walls was examined as a function of pH, growth phase, and growth media (for intact cells only) using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Infrared spectra of aqueous model organic molecules, representatives of the common functional groups found in bacterial cell walls (i.e., hydroxyl, carboxyl, phosphoryl, and amide groups), were also examined in order to assist the interpretation of the infrared spectra of bacterial samples. The surface sensitivity of the ATR-FTIR spectroscopic technique was evaluated using diatom cells, which possess a several-nanometers-thick layer of glycoprotein on their silica shells. The ATR-FTIR spectra of bacterial surfaces exhibit carboxyl, amide, phosphate, and carbohydrate related features, and these are identical for both Gram-positive and Gram-negative cells. These results provide direct evidence to the previously held conviction that the negative charge of bacterial surfaces is derived from the deprotonation of both carboxylates and phosphates. Variation in solution pH has only a minor effect on the secondary structure of the cell wall proteins. The cell surface functional group chemistry is altered neither by the growth phase nor by the growth medium of bacteria. This study reveals the universality of the functional group chemistry of bacterial cell surfaces.

Linking Diversity and Stable Isotope Fractionation in Ammonia-Oxidizing Bacteria

The link between similarity in amino acid sequence for ammonia monooxygenase (AMO) and isotopic discrimination for ammonia oxidation ( l AMO ) was investigated in g -subdivision ammonia-oxidizing bacteria. The isotope effects for ammonia oxidation in pure cultures of the nitrifying strains Nitrosomonas marina , Nitrosomonas C-113a, Nitrosospira tenuis , Nitrosomonas europaea , and Nitrosomonas eutropha ranged from 14.2 to 38.2. The differences in isotope effects could not be readily explained by differential rates of ammonia oxidation, transport of NH 4 + , or accumulation of NH 2 OH or N 2 O among the strains. The major similarities and differences observed in l AMO are, however, paralleled by similarities and differences in amino acid sequences for the f -subunit of AMO (AmoA). Robust differences in l AMO among nitrifying bacteria may be expected to influence the stable isotopic signatures of nitrous oxide (N 2 O) produced in various environments.

Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment

ABSTRACT The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 107 copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications.

Black Sea methane geochemistry

Methane concentrations and oxidation rates were measured in the water column and sediments of the Black Sea at a central station during leg 5 of the 1988 U.S.—Turkey Black Sea Expedition. Methane concentrations were 10 nM in the upper 100 m, increased to 11 μM at 550 m, and were uniform to the bottom. Water column methane oxidation rates were measured using two independent radiotracer techniques: tracer level additions of 3H−CH4, and non-tracer level additions of 14C−CH4. The methods agree within a factor of two. Methane oxidation rates were low in the surface 100 m and increased to relatively uniform values of 0.6μM y−1 below 500 m. Sediment methane concentration and oxidation rate distributions showed that shelf and slope sediments were methane sources, while deep basin sediments were methane sinks. These measurements were used to construct a methane budget for Black Sea waters. Microbially mediated anaerobic methane oxidation is the dominant water column methane sink, followed by evasion to the atmosphere, abyssal plain sediment consumption and outflow at the Bosporus. The source of methane appears to be anoxic, high deposition rate shelf and slope sediments. The water column oxidation rate measurements suggest a short (5–20 year) residence time for methane in the Black Sea, indicating a higher geochemical activity than previously believed. The quantity of carbon participating in the Black Sea methane cycle is equivalent to about 0.5% of the primary production.

Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments.

Anaerobic ammonium oxidation (anammox) has recently been recognized as a pathway for the removal of fixed N from aquatic ecosystems. However, the quantitative significance of anammox in estuarine sediments is variable, and measurements have been limited to a few estuaries. We measured anammox and conventional denitrification activities in sediments along salinity gradients in the Chesapeake Bay and two of its sub-estuaries, the Choptank River and Patuxent River. Homogenized sediments were incubated with 14/15N amendments of