Spatial and seasonal patterns in sediment nitrogen remineralization and ammonium concentrations in San Francisco Bay, California

Nitrogen remineralization and extractable ammonium concentrations were measured in sediments from several locations in North and South San Francisco bays. In South Bay. remineralization rates decreased with depth in sediment and were highest in the spring following the seasonal phytoplankton bloom. At the channel stations, peak remineralization lagged peak water-column phytoplankton biomass (as measured by chlorophyll a) by a month. Remineralization rates were generally higher in South Bay than North Bay. The lower remineralization rates in North Bay may be a result of anomalously low phytoplankton production and thus reduced deposition to the sediments, as well as low riverine organic inputs to the upper estuary in recent years. Remineralization rates were positively correlated to carbon and nitrogen content of the sediments. In general, ammonium profiles in South Bay sediments showed no increase in deeper (4-8 cm) sediments. In North Bay, ammonium concentrations were greatest at stations with highest remineralization rates, and, in contrast to South Bay, extractable ammonium increased in deeper sediment. Differences in ammonium pools between North Bay and South Bay may be a result of increased irrigation by deep-dwelling macrofauna, which are more abundant in South Bay.Journal Articl

Production, respiration and net ecosystem metabolism in U.S. estuaries

Primary production, respiration, and net ecosystem metabolism (NEM) are useful indicators of ecosystem level trophic conditions within estuaries. In this study, dissolved oxygen data collected every half hour between January 1996 to December 1998 by the National Estuarine Research Reserve System Wide Monitoring Program were used to calculate primary production, respiration, and net ecosystem metabolism. Data from two sites at each of 14 Reserves were analyzed. On average, three quarters of the data available could be used to calculate metabolic rates. Data from two of the Reserves were used to evaluate the assumption of homogeneity of water masses moving past the oxygen sensor. Temperature was the single most important factor controlling metabolic rates at individual sites, although salinity was also important at about half the sites. On an annual basis, respiration exceeded gross primary production demonstrating that all but 4 of the 28 sites were heterotrophic.Journal ArticleFinal article publishe

Factors controlling net ecosystem metabolism in U.S. estuaries

High frequency dissolved oxygen data were analyzed to calculate primary production, respiration and net ecosystem metabolism (NEM) from 42 sites within 22 National Estuarine Research Reserves (NERR), 1995–2000. NERR sites are characterized by a variety of dominant plant communities including phytoplankton, salt marsh, seagrass, macroalgae, freshwater macrophyte, and mangrove, and are representative of the coastal bioregions of the United States. As expected from the wide diversity of sites, metabolic rates were temporally and spatially variable with the highest production and respiration occurring during the summer in Southeastern estuaries. Sites within different regions exhibited consistent seasonal trends in production, respiration, and NEM. Temperature was the most important environmental factor explaining within-site variation in metabolic rates; nutrient concentrations were the second most important factor. All but three of the 42 sites were heterotrophic (respiration was greater than production) on an annual basis. Habitat adjacent to the monitoring site, estuarine area, and salinity explained 58% of the variation in NEM. Open water sites or sites adjacent to mangroves or in marsh creeks were heterotrophic, while sites in or adjacent to submerged aquatic vegetation (eelgrass or macroalgal beds) were either autotrophic or near balance. Estuarine area was also a significant factor explaining variability in NEM; larger systems were closer to balance than smaller systems that trended toward heterotrophy. Freshwater sites were more heterotrophic than saline sites. Nutrient loading explained 68% of the variation in NEM among some of the sites. When these estimates were compared to the literature, metabolic rates from the NERR sites were much larger, often two to five times greater than rates from other estuarine and coastal systems. One explanation is that these small, generally shallow sites located near shore may have greater allochthonous organic inputs as well as significant benthic primary production than the large, deeper systems represented by the literature.Journal ArticleFinal article publishe

Progress report submitted to the U.S. Environmental Protection Agency, Region 4: Atmospheric deposition of mercury and trace metals to the Pensacola Bay watershed

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Nitrogen cycling in sediments with estuarine populations of Potamogeton perfoliatus and Zostera marina

Rates of nitrogen transformations and concentrations of extractable NH₄⁺ and NO₃⁻ (plus NO₂⁻) were measured in estuarine sediments vegetated with the submersed macrophytes Potamogeton perfoliatus and Zostera marina, and in adjacent bare sediments, 3 or 4 times during the growing season. Nitrification and denitrification potentials were measured in substrate-amended sediment slurries at 5 depth intervals to provide a measure of bacterial activity. In general, rates were significantly higher in vegetated compared to bare sediments. It appears that both plant species affected nitrogen transformations through several similar mechanisms, while the microbial community, in turn, regulated nitrogen available for plant growth. In P. perfoliatus beds,ammonification and potential nitrification rates were correlated. Both exhibited summer maxima coinciding with peak plant biomass and productivity. Although vertically integrated (0-12 cm) ammonification rates were about twice as high in vegetated than in bare sediments, NH₄⁺ pools were significantly lower, probably due to high plant nitrogen demand. In contrast, denitrification,rates were highest in spring when NO₃⁻ concentrations peaked, and were significantly correlated to nitrification rates in both spring and falL Denitrification was only about 20% of total NO₃⁻ reduction, suggesting that NH₄⁺ production from NO₃⁻ may be important in conserving nitrogen within the grassbed. In sediments with Z. marina, rates of ammonification, and nitrification and denitrification potentials each exhibited a distinct seasonal cycle, indicating that rates were not as tightly coupled as in P. perfoliatus beds. High ammonification rates exceeded plant demand leading to NH₄⁺ accumulation. Potential nitrification rates were highest in vegetated sediments during falL Denitrification rates, which were also greater in vegetated than in bare sediments, were highest in spring when NO₃⁻ concentrations were high. Potential denitrification rates comprised about 10 % of total NO₃⁻ reduction, indicating that NO₃⁻ reduction to NH₄⁺ dominated. The microbial communities responsible for key nitrogen transformations in the sediments were enhanced by both P. perfoliatus and Z. marina: ammonification by inputs of organic nitrogen; nitrification by release of O₂ by plant roots; and denitrification by production of NO₃⁻.final article publishedJournal Articl

The effects of human activities and extreme meteorological events on sediment nitrogen dynamics in an urban estuary, Escambia Bay, Florida, USA

This study examined how sediment-sorbed PCBs and several large storms affected sediment nutrient dynamics based on potential nitrification rates and benthic flux measurements. PCBs were hypothesized to negatively affect potential nitrification rates due to the sensitivity of nitrifying bacteria. Sediment disturbance caused by the succession of storms, which can enhance nutrient inputs and phytoplankton production, was hypothesized to enhance both potential nitrification rates and benthic flux measurements as a result of higher nutrient and organic matter concentrations. Potential nitrification rates, benthic fluxes (NO₃⁻ + NO₂⁻, NH₄⁺, and DIP), sediment PCB content, water content, organic content, salinity, bottom water dissolved oxygen, and sediment chlorophyll were measured at 13 different sites in Escambia Bay during the summer of 2005. Potential nitrification rates were highest at deep, organic-rich sites. Total PCB content did not have a direct effect on potential nitrification rates. An analysis of recent changes in benthic processes in relation to extreme meteorological events was performed by comparing the 2005 results with data from 2000, 2003, and 2004. Storm effects on sediment biogeochemistry were mixed with sediment nitrogen dynamics enhanced at some sites but not others. In addition, SOC and NH₄⁺ fluxes increased in deeper channel sites after Hurricanes Ivan and Dennis, which could be attributed to the deposition of phytoplankton blooms. Sediment nutrient dynamics in Escambia Bay appear to be resilient to these extreme meteorological events since there were no significant effects on sediment processes in the Bay as a whole.Journal Articl

Influence of the submersed plant, Potamogeton perfoliatus, on nitrogen cycling in estuarine sediments

Effects of Potamogeton perfoliatus on N transformations in sediments were examined with ¹⁵N isotope techniques. Rates of ammonification, nitrification, denitrification, and plant uptake of nitrogen were measured in intact sediments with and without P. perfoliatus twice during the growing season (May and July). Sediments were injected with ¹⁵NH₄+ and the appearance of ¹⁵N over time in overlying water, pore water, and plant tissues was measured. Most of the ¹⁵N added was recovered. Rates of bacterial NH₄+ utilization (including NH₄+ assimilation and nitrification) were similar to gross ammonification rates in vegetated and bare sediments, although rates were highly variable. Root (and rhizome) uptake represented -90% of total N uptake by the plants in May, but only 20% in July. Tissue-specific (root or shoot) uptake rates were similar in May and July, although shoot (leaves plus stems) biomass increased faster than root biomass from May to July. Between 70 and 75% of the N taken up by roots was translocated to shoots. Denitrification rates, calculated from the appearance of ¹⁵N-N₂ in the overlying and pore water, were significantly greater in vegetated than in bare sediments in July. Nitrification and denitrification were closely coupled, and denitrification in the root zone represented - 16% of total denitrification. In vegetated sediments, - 75% of the ¹⁵N lost from sediments was denitrified, and 25% was taken up by the plants. P. perfoliatus had a significant influence on sediment N cycling by direct uptake of NH₄ and NO₃ and by indirect mechanisms leading to enhanced nitrification and denitrification.Journal Articl

Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA: Implications for net ecosystem metabolism

We present results of an intensive sampling program designed to measure weekly changes in ecosystem respiration (oxygen consumption in the water column and sediments) around the 1996 spring bloom in South San Francisco Bay, California, USA. Measurements were made at a shallow site (2 m, where mean photic depth was 60% of the water colunln height) and a deep site (15 m, mean photic depth was only 20% of the water column). We also estimated phytoplankton primary producbon weekly at both sites to develop estimates of net oxygen flux as the sum of pelagic production (PP), pelagic respiration (PR) and benthic respiration (BR). Over the 14 wk period from February 5 to May 14, PP ranged from 2 to 210, PR from 9 to 289, and BR from 0.1 to 48 mmol O₂ m⁻² d⁻¹, illustrating large variability of estuarine oxygen fluxes at the weekly time scale. Pelagic production exceeded total respiration at the shallow site, but not at the deep site, demonstrating that the shallow domains are net autotrophic but the deep domains are net heterotrophic, even during the period of the spring bloom. If we take into account the potential primary production by benthic microalgae, the estuary as a whole is net autotrophic during spring, net heterotrophic during the nonbloom seasons, and has a balanced net metabolism over a full annual period. The seasonal shift from net autotrophy to heterotrophy during the transition from spring to summer was accompanied by a large shift from dominance by pelagic respiration to dominance by benthic respiration. This suggests that changes in net ecosystem metabolism can reflect changes in the pathways of energy flow in shallow coastal ecosystems.Journal ArticleFinal article publishe

Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments

Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm⁻³ d⁻¹) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm⁻³ d⁻¹ and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm⁻³ d⁻¹. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.Journal ArticleFinal article publishe

Living oysters and their shells as sites of nitrification and denitrification

Oysters provide a critical habitat, are a food resource for higher trophic levels and support important commercial fisheries throughout the world. Oyster reefs can improve water quality by removing phytoplankton. While sediment denitrification may be enhanced adjacent to oyster reefs, little is known about nitrification and denitrification associated with living oysters and their shells. We measured nitrification and denitrification in living oysters (Crassostrea virginica and Crassostrea gigas) and empty oyster shells. Nitrification was similar between live oysters and empty oyster shells, however, denitrification was enhanced significantly on living oysters compared to shells. This is the first demonstration of nitrification and denitrification associated with living oysters and their shells. Our data suggest that loss of historic oyster reefs has likely affected the resilience of estuaries to eutrophication. The additional benefit of oyster mediated denitrification should be considered in restoration of oyster reefs as a tool for managing eutrophication.Journal Articl