Jane M. Caffrey

Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia

Nitrification, the oxidation of NH4+ to NO2− and subsequently to NO3−, plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.

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.

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.

Nitrate Sources and Sinks in Elkhorn Slough, California: Results from Long-term Continuous in situ Nitrate Analyzers

Nitrate and water quality parameters (temperature, salinity, dissolved oxygen, turbidity, and depth) were measured continuously with in situ NO3 analyzers and water quality sondes at two sites in Elkhorn Slough in Central California. The Main Channel site near the mouth of Elkhorn Slough was sampled from February to September 2001. Azevedo Pond, a shallow tidal pond bordering agricultural fields further inland, was sampled from December 1999 to July 2001. Nitrate concentrations were recorded hourly while salinity, temperature, depth, oxygen, and turbidity were recorded every 30 min. Nitrate concentrations at the Main Channel site ranged from 5 to 65 μM. The propagation of an internal wave carrying water from ≈100 m depth up the Monterey Submarine Canyon and into the lower section of Elkhorn Slough on every rising tide was a major source of nitrate, accounting for 80–90% of the nitrogen load during the dry summer period. Nitrate concentrations in Azevedo Pond ranged from 0–20 μM during the dry summer months. Nitrate in Azevedo Pond increased to over 450 μM during a heavy winter precipitation event, and interannual variability driven by differences in precipitation was observed. At both sites, tidal cycling was the dominant forcing, often changing nitrate concentrations by 5-fold or more within a few hours. Water volume flux estimates were combined with observed nitrate concentrations to obtain nitrate fluxes. Nitrate flux calculations indicated a loss of 4 mmol NO3 m−2 d−1 for the entire Elkhorn Slough and 1 mmol NO3 m−2 d−1 at Azevedo Pond. These results suggested that the waters of Elkhorn Slough were not a major source of nitrate to Monterey Bay but actually a nitrate sink during the dry season. The limited winter data at the Main Channel site suggest that nitrate was exported from Elkhorn Slough during the wet season. Export of ammonium or dissolved organic nitrogen, which we did not monitor, may balance some or all of the NO3 flux.

Thunderstorms Increase Mercury Wet Deposition

Mercury (Hg) wet deposition, transfer from the atmosphere to Earths surface by precipitation, in the United States is highest in locations and seasons with frequent deep convective thunderstorms, but it has never been demonstrated whether the connection is causal or simple coincidence. We use rainwater samples from over 800 individual precipitation events to show that thunderstorms increase Hg concentrations by 50% relative to weak convective or stratiform events of equal precipitation depth. Radar and satellite observations reveal that strong convection reaching the upper troposphere (where high atmospheric concentrations of soluble, oxidized mercury species (Hg(II)) are known to reside) produces the highest Hg concentrations in rain. As a result, precipitation meteorology, especially thunderstorm frequency and total rainfall, explains differences in Hg deposition between study sites located in the eastern United States. Assessing the fate of atmospheric mercury thus requires bridging the scales of global transport and convective precipitation.

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.

A Historical Perspective on Eutrophication in the Pensacola Bay Estuary, FL, USA

In this chapter, we provide a brief description of the Pensacola Bay estuary, examining the available historical data for evidence of trends in eutrophication within the estuary. Common to many industrialized estuaries, Pensacola Bay has been subjected to unregulated point sources of nutrients and other contaminants, peaking during the 1950s and 1960s. Also, over the past 60 years, the region has experienced a fivefold increase in population in the watershed and a doubling of river nitrate concentrations. Today, the estuary exhibits classical symptoms of eutrophication, including extensive summer hypoxia, significant loss of sea grass habitat, and phytoplankton dynamics that respond strongly to seasonal and interannual variation in freshwater flow. Surprisingly, Pensacola Bay appears to have low nutrient concentrations, moderate productivity, and high water transparency, characteristics that appear to have persisted during a period of rapid human population growth. We find the lack of demonstrable changes in the distribution of phytoplankton biomass or distribution and severity of hypoxia during a period of increasing human population pressures enigmatic.

Designing a relational database for tracking and analysis of atmospheric deposition of mercury and trace metals in the Pensacola (Florida) Bay Watershed

The need to track and analyse the atmospheric deposition of mercury and trace metals in the Pensacola (Florida) Bay Watershed in recent years has resulted in the need for a data management system that will allow data to be efficiently stored, checked for errors, manipulated, retrieved for analysis and shared within the research community. In this paper, we describe a relational database that was developed as a data management tool to address the needs of those maintaining and using atmospheric deposition of mercury and trace metal data in the Pensacola Bay Watershed area. We present the overall design of the database and show useful queries that can be used to clean and maintain the integrity of the data, perform calculations on the data, join and union tables and retrieve the data for presentation and analysis.

Water Quality Trends Following Anomalous Phosphorus Inputs to Grand Bay, Mississippi, USA

Grand Bay National Estuarine Research Reserve (GBNERR) is a 7500 ha protected area in Jackson County, MS. In 2005, a levee breach at a fertilizer manufacturing facility released highly acidic and phosphate—rich wastewater into the reserve. A second spill occurred in September 2012 following Hurricane Isaac. We used orthophosphate (PO4 3—) concentrations to categorize the 2 events, post— events, and non—impact periods between the 2 spills. We examined spatial and temporal patterns in nutrients, chlorophyll, pH, and other parameters within and between monitoring stations. After the first event, pH at the Bangs Lake water quality station decreased to 3.7 and PO4 3— increased to over 4 mg P/l. Orthophosphate returned to background concentrations near the detection limit after approximately one year. Sampling 3 weeks after Hurricane Isaac showed PO4 3— concentrations over 1 mg P/l in Bangs Lake. Elevated PO4 3— levels were detected at other monitoring locations for 3—5 months, depending on distance from the fertilizer facility. Multiple comparison tests of trends within stations showed that both events had statistically similar PO4 3— concentrations, although the magnitudes and the time to return to baseline concentrations differed between stations. Temporal patterns of other nutrients had apparent long—term trends, particularly chlorophyll a, which showed an increase from 18—56% depending on station. This study provides a rare description of decadal water quality trends in a shallow, temperate estuary in response to discrete spill events. The results provide new information on the effects of phosphorus inputs to nitrogen—limited systems, having management implications for Gulf Coast estuaries.