Alexander E. Parker

Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary

Primary production in the Northern San Francisco Estuary (SFE) has been declining despite heavy loading of anthropogenic nutrients. The inorganic nitrogen (N) loading comes primarily from municipal wastewater treatment plant (WTP) discharge as ammonium (NH(4)). This study investigated the consequences for river and estuarine phytoplankton of the daily discharge of 15 metric tons NH(4)-N into the Sacramento River that feeds the SFE. Consistent patterns of nutrients and phytoplankton responses were observed during two 150-km transects made in spring 2009. Phytoplankton N productivity shifted from NO(3) use upstream of the WTP to productivity based entirely upon NH(4) downstream. Phytoplankton NH(4) uptake declined downstream of the WTP as NH(4) concentrations increased, suggesting NH(4) inhibition. The reduced total N uptake downstream of the WTP was accompanied by a 60% decline in primary production. These findings indicate that increased anthropogenic NH(4) may decrease estuarine primary production and increase export of NH(4) to the coastal ocean.

Life Histories, Salinity Zones, and Sublethal Contributions of Contaminants to Pelagic Fish Declines Illustrated with a Case Study of San Francisco Estuary, California, USA

Human effects on estuaries are often associated with major decreases in abundance of aquatic species. However, remediation priorities are difficult to identify when declines result from multiple stressors with interacting sublethal effects. The San Francisco Estuary offers a useful case study of the potential role of contaminants in declines of organisms because the waters of its delta chronically violate legal water quality standards; however, direct effects of contaminants on fish species are rarely observed. Lack of direct lethality in the field has prevented consensus that contaminants may be one of the major drivers of coincident but unexplained declines of fishes with differing life histories and habitats (anadromous, brackish, and freshwater). Our review of available evidence indicates that examining the effects of contaminants and other stressors on specific life stages in different seasons and salinity zones of the estuary is critical to identifying how several interacting stressors could contribute to a general syndrome of declines. Moreover, warming water temperatures of the magnitude projected by climate models increase metabolic rates of ectotherms, and can hasten elimination of some contaminants. However, for other pollutants, concurrent increases in respiratory rate or food intake result in higher doses per unit time without changes in the contaminant concentrations in the water. Food limitation and energetic costs of osmoregulating under altered salinities further limit the amount of energy available to fish; this energy must be redirected from growth and reproduction toward pollutant avoidance, enzymatic detoxification, or elimination. Because all of these processes require energy, bioenergetics methods are promising for evaluating effects of sublethal contaminants in the presence of other stressors, and for informing remediation. Predictive models that evaluate the direct and indirect effects of contaminants will be possible when data become available on energetic costs of exposure to contaminants given simultaneous exposure to non-contaminant stressors.

Microbial community composition of transiently wetted Antarctic Dry Valley soils

During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

Phytoplankton communities from San Francisco Bay Delta respond differently to oxidized and reduced nitrogen substrates—even under conditions that would otherwise suggest nitrogen sufficiency

The effect of equivalent additions of nitrogen (N, 30-40 μM-N) in different forms (ammonium, NH4+, and nitrate, NO3-) under conditions of different light exposure on phytoplankton community composition was studied in a series of four, 5-day enclosure experiments on water collected from the nutrient-rich San Francisco Bay Delta over two years. Overall, proportionately more chlorophyll a and fucoxanthin (generally indicative of diatoms) was produced per unit N taken up in enclosures enriched with NO3- and incubated at reduced (~15% of ambient) light intensity than in treatments with NO3- with high (~60% of ambient) light exposure or with NH4+ under either light condition. In contrast, proportionately more chlorophyll b (generally indicative of chlorophytes) and zeaxanthin (generally indicative of cyanobacteria) was produced in enclosures enriched with NH4+ and incubated under high light intensity than in treatments with low light or with added NO3- at either light level. Rates of maximal velocities (Vmax) of uptake of N substrates, measured using 15N tracer techniques, in all enclosures enriched with NO3- were higher than those enriched with NH4+. Directionality of trends in enclosures were similar to phytoplankton community shifts observed in transects of the Sacramento River to Suisun Bay, a region in which large changes in total N quantity and form occur. These data substantiate the growing body of experimental evidence that dichotomous microbial communities develop when enriched with the same absolute concentration of oxidized vs. reduced N forms, even when sufficient N nutrient was available to the community prior to the N inoculations.

Differential Supply of Autochthonous Organic Carbon and Nitrogen to the Microbial Loop in the Delaware Estuary

Using stable isotope tracer techniques in 4-h bottle incubations, the importance of organic matter transfer from phytoplankton to heterotrophic bacteria (bacteria) has been re-evaluated in the Delaware Estuary, considering carbon (C) and nitrogen (N) cycles separately. The hypothesis is that the transfer of C and N from phytoplankton to bacteria varies both temporally and spatially along estuarine gradients in response to variation in factors such as terrestrial organic C supply, inorganic N speciation and concentrations, and extracellular release of dissolved organic matter by phytoplankton. The percentage of autochthonous dissolved organic C being assimilated by bacteria varied between 3% and 10% of primary production and was not related to the rate of primary production. The transfer of N was considerably more variable when compared to C transfer, averaging ca. 20% of phytoplankton N assimilation; individual experiments yielded rates as high as 50%. Unlike C, autochthonous dissolved organic N transfer appears to vary with the magnitude of primary production, and its assimilation by bacteria accounted for 0–56% of the total measured bacterial N uptake. The results highlight the importance of separate consideration of C and N elemental cycles in evaluating sources of organic matter to the estuarine microbial loop.

Reevaluating the Generality of an Empirical Model for Light-Limited Primary Production in the San Francisco Estuary

Depth-integrated primary production (ΣP, in grams of carbon per square meter per day) was measured using 14C in the northern San Francisco Estuary (SFE) from March through August of 2006 and 2007. Determinations of ΣP were then used to calibrate a published light-utilization model that relates ΣP to a composite parameter of chlorophyll, solar irradiance, and photic zone depth. The resultant calibration coefficient, Ψ, varied by a factor of nearly two between 2006 and 2007 and was lower than determined in previous calibrations for the estuary. The now chronically low chlorophyll concentrations in the SFE have resulted in lower predictive power of the light-utilization model. The variation in Ψ was likely the result of interannual variation in phytoplankton assimilation number. These results suggest that using a single Ψ may yield large errors in estimated estuarine production when applied overbroad spatial and temporal scales. Given the food-limited condition of the SFE, it appears that direct measurements of primary production are necessary for accurately characterizing the base of the estuarine food web.

Ecosystem-Scale Rates of Primary Production Within Wetland Habitats of the Northern San Francisco Estuary

Salt marsh restoration is hypothesized to provide shoreline stabilization, increased fish habitat, and organic carbon subsidies for estuarine food webs. Organic carbon comes from diverse primary producers that differ in carbon fixation rates and areal extent within wetland systems. This study was designed to obtain some of the first estimates of the relative contribution of different primary producers to total organic carbon production within open water and tidally flooded wetlands of the northern San Francisco Estuary (SFE). Carbon fixation rates of phytoplankton, microphytobenthos, and low marsh emergent vegetation were measured in two natural and four restoring wetlands in 2004. Areal (m2) rates of carbon fixation were greatest for low marsh vegetation, while phytoplankton and microphytobenthos rates were one and two orders of magnitude lower, respectively. However, when areal production rates were scaled to the amount of habitat available for each primary producer group, the relative importance of each group varied by location. Given that each primary producer group supports a different subset of estuarine consumers, the type of food subsidy desired should influence the amount open water channel, mudflat and low marsh area restored. Large-scale wetland restoration activities should consider the types of primary producers likely to occupy restored habitats when estimating future food web impacts.