The role of ammonium and nitrate in spring bloom development in San Francisco Bay

Dugdale, Richard C.; Wilkerson, Frances P.; Hogue, Victoria E.; Marchi, A.

doi:10.1016/j.ecss.2006.12.008

Cited by 223 publications

(213 citation statements)

References 32 publications

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“…They attributed summer diatom blooms in Suisun Bay prior to 1987 to accumulation of phytoplankton biomass rather than a high growth rate (Cloern 1979;Cole and Cloern 1984 reported by Cole and Cloern (1984); the slight seasonal increase that we observed for P B M(24) occurred in parallel with the movement of the sampling area from Central Bay to Suisun Bay and the western Delta Cole and Cloern (1984) for spring. It has been hypothesized that growth rates of phytoplankton in the northern SFE have potentially decreased as a result of increased NH 4 loading (Dugdale et al 2007;, contaminants (Brooks et al 2012), and shifts in phytoplankton community composition (Lehman 2000;Glibert et al 2011). The decline in both P (24) reported by Alpine and Cloern (1992) was much higher than other estimates of P B M(24) reported for the SFE (Table 1) but similar to values reported for some other estuaries (e.g., Pennock and Sharp 1986).…”

Section: Discussioncontrasting

confidence: 53%

“…Like many other urbanized estuaries around the world, the SFE has experienced perturbations in key ecosystem drivers, including sediment and nutrient loads (Schoellhamer 2011;Jassby 2008), quantity and diversity of toxic pollutants (Brooks et al 2012), decreased phytoplankton biomass, and a loss of diatoms (e.g., Alpine and Cloern 1992;Kimmerer 2004;Dugdale et al 2007), and changes in zooplankton and fish (Mueller-Solger et al 2002;Kimmerer 2005). Although the original authors of the light-utilization model for the SFE (Cole and Cloern 1984) predicted that the empirical efficiency factor y would likely respond to such changes, this parameter has been previously recalculated for the northern estuary only twice (Alpine and Cloern 1992;Jassby et al 2002).…”

Section: Discussionmentioning

confidence: 99%

“…Smaller autotrophs including flagellates and cyanobacteria now appear to dominate the autotrophic community (Lehman 2000;Glibert et al 2011). Phytoplankton community structure was likely altered via size-selective grazing by the clams (Werner and Hollibaugh 1993) although additional drivers, including pesticides (Brooks et al 2012), changing nitrogen-to-phosphorus ratio (Glibert et al 2011), and increased ammonium loads (Dugdale et al 2007;Glibert et al 2011;) have also been implicated. At the same time, reduced sediment loads to the northern SFE, a consequence of damming upstream tributaries (Jassby 2008;Schoellhamer 2011) has resulted in increased water transparency and more favorable conditions for phytoplankton growth.…”

Section: Introductionmentioning

confidence: 99%

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

Parker

Kimmerer

Lidström

2012

Estuaries and Coasts

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Depth-integrated primary production (ΣP, in grams of carbon per square meter per day) was measured using 14 C 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, y, 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 lightutilization model. The variation in y was likely the result of interannual variation in phytoplankton assimilation number. These results suggest that using a single y 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.

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Section: Discussioncontrasting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Parker

Kimmerer

Lidström

2012

Estuaries and Coasts

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“…10 mmol L 21 . This somewhat surprising observation, discussed by Yoshiyama and Sharp (2006), was recently shown to also occur in the San Francisco Bay (Dugdale et al 2007). …”

Section: Discussionmentioning

confidence: 98%

Estuarine oxygen dynamics: What can we learn about hypoxia from long‐time records in the Delaware Estuary?

Sharp

2009

Limnology & Oceanography

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Hypoxia and anoxia occurred in the upper Delaware Estuary throughout much of the 20th century and diminished over the past several decades. I reviewed 30 yr of data from my laboratory's research efforts, 40 yr of consistent monitoring data from a multistate agency, results from inconsistent data collection from the past century, and anecdotal information to construct a long-time picture of the decline and increase of dissolved oxygen concentrations (DO) in the urban region of the estuary. The primary cause of the DO decline appeared to be inputs or allochthonous materials from urban sources (reduced nitrogen and carbon). In spite of extremely high nutrient concentrations, excess algal production did not influence DO anywhere along the tidal freshwater stretch or the saline portion of the well-mixed Delaware Estuary; and it does not have an influence today. The nutrient loading to the Delaware Estuary is very high, yet the typical signs of eutrophication are not obvious. Based on a model of apparent oxygen utilization, the Delaware Bay apparently had higher primary production 50 yr ago, a time when nutrient concentrations were as high or higher than today, shellfish and finfish production were apparently also higher, and DO was close to saturation. This analysis is offered as guidance in assessing and managing estuarine eutrophication, which is too often considered narrowly to be the result of inadvertent overfertilization by nutrients or a single nutrient element.

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“…Microbial communities were harvested after 24 h by filtration through a 0.22-mM polycarbonate filter that was then immediately frozen at À80 1C. Background concentrations of ammonium in the SF Bay range from 1 to 14 mM (Dugdale et al, 2007); typical estuarine glucose concentrations are 5-100 nM (Hanson and Snyder, 1980). In a second SF Bay experiment, water samples were incubated as described above, but for less time (12 h) and lower labeled substrate concentrations.…”

Section: Methodsmentioning

confidence: 99%

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

et al. 2011

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Most microorganisms remain uncultivated, and typically their ecological roles must be inferred from diversity and genomic studies. To directly measure functional roles of uncultivated microbes, we developed Chip-stable isotope probing (SIP), a high-sensitivity, high-throughput SIP method performed on a phylogenetic microarray (chip). This approach consists of microbial community incubations with isotopically labeled substrates, hybridization of the extracted community rRNA to a microarray and measurement of isotope incorporation-and therefore substrate use-by secondary ion mass spectrometer imaging (NanoSIMS). Laboratory experiments demonstrated that Chip-SIP can detect isotopic enrichment of 0.5 atom % 13 C and 0.1 atom % 15 N, thus permitting experiments with short incubation times and low substrate concentrations. We applied Chip-SIP analysis to a natural estuarine community and quantified amino acid, nucleic acid or fatty acid incorporation by 81 distinct microbial taxa, thus demonstrating that resource partitioning occurs with relatively simple organic substrates. The Chip-SIP approach expands the repertoire of stable isotope-enabled methods available to microbial ecologists and provides a means to test genomics-generated hypotheses about biogeochemical function in any natural environment.

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The role of ammonium and nitrate in spring bloom development in San Francisco Bay

Cited by 223 publications

References 32 publications

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

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

Estuarine oxygen dynamics: What can we learn about hypoxia from long‐time records in the Delaware Estuary?

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

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