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Baxa D.V.,University of California at Davis | Kurobe T.,University of California at Davis | Ger K.A.,University of California at Davis | Lehman P.W.,500 Industrial Blvd | Teh S.J.,University of California at Davis
Harmful Algae | Year: 2010

Developing an effective and rapid method to identify and estimate the abundance of Microcystis is warranted in the San Francisco Estuary (SFE) in view of expanding cyanobacterial blooms dominated by Microcystis spp. Blooms that occurred in the estuary from July to September 2007 were initially assessed using a standard polymerase chain reaction (PCR) employing primers designed for the conserved Microcystis-specific 16S ribosomal DNA (rDNA) region. The presence of microcystin-producing (MC+) toxic Microcystis was observed in cyanobacterial and water samples as shown by the amplification of the MC toxin synthetase genes mcyB and mcyD by standard PCR. The goal of this study was to develop a real-time quantitative PCR (qPCR) based on the 16S rDNA and mcyD gene sequences of Microcystis found in the SFE to quantify the proportion of toxic Microcystis with mcyD genes among total Microcystis or cyanobacterial population. Cyanobacterial samples collected by diagonal net tows of the water column showed that the ratio of gene copies was dominant for Microcystis among cyanobacteria (28-96%), and Microcystis carrying mcyD genes formed 0.4-20% of the total Microcystis spp. Total Microcystis was also abundant (7.7 × 104 to 9.9 × 107 cells L-1) in ambient surface waters, and the range of Microcystis cell equivalents with mcyD genes (4.1 × 102 to 2.2 × 107 cells L-1) indicated a large variation in the ratio of toxic Microcystis among total Microcystis (0.01-27%). Differences in the proportion of toxic and nontoxic Microcystis, as deduced from the cell equivalents of total Microcystis, were observed across the sampling locations and seasons where concentrations of total MCs (0.007-10.81 μg/L) also varied. By revealing trends in the sources and magnitude of toxic and nontoxic Microcystis, qPCR can contribute to rapid risk assessment and prediction of strategies designed to manage the adverse effects of cyanobacterial blooms in the SFE. © 2010 Elsevier B.V. Source

Massoudieh A.,Catholic University of America | Loboschefsky E.,University of California at Davis | Sommer T.,500 Industrial Blvd | Ginn T.,University of California at Davis | And 2 more authors.
Ecological Modelling | Year: 2011

Most models developed for the movement and fate of eggs and larvae of aquatic species are based on a particle tracking approach. Although this method has many advantages due to its high flexibility, particle tracking may become computationally intensive for complex geometries and when large numbers of particles are needed to simulate the population properly. In continuous models based on advection and dispersion mechanisms, the computational burden is independent of the size of the population. We developed a continuous fate and transport model for striped bass eggs and larvae in the San Francisco Bay-Delta. The model predicts the concentration of eggs and larvae at any location over time. The method of moments was used to account for the effect of temperature and age on the transition of eggs to larvae and larvae to juveniles. Egg and larval mortality were represented as functions of temperature, and eggs also experienced settling mortality. The fate and transport model used the same one-dimensional spatial grid as the existing Delta Simulation Model II (DSM2) hydrodynamics model. DSM2 output of flow rates, water depths, and cross-sectional areas were inputted into the fate and transport model to determine transport. The model was applied to striped bass eggs and larvae data collected during years 1990-1994; agreement between the modeled and the measured data was acceptable in most cases. Exploratory simulations were performed to demonstrate how the model could be used to evaluate the effects on egg and larval survival and total juvenile production of water diversions for supply and agricultural use and changes in the long-term mean water temperature. The model can be further used to examine the impact of various operation strategies in the San Francisco Bay-Delta, where diversion losses of early life stages of fishes remain a major management issue. © 2011 Elsevier B.V. Source

Quinones R.M.,University of California at Davis | Grantham T.E.,University of California at Davis | Harvey B.N.,500 Industrial Blvd | Kiernan J.D.,National Oceanic and Atmospheric Administration | And 3 more authors.
Reviews in Fish Biology and Fisheries | Year: 2014

Dam removal is often proposed for restoration of anadromous salmonid populations, which are in serious decline in California. However, the benefits of dam removal vary due to differences in affected populations and potential for environmental impacts. Here, we develop an assessment method to examine the relationship between dam removal and salmonid conservation, focusing on dams that act as complete migration barriers. Specifically, we (1) review the effects of dams on anadromous salmonids, (2) describe factors specific to dam removal in California, (3) propose a method to evaluate dam removal effects on salmonids, (4) apply this method to evaluate 24 dams, and (5) discuss potential effects of removing four dams on the Klamath River. Our flexible rating system can rapidly assess the likely effects of dam removal, as a first step in the prioritization of multiple dam removals. We rated eight dams proposed for removal and compared them with another 16 dams, which are not candidates for removal. Twelve of the 24 dams evaluated had scores that indicated at least a moderate benefit to salmonids following removal. In particular, scores indicated that removal of the four dams on the Klamath River is warranted for salmonid conservation. Ultimately, all dams will be abandoned, removed, or rebuilt even if the timespan is hundreds of years. Thus, periodic evaluation of the environmental benefits of dam removal is needed using criteria such as those presented in this paper. © 2014, The Author(s). Source

Brandl S.,University of California at Davis | Schumer G.,Cramer Fish science | Schreier B.M.,500 Industrial Blvd | Conrad J.L.,500 Industrial Blvd | And 2 more authors.
Molecular Ecology Resources | Year: 2015

The effect of predation on native fish by introduced species in the San Francisco Estuary-Delta (SFE) has not been thoroughly studied despite its potential to impact species abundances. Species-specific quantitative PCR (qPCR) is an accurate method for identifying species from exogenous DNA samples. Quantitative PCR assays can be used for detecting prey in gut contents or faeces, discriminating between cryptic species, or detecting rare aquatic species. We designed ten TaqMan qPCR assays for fish species from the SFE watershed most likely to be affected by non-native piscivores. The assays designed are highly specific, producing no signal from co-occurring or related species, and sensitive, with a limit of detection between 3.2 and 0.013 pg/μL of target DNA. These assays will be used in conjunction with a high-throughput qPCR platform to compare predation rates between native and non-native piscivores and assess the impacts of predation in the system. © 2014 John Wiley & Sons Ltd. Source

Lehman P.W.,500 Industrial Blvd | Mayr S.,Central district | Mecum L.,001 N. Wilson Way | Enright C.,500 Industrial Blvd
Aquatic Ecology | Year: 2010

It is hypothesized that perennial freshwater tidal wetland habitat exports inorganic and organic material needed to support the estuarine food web and to create favorable habitat for aquatic organisms in San Francisco Estuary. It is also hypothesized that most of the material flux in this river-dominated region is controlled by river flow. The production and export of material by Liberty Island were measured and compared using discrete monthly and continuous (15 min) measurements of a suite of inorganic and organic materials and flow between 2004 and 2005. Seasonal material flux was estimated from monthly discrete data for inorganic nutrients, suspended solids and salts, organic carbon and nitrogen and phytoplankton and zooplankton group carbon and chlorophyll a and pheophytin pigment. Estimates of material flux from monthly values were compared with measured daily material flux values for chlorophyll a concentration, salt and suspended solids obtained from continuous measurements (15 min) using YSI water quality sondes. Phytoplankton carbon produced within the wetland was estimated by in situ primary productivity. Most inorganic and organic materials were exported from the wetland on an annual basis, but the magnitude and direction varied seasonally. Dissolved inorganic nutrients such as nitrate, soluble phosphorus, total phosphorus and silica as well as total suspended solids were exported in the summer while total and dissolved organic carbon were exported in the winter. Salts like chloride and bromide were exported in the fall. Chlorophyll a and pheophytin were exported in the fall and associated with diatom and cyanobacteria carbon. Mesozooplankton carbon was dominated by calanoid copepods and exported most of the year except summer. Continuous sampling revealed high hourly and daily variation in chlorophyll a, salt and total suspended solids flux due to high frequency changes in concentration and tidal flow. In fact, tidal flow rather than river discharge was responsible for 90% or more of the material flux of the wetland. These studies indicate that freshwater tidal wetlands can be a source of inorganic and organic material but the export of material is highly variable spatially and temporally, varies most closely with tidal flow and requires high frequency measurements of both tidal flow and material concentration for accurate estimates. © Springer Science+Business Media B.V. 2009. Source

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