Southern California Coastal Water Research Project SCCWRP

Costa Mesa, CA, United States

Southern California Coastal Water Research Project SCCWRP

Costa Mesa, CA, United States
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Gregory J.B.,National Oceanic and Atmospheric Administration | Webster L.F.,National Oceanic and Atmospheric Administration | Griffith J.F.,Southern California Coastal Water Research Project SCCWRP | Stewart J.R.,National Oceanic and Atmospheric Administration | Stewart J.R.,University of North Carolina at Chapel Hill
Journal of Virological Methods | Year: 2011

Norovirus is associated commonly with human sewage and is responsible for numerous cases of waterborne and foodborne gastroenteritis every year. Assays using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) have been developed for norovirus, however, accurate detection and quantitation remain problematic owing to a lack of suitable positive controls. To improve enumeration of norovirus genomes from water, a synthetic norovirus genogroup II quantitation standard and competitive internal positive control were developed. The quantitation standard demonstrates identical amplification efficiency as wildtype norovirus and can be used as a viral surrogate in labs with restricted access to norovirus. The internal control quantifies sample inhibition, allowing for accurate quantitation of norovirus from complex environmental samples. Seawater samples spiked with sewage or bird guano were evaluated using the norovirus assay as part of a methods comparison study. Inhibition was detected in nine of 36 (25%) samples, two of which proved to be positive upon re-analysis. Results support the specificity of this assay for human-source (sewage) fecal contamination. Overall, use of this quantitation standard and internal control signify a great advance over traditional positive controls and suggest that molecular techniques for viral analysis could become standardized for routine water quality monitoring. © 2010 Elsevier B.V.

Johnston C.,Jardon & Howard Technologies Incorporated | Johnston C.,National Oceanic and Atmospheric Administration | Ufnar J.A.,Vanderbilt University | Griffith J.F.,Southern California Coastal Water Research Project SCCWRP | And 3 more authors.
Journal of Applied Microbiology | Year: 2010

Aims: To develop a quantitative, real-time PCR assay to detect the nifH gene of Methanobrevibacter smithii. Methanobrevibacter smithii is a methanogenic archaea found in the intestinal tract of humans that may be a useful indicator of sewage pollution in water.Methods and Results: Quantification standards were prepared from Meth. smithii genomic DNA dilutions, and a standard curve was used to quantify the target gene and calculate estimated genome equivalency units. A competitive internal positive control was designed and incorporated into the assay to assess inhibition in environmental extracts. Testing the assay against a panel of 23 closely related methanogen species demonstrated specificity of the assay for Meth. smithii. A set of 36 blind water samples was then used as a field test of the assay. The internal control identified varying levels of inhibition in 29 of 36 (81%) samples, and the Meth. smithii target was detected in all water samples with known sewage input.Conclusions: The quantitative PCR assay developed in this study is a sensitive and rapid method for the detection of the Meth. smithii nifH gene that includes an internal control to assess inhibition. Further research is required both to better evaluate host specificity of this assay and the correlation with human health risks.Significance and Impact of the Study: This research is the first description of the development of a rapid and sensitive quantitative assay for a methanogenic archaeal indicator of sewage pollution. Journal of Applied Microbiology. © 2010 The Society for Applied Microbiology. No claim to US Government works.

Stewart J.R.,University of North Carolina at Chapel Hill | Boehm A.B.,Stanford University | Dubinsky E.A.,Lawrence Berkeley National Laboratory | Fong T.-T.,Tetra Tech Inc. | And 9 more authors.
Water Research | Year: 2013

Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions. © 2013 Elsevier Ltd.

Fernandez L.A.,U.S. Environmental Protection Agency | Fernandez L.A.,Northeastern University | Lao W.,Southern California Coastal Water Research Project SCCWRP | Maruya K.A.,Southern California Coastal Water Research Project SCCWRP | Burgess R.M.,U.S. Environmental Protection Agency
Environmental Science and Technology | Year: 2014

Passive samplers were deployed to the seafloor at a marine Superfund site on the Palos Verdes Shelf, California, USA, and used to determine water concentrations of persistent organic pollutants (POPs) in the surface sediments and near-bottom water. A model of Fickian diffusion across a thin water boundary layer at the sediment-water interface was used to calculate flux of contaminants due to molecular diffusion. Concentrations at four stations were used to calculate the flux of DDE, DDD, DDMU, and selected PCB congeners from sediments to the water column. Three passive sampling materials were compared: PE strips, POM strips, and SPME fibers. Performance reference compounds (PRCs) were used with PE and POM to correct for incomplete equilibration, and the resulting POP concentrations, determined by each material, agreed within 1 order of magnitude. SPME fibers, without PRC corrections, produced values that were generally much lower (1 to 2 orders of magnitude) than those measured using PE and POM, indicating that SPME may not have been fully equilibrated with waters being sampled. In addition, diffusive fluxes measured using PE strips at stations outside of a pilot remedial sand cap area were similar to those measured at a station inside the capped area: 240 to 260 ng cm-2 y-1 for p,p′-DDE the largest diffusive fluxes of POPs were calculated at station 8C, the site where the highest sediment concentrations have been measured in the past, 1100 ng cm-2 y-1 for p,p′-DDE. © 2014 American Chemical Society.

Crain B.J.,Humboldt State University | White J.W.,Humboldt State University | Steinberg S.J.,Humboldt State University | Steinberg S.J.,Southern California Coastal Water Research Project SCCWRP
Biodiversity and Conservation | Year: 2011

The emerging interest in the biological and conservation significance of locally rare species prompts a number of questions about their correspondence with other categories of biodiversity, especially global rarity. Here we present an analysis of the correspondence between the distributions of globally and locally rare plants. Using biological hotspots of rarity as our framework, we evaluate the extent to which conservation of globally rare plants will act as a surrogate for conservation of locally rare taxa. Subsequently, we aim to identify gaps between rarity hotspots and protected land to guide conservation planning. We compiled distribution data for globally and locally rare plants from botanically diverse Napa County, California into a geographic information system. We then generated richness maps highlighting hotspots of global and local rarity. Following this, we overlaid the distribution of these hotspots with the distribution of protected lands to identify conservation gaps. Based on occupancy of 1 km 2 grid cells, we found that over half of Napa County is occupied by at least one globally or locally rare plant. Hotspots of global and local rarity occurred in a substantially smaller portion of the county. Of these hotspots, less than 5% were classified as multi-scale hotspots, i. e. they were hotspots of global and local rarity. Although, several hotspots corresponded with the 483 km 2 of protected lands in Napa County, some of the richest areas did not. Thus, our results show that there are important conservation gaps in Napa County. Furthermore, if only hotspots of global rarity are preserved, only a subset of locally rare plants will be protected. Therefore, conservation of global, local, and multi-scale hotspots needs serious consideration if the goals are to protect a larger variety of biological attributes, prevent extinction, and limit extirpation in Napa County. © 2011 Springer Science+Business Media B.V.

Stein E.D.,Southern California Coastal Water Research Project SCCWRP | Cover M.R.,California State University, Stanislaus | Elizabeth Fetscher A.,Southern California Coastal Water Research Project SCCWRP | O'Reilly C.,California Ocean Protection Council | And 2 more authors.
Journal of the American Water Resources Association | Year: 2013

Armoring of streambanks is a common management response to perceived threats to adjacent infrastructure from flooding or erosion. Despite their pervasiveness, effects of reach-scale bank armoring have received less attention than those of channelization or watershed-scale hydromodification. In this study, we explored mechanistic ecosystem responses to armoring by comparing conditions upstream, within, and downstream of six stream reaches with bank armoring in Southern California. Assessments were based on four common stream-channel assessment methods: (1) traditional geomorphic measures, (2) the California Rapid Assessment Method for wetlands, (3) bioassessment with benthic macroinvertebrates, and (4) bioassessment with stream algae. Although physical responses varied among stream types (mountain, transitional, and lowland), armored segments generally had lower slopes, more and deeper pools and fewer riffles, and increased sediment deposition. Several armored segments exhibited channel incision and bank toe failure. All classes of biological indicators showed subtle, mechanistic responses to physical changes. However, extreme heterogeneity among sites, the presence of catchment-scale disturbances, and low sample size made it difficult to ascribe observed patterns solely to channel armoring. The data suggest that species-level or functional group-level metrics may be more sensitive tools than integrative indices of biotic integrity to local-scale effects. © 2013 American Water Resources Association.

Maruya K.A.,Southern California Coastal Water Research Project SCCWRP | Landrum P.F.,Southern Illinois University Carbondale | Burgess R.M.,U.S. Environmental Protection Agency | Shinek J.P.,Harvard University
Integrated Environmental Assessment and Management | Year: 2012

The recently adopted sediment quality assessment framework for evaluating bay and estuarine sediments in the state of California incorporates bulk sediment chemistry as a key line of evidence (LOE) but does not address the bioavailability of measured contaminants. Thus, the chemistry-based LOE likely does not provide an accurate depiction of organism exposure in all cases, nor is it particularly well suited for assessment of causality. In recent years, several methods for evaluating the bioavailability of sediment-associated contaminants have emerged, which, if optimized and validated, could be applied to improve the applicability and broaden the scope of sediment quality assessment. Such methods include equilibrium-based biomimetic extractions using either passive sampling devices (PSDs) or measures of rapidly desorbing contaminant pools, which provide information compatible with existing mechanistic approaches. Currently, these methods show promise in relating bioaccessible chemicals to effects endpoints, including bioaccumulation of hydrophobic organic compounds and/or toxicity due to metals. Using these methods, a bioavailability LOE for organics is proposed based on PSD and equilibrium partitioning theory that can be employed as an independent LOE or in assessing causality in tiered toxicity identification evaluations. Current and future research should be aimed at comparing the performance of PSDs and their relationships with effects concentrations, field validation of the most promising methods, addressing contaminant mixtures, further developing the parameterization of the proposed bioavailability LOE, and providing a better understanding of the underlying diagenetic cycling of metal contaminants that lead to exposure, affect bioavailability, and drive adverse outcomes. © 2010 SETAC.

Fernandez L.A.,U.S. Environmental Protection Agency | Lao W.,Southern California Coastal Water Research Project SCCWRP | Maruya K.A.,Southern California Coastal Water Research Project SCCWRP | White C.,U.S. Environmental Protection Agency | Burgess R.M.,U.S. Environmental Protection Agency
Environmental Science and Technology | Year: 2012

Passive sampling was used to deduce water concentrations of persistent organic pollutants (POPs) in the vicinity of a marine Superfund site on the Palos Verdes Shelf, California, USA. Precalibrated solid phase microextraction (SPME) fibers and polyethylene (PE) strips that were preloaded with performance reference compounds (PRCs) were codeployed for 32 d along an 11-station gradient at bottom, surface, and midwater depths. Retrieved samplers were analyzed for DDT congeners and their breakdown products (DDE, DDD, DDMU, and DDNU) and 43 PCB congeners using GC-EI- and NCI-MS. PRCs were used to calculate compound-specific fractional equilibration achieved in situ for the PE samplers, using both an exponential approach to equilibrium (EAE) and numerical integration of Fickian diffusion (NI) models. The highest observed concentrations were for p,p′-DDE, with 2200 and 990 pg/L deduced from PE and SPME, respectively. The difference in these estimates could be largely attributed to uncertainty in equilibrium partition coefficients, unaccounted for disequilibrium between samplers and water, or different time scales over which the samplers average. The concordance between PE and SPME estimated concentrations for DDE was high (R2 = 0.95). PCBs were only detected in PE samplers, due to their much larger size. Near-bottom waters adjacent to and down current from sediments with the highest bulk concentrations exhibited aqueous concentrations of DDTs and PCBs that exceeded Ambient Water Quality Criteria (AWQC) for human and aquatic health, indicating the need for future monitoring to determine the effectiveness of remedial activities taken to reduce adverse effects of contaminated surface sediments. © 2012 American Chemical Society.

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