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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. Source


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. Source


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. Source


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 8 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. Source


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. Source

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