Search results

Title: The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
Author: Keeling, Burki, Wilcox, Allam, Allen, Amaral-Zettler, Armbrust, Archibald, Bharti, Bell, Beszteri, Bidle, Cameron, Campbell, Caron, Cattolico, Collier, Coyne, Davy, Deschamps, Dyhrman, Edvardsen, Gates, Gobler, Greenwood, Guida, Jacobi, Jakobsen, James, Jenkins, John, Johnson, Juhl, Kamp, Katz, Kiene, Kudryavtsev, Leander, Lin, Lovejoy, Lynn, Marchetti, McManus, Nedelcu, Menden-Deuer, Miceli, Mock, Montresor, Moran, Murray, Nadathur, Nagai, Ngam, Palenik, Pawlowski, Petroni, Piganeau, Posewitz, Rengefors, Romano, Rumpho, Rynearson, Schilling, Schroeder, Simpson, Slamovits, Smith, Smith, Smith, Sosik, Stief, Theriot, Twary, Umale, Vaulot, Wawrik, Wheeler, Wilson, Xu, Zingone, Worden
Date: 2014-01-01T00:00:00Z

Title: Phylogenetic relationships of yessotoxin-producing dinoflagellates, based on the large subunit and internal transcribed spacer ribosomal DNA domains
Description: Yessotoxin (YTX) is a globally distributed marine toxin produced by some isolates of the dinoflagellate species Protoceratium reticulatum, Lingulodinium polyedrum, and Gonyaulax spinifera within the order Gonyaulacales. The process of isolating cells and testing each isolate individually for YTX production during toxic blooms are labor intensive, and this impedes our ability to respond quickly to toxic blooms. In this study, we used molecular sequences from the large subunit and internal transcribed spacer genomic regions in the ribosomal operon of known YTX-producing dinoflagellates to determine if genetic differences exist among geographically distinct populations or between toxic and nontoxic isolates within species. In all analyses, all three YTX-producing species fell within the Gonyaulacales order in agreement with morphological taxonomy. Phylogenetic analyses of available rRNA gene sequences indicate that the capacity for YTX production appears to be confined to the order Gonyaulacales. These findings indicate that Gonyaulacoloid dinoflagellate species are the most likely to produce YTX and thus should be prioritized for YTX screening during events. Dinoflagellate species that fall outside of the Gonyaulacales order are unlikely to produce YTX. Although the rRNA operon offers multiple sequence domains to resolve species level diversification within this dinoflagellate order, these domains are not sufficiently variable to provide robust markers for YTX toxicity. © 2009, American Society for Microbiology. All Rights Reserved., Cited By (since 1996):8, CODEN: AEMID, Downloaded from: http://aem.highwire.org/content/75/1/54.full.pdf+html (13 June 2014).
Author: Howard, Smith, Kudela
Date: 2009-01-01T00:00:00Z

Title: Evolution of Macrocystis spp. (Phaeophyceae) as determined by ITS1 and ITS2 sequences
Description: Macrocystis (Lessoniaceae) displays an antitropical distribution, occurring in temperate subtidal regions along western North America in the northern hemisphere and throughout the southern hemisphere. We used the noncoding rDNA internal transcribed spacer regions (ITS1 and ITS2) to examine relatedness among (1) Macrocystis and several genera of Laminariales, (2) four species of Macrocystis (M. integrifolia Bory from the northern hemisphere, M. angustifolia Bory and M. laevis Hay from the southern hemisphere, and M. pyrifera [L.] C. Ag. from both hemispheres), and (3) multiple clones of several individuals. Of the taxa included in our phylogenetic analysis, the elk kelp, Pelagophycus porra (Lem.) Setch., was the sister taxon to Macrocystis spp. Macrocystis individuals from the southern hemisphere (representing three species) formed a strongly to moderately supported clade, respectively, when the ITS1 and ITS2 sequences were analyzed separately. No distinction was detected between the two species in the northern hemisphere. Thus, Macrocystis may be a monospecific genus (M. pyrifera). A northern-hemisphere-to-southern-hemisphere pattern of dispersal was inferred, because northern-hemisphere individuals were more diverse and displayed paraphyletic clades, whereas southern-hemisphere individuals were less diverse and formed a monophyletic clade. High intraindividual variation in ITS1 sequences was observed in one individual from Santa Catalina Island (CA), suggesting very recent and rapid mixing of genotypes from areas to the north and Baja California (Mexico) or introgressive hybridization with Pelagophycus., Cited By (since 1996):67, Seaweeds, CODEN: JPYLA
Author: Coyer, Smith, Andersen
Date: 2001-01-01T00:00:00Z

Title: Macrofaunal abundance and composition on the West Antarctic Peninsula continental shelf,
Description: To assess the impact and fate of the summer phytoplankton bloom on Antarctic benthos, we evaluated temporal and spatial patterns in macrofaunal abundance and taxonomic composition along a transect crossing the West Antarctic Peninsula (WAP) continental shelf. As part of the FOODBANCS project, we sampled three sites at 550-625 m depths during five cruises occurring in November 1999, February-March 2000, June 2000, October 2000 and March 2001. We used a combination of megacore and box-core samplers to take 81 samples, and collected over 30,000 macrofaunal individuals, one of the largest sampling efforts on the Antarctic shelf to date. Comparison of the two sampling methodologies (box core and megacore) indicates similar macrofaunal densities, but with significant differences in taxonomic composition, a reflection of the different spatial scales of sampling. Macrofaunal abundances on the WAP shelf were relatively high compared to other Antarctic shelf settings. At two of the three sampling sites, macrofaunal abundance remained constant throughout the year, which is consistent with the presence of a sediment 'food bank'. Differences were observed in taxonomic composition at the site closest to the coast (Station A), driven by higher abundances of sub-surface-deposit feeders. A significant temporal response was observed in the ampharetid polychaetes at Station A, with an abundance peak in the late fall post-bloom period; this may have resulted from juvenile recruitment during the summer bloom. Familial composition of macrofaunal polychaetes on the WAP shelf is more closely related to deep-sea abyssal fauna than to other shelf regions, and we hypothesize that this is a result of both local ecological conditions (low temperatures) and a reflection of historical processes such as extinctions on the Antarctic shelf during previous glacial maxima followed by recolonization from the deep sea. © 2008 Elsevier Ltd. All rights reserved., Cited By (since 1996):4, Invertebrates, Antarctica, CODEN: DSROE, ,
Author: Glover, Smith, Mincks, Sumida, Thurber
Date: 2008-01-01T00:00:00Z

Title: Transport makes the difference,
Description: , CODEN: JPYLA, , ,
Author: Smith
Date: 2000-01-01T00:00:00Z

Title: Ozone depletion: Ultraviolet radiation and phytoplankton biology in Antarctic waters,
Description: The springtime stratospheric ozone (O 3) layer over the Antarctic is thinning by as much as 50 percent, resulting in increased midultraviolet (UVB) radiation reaching the surface of the Southern Ocean. There is concern that phytoplankton communities confined to near-surface waters of the marginal ice zone will be harmed by increased UVB irradiance penetrating the ocean surface, thereby altering the dynamics of Antarctic marine ecosystems. Results from a 6-week cruise (Icecolors) in the marginal ice zone of the Bellingshausen Sea in austral spring of 1990 indicated that as the O 3 layer thinned: (i) sea surface- and depth-dependent ratios of UVB irradiance (280 to 320 nanometers) to total irradiance (280 to 700 nanometers) increased and (ii) UVB inhibition of photosynthesis increased. These and other Icecolors findings suggest that O 3-dependent shifts of in-water spectral irradiances alter the balance of spectrally dependent phytoplankton processes, including photoinhibition, photoreactivation, photoprotection, and photosynthesis. A minimum 6 to 12 percent reduction in primary production associated with O 3 depletion was estimated for the duration of the cruise., Cited By (since 1996):544, CODEN: SCIEA, ,
Author: Smith, Prézelin, Baker, Bidigare, Boucher, Coley, Karentz, Macintyre, Matlick, Menzies, Ondrusek, Wan, Waters
Date: 1992-01-01T00:00:00Z

Title: FISH-Flow: A quantitative molecular approach for describing mixed clade communities of Symbiodinium
Description: Our understanding of reef corals and their fate in a changing climate is limited by our ability to monitor the diversity and abundance of the dinoflagellate endosymbionts that sustain them. This study combined two well-known methods in tandem: fluorescent in situ hybridization (FISH) for genotype-specific labeling of Symbiodinium and flow cytometry to quantify the abundance of each symbiont clade in a sample. This technique (FISH-Flow) was developed with cultured Symbiodinium representing four distinct clades (based on large subunit rDNA) and was used to distinguish and quantify these types with high efficiency and few false positives. This technique was also applied to freshly isolated symbionts of Orbicella faveolata and Orbicella annularis. Isolates from acutely bleached coral tissues had significantly lower labeling efficiency; however, isolates from healthy tissue had efficiencies comparable to cultured Symbiodinium trials. RNA degradation in bleaching samples may have interfered with labeling of cells. Nevertheless, we were able to determine that, with and without thermal stress, experimental columns of the coral O. annularis hosted a majority of clade B and B/C symbionts on the top and side of the coral column, respectively. We demonstrated that, for cultured Symbiodinium and Symbiodinium freshly isolated from healthy host tissues, the relative ratio of clades could be accurately determined for clades present at as low as 7 % relative abundance. While this method does not improve upon PCR-based techniques in identifying clades at background levels, FISH-Flow provides a high precision, flexible system for targeting, quantifying and isolating Symbiodinium genotypes of interest. © 2013 Springer-Verlag Berlin Heidelberg.
Author: McIlroy, Smith, Geller
Date: 2014-01-01T00:00:00Z

Title: Surveillance for zoonotic and selected pathogens in harbor seals phoca vitulina from central California
Description: The infection status of harbor seals Phoca vitulina in central California, USA, was evaluated through broad surveillance for pathogens in stranded and wild-caught animals from 2001 to 2008, with most samples collected in 2007 and 2008. Stranded animals from Mendocino County to San Luis Obispo County were sampled at a rehabilitation facility: The Marine Mammal Center (TMMC, n = 175); wild-caught animals were sampled at 2 locations: San Francisco Bay (SF, n = 78) and Tomales Bay (TB, n = 97), that differed in degree of urbanization. Low prevalences of Salmonella, Campylobacter, Giardia, and Cryptosporidium were detected, in the feces of stranded and wild-caught seals. Clostridium perfringens and Escherichia coli were more prevalent in the feces of stranded (58% [78 out of 135] and 76% [102 out of 135]) than wild-caught (42% [45 out of 106] and 66% [68 out of 106]) seals, whereas Vibrio spp. were 16 times more likely to be cultured from the feces of seals from SF than TB or TMMC (p < 0.005). Brucella DNA was detected in 3.4% of dead stranded harbor seeds (2 out of 58). Type A influenza was isolated from feces of 1 out of 96 wild-caught seals. Exposure to Toxoplasma gondii, Sarcocystis neurona, and type A influenza was only detected in the wild-caught harbor seals (post-weaning age classes), whereas antibody titers to Leptospira spp. were detected in stranded and wild-caught seals. No stranded (n = 109) or wild-caught (n = 217) harbor seals had antibodies to phocine distemper virus, although a single low titer to canine distemper virus was detected. These results highlight the role of harbor seals as sentinel species for zoonotic and terrestrial pathogens in the marine environment., Harbor Seals
Author: Greig, Gulland, Smith, Conrad, Field, Fleetwood, Harvey, Ip, Jang, Packham, Wheeler, Hall

Title: Using the molecular toolbox to compare harmful algal blooms in upwelling systems,
Description: Harmful algal blooms (HABs) are now generally recognized as occurring over a wide range of habitats from oligotrophic to hypernutrified, and appear to be expanding globally. Unlike many other ecosystems impacted by HABs, upwelling systems worldwide share a common set of physical parameters and are likely to respond similarly, regardless of locale. The Core Research Project on HABs in Upwelling Systems, a component of the scientific programme on the Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB), promotes a comparative approach to identify the similarities and differences in the manifestation of HAB events in these systems. As applied to the goals of this programme, molecular techniques are a powerful suite of tools for HAB species identification, for determining genetic similarity within morphologically indistinguishable species, and ultimately, for assessing spatial and temporal patterns in ecophysiological responses in these upwelling systems. Knowledge of HAB organisms will be enhanced by comparing and contrasting the responses of these organisms in similar upwelling regions. Here, we provide an update on the availability of molecular and genetic tools for comparative HAB programmes in upwelling systems, focusing on four broad applications: cell enumeration and identification, molecular phylogenetics, functional/comparative genomics, and applications of high throughput sequencing methods. We highlight the rapid evolution, the promise, and the potential pitfalls, of the molecular toolbox, focusing on specific examples of how scientists and resource managers currently apply these methods. Specific examples are developed using relevant case studies from the California, Benguela and Iberian systems. We summarise by providing a synthesis of future research directions and goals that would be particularly relevant to advancing the comparative method for HAB genetics with an emphasis on upwelling systems. © 2010 Elsevier Ltd. All rights reserved., Cited By (since 1996):6, CODEN: POCNA, , , Oceanography
Author: Kudela, Howard, Jenkins, Miller, Smith
Date: 2010-01-01T00:00:00Z

Title: Causality of an extreme harmful algal bloom in Monterey Bay, California, during the 2014-2016 northeast Pacific warm anomaly
Description: Export Date: 26 June 2017, Article in Press, An ecologically and economically disruptive harmful algal bloom (HAB) affected much of the northeast Pacific margin in 2015, during a prolonged oceanic warm anomaly. Caused by diatoms of the genus Pseudo-nitzschia, this HAB produced the highest particulate concentrations of the biotoxin domoic acid (DA) ever recorded in Monterey Bay, California. Bloom inception followed strong upwelling during the spring transition, which introduced nutrients and eliminated the warm anomaly locally. Subsequently, moderate and intermittent upwelling created favorable conditions for growth and accumulation of HAB biomass, which was dominated by a highly toxigenic species, P. australis. High cellular DA concentrations were associated with available nitrogen for DA synthesis coincident with silicate exhaustion. This nutrient influence resulted from two factors: (1) disproportionate depletion of silicate in upwelling source waters during the warm anomaly, the most severe depletion observed in 24 years, and (2) silicate uptake by the dense diatom bloom
Author: Ryan, Kudela, Birch, Blum, Bowers, Chavez, Doucette, Hayashi, Marin, Mikulski, Pennington, Scholin, Smith, Woods, Zhang

Title: Characterization of a cDNA encoding glutamine synthetase from the marine diatom Skeletonema costatum (Bacillariophyceae),
Description: A cDNA-encoding glutamime synthetase (GS) was isolated from the marine diatom Skeletonema costatum (Greville) Cleve by PCR amplification. Nucleic acid and deduced amino acid sequences of the diatom GS were greater than 50% identical to GS from green algae and vascular plants, and phylogenetic analysis established the diatom GS as a member of the GSII gene family. The presence of an N-terminus signal sequence, identified on the basis of sequence similarity with other chloroplast-localized proteins from diatoms, suggests that the encoded GS isoenzyme is localized to the chloroplast. The GS mRNA was present in log-phase cells grown with either nitrate or ammonium as the sole added nitrogen source. Results from Southern blot analysis of genomic DNA suggested that the cDNA isolated in this study was either a member of a small, highly conserved gene family or that there was allelic variation within the region examined. Phylogenetic analyses further indicated that genes encoding GS from the diatom and two species of green algae diverged prior to the gene duplication, to the isoenzymes in vascular plants, supporting the hypothesis that GS isoenzymes in diatoms, green algae, and vascular plants arose through independent evolutionary events., Cited By (since 1996):16, Seaweeds, CODEN: JPYLA, ,
Author: Robertson, Smith, Alberte
Date: 1999-01-01T00:00:00Z

Title: Demography and elasticity of the diamond stingray, Dasyatis dipterura,
Description: Despite their abundance in near-shore tropical and subtropical marine environments, which support much of the world's elasmobranch fisheries, population dynamics and impacts of fisheries on stingrays are poorly documented. Age-structured demographic models were developed using empirical estimates of fecundity, longevity and maturity to project population growth parameters and potential responses to fishing mortality of Dasyatis dipterura from the Bahía Magdalena lagoon complex, México. Monte Carlo simulation was incorporated to include uncertainty in life history parameters into model projections. Six models were developed using deterministic and probabilistic approaches under unexploited and exploited (fishing mortality ≤ 0.05 year-1) conditions. Mean annual population growth rates (γ) of 1.05-1.06 (5-6% increase), net reproductive rates of 2.3-2.4 and generation times of 14.9-16.5 years were projected from simulations. The introduction of a low fishing mortality into probabilistic models produced γ of 1.01 year-1. Elasticity analysis indicated that population growth rates for D. dipterura are more strongly influenced by the survival of juvenile and adult stages than by survival of neonates or changes in fecundity. Demographic analyses indicated that D. dipterura has a low intrinsic growth potential and limited resilience to fishing pressure. Localised depletion or population collapses are therefore likely to occur through unrestricted, unmonitored fishing effort. © CSIRO 2008., Cited By (since 1996):13, ,
Author: Smith, Cailliet, Cort́s
Date: 2008-01-01T00:00:00Z

Title: Pseudo-nitzschia species composition varies concurrently with domoic acid concentrations during two different bloom events in the Southern California Bight
Description: The San Pedro Shelf (SPS) region of the Southern California Bight has witnessed an increase of Pseudo-nitzschia spp. blooms during the past decade, although the domoic acid (DA) concentrations observed during these events have varied considerably. This study compared the extent, timing and environmental controls of Pseudo-nitzschia blooms that were observed in two consecutive years on the SPS. Environmental conditions were characterized during shipboard surveys during spring 2013 and 2014 along an onshore–offshore transect at surface and subsurface depths. A Pseudo-nitzschia bloom of similar cell abundances was observed during each year, yet maximal DA concentrations differed by nearly two orders of magnitude. Environmental parameters were favorable for Pseudo-nitzschia spp. growth in both years, but few factors could be identified that specifically pertained to DA, with the exception that toxicity correlated negatively with dissolved silicic acid concentrations. Automated ribosomal intergenic spacer analysis for Pseudo-nitzschia species indicated that the relative abundance of toxin-producing species had a strong influence on DA concentrations between years, with high-DA concentrations corresponding to Pseudo-nitzschia communities dominated by P. australis/P. seriata. Factors explaining the preferential growth of particular Pseudo-nitzschia species remain enigmatic but are important for predicting toxic events attributable to these taxa.
Author: Smith, Gellene, Hubbard, Bowers, Kudela, Hayashi, Caron

Title: Calibration and evaluation of five indicators of benthic community condition in two California bay and estuary habitats,
Description: Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection. © 2008 Elsevier Ltd. All rights reserved., Cited By (since 1996):15, Invertebrates, CODEN: MPNBA, ,
Author: Ranasinghe, Weisberg, Smith, Montagne, Thompson, Oakden, Huff, Cadien, Velarde, Ritter
Date: 2009-01-01T00:00:00Z

Title: SeaWiFS satellite ocean color data from the Southern Ocean,
Description: SeaWiFS estimates of surface chlorophyll. concentrations are reported for the region of the U.S. JGOFS study in the Southern Ocean (∼ 170 °W, 60 °S). Elevated chlorophyll was observed at the Southern Ocean fronts, near the edge of the seasonal ice sheet, and above the Pacific-Antarctic Ridge. The elevated chlorophyll levels associated with the Pacific-Antarctic Ridge are surprising since even the crest of the ridge is at depths > 2000 m. This elevated phytoplankton biomass is likely the result of mesoscale physical-biological interactions where the Antarctic Circumpolar Current (ACC) encounters the ridge. Four cruises surveyed this region between October 1997 and March 1998, as part of the U.S. JGOFS. Satellite-derived chlorophyll concentrations were compared with in situ extracted chlorophyll measurements from these cruises. There was good agreement (r 2 of 0.72, from a linear regression of shipboard vs. satellite chlorophyll), although SeaWiFS underestimated chlorophyll concentrations relative to the ship data. Copyright 1999 by the American Geophysical Union., Cited By (since 1996):83, CODEN: GPRLA, ,
Author: Moore, Abbott, Richman, Smith, Cowles, Coale, Gardner, Barber
Date: 1999-01-01T00:00:00Z

Title: Reproductive biology of two commercially exploited skates, Raja binoculata and R. rhina, in the western Gulf of Alaska,
Description: This study provides the first detailed information on the reproductive biology of two large and abundant eastern North Pacific Ocean skate species: big skate (Raja binoculata) and longnose skate (Raja rhina). Skates were collected in the western Gulf of Alaska during 2005 and 2006 after a targeted fishery for these two species developed around Kodiak Island, Alaska; both species are also taken as by-catch to other fisheries. A total of 307 females (20.1-183.3 cm TL) and 138 males (19.5-143.7 cm TL) R. binoculata, and 354 females (18.1-145.0 cm TL) and 318 males (21.1-135.8 cm TL) R. rhina were collected. Female R. binoculata were found to attain first (e.g., smallest individual) maturity at 125.8 cm TL and 50% at 148.6 cm TL. Males were found to attain first and 50% maturity at 124.0 and 119.2 cm TL, respectively. No gravid female R. binoculata, with egg cases in utero, were encountered during the study. Female R. rhina were found to attain first and 50% maturity at 102.2 and 113.1 cm TL, respectively. Gravid female R. rhina, with egg cases in utero, were recorded throughout the sampling period. Males attained first maturity at 101.0 cm TL and 50% maturity at 102.9 cm TL. Histological analysis did not reveal significant changes in spermatocyst production for either species during the sampling period. Both species appear to be reproductively active year-round as no seasonal cycle was evident. This study provides new and essential information on the reproductive biology of these two commercially targeted skate species. © 2008 Elsevier B.V. All rights reserved., Cited By (since 1996):8, CODEN: FISRD, ,
Author: Ebert, Smith, Cailliet
Date: 2008-01-01T00:00:00Z

Title: Microsatellite Markers for Population Genetic Applications in the Domoic Acid-producing Diatom Pseudo-nitzschia australis Frenguelli (Bacillariophyceae)
Description: Microsatellites are commonly used markers in population genetics and are increasingly being employed to determine population structure in phytoplankton populations. We have developed seven polymorphic microsatellite markers for the domoic-acid producing diatom Pseudo-nitzschia australis. Using these markers, thirty P. australis isolates were genotyped, 10 isolates were from Monterey Bay, California and 20 were from off the northern coast of Oregon. The number of alleles per locus ranged from two to eight and observed heterozygosities ranged from 0.11 to 0.70. All but two of the isolates were genetically distinct and initial population differentiation analysis indicated no significant differences between the Pacific Northwest isolates and the Monterey Bay isolates. Pseudo-nitzschia australis microsatellites appear to be species specific based on cross amplification tests with Pseudo-nitzschia fraudulenta (Cleve) Hasle, Pseudo-nitzschia seriata (Cleve) H.Peragallo, Pseudo-nitzschia pungens (Grunow ex Cleve) and Pseudo-nitzschia multiseries (Hasle) Hasle.
Author: Adams, Schwenke, Smith, Trainer

Title: How many organisms are in ballast water discharge? A framework for validating and selecting compliance monitoring tools
Description: As regulations governing the discharge of living organisms in ships' ballast water enter into force, tools to rapidly and easily measure compliance with the discharge standards will be essential. To assess, validate, and select compliance tools, a framework-consisting of three parts-is presented: proof-of-concept, validation and verification, and final selection stages. Next, a case study describing the proof-of-concept stage is discussed. Specifically, variable fluorescence was evaluated as an approach for determining compliance with the discharge standard for living organisms ≥10. μm and <50. μm (typically protists). Preliminary laboratory experiments were conducted, which were followed by an expert workshop to gauge the feasibility of this approach and propose hypothetical thresholds indicating when the discharge standard is undoubtedly exceeded. Subsequently, field trials were conducted to assess this approach and recommended thresholds. All results were favorable, indicating the validation and verification stages are merited to further evaluate fluorometers as compliance monitoring tools., article
Author: Drake, Tamburri, First, Smith, Johengen

Title: Evaluation and use of sediment toxicity reference sites for statistical comparisons in regional assessments,
Description: Sediment reference sites were used to establish toxicity standards against which to compare results from sites investigated in San Francisco Bay (California, USA) monitoring programs. The reference sites were selected on the basis of low concentrations of anthropogenic chemicals, distance from active contaminant sources, location in representative hydrographic areas of the Bay, and physical features characteristic of depositional areas (e.g., fine grain size and medium total organic carbon [TOC]). Five field-replicated sites in San Francisco Bay were evaluated over three seasons. Samples from each site were tested with nine toxicity test protocols and were analyzed for sediment grain size and concentrations of trace metals, trace organics, ammonia, hydrogen sulfide, and TOC. The candidate sites were found to have relatively low concentrations of measured chemicals and generally exhibited low toxicity. Toxicity data from the reference sites were then used to calculate numerical tolerance limits to be used as threshold values to determine which test sites had significantly higher toxicity than reference sites. Tolerance limits are presented for four standard test protocols, including solid-phase sediment tests with the amphipods Ampelisca abdita and Eohaustorius estuarius and sea urchin Strongylocentrotus purpuratus embryo/larval development tests in pore water and at the sediment-water interface (SWI). Tolerance limits delineating the lowest 10th percentile (0.10 quantile) of the reference site data distribution were 71% of the control response for Ampelisca, 70% for Eohaustorius, 94% for sea urchin embryos in pore water, and 87% for sea urchins embryos exposed at the SWI. The tolerance limits are discussed in terms of the critical values governing their calculation and the management implications arising from their use in determining elevated toxicity relative to reference conditions., Cited By (since 1996):19, Rocks and Cores, CODEN: ETOCD, ,
Author: Hunt, Anderson, Phillips, Newman, Tjeerdema, Fairey, Puckett, Stephenson, Smith, Wilson, Taberski
Date: 2001-01-01T00:00:00Z

Title: Evaluating ecological states of rocky intertidal communities: A Best Professional Judgment exercise
Description: A Best Professional Judgment (BPJ) exercise was performed to determine the level of agreement among experts in evaluating the ecological states of western North American rocky intertidal communities. Species-abundance and environmental data from 12 central and 11 southern California sites were provided to 14 experts who independently ranked communities from best to worst and assigned each to one of five categories based on the degree of deviation from an expected natural biological state. Experts achieved Spearman correlations of 0.49 (central California) and 0.30 (southern California) in their rankings and averaged 75.4% and 70.0% Euclidean Similarity (ES) in their community evaluations. These ES values compare favorably with agreement levels found for similar exercises with soft bottom macroinvertebrate assemblages. The experts emphasized macrophytes with functional characteristics related to morphology and sessile macroinvertebrates in their assessments. Several challenges were noted in interpreting rocky intertidal data sets, the most prominent of which are high spatial and temporal variation and site-to-site differences in natural disturbance regimes, features that lead to multiple, expected community states. Experts required detailed, physical habitat descriptions to develop community composition expectations that differed for different shore types, and expressed concern about evaluating rocky intertidal communities based on only a single sampling event. Distinguishing natural from anthropogenic disturbance without information on the sources and magnitudes of anthropogenic perturbation was also found to be challenging because the biological responses to these stressors are often similar. This study underscores the need for long-term data sets that describe the dynamics of populations and communities and rigorous testing of expert judgments to firmly establish broadly applicable and consistent links between community states and anthropogenic stressors on rocky shores. © 2015 Elsevier Ltd., Export Date: 11 September 2015
Author: Murray, Weisberg, Raimondi, Ambrose, Bell, Blanchette, Burnaford, Dethier, Engle, Foster, Miner, Nielsen, Pearse, Richards, Smith
Date: 2016-01-01T00:00:00Z

Title: Validated age and growth of the leopard shark, Triakis semifasciata, with comments on reproduction,
Description: The age, growth, and sexual maturation of the leopard shark, Triakis semifasciata, from central California were studied. Growth band counts in vertebral centra of 162 leopard sharks produced von Bertalanffy growth curves with L ∞, K. and t o parameters of 1536 mm. 0.082, and -2.31, respectively, for both sexes combined. The L 8 value for females (1602 mm TL) was slightly but insignificantly higher than for males (1499 mm TL), but the K and t o values were almost identical. Seasonal changes in size modes of young-of-the-year leopard sharks, centrum edge characteristics, and growth and tetracycline mark-recapture from the field were used to validate annual deposition of vertebral centrum band pairs. Sexual maturity was evaluated by the gonads and presence of sperm and eggs; males mature at 7 yr and at about 63% of asymptotic length, and females mature at 10 yr, and at about 72% of asymptotic length. This slow growth, late maturity, and relatively low fecundity may increase their susceptibility to over-exploitation. © 1992 Kluwer Academic Publishers., Cited By (since 1996):53, Fish and Fisheries, CODEN: EBFID, ,
Author: Kusher, Smith, Cailliet
Date: 1992-01-01T00:00:00Z

Title: Pseudo-nitzschia species composition varies concurrently with domoic acid concentrations during two different bloom events in the Southern California Bight
Description: The San Pedro Shelf (SPS) region of the Southern California Bight has witnessed an increase of Pseudo-nitzschia spp. blooms during the past decade, although the domoic acid (DA) concentrations observed during these events have varied considerably. This study compared the extent, timing and environmental controls of Pseudo-nitzschia blooms that were observed in two consecutive years on the SPS. Environmental conditions were characterized during shipboard surveys during spring 2013 and 2014 along an onshore–offshore transect at surface and subsurface depths. A Pseudo-nitzschia bloom of similar cell abundances was observed during each year, yet maximal DA concentrations differed by nearly two orders of magnitude. Environmental parameters were favorable for Pseudo-nitzschia spp. growth in both years, but few factors could be identified that specifically pertained to DA, with the exception that toxicity correlated negatively with dissolved silicic acid concentrations. Automated ribosomal intergenic spacer analysis for Pseudo-nitzschia species indicated that the relative abundance of toxin-producing species had a strong influence on DA concentrations between years, with high-DA concentrations corresponding to Pseudo-nitzschia communities dominated by P. australis/P. seriata. Factors explaining the preferential growth of particular Pseudo-nitzschia species remain enigmatic but are important for predicting toxic events attributable to these taxa., Published
Author: Smith, Bowers, Moisander

Title: Variable responses of temperate calcified and fleshy macroalgae to elevated pCO2 and warming
Description: Anthropogenic carbon dioxide (CO2) emissions simultaneously increase ocean temperatures and reduce ocean surface pH, a process termed ocean acidification (OA). OA is expected to negatively affect the growth and physiology of many calcified organisms, but the response of non-calcified (fleshy) organisms is less well understood. Rising temperatures and pCO2 can enhance photosynthetic rates (within tolerance limits). Therefore, warming may interact with OA to alter biological responses of macroalgae in complicated ways. Beyond thresholds of physiological tolerance, however, rising temperatures could further exacerbate negative responses to OA. Many studies have investigated the effects of OA or warming independently of each other, but few studies have quantified the interactive effects of OA and warming on marine organisms. We conducted four short-term independent factorial CO2 enrichment and warming experiments on six common species of calcified and fleshy macroalgae from southern California to investigate the independent and interactive effects of CO2 and warming on growth, carbonic anhydrase (CA) enzyme activity, pigment concentrations, and photosynthetic efficiency. There was no effect of elevated pCO2 on CA activity, pigment concentration, and photosynthetic efficiency in the macroalgal species studies.However,we found that calcareous algae suffered reduced growth rates under high pCO2 conditions alone, although the magnitude of the effect varied by species. Fleshy algae had mixed responses of growth rates to high pCO2, indicating that the effects of pCO2 enrichment are inconsistent across species. The combined effects of elevated pCO2 and warming had a significantly negative impact on growth for both fleshy and calcareous algae; calcareous algae experienced five times more weight loss than specimens in ambient control conditions and fleshy growth was reduced by 76%. Our results demonstrate the need to study the interactive effects of multiple stressors associated with global change on marine communities., http://icesjms.oxfordjournals.org/content/early/2015/09/25/icesjms.fsv168.abstract, Advanced view
Author: Kram, Price, Donham, Johnson, Kelly, Hamilton, Smith
Date: 2015-09-25T00:00:00Z

Title: Condensation of the isoprenoid and amino precursors in the biosynthesis of domoic acid
Description: Understanding how environmental signals regulate production of domoic acid in blooms of Pseudo-nitzschia spp. at a molecular level requires description of the biochemical pathway to this kainoid neurotoxin. Precursor feeding studies have suggested domoic acid arises from the condensation of the C 10 isoprenoid geranyl diphosphate with glutamate, but the specific reactions leading to domoic acid from these precursors remain undescribed. Here, we develop a method to derivatize domoic acid with propyl chloroformate that enables gas chromatography-mass spectrometry (GC-MS) analysis to measure incorporation of stable isotopes into domoic acid generated in cultures incubated with isotopically-labeled substrates. We apply this method to demonstrate that both 2H from [1- 2H 2]geraniol are incorporated into domoic acid, suggesting that the condensation of geranyl diphosphate with an amino group occurs by nucleophilic substitution of the diphosphate rather than by oxidation of geraniol to the aldehyde before reaction with an amino group to form an imine. Ultimately, these and similar studies will facilitate the identification of DA biosynthetic enzymes and genes which will enable the study of how environmental factors regulate DA biosynthesis at the molecular level. © 2011 Elsevier Ltd., Seaweeds, CODEN: TOXIA
Author: Savage, Smith, Clark, Saucedo
Date: 2012-01-01T00:00:00Z

Title: Southern Ocean Iron Enrichment Experiment,
Description: The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide., Cited By (since 1996):316, Oceanography, CODEN: SCIEA, ,
Author: Coale, Johnson, Chavez, Buesseler, Barber, Brzezinski, Cochlan, Millero, Falkowski, Bauer, Wanninkhof, Kudela, Altabet, Hales, Takahashi, Landry, Bidigare, Wang, Chase, Strutton, Friederich, Gorbunov, Lance, Hilting, Hiscock, Demarest, Hiscock, Sullivan, Tanner, Gordon, Hunter, Elrod, Fitzwater, Jones, Tozzi, Koblizek, Roberts, Herndon, Brewster, Ladizinsky, Smith, Cooper, Timothy, Brown, Selph, Sheridan, Twining, Johnson
Date: 2004-01-01T00:00:00Z

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