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: 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: 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: Diet Composition and Trophic Ecology of Northeast Pacific Ocean Sharks
Description: Although there is a general perception of sharks as large pelagic, apex predators, most sharks are smaller, meso- and upper-trophic level predators that are associated with the seafloor. Among 73 shark species documented in the eastern North Pacific (ENP), less than half reach maximum lengths > 200 cm, and 78% occur in demersal or benthic regions of the continental shelf or slope. Most small (≤ 200 cm) species (e.g., houndsharks) and demersal, nearshore juveniles of larger species (e.g., requiem sharks) consume small teleosts and decapod crustaceans, whereas large species in pelagic coastal and oceanic environments feed on large teleosts and squids. Several large, pelagic apex predator species occur in the ENP, but the largest species (i.e., Basking Shark, Whale Shark) consume zooplankton or small nekton. Size-based dietary variability is substantial for many species, and segregation of juvenile and adult foraging habitats also is common (e.g., Horn Shark, Shortfin Mako). Temporal dietary differences are most pronounced for temperate, nearshore species with wide size ranges, and least pronounced for smaller species in extreme latitudes and deep-water regions. Sympatric sharks often occupy various trophic positions, with resource overlap differing by space and time and some sharks serving as prey to other species. Most coastal species remain in the same general region over time and feed opportunistically on variable prey inputs (e.g., season migrations, spawning, or recruitment events), whereas pelagic, oceanic species actively seek hot spots of prey abundance that are spatiotemporally variable. The influence of sharks on ecosystem structure and regulation has been downplayed compared to that of large teleosts species with higher per capita consumption rates (e.g., tunas, billfishes). However, sharks also exert indirect influences on prey populations by causing behavioural changes that may result in restricted ranges and reduced fitness. Except for food web modelling efforts in Alaskan waters, the trophic impacts of sharks are poorly incorporated into current ecosystem approaches to fisheries management in the NEP.
Author: Bizzarro, Carlisle, Smith, Cortés

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: 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: 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: Developing standards for dissolved iron in seawater
Description: Cited By (since 1996):114
Author: Johnson, Boyle, Bruland, Coale, Measures, Moffett, Aguilar-Islas, Barbeau, Bergquist, Bowie, Buck, Cai, Chase, Cullen, Doi, Elrod, Fitzwater, Gordon, King, Laan, Laglera-Baquer, Landing, Lohan, Mendez, Milne, Obata, Ossiander, Plant, Sarthou, Sedwick, Smith, Sohst, Tanner, Van den Berg, Wu
Date: 2007-01-01T00:00:00Z

Title: Species-specific consequences of ocean acidification for the calcareous tropical green algae Halimeda
Description: Ocean acidification (OA), resulting from increasing dissolved carbon dioxide (CO2) in surface waters, is likely to affect many marine organisms, particularly those that calcify. Recent OA studies have demonstrated negative and/or differential effects of reduced pH on growth, development, calcification and physiology, but most of these have focused on taxa other than calcareous benthic macroalgae. Here we investigate the potential effects of OA on one of the most common coral reef macroalgal genera, Halimeda. Species of Halimeda produce a large proportion of the sand in the tropics and are a major contributor to framework development on reefs because of their rapid calcium carbonate production and high turnover rates. On Palmyra Atoll in the central Pacific, we conducted a manipulative bubbling experiment to investigate the potential effects of OA on growth, calcification and photophysiology of 2 species of Halimeda. Our results suggest that Halimeda is highly susceptible to reduced pH and aragonite saturation state but the magnitude of these effects is species specific. H. opuntia suffered net dissolution and 15% reduction in photosynthetic capacity, while H. taenicola did not calcify but did not alter photophysiology in experimental treatments. The disparate responses of these species to elevated CO2 partial pressure (pCO2) may be due to anatomical and physiological differences and could represent a shift in their relative dominance in the face of OA. The ability for a species to exert biological control over calcification and the species specific role of the carbonate skeleton may have important implications for the potential effects of OA on ecological function in the future. © 2011 Inter-Research., Cited By (since 1996):12, Seaweeds, CODEN: MESED
Author: Price, Hamilton, Tootell, Smith
Date: 2011-01-01T00:00:00Z

Title: Glacial meltwater dynamics in coastal waters west of the Antarctic peninsula,
Description: The annual advance and retreat of sea ice has been considered a major physical determinant of spatial and temporal changes in the structure of the Antarctic coastal marine ecosystem. However, the role of glacial meltwater on the hydrography of the Antarctic Peninsula ecosystem has been largely ignored, and the resulting biological effects have only been considered within a few kilometers from shore. Through several lines of evidence collected in conjunction with the Palmer Station Long-Term Ecological Research Project, we show that the freshening and warming of the coastal surface water over the summer months is influenced not solely by sea ice melt, as suggested by the literature, but largely by the influx of glacial meltwater. Moreover, the seasonal variability in the amount and extent of the glacial meltwater plume plays a critical role in the functioning of the biota by influencing the physical dynamics of the water (e.g., water column stratification, nearshore turbidity). From nearly a decade of observations (1991-1999), the presence of surface meltwater is correlated not only to phytoplankton blooms nearshore, but spatially over 100 km off-shore. The amount of meltwater will also have important secondary effects on the ecosystem by influencing the timing of sea ice formation. Because air temperatures are statistically increasing along the Antarctic Peninsula region, the presence of glacial meltwater is likely to become more prevalent in these surface waters and continue to play an ever-increasing role in driving this fragile ecosystem., Cited By (since 1996):69, CODEN: PNASA, ,
Author: Dierssen, Smith, Vernet
Date: 2002-01-01T00:00:00Z

Title: Trace metals in mussels transplanted to San Francisco Bay,
Description: Mussels (Mytilus californianus) transplanted to San Francisco Bay exhibited elevated trace metal concentrations compared with those in other mussel watch studies on the west coast of the United States. The highest concentrations of Ag, Cu, Hg, Mn, Pb and Zn were at the South Bay stations, and often in the Redwood Creek area. Ag and Hg concentrations were linearly correlated with station distance from the North Bay (San Pablo Bay), indicating that the South Bay is a major reservoir of these pollutants within San Francisco Bay. © 1986., Cited By (since 1996):7, CODEN: ETOCD, ,
Author: Smith, Stephenson, Flegal
Date: 1986-01-01T00:00:00Z

Title: Cytometric quantification of nitrate reductase by immunolabeling in the marine diatom Skeletonema costatum,
Description: Background: The uptake of nitrate by phytoplankton is a central issue in biological oceanography due to its importance to primary production and vertical flux of biogenic carbon. Nitrate reductase catalyzes the first step of nitrate assimilation, the reduction of NO'3 to NO 2. A cytometric protocol to detect and quantify relative changes in nitrate reductase (NR) protein content of the marine centric diatom Skeletonema costatum is presented. Methods: Immunolabeling of NR protein was achieved with polyclonal antibodies raised against S. costatum NR. Antisera specific to a NR protein subunit and to a NR polypeptide sequence were compared and cytometric results of NR protein abundance were related to Western analyses. Changes in cellular NR abundance and activity were followed during an upwelling simulation experiment in which S. costatum was exposed to a shift from ammonia to nitrate as major nitrogen source. Results: NR protein could be detected in NO 3-grown cells and at extremely low levels hardly discernible by Western Blot densiometry in NH 4-grown cells. The protocol allowed observation of early stages of NR induction during an upwelling simulation. NR abundance increased after the nutrient shift to reach a new physiological 'steady- state' 96 hrs later. NR activity exhibited diel variation with maxima at mid- day. NR abundance as estimated by both flow cytometry and Western analysis exhibited a hyperbolic relationship to NR activity. This pattern suggests post-translational activation of NR protein. Conclusions: The presented protocol allows the differentiation of NH 4- versus NO 3-grown algae as well as the monitoring of early stages in the induction of nitrate assimilatory capacities. (C) 2000 Wiley-Liss, Inc., Cited By (since 1996):8 Seaweeds, CODEN: CYTOD, ,
Author: Jochem, Smith, Gao, Zimmerman, Cabello-Pasini, Kohrs, Alberte
Date: 2000-01-01T00:00:00Z

Title: Determination of tributyltin in tissues and sediments by graphite furnace atomic absorption spectrometry,
Description: A method for the determination of tributyltin (TBT) in tissue and sediments has been developed for environmental samples. The technique involves extraction with methylene chloride and isolation of TBT from mono- and dibutyltin with a sodium hydroxide wash. The TBT is then back extracted and converted to elemental Sn with nitric acid. Analysis is by Zeeman graphite furnace atomic absorption spectrophotometry. Recoveries of spiked samples were between 99 % and 111% for mussel and fish tissues and 72% and 99% for various sediments. The limit of quantification was 0.0025 μg/g for tissue (on a wet weight basis). This technique was developed in response to our need to process large numbers of environmental samples with a minimum time investment., Cited By (since 1996):9, ,
Author: Stephenson, Smith
Date: 1988-01-01T00:00:00Z

Title: Domoic acid contamination within eight representative species from the benthic food web of Monterey Bay, California, USA
Description: Benthic food webs often derive a significant fraction of their nutrient inputs from phytoplankton in the overlying waters. If the phytoplankton include harmful algal species like Pseudonitzschia australis, a diatom capable of producing the neurotoxin domoic acid (DA), the benthic food web can become a depository for phycotoxins. We tested the general hypothesis that DA contaminates benthic organisms during local blooms of P. australis, a widespread toxin producer along the US west coast. To test for trophic transfer and uptake of DA into the benthic food web, we sampled 8 benthic species comprising 4 feeding groups: filter feeders (Emerita analoga and Urechis caupo); a predator (Citharichthys sordidus); scavengers (Nassarius fossatus and Pagurus samuelis) and deposit feeders (Neotrypaea californiensis, Dendraster excentricus and Olivella biplicata). Sampling occurred before, during and after blooms of P. australis in Monterey Bay, CA, USA during 2000 and 2001. DA was detected in all 8 species, with contamination persisting over variable time scales. Maximum DA levels in N. fossatus (674 ppm), E. analoga (278 ppm), C. sordidus (515 ppm), TV. californiensis (145 ppm), P. samuelis (56 ppm), D. excentricus (15 ppm) and O. biplicata (3 ppm) coincided with P. australis blooms, while DA levels in U. caupo remained above 200 ppm (max. = 751 ppm) throughout the study period. DA in 6 species exceeded levels thought to be safe for higher level consumers (i.e. ≥20 ppm) and thus is likely to have deleterious effects on marine birds, sea lions and the endangered California sea otter, known to prey upon these benthic species. © Inter-Research 2008., Cited By (since 1996):17, Ecology, CODEN: MESED
Author: Kvitek, Goldberg, Smith, Doucette, Silver
Date: 2008-01-01T00:00:00Z

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