Search results | Digital Commons of Moss Landing Marine Laboratories

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: 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: 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: 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: 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: 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: 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. © 2014.
Author: Drake, Tamburri, First, Smith, Johengen
Date: 2014-01-01T00:00:00Z

Title: The Applicability of Sonars for Habitat Mapping: a Bibliography
Author: Smith, McConnaughey

Title: An evaluation of ISFET sensors for coastal pH monitoring applications
Description: Abstract The accuracy and precision of ion sensitive field effect transistor (ISFET) pH sensors have been well documented, but primarily by ocean chemistry specialists employing the technology at single locations. Here we examine their performance in a network context through comparison to discrete measurements of pH, using different configurations of the Honeywell DuraFET pH sensor deployed in six coastal settings by operators with a range of experience. Experience of the operator had the largest effect on performance. The average difference between discrete and ISFET pH was 0.005 pH units, but ranged from −0.030 to 0.083 among operators, with more experienced operators within ± 0.02 pH units of the discrete measurement. In addition, experienced operators achieved a narrower range of variance in difference between discrete bottle measurements and ISFET sensor readings compared to novice operators and novice operators had a higher proportion of data failing quality control screening. There were no statistically significant differences in data uncertainty associated with sensor manufacturer or deployment environment (pier-mounted, flowthrough system, and buoy-mounted). The variation we observed among operators highlights the necessity of best practices and training when instruments are to be used in a network where comparison across data streams is desired. However, while opportunities remain for improving the performance of the ISFET sensors when deployed by less experienced operators, the uncertainty associated with their deployment and validation was several-fold less than the observed natural temporal variability in pH, demonstrating the utility of these sensors in tracking local changes in acidification.
Author: McLaughlin, Dickson, Weisberg, Coale, Elrod, Hunter, Johnson, Kram, Kudela, Martz, Negrey, Passow, Shaughnessy, Smith, Tadesse, Washburn, Weis
Date: 2017-04-01T00:00:00Z

Title: Causality of an extreme harmful algal bloom in Monterey Bay, California, during the 2014–2016 northeast Pacific warm anomaly
Description: 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., Published
Author: Bowers, Smith