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  • 1
    Publication Date: 2023-02-12
    Keywords: ALOHA2002-12-14; Calculated after Luo et al. (2012); CIII, abundance expressed in number of nifH gene copies; Comment; Date/Time of event; DEPTH, water; Diazotrophs, total biomass as carbon; Event label; Fluorescence-based quantitative real-time PCR (qPCR); Hawaiian Islands, North Central Pacific; Latitude of event; Longitude of event; MAREDAT_Diazotrophs_Collection; Trichodesmium, abundance expressed in number of nifH gene copies; Trichodesmium, biomass as carbon; Trichodesmium abundance, total; Unicellular cyanobacteria, biomass; Unicellular cyanobacteria-A, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-A, biological trait, ratio expressed in mass of carbon per amount of nifH gene copies; Unicellular cyanobacteria-B, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-B, biological trait, ratio expressed in mass of carbon per amount of nifH gene copies
    Type: Dataset
    Format: text/tab-separated-values, 75 data points
    Location Call Number Limitation Availability
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  • 2
    Publication Date: 2023-02-26
    Keywords: ALOHA2002-12-13; ALOHA2002-12-14; ALOHA2002-12-15; Calculated after Luo et al. (2012); Date/Time of event; DEPTH, water; Diazotrophs, total biomass as carbon; Event label; Fluorescence-based quantitative real-time PCR (qPCR); Hawaiian Islands, North Central Pacific; Heterocyst, biomass; Latitude of event; Longitude of event; MAREDAT_Diazotrophs_Collection; Richelia, abundance expressed in number of nifH gene copies; Richelia, associated species; Richelia, biological trait, ratio expressed in mass of carbon per amount of nifH gene copies; Sample comment; Trichodesmium, abundance expressed in number of nifH gene copies; Trichodesmium, biomass as carbon; Trichodesmium abundance, total; Unicellular cyanobacteria, biomass; Unicellular cyanobacteria-A, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-A, biological trait, ratio expressed in mass of carbon per amount of nifH gene copies; Unicellular cyanobacteria-B, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-B, biological trait, ratio expressed in mass of carbon per amount of nifH gene copies
    Type: Dataset
    Format: text/tab-separated-values, 341 data points
    Location Call Number Limitation Availability
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  • 3
    Publication Date: 2024-03-22
    Description: The oceans' uptake of anthropogenic carbon dioxide (CO2) decreases seawater pH and alters the inorganic carbon speciation – summarized in the term ocean acidification (OA). Already today, coastal regions experience episodic pH events during which surface layer pH drops below values projected for the surface ocean at the end of the century. Future OA is expected to further enhance the intensity of these coastal extreme pH events. To evaluate the influence of such episodic OA events in coastal regions, we deployed eight pelagic mesocosms for 53 days in Raunefjord, Norway, and enclosed 56–61 m**3 of local seawater containing a natural plankton community under nutrient limited post-bloom conditions. Four mesocosms were enriched with CO2 to simulate extreme pCO2 levels of 1978-2069 μatm while the other four served as untreated controls. Here, we present results from multivariate analyses on OA-induced changes in the phyto-, micro-, and mesozooplankton community structure. Pronounced differences in the plankton community emerged early in the experiment, and were amplified by enhanced top-down control throughout the study period. The plankton groups responding most profoundly to high CO2 conditions were cyanobacteria (negative), chlorophyceae (negative), auto- and heterotrophic microzooplankton (negative), and a variety of mesozooplanktonic taxa, including copepoda (mixed), appendicularia (positive), hydrozoa (positive), fish larvae (positive), and gastropoda (negative). The restructuring of the community coincided with significant changes in the concentration and elemental stoichiometry of particulate organic matter. Results imply that extreme CO2 events can lead to a substantial reorganization of the planktonic food web, affecting multiple trophic levels from phytoplankton to primary and secondary consumers.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Ammonium; Aragonite saturation state; Aragonite saturation state, standard deviation; Bicarbonate ion; Bicarbonate ion, standard deviation; Biogenic silica; Biomass/Abundance/Elemental composition; Calcite saturation state; Calcite saturation state, standard deviation; Calculated using seacarb; Calculated using seacarb after Nisumaa et al. (2010); Calculated using seacarb after Orr et al. (2018); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbon, organic, particulate; Carbon, organic, particulate/Nitrogen, organic, particulate ratio; Carbon, organic, particulate/Phosphorus, particulate ratio; Carbon, total, particulate; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Chlorophyceae indeterminata, biomass as carbon; Chlorophyll a; Chlorophyll a, standard deviation; Chrysophyceae indeterminata, biomass as carbon; Coast and continental shelf; Community composition and diversity; Cryptophyceae indeterminata, biomass as carbon; Cyanophyceae, biomass as carbon; DATE/TIME; Day of experiment; Diatoms indeterminata, biomass as carbon; Dinophyceae indeterminata, biomass as carbon; Entire community; Event label; Field experiment; Fjord; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Fugacity of carbon dioxide in seawater, standard deviation; KOSMOS_2015; KOSMOS_2015_Mesocosm-M1; KOSMOS_2015_Mesocosm-M2; KOSMOS_2015_Mesocosm-M3; KOSMOS_2015_Mesocosm-M4; KOSMOS_2015_Mesocosm-M5; KOSMOS_2015_Mesocosm-M6; KOSMOS_2015_Mesocosm-M7; KOSMOS_2015_Mesocosm-M8; KOSMOS_2015_Mesocosm-M9; KOSMOS Bergen; MESO; Mesocosm experiment; Mesocosm label; Mesocosm or benthocosm; Nitrate; Nitrate and Nitrite; Nitrite; Nitrogen, organic, particulate; Nitrogen, organic, particulate/Phosphorus, organic, particulate ratio; Nitrogen, total, particulate; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Particulate inorganic carbon/particulate organic carbon ratio; Pelagos; pH; pH, standard deviation; Phosphate; Phosphate, total, particulate; Potentiometric titration; Prasinophyceae indeterminata, biomass as carbon; Primary production/Photosynthesis; Prymnesiophyceae indeterminata, biomass as carbon; Ratio; Salinity; Salinity, standard deviation; Silicate; Temperate; Temperature, water; Temperature, water, standard deviation; Type
    Type: Dataset
    Format: text/tab-separated-values, 18566 data points
    Location Call Number Limitation Availability
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  • 4
    Publication Date: 2024-05-02
    Description: To gain a better understanding of what drives Pseudo-nitzschia australis growth and toxicity during upwelling and marine heatwave events, multiple-driver scenario or 'cluster' experiments were conducted using temperature, pCO2, and nutrient levels reflecting conditions during upwelling (13 ◦C, 900 ppm pCO2, replete nutrients) and two intensities of marine heatwaves (19 ◦C or 20.5 ◦C, 250 ppm pCO2, reduced macronutrients). We also conducted single-driver experiments to gain a mechanistic understanding of which drivers most impact P. australis growth and toxicity.
    Keywords: Alkalinity, total; Aragonite saturation state; Bacillariophyta; Bicarbonate ion; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chromista; Domoic acid per cell; Domoic acid production per particulate organic carbon; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Immunology/Self-protection; Laboratory experiment; Laboratory strains; Macro-nutrients; Net primary production of carbon per particulate organic carbon; Net primary production of carbon per particulate organic nitrogen; Not applicable; OA-ICC; Ocean Acidification International Coordination Centre; Other studied parameter or process; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Particulate domoic acid per particulate organic carbon; Pelagos; pH; Phytoplankton; Primary production/Photosynthesis; Pseudo-nitzschia australis; Replicate; Salinity; Single species; Species, unique identification; Species, unique identification (Semantic URI); Species, unique identification (URI); Temperature; Temperature, water; Treatment; Type of study
    Type: Dataset
    Format: text/tab-separated-values, 867 data points
    Location Call Number Limitation Availability
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  • 5
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.
    Description: Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of 〈0.05, and a total of 136 proteins were differentially abundant (p〈0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.
    Description: This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 3 (2012): 385, doi:10.3389/fmicb.2012.00385.
    Description: Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability 〈 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.
    Description: This research was funded by the National Science Foundation grant #OCE-0723667 (to Sonya T. Dyhrman, Mak A. Saito, Bethany D. Jenkins, and Tatiana A. Rynearson). Harriet Alexander is funded under a National Defense Science and Engineering Graduate (NDSEG) Fellowship.
    Keywords: Thalassiosira pseudonana ; Diatom ; Phytoplankton ; Housekeeping genes ; RT-qPCR ; Transcriptome ; Relative gene expression ; Reference gene
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
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  • 7
    Publication Date: 2022-10-31
    Description: Dataset: AE1812 incubation Chl a
    Description: Chlorophyll a concentrations from addition incubation experiments performed aboard AE1812 while transecting from the Sargasso Sea to Coastal Rhode Island in May 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/820938
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1558490
    Keywords: Chlorophyll a ; Subsurface chlorophyll maximum ; In situ samples ; On deck incubations
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
    Location Call Number Limitation Availability
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  • 8
    Publication Date: 2022-10-31
    Description: Dataset: Dissolved trace metal (Mn, Fe, Co, Ni, Cu, Zn, Cd, Pb) concentration
    Description: Concentrations of dissolved (〈0.2 µm) manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), cadmium (Cd), lead (Pb) in surface (~2 m) samples collected between 15 August 2018 and 6 September 2018 during EXports Processes in the Oceans from RemoTe Sensing (EXPORTS) cruise aboard RV Roger Revelle RR1813 at Ocean Station PAPA (Station P). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/869683
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1756816, NSF Division of Ocean Sciences (NSF OCE) OCE-1756433, NSF Division of Ocean Sciences (NSF OCE) OCE-1756442
    Keywords: Dissolved trace metals ; Ocean Station Papa ; Line P ; EXPORTS ; EXPORTS-NP
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
    Location Call Number Limitation Availability
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  • 9
    Publication Date: 2022-10-31
    Description: Dataset: NBP1608 TMs: stations
    Description: Dissolved trace metal concentrations from depth profiles during RVIB Nathaniel B. Palmer cruise NBP16-08 in the Southern Ocean from 2016-09-11 to 2016-10-10. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/781773
    Description: NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1443483, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1443474, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1443646
    Description: 2020-06-01
    Keywords: Trace metals ; Southern Ocean
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
    Location Call Number Limitation Availability
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  • 10
    Publication Date: 2022-10-31
    Description: Dataset: AE1812 Alkaline phosphatase
    Description: This dataset reports alkaline phosphatase activities (APA) for 3 incubation runs and 33 in situ samples collected on RV/Atlantic Explorer cruise AE1812 in May 2018. The samples were collected between Bermuda and Rhode Island. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/739973
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1558506
    Keywords: Alkaline phosphatase ; Diatoms
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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