Jenkins Bethany D.

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Jenkins
First Name
Bethany D.
ORCID
0000-0003-2319-3098

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  • Working Paper
    Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements
    (Woods Hole Oceanographic Institution, 2022-03) Berube, Paul M. ; Gifford, Scott M. ; Hurwitz, Bonnie ; Jenkins, Bethany D. ; Marchetti, Adrian ; Santoro, Alyson E.
    In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from Canada and France, met to develop a framework for standardization and intercalibration (S&I) of ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and metatranscriptomics). During the three-day workshop, participants discussed numerous topics, including: a) sample biomass collection and nucleic acid preservation for downstream analysis, b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f ) integration of bioinformatic considerations. This report provides a summary of these and other topics covered during the workshop and a series of recommendations for future S&I activities for na’omics approaches.
  • Dataset
    32Si data from EXPORTS cruise RR1813 on R/V Roger Revelle in the Subarctic North Pacific near Station PAPA from August to September 2018
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-02-06) Brzezinski, Mark A. ; Buck, Kristen N. ; Jenkins, Bethany D.
    This dataset includes depth profiles in the euphotic zone of nutrient (nitrate, silicate, phosphate) concentrations and profiles of silicic acid uptake rates from EXPORTS cruise RR1813. The EXPORTS field campaign in the subarctic North Pacific sampled an ecosystem characterized as high nutrient low chlorophyll (HNLC) due to low iron (Fe) levels that are primary controllers constraining phytoplankton utilization of other nutrients. It has been a paradigm in low Fe, HNLC systems that diatoms grow at elevated Si:C and Si:N ratios and should be efficiently exported as particles significantly enriched in Si relative to C. However, Fe limitation also alters diatoms species composition and the high Si demand imposed by low Fe can drive HNLC regions to Si limitation or Si/Fe co-limitation. Thus, the degree of Si and/or Fe stress in HNLC waters can all alter diatom taxonomic composition, the elemental composition of diatom cells, and the path cells follow through the food web ultimately altering diatom carbon export. Within each ecosystem state examined in the EXPORTS program, nutrient biogeochemistry, diatom and phytoplankton community structure, and global diatom gene expression patterns (metatranscriptomics) are characterized in the lit ocean. Nutrient amendment experiments with tracer addition (14C, 32Si) are used to quantify the level of Si and Fe stress being experienced by the phytoplankton and to contextualize taxa-specific metatranscriptome responses for resolving gene expression profiles in the in situ communities. 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/785856
  • Dataset
    Pseudo-nitzschia spp. cell counts, nutrients water temperature and salinity, and concentrations of the toxin domoic acid from weekly samples and offshore cruises with the Northeast U.S. Shelf (NES) Long-Term Ecological Research (LTER)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-04-29) Jenkins, Bethany D. ; Bertin, Matthew
    This dataset is related to approximately weekly sampling of Narragansett Bay, RI in tandem with the University of Rhode Island (URI) Graduate School of Oceanography (GSO) Long-Term Plankton Time Series (LTPTS) and Fish Trawl Survey to examine species assemblages and toxicity of the diatom genus Pseudo-nitzschia spp. This includes nutrient concentrations, cell counts, water temperature and salinity, and concentrations of the toxin domoic acid from these weekly samples and more, including offshore cruises with the Northeast U.S. Shelf (NES) Long-Term Ecological Research (LTER). 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/847448
  • Dataset
    Amplicon sequence variants (ASVs) recovered from samples and their related identification as Pseudo-nitzschia taxa and the methods used
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-04-29) Jenkins, Bethany D. ; Bertin, Matthew
    This dataset is related to approximately weekly sampling of Narragansett Bay, RI in tandem with the University of Rhode Island (URI) Graduate School of Oceanography (GSO) Long-Term Plankton Time Series (LTPTS) and Fish Trawl Survey to examine species assemblages and toxicity of the diatom genus Pseudo-nitzschia spp. This dataset includes the amplicon sequence variants (ASVs) recovered from samples and their related identification as Pseudo-nitzschia taxa and the methods used related to the Sterling et al manuscript. These data are connected to NCBI Bioproject PRJNA690940 & GenBank Accession Numbers MW447658 – MW447770, which will be released January 2025 or when the associated manuscript is published, whichever occurs first. 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/847469
  • Dataset
    Presence or absence of amplicon sequence variants (ASVs) recovered from samples which are described in DATASET 01, Pseudo-nitzschia spp. from weekly samples and offshore cruises with the Northeast U.S. Shelf (NES) Long-Term Ecological Research (LTER)
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-04-29) Jenkins, Bethany D. ; Bertin, Matthew
    This dataset is related to approximately weekly sampling of Narragansett Bay, RI in tandem with the University of Rhode Island (URI) Graduate School of Oceanography (GSO) Long-Term Plankton Time Series (LTPTS) and Fish Trawl Survey to examine species assemblages and toxicity of the diatom genus Pseudo-nitzschia spp. This dataset includes the presence or absence of amplicon sequence variants (ASVs) recovered from samples which are described in DATASET 01. 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/847495
  • Article
    Emerging harmful algal blooms caused by distinct seasonal assemblages of a toxic diatom
    (Association for the Sciences of Limnology and Oceanography, 2022-10-07) Sterling, Alexa R. ; Kirk, Riley D. ; Bertin, Matthew J. ; Rynearson, Tatiana A. ; Borkman, David G. ; Caponi, Marissa C. ; Carney, Jessica ; Hubbard, Katherine A. ; King, Meagan A. ; Maranda, Lucie ; McDermith, Emily J. ; Santos, Nina R. ; Strock, Jacob P. ; Tully, Erin M. ; Vaverka, Samantha B. ; Wilson, Patrick D. ; Jenkins, Bethany D.
    Diatoms in the Pseudo‐nitzschia genus produce the neurotoxin domoic acid. Domoic acid bioaccumulates in shellfish, causing illness in humans and marine animals upon ingestion. In 2017, high domoic acid levels in shellfish meat closed shellfish harvest in Narragansett Bay, Rhode Island for the first and only time in history, although abundant Pseudo‐nitzschia have been observed for over 60 years. To investigate whether an environmental factor altered endemic Pseudo‐nitzschia physiology or new domoic acid‐producing strain(s) were introduced to Narragansett Bay, we conducted weekly sampling from 2017 to 2019 and compared closure samples. Plankton‐associated domoic acid was quantified by LC‐MS/MS and Pseudo‐nitzschia spp. were identified using a taxonomically improved high‐throughput rDNA sequencing approach. Comparison with environmental data revealed a detailed understanding of domoic acid dynamics and seasonal multi‐species assemblages. Plankton‐associated domoic acid was low throughout 2017–2019, but recurred in fall and early summer maxima. Fall domoic acid maxima contained known toxic species as well as a novel Pseudo‐nitzschia genotype. Summer domoic acid maxima included fewer species but also known toxin producers. Most 2017 closure samples contained the particularly concerning toxic species, P. australis, which also appeared infrequently during 2017–2019. Recurring Pseudo‐nitzschia assemblages were driven by seasonal temperature changes, and plankton‐associated domoic acid correlated with low dissolved inorganic nitrogen. Thus, the Narragansett Bay closures were likely caused by both resident assemblages that become toxic depending on nutrient status as well as the episodic introductions of toxic species from oceanographic and climatic shifts.
  • Dataset
    Underway dissolved macronutrient concentrations collected on RVIB Nathaniel B. Palmer cruise NBP 16-08 from September to October 2016
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-03) Buck, Kristen N. ; Chappell, Phoebe Dreux ; Jenkins, Bethany D.
    Underway dissolved macronutrient concentrations collected on RVIB Nathaniel B. Palmer cruise NBP 16-08 from September to October 2016. 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/742549
  • Dataset
    ​Dissolved trace metal concentrations for Incubation 3, initiated September 27th, 2016 on RVIB Nathaniel B. Palmer cruise NBP16-08 in the Southern Ocean
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-24) Buck, Kristen N. ; Chappell, Phoebe Dreux ; Jenkins, Bethany D.
    ​Dissolved trace metal concentrations for Incubation 3, initiated September 27th, 2016 on RVIB Nathaniel B. Palmer cruise NBP16-08 in the Southern Ocean. 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/781841
  • Dataset
    Chlorophyll and phaeopigment concentrations from incubation experiments performed with amended Southern Drake Passage on RVIB Nathaniel B. Palmer cruise NBP 16-08 from September to October 2016
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-03-18) Chappell, Phoebe Dreux ; Buck, Kristen ; Jenkins, Bethany D.
    This dataset includes chlorophyll and phaeopigment concentrations from incubation experiments performed with amended Southern Drake Passage on RVIB Nathaniel B. Palmer cruise NBP 16-08 from September to October 2016. 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/742206
  • Dataset
    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
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-12-19) Buck, Kristen N. ; Chappell, Phoebe Dreux ; Jenkins, Bethany D.
    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
  • Dataset
    Chlorophyll a concentrations from addition incubation experiments performed aboard AE1812 while transecting from the Sargasso Sea to Coastal Rhode Island in May 2018.
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-08-26) Rynearson, Tatiana ; Jenkins, Bethany D.
    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
  • Dataset
    Alkaline phosphatase activities for in situ and incubation samples from RV/Atlantic Explorer cruise AE1812 cruise transect from Bermuda to Rhode Island in May 2018.
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-06-29) Dyhrman, Sonya T. ; Jenkins, Bethany D. ; Rynearson, Tatiana
    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
  • Dataset
    Chlorophyll a concentrations measured along the cruise track of AE1812 which transected from the Sargasso Sea to Coastal Rhode Island during May 2018.
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-08-26) Rynearson, Tatiana ; Jenkins, Bethany D.
    Chlorophyll a concentrations measured along the cruise track of AE1812 which transected from the Sargasso Sea to Coastal Rhode Island during 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/820948
  • Article
    Meeting report : Ocean ‘omics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013)
    (Genomic Standards Consortium, 2014) Gilbert, Jack A. ; Dick, Gregory J. ; Jenkins, Bethany D. ; Heidelberg, John F. ; Allen, Eric E. ; Mackey, Katherine R. M. ; DeLong, Edward F.
    The National Science Foundation’s EarthCube End User Workshop was held at USC’s Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterise the needs and tools available to the community focusing on microbial and physical oceanography research with a particular focus on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analysing the existing data, and on the need for the construction and curation of diverse federated databases, as well as development of shared interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyberinfrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.
  • Article
    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
    (Public Library of Science, 2014-06-24) Keeling, Patrick J. ; Burki, Fabien ; Wilcox, Heather M. ; Allam, Bassem ; Allen, Eric E. ; Amaral-Zettler, Linda A. ; Armbrust, E. Virginia ; Archibald, John M. ; Bharti, Arvind K. ; Bell, Callum J. ; Beszteri, Bank ; Bidle, Kay D. ; Cameron, Connor T. ; Campbell, Lisa ; Caron, David A. ; Cattolico, Rose Ann ; Collier, Jackie L. ; Coyne, Kathryn J. ; Davy, Simon K. ; Deschamps, Phillipe ; Dyhrman, Sonya T. ; Edvardsen, Bente ; Gates, Ruth D. ; Gobler, Christopher J. ; Greenwood, Spencer J. ; Guida, Stephanie M. ; Jacobi, Jennifer L. ; Jakobsen, Kjetill S. ; James, Erick R. ; Jenkins, Bethany D. ; John, Uwe ; Johnson, Matthew D. ; Juhl, Andrew R. ; Kamp, Anja ; Katz, Laura A. ; Kiene, Ronald P. ; Kudryavtsev, Alexander N. ; Leander, Brian S. ; Lin, Senjie ; Lovejoy, Connie ; Lynn, Denis ; Marchetti, Adrian ; McManus, George ; Nedelcu, Aurora M. ; Menden-Deuer, Susanne ; Miceli, Cristina ; Mock, Thomas ; Montresor, Marina ; Moran, Mary Ann ; Murray, Shauna A. ; Nadathur, Govind ; Nagai, Satoshi ; Ngam, Peter B. ; Palenik, Brian ; Pawlowski, Jan ; Petroni, Giulio ; Piganeau, Gwenael ; Posewitz, Matthew C. ; Rengefors, Karin ; Romano, Giovanna ; Rumpho, Mary E. ; Rynearson, Tatiana A. ; Schilling, Kelly B. ; Schroeder, Declan C. ; Simpson, Alastair G. B. ; Slamovits, Claudio H. ; Smith, David R. ; Smith, G. Jason ; Smith, Sarah R. ; Sosik, Heidi M. ; Stief, Peter ; Theriot, Edward ; Twary, Scott N. ; Umale, Pooja E. ; Vaulot, Daniel ; Wawrik, Boris ; Wheeler, Glen L. ; Wilson, William H. ; Xu, Yan ; Zingone, Adriana ; Worden, Alexandra Z.
    Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
  • Article
    The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response
    (Public Library of Science, 2012-03-29) Dyhrman, Sonya T. ; Jenkins, Bethany D. ; Rynearson, Tatiana A. ; Saito, Mak A. ; Mercier, Melissa L. ; Alexander, Harriet ; Whitney, LeAnn P. ; Drzewianowski, Andrea ; Bulygin, Vladimir V. ; Bertrand, Erin M. ; Wu, Zhijin ; Benitez-Nelson, Claudia R. ; Heithoff, Abigail
    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.
  • Working Paper
    EXPORTS Measurements and Protocols for the NE Pacific Campaign
    (NASA STI Program and Woods Hole Oceanographic Institution, 2021-02) Behrenfeld, Michael J. ; Benitez-Nelson, Claudia R. ; Boss, Emmanuel S. ; Brzezinski, Mark A. ; Buck, Kristen N. ; Buesseler, Ken O. ; Burd, Adrian B. ; Carlson, Craig A. ; Cassar, Nicolas ; Cetinić, Ivona ; Close, Hilary G. ; Craig, Susanne E. ; D'Asaro, Eric A. ; Durkin, Colleen A. ; Estapa, Margaret L. ; Fassbender, Andrea ; Fox, James ; Freeman, Scott ; Gifford, Scott M. ; Gong, Weida ; Graff, Jason R. ; Gray, Deric ; Guidi, Lionel ; Halsey, Kim ; Hansell, Dennis A. ; Haëntjens, Nils ; Horner, Tristan J. ; Jenkins, Bethany D. ; Jones, Janice L. ; Karp-Boss, Lee ; Kramer, Sasha J. ; Lam, Phoebe J. ; Lee, Craig M. ; Lee, Jong-Mi ; Liu, Shuting ; Mannino, Antonio ; Maas, Amy E. ; Marchal, Olivier ; Marchetti, Adrian ; McDonnell, Andrew M. P. ; McNair, Heather ; Menden-Deuer, Susanne ; Morison, Francoise ; Nelson, Norman B. ; Nicholson, David P. ; Niebergall, Alexandria K. ; Omand, Melissa M. ; Passow, Uta ; Perry, Mary J. ; Popp, Brian N. ; Proctor, Chris ; Rafter, Patrick ; Roca-Martí, Montserrat ; Roesler, Collin S. ; Rubin, Edwina ; Rynearson, Tatiana A. ; Santoro, Alyson E. ; Siegel, David A. ; Sosik, Heidi M. ; Soto Ramos, Inia ; Stamieszkin, Karen ; Steinberg, Deborah K. ; Stephens, Brandon M. ; Thompson, Andrew F. ; Van Mooy, Benjamin A. S. ; Zhang, Xiaodong
    EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led and NSF co-funded field campaign that will provide critical information for quantifying the export and fate of upper ocean net primary production (NPP) using satellite information and state of the art technology.
  • Dataset
    ​Dissolved trace metal concentrations for Incubation 2, initiated September 24th, 2016 on RVIB Nathaniel B. Palmer cruise NBP16-08 in the Southern Ocean
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-24) Buck, Kristen N. ; Chappell, Phoebe Dreux ; Jenkins, Bethany D.
    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/781827
  • Dataset
    32Si and 14C production data (experimental) from EXPORTS cruise RR1813 on R/V Roger Revelle in the Subarctic North Pacific near Station PAPA from August to September 2018
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-02-06) Brzezinski, Mark A. ; Buck, Kristen N. ; Jenkins, Bethany D.
    This dataset includes 32Si and 14C production data (experimental) from EXPORTS cruise RR1813. The EXPORTS field campaign in the subarctic North Pacific sampled an ecosystem characterized as high nutrient low chlorophyll (HNLC) due to low iron (Fe) levels that are primary controllers constraining phytoplankton utilization of other nutrients. It has been a paradigm in low Fe, HNLC systems that diatoms grow at elevated Si:C and Si:N ratios and should be efficiently exported as particles significantly enriched in Si relative to C. However, Fe limitation also alters diatoms species composition and the high Si demand imposed by low Fe can drive HNLC regions to Si limitation or Si/Fe co-limitation. Thus, the degree of Si and/or Fe stress in HNLC waters can all alter diatom taxonomic composition, the elemental composition of diatom cells, and the path cells follow through the food web ultimately altering diatom carbon export. Within each ecosystem state examined in the EXPORTS program, nutrient biogeochemistry, diatom and phytoplankton community structure, and global diatom gene expression patterns (metatranscriptomics) are characterized in the lit ocean. Nutrient amendment experiments with tracer addition (14C, 32Si) are used to quantify the level of Si and Fe stress being experienced by the phytoplankton and to contextualize taxa-specific metatranscriptome responses for resolving gene expression profiles in the in situ communities. 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/786013
  • Article
    Identifying reference genes with stable expression from high throughput sequence data
    (Frontiers Media, 2012-11-09) Alexander, Harriet ; Jenkins, Bethany D. ; Rynearson, Tatiana A. ; Saito, Mak A. ; Mercier, Melissa L. ; Dyhrman, Sonya T.
    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.