http://lod.bco-dmo.org/id/dataset/936856
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-09-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pseudo-nitzschia spp. presence-absence and environmental data in Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023
2024-10-14
publication
2024-10-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-14
publication
https://doi.org/10.26008/1912/bco-dmo.936856.1
Bethany D. Jenkins
University of Rhode Island
principalInvestigator
Matthew Bertin
University of Rhode Island
principalInvestigator
Riley Kirk
University of Rhode Island
principalInvestigator
Tatiana A. Rynearson
University of Rhode Island
principalInvestigator
Alexa Sterling
University of Rhode Island
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Roche, K. M., Church, I., Sterling, A., Rynearson, T. A., Bertin, M., Kim, A., Kirk, R., Jenkins, B. D. (2024) Pseudo-nitzschia spp. presence-absence and environmental data in Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.936856.1 [access date]
Dataset Description: <p>Acknowledgement:</p>
<p>We acknowledge the NSF RI C-AIM EPSCoR Cooperative Agreement (OIA-1004057) for research support. Sequencing was performed at the University of Rhode Island Molecular Informatics Core supported by the Institutional Development Award (IDeA) Network for Biomedical Research Excellence from the National Institute of General Medical Sciences of the National Institutes of Health (P20GM103430).</p> Methods and Sampling: <p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px">Samples were selected from the NES-LTER transect and various time series sites in <span style="color:rgb(0, 0, 0)">Narragansett Bay, Rhode Island (</span>NB</span>) during winter and summer periods from January 2018 through February 2023 to compare seasonal and regional patterns of <em>Pseudo-nitzschia</em> species composition and DA, as well as environmental drivers. NB and NES will henceforth be referred to as subregions of the larger Northeast U.S. Continental Shelf region, with NES specifically referring to the area spanned by the NES-LTER transect. Samples were collected on NES-LTER cruises (<em>R/V</em> Endeavor, <em>R/V</em> Atlantis) from 11 stations along a 150 km transect (n=77) each winter (January-February) and summer (July-August). Samples from three to four stations per cruise were used in this dataset spanning innershelf (L1), midshelf (L3, L4) and outershelf (L7, L8, L10) sections of the transect. The northernmost station, L1, is about 50 km from the mouth of NB. To collect plankton biomass for nucleic acid isolation, CTD rosette seawater from the surface and subsurface chlorophyll maximum (SCM) were passed via peristaltic pump over 25 mm 5 µm pore size filters (Sterlitech, Kent, WA, USA). Biomass filters were either flash frozen in liquid nitrogen (2018-2022) or placed in DNA/RNA shield (winter 2023; Zymo Research, Irvine, CA, USA) and stored in a -80°C freezer. The SCM depth varied as observed by <em>in situ</em> chlorophyll fluorescence, with a median depth of 28 m for summer and 19 m for winter samples. In cases where the SCM was not well defined due to water column mixing that typically took place in winter at nearshore stations, a sampling depth between 20 and 30 m was targeted.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">In NB, surface seawater samples were collected from various sites in the East and West Passages including the Narragansett Bay Long-Term Plankton Time Series (NBPTS) site, Whale Rock (WR), Castle Hill Beach (CHB), East Passage (EP), and University of Rhode Island Graduate School of Oceanography (GSO) dock. Seawater was transported back to the laboratory and passed over 25 mm 5 µm pore size filters (Sterlitech, Kent, WA, USA) using a peristaltic pump before flash freezing in liquid nitrogen and storage at -80°C. To fill in several missing dates from this time series, six samples collected separately in the NBPTS (https://web.uri.edu/gso/research/plankton/) sampling program were used. These samples differed in collection methodology only by the filter pore size used (0.22 µm, Express Plus, Millipore Sigma) and vacuum as opposed to peristaltic filtration.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">DNA was extracted from most NB and NES samples (n=219) using a modified version of the DNeasy Plant Kit (Qiagen, Germantown, MD, USA) that included a 1-minute bead beating step (0.1 mm and 0.5 mm Zirconia/Silica beads, BioSpec Products, Bartlesville, OK, USA) and two part elution into a total of 45 µL Buffer AE. Similarly, the six NBPTS samples were extracted using a modified version of the DNeasy Blood &amp; Tissue kit (Qiagen, Germantown, MD, USA) with a 1-minute bead beating step and final elution into 50 µL Buffer AE. Some NES samples (n=18) were extracted using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) with a 1-minute bead beating step (0.4 mm Zirconium Beads, OPS Diagnostics, Lebanon, NJ, USA) and final elution into 50 µL nuclease-free water. DNA from each sample was amplified with a primer set that targets the eukaryotic internal transcribed spacer region 1 (ITS1) and effectively distinguishes <em>Pseudo-nitzschia</em> species (White et al., 1990; Sterling et al., 2022). Briefly, DNA was diluted to 1-4 ng/µL and 2 µL of template was added to 25 µL PCR reactions with Phusion Hot Start High-Fidelity Master Mix (Thermo Fisher Scientific Inc., Waltham, MA, USA) and HPLC-purified forward and reverse primers at 0.5 µM concentration with Illumina MiSeq adapters (Integrated DNA Technologies, Coralville, IA, USA). A stepwise thermocycle was used as described in Sterling et al. (2022).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">DNA amplicons were sequenced at the Rhode Island-INBRE Molecular Informatics Core on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA, USA). There, libraries were prepared by cleaning ITS1 PCR products with KAPA pure beads (KAPA Biosystems, Woburn, MA, USA) and attaching sequencing indices and adapters using PCR. This amplification was performed with the Illumina Nextera XT Index Kit (Illumina, San Diego, CA, USA) and Phusion High Fidelity Master Mix, followed by a second round of cleaning with KAPA pure beads and visualization with gel electrophoresis. The quality of select samples was assessed on a Bioanalyzer DNA1000 chip (Agilent Technologies, Santa Clara, CA, USA) and all samples were quantified on a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA). The final library was pooled, quantified with qPCR on a LightCycler480 (Roche, Pleasanton, CA, USA) using a KAPA Biosystems Illumina Kit (KAPA Biosystems, Woburn, MA, USA), and sequenced on the Illumina MiSeq using v3 chemistry and 2x250 paired-end reads. Samples were sequenced across five separate MiSeq runs using identical methods and negative controls.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">Various biological, chemical, and physical data were collected during each sampling event. In NB, surface temperature and salinity were measured using multiparameter sondes (6920 V2 for samples collected at NBPTS and WR; ProDSS for samples collected at CHB and GSO dock; YSI, Yellow Springs, Ohio, USA). During NES sampling, temperature and salinity were measured using two SBE911 CTD sensors (Sea Bird Electronics, Bellevue, WA, USA) and the mean of the two measurements was used in the final analysis. Dissolved macronutrient samples were collected by freezing 0.2 µm seawater filtrate at -20°C. NB site nutrients were analyzed at the University of Rhode Island Marine Science Research Facility (URI MSRF, Narragansett, RI, USA) on a QuickChem 8500 (Lachat, Milwaukee, WI, USA) while NES samples were measured at the Woods Hole Oceanographic Institution’s Nutrient Analytical Facility (Woods Hole, MA, USA) on a four-channel segmented flow AA3 HR Autoanalyzer (SEAL Analytical, Mequon, WI, USA). Both instruments measured nitrite + nitrate, ammonium, silicate, and phosphate. Nitrite + nitrate and ammonium values were summed and used in the analysis as dissolved inorganic nitrogen (DIN). Any measurements below each instrument’s limit of detection for each nutrient type were replaced with zero.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">Biomass for particle-associated DA analysis was collected, extracted, and analyzed via liquid chromatography with tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring. All samples were chromatographically separated in an identical fashion to Sterling et al. (2022), and the majority of samples (n=167) were analyzed using a 4500 QTRAP mass spectrometer (SCIEX, Framingham, MA, USA). A subset of samples (n=42) were measured using a 1290 Infinity II UHPLC system coupled to a 6470 Triple Quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA, USA). The peak of DA eluted at 10.41 min. Analysis was carried out in positive mode, and three transitions from the protonated DA molecule were used and optimized for quantification: <em>m/z</em> 312 → 266, <em>m/z</em> 312 → 161, and <em>m/z</em> 312 → 105 determined by MassHunter Optimizer (Agilent, Santa Clara, CA, USA) including the optimized fragmentor (112), collision energy (20, 28, 48), and cell accelerator voltage (4) settings. The <em>m/z</em> 312 → 266 transition was used for quantification following acquisition from both mass spectrometry instruments. Particle-associated DA was quantified to ng particulate DA L<sup>-1</sup> of filtered seawater using an external calibration curve created with pure DA standards of increasing concentrations included in each analysis (DA Certified Reference Material, National Research Council Canada, Halifax, Nova Scotia).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif"><em>Pseudo-nitzschia </em>spp. abundance was quantified using light microscopy cell counts of live (NBPTS site) and preserved (all other sites) samples. For preserved samples, acidic Lugol’s solution was added to whole seawater for a final concentration of 1% Lugol’s and stored at 4°C until enumeration. A Sedgewick-Rafter counting chamber (Science First/Wildco, Yulee, FL, USA) and a BX40 light microscope (Olympus, Tokyo, Japan) were used to identify and enumerate cells at the genus level, since many <em>Pseudo-nitzschia</em> species are morphologically cryptic under light microscopy (Bates et al., 2018).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px">Sampling Locations</span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Narragansett Bay sites: </span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Narragansett Bay Long Term Plankton Time Series (41.57 N -71.39 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Whale Rock (41.43 N -71.42 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">East Passage (41.45 N -71.38 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Castle Hill Beach (41.46 N -71.36 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Graduate School of Oceanography dock (41.49 N -71.42 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">NES stations: </span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">L1 (41.20 N -70.88 W), L3 (40.86 N -70.88 W), L4 (40.70 N -70.88 W), L7 (40.23 N -70.88 W), L8 (40.14 N -70.77 W), L10 (39.93 N -70.88 W)</span></span></span></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1655686 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1655686
Funding provided by NSF Office of Integrative Activities (NSF OIA) Award Number: OIA-1655221 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1655221
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA18OAR4170094
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2322676 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2322676
completed
Bethany D. Jenkins
University of Rhode Island
401-874-7551
Department of Cell and Molecular Biology and Graduate School of Oceanography 279 CBLS, 120 Flagg Road
Kingston
RI
02881
USA
bdjenkins@uri.edu
pointOfContact
Matthew Bertin
University of Rhode Island
401 874 5016
mbertin@uri.edu
pointOfContact
Riley Kirk
University of Rhode Island
rileykirk@uri.edu
pointOfContact
Tatiana A. Rynearson
University of Rhode Island
401-874-6022
Graduate School of Oceanography, University of Rhode Island 215 South Ferry Rd.
Narragansett
RI
02882
USA
rynearson@uri.edu
pointOfContact
Alexa Sterling
University of Rhode Island
Sterling.Alexa@epa.gov
pointOfContact
asNeeded
Dataset Version: 1
Unknown
library_ID
Sample_Date
Site
Site_Abbreviation
Lat
Lon
Depth_category
Depth
Season
LTER_cruise
CTD_cast
Niskin
pDA
Pseudonitzschia
Temp
Salinity
Phosphate
Silicate
Nitrate_and_Nitrite
Nitrite
Ammonium
Nitrate
DIN
Pseudo_nitzschia_americana
Pseudo_nitzschia_australis
Pseudo_nitzschia_caciantha
Pseudo_nitzschia_calliantha
Pseudo_nitzschia_cuspidata
Pseudo_nitzschia_delicatissima
Pseudo_nitzschia_fraudulenta
Pseudo_nitzschia_galaxiae
Pseudo_nitzschia_hasleana
Pseudo_nitzschia_inflatula
Pseudo_nitzschia_mannii
Pseudo_nitzschia_multiseries
Pseudo_nitzschia_multistriata
Pseudo_nitzschia_plurisecta
Pseudo_nitzschia_pungens
Pseudo_nitzschia_pungens_var_aveirensis
Pseudo_nitzschia_pungens_var_cingulata
Pseudo_nitzschia_qiana
Pseudo_nitzschia_sabit
Pseudo_nitzschia_subpacifica
Pseudo_nitzschia_turgidula
NCBI_BioSample
NCBI_BioProject
Illumina MiSeq Platform
SBE911 CTD sensors
Lachat QuickChem 8500
6470 Triple Quadrupole mass spectrometer
SCIEX 4500 Qtrap mass spectrometer
BX40 light microscope
AA3 HR Autoanalyzer
Sedgewick Rafter Counting Chamber
Eppendorf Mastercycler EP Thermal Cycler Series
1290 Infinity II UHPLC system
YSI ProDSS multiparameter meter
theme
None, User defined
No BCO-DMO term
date
site
Site_ID
latitude
longitude
depth
season
Cruise identfier
cast
Niskin bottle number
domoic acid
cell_concentration
water temperature at measurement depth
salinity
Dissolved Inorganic Phosphate
silicate, silicon dioxide SiO2
nitrate plus nitrite
Nitrite
Ammonium
Nitrate
Dissolved Inorganic Nitrogen
flag
NCBI BioSample accession
NCBI BioProject accession
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD Sea-Bird 911
Lachat QuikChem 8500 flow injection analysis system
Mass Spectrometer
Mass Spectrometer
Microscope - Optical
Seal Analytical AutoAnalyser 3HR
Sedgewick Rafter Counting Chamber
Thermal Cycler
Ultra-high-performance liquid chromatography
YSI Professional Plus Multi-Parameter Probe
instrument
BCO-DMO Standard Instruments
EN608
EN617
EN627
EN644
EN649
EN655
EN661
EN668
AT46
EN687
EN695
service
Deployment Activity
Narragansett Bay in Rhode Island, USA and offshore Atlantic Ocean transect across the Northeast U.S. Shelf (NES)
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Long Term Ecological Research network
http://www.lternet.edu/
Long Term Ecological Research network
adapted from http://www.lternet.edu/
The National Science Foundation established the LTER program in 1980 to support research on long-term ecological phenomena in the United States. The Long Term Ecological Research (LTER) Network is a collaborative effort involving more than 1800 scientists and students investigating ecological processes over long temporal and broad spatial scales. The LTER Network promotes synthesis and comparative research across sites and ecosystems and among other related national and international research programs. The LTER research sites represent diverse ecosystems with emphasis on different research themes, and cross-site communication, network publications, and research-planning activities are coordinated through the LTER Network Office.
2017 LTER research site map obtained from https://lternet.edu/site/lter-network/
LTER
largerWorkCitation
program
Northeast U.S. Shelf Long Term Ecological Research site
https://nes-lter.whoi.edu/
Northeast U.S. Shelf Long Term Ecological Research site
<p><strong>Continuing Award OCE-2322676<br />
<em>Sep 2023 to Aug 2028 (estimated)</em><br />
LTER: Scales of Variability in Ecosystem Dynamics and Production on the Changing Northeast U.S. Shelf (NES II)</strong><br />
<strong><em>NSF Award Abstract:</em></strong></p>
<p>The Northeast U.S. Shelf (NES) is the region of the Northwest Atlantic Ocean that overlies the continental shelf from North Carolina to Maine. The NES has a long history of intense human utilization and provides an array of ecosystem services including shipping, recreation, conservation, and energy development. The NES also comprises a seasonally dynamic and productive ecosystem, supporting renowned fisheries, whose integrity is critical to the health of the Northeast U.S. economy. The NES ecosystem's productivity is fueled by planktonic organisms that interact with each other in complex food webs whose structure depends on environmental conditions (e.g., temperature, light, and nutrient levels). These conditions are rapidly changing because of climate-change-related warming and human utilization. For example, the NES is seeing the largest development of coastal wind farms in the U.S. to date. Phase II of the Northeast U.S. Shelf Long-Term Ecological Research program (NES-LTER II) advances our ability to predict how anthropogenic impacts will affect the dynamics of the shelf's planktonic food webs and their ability to support the productivity of higher trophic levels, from fish to whales and humans. Because the NES is subject to long-term challenges that will impact many people, the project emphasizes an active education component for helping to train the next generation of marine scientists and outreach activities to increase public understanding of marine science and technology. The project team conducts education and outreach via three main components: (1) training and mentoring for early career researchers from undergraduates to postdoctoral researchers in LTER research; (2) an LTER Schoolyard program that engages middle and high school teachers and students; and (3) public outreach through targeted events, the project website, and social media channels.</p>
<p>Patterns of ecosystem change over seasons to decades have been documented in the NES, but the key mechanisms linking changes in the physical environment, planktonic food webs, and higher trophic levels remain poorly understood. As a result, predictive capability is limited and management strategies are largely reactive. To address these needs, NES II is targeting a mechanistic understanding of how food web structure and function responds to environmental conditions, natural variability and human induced changes. NES II combines observations that provide regional-scale context, process cruises along a high gradient cross-shelf transect, high-frequency time series at an inner-shelf location, coupled biological-physical food web models, and targeted population models. In addition, the research team is investigating how community structure and trophic transfer are impacted by disturbances including (i) the increasing prevalence of heat waves, (ii) intrusions of offshore water associated with increasing instability in the Gulf Stream, and (iii) offshore wind farms now under construction on the NES. The long-term research plan is guided by the overarching science question: "How is climate change impacting the pelagic NES ecosystem and, in particular, affecting the relationship between compositional (e.g., species diversity and size structure) and aggregate (e.g., rates of primary production, and transfer of energy to higher trophic levels) variability?" The investigators are assessing the extent to which the NES ecosystem possesses a biodiversity reservoir that is resilient to dramatic changes in the environment and that will allow the ecosystem to maintain overall productivity.<br />
</p>
<p><strong>Prior Award<br />
<em>Sep 2017 to Feb 2024</em><br />
LTER: Linking Pelagic Community Structure with Ecosystem Dynamics and Production Regimes on the Changing Northeast US Shelf</strong><em> </em><br />
Summary information including abstract, PIs, and other award details are included in the Funding History PDF in the Files section below.</p>
<p><strong>Additional Information:</strong><br />
The NES-LTER project includes collaboration with the National Marine Fisheries Service / Northeast Fisheries Science Center [NMFS/NEFSC] in particular for sharing data related to Project EcoMon Zooplankton <a class="moz-txt-link-freetext" href="https://www.bco-dmo.org/project/2106">https://www.bco-dmo.org/project/2106.</a></p>
<p><strong>This project is supported by continuing grants with slight name variations:</strong></p>
<ul>
<li><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px"> LTER: Linking Pelagic Community Structure with Ecosystem Dynamics and Production Regimes on the Changing Northeast US Shelf</span></li>
<li><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px"> LTER: Scales of Variability in Ecosystem Dynamics and Production on the Changing Northeast U.S. Shelf (NES II)</span></li>
</ul>
NES LTER
largerWorkCitation
project
RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling
https://osprey.bco-dmo.org/project/836631
RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling
<p>NSF Award Abstract:</p>
<p>Non-technical Description<br />
The University of Rhode Island (URI) will establish the Consortium for Coastal Ecology Assessment, Innovation, and Modeling (C-AIM) to coordinate research, education, and workforce development across Rhode Island (RI) in coastal marine science and ecology. C-AIM addresses fundamental research questions using observations, computational methods, and technology development applied to Narraganset Bay (NB), the largest estuary in New England and home to important ecosystem services including fisheries, recreation, and tourism. The research will improve understanding of the microorganisms in NB, develop new models to predict pollution and harmful algal bloom events in NB, build new sensors for nutrients and pollutants, and provide data and tools for stakeholders in the state. Observational capabilities will be coordinated in an open platform for researchers across RI; it will provide real-time physical, chemical, and biological observations ? including live streaming to mobile devices. C-AIM will also establish the RI STEAM (STEM + Art) Imaging Consortium to foster collaboration between artists, designers, engineers, and scientists. Research internships will be offered to undergraduate students throughout the state and seed funding for research projects will be competitively awarded to Primarily Undergraduate Institution partners.</p>
<p>Technical Description<br />
C-AIM will employ observations and modeling to assess interactions between organisms and ecosystem function in NB and investigate ecological responses to environmental events, such as hypoxia and algal blooms. Observations of the circulation, biogeochemistry, and ecosystem will be made using existing and new instrument platforms. The Bay Observatory ? a network of observational platforms around NB - will be networked to trigger enhanced water sampling and sensing during specific environmental events, such as hypoxic conditions or phytoplankton blooms. Biogeochemical, ecological, and coastal circulation models will be integrated and coupled to focus on eutrophication and pollutant loading. Data and models will be integrated on multiple scales, from individual organisms and trophic interactions to food-web responses, and from turbulence to the regional ocean circulation. New sensing technologies for nutrients and pollutants will be developed, including affordable, micro-fluidic (Lab-on-a-Chip) devices with antifouling capabilities. The results will be synthesized and communicated to stakeholders.</p>
C-AIM
largerWorkCitation
project
Narragansett Bay Long-Term Plankton Time Series
https://web.uri.edu/gso/research/plankton/
Narragansett Bay Long-Term Plankton Time Series
<p>The Narragansett Bay Long-Term Plankton Time Series is one of the world’s longest-running plankton surveys. Beginning in 1957, weekly samples have been collected to assess the phytoplankton community and characterize the physical parameters of Narragansett Bay.</p>
<p>Samples are collected once per week -regardless of tidal stage- for temperature, salinity, turbidity, size-fractionated chlorophyll a and nutrients. Microplankton community composition (size range >10μm, both species identification and abundance) is determined using a light microscope to quantify live samples. The species list for the >10μm size fraction includes 246 different species or species complexes of protists. Samples are also collected for the determination of copepod and ctenophore concentrations.</p>
<p>Funding for the time series has come from the University of Rhode Island since 1999. Ship time is frequently provided by the U.S. Department of Fish and Wildlife.</p>
<p><strong>This Time Series is related to the following projects at BCO-DMO:</strong></p>
<ul>
<li>Connecting local, regional and global scales of gene flow in planktonic marine diatoms (<a href="https://www.bco-dmo.org/project/511708">https://www.bco-dmo.org/project/511708</a>)</li>
<li>Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients (<a href="https://www.bco-dmo.org/project/712787">https://www.bco-dmo.org/project/712787</a>)</li>
<li>LTER: Linking Pelagic Community Structure with Ecosystem Dynamics and Production Regimes on the Changing Northeast US Shelf (<a href="https://www.bco-dmo.org/project/747769">https://www.bco-dmo.org/project/747769</a>)</li>
<li>Quantifying Temperature Dependence In Growth & Grazing Rates of Planktonic Herbivores (<a href="https://www.bco-dmo.org/project/739232">https://www.bco-dmo.org/project/739232</a>)</li>
<li>RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling (<a href="https://www.bco-dmo.org/project/836631">https://www.bco-dmo.org/project/836631</a>)</li>
</ul>
NBPTS
largerWorkCitation
project
eng; USA
oceans
Narragansett Bay in Rhode Island, USA and offshore Atlantic Ocean transect across the Northeast U.S. Shelf (NES)
-71.42
-70.77
39.93
41.57
2018-01-31
2023-01-16
From projects that focused on the following 2 locations: 1. Northeast U.S. Continental Shelf Large Marine Ecosystem: 35.2019 to 46.0906 latitude, -77.3492 to -63.3608 longitude 2. Narragansett Bay, Rhode Island
0
BCO-DMO catalogue of parameters from Pseudo-nitzschia spp. presence-absence and environmental data in Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/940182.rdf
Name: library_ID
Units: unitless
Description: <p>Sequencing identifying number that associates environmental data with sequencing data matrix.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940183.rdf
Name: Sample_Date
Units: unitless
Description: <p>Sample collection date</p>
http://lod.bco-dmo.org/id/dataset-parameter/940184.rdf
Name: Site
Units: unitless
Description: <p>Sample collection site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/940185.rdf
Name: Site_Abbreviation
Units: unitless
Description: <p>Sample collection site name abbreviated</p>
http://lod.bco-dmo.org/id/dataset-parameter/940186.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of sampling site (N = positive)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940187.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of sampling site (W = negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940188.rdf
Name: Depth_category
Units: unitless
Description: <p>Qualitative depth category used in analysis to indicate sampling depth. Surface means that the sample was collected within the upper 5 m of the water column and SCM stands for subsurface chlorophyll maximum which was determined by chlorophyll fluorescence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940189.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940190.rdf
Name: Season
Units: unitless
Description: <p>Season of sample collection used in analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/940191.rdf
Name: LTER_cruise
Units: unitless
Description: <p>NES LTER cruise deployment name. NA = not applicable</p>
http://lod.bco-dmo.org/id/dataset-parameter/940192.rdf
Name: CTD_cast
Units: unitless
Description: <p>Number of CTD cast on NES LTER cruise. One sample indicates "flow" because it was collected from the ship flow-through system instead of a CTD cast. One sample indicates "bucket" because it was collected using a bucket and rope from surface seawater. NA = not applicable</p>
http://lod.bco-dmo.org/id/dataset-parameter/940193.rdf
Name: Niskin
Units: unitless
Description: <p>Number of niskin bottle from CTD casts on NES LTER cruise. One sample indicates "flow" because it was collected from the ship flow-through system instead of a CTD cast. One sample indicates "bucket" because it was collected using a bucket and rope from surface seawater. NA = not applicable</p>
http://lod.bco-dmo.org/id/dataset-parameter/940194.rdf
Name: pDA
Units: nanograms/liter (ng/L)
Description: <p>Particulate domoic acid concentration measured by LC-MS/MS of > 5um filters</p>
http://lod.bco-dmo.org/id/dataset-parameter/940195.rdf
Name: Pseudonitzschia
Units: cells/liter
Description: <p>Number of individual cells identified as belonging to the diatom genus Pseudo-nitzschia [NCBI:txid41953] calculated in one liter (L) of surface seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/940196.rdf
Name: Temp
Units: Degrees Celsius (°C)
Description: <p>Seawater temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/940197.rdf
Name: Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Seawater salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/940198.rdf
Name: Phosphate
Units: microMolar (uM)
Description: <p>Concentration of dissolved inorganic phosphate in seawater sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940199.rdf
Name: Silicate
Units: microMolar (uM)
Description: <p>Concentration of dissolved inorganic silicate in seawater sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940200.rdf
Name: Nitrate_and_Nitrite
Units: microMolar (uM)
Description: <p>Concentration of dissolved nitrate and nitrite in seawater sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940201.rdf
Name: Nitrite
Units: microMolar (uM)
Description: <p>Concentration of dissolved nitrite in seawater sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940202.rdf
Name: Ammonium
Units: microMolar (uM)
Description: <p>Concentration of dissolved ammonium in seawater sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940203.rdf
Name: Nitrate
Units: microMolar (uM)
Description: <p>Concentration of dissolved nitrate in seawater sample calculated by subtracting the concentration of nitrite from the nitrate plus nitrite measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/940204.rdf
Name: DIN
Units: microMolar (uM)
Description: <p>Concentration of dissolved inorganic nitrogen in seawater sample calculated by summing the nitrate plus nitrite and ammonium measurements</p>
http://lod.bco-dmo.org/id/dataset-parameter/940205.rdf
Name: Pseudo_nitzschia_americana
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940206.rdf
Name: Pseudo_nitzschia_australis
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940207.rdf
Name: Pseudo_nitzschia_caciantha
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940208.rdf
Name: Pseudo_nitzschia_calliantha
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940209.rdf
Name: Pseudo_nitzschia_cuspidata
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940210.rdf
Name: Pseudo_nitzschia_delicatissima
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940211.rdf
Name: Pseudo_nitzschia_fraudulenta
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940212.rdf
Name: Pseudo_nitzschia_galaxiae
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940213.rdf
Name: Pseudo_nitzschia_hasleana
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940214.rdf
Name: Pseudo_nitzschia_inflatula
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940215.rdf
Name: Pseudo_nitzschia_mannii
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940216.rdf
Name: Pseudo_nitzschia_multiseries
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940217.rdf
Name: Pseudo_nitzschia_multistriata
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940218.rdf
Name: Pseudo_nitzschia_plurisecta
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940219.rdf
Name: Pseudo_nitzschia_pungens
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940220.rdf
Name: Pseudo_nitzschia_pungens_var_aveirensis
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940221.rdf
Name: Pseudo_nitzschia_pungens_var_cingulata
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940222.rdf
Name: Pseudo_nitzschia_qiana
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940223.rdf
Name: Pseudo_nitzschia_sabit
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940224.rdf
Name: Pseudo_nitzschia_subpacifica
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940225.rdf
Name: Pseudo_nitzschia_turgidula
Units: unitless
Description: <p>presence (1) or absence (0) of the species in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940226.rdf
Name: NCBI_BioSample
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/940227.rdf
Name: NCBI_BioProject
Units: unitless
Description: <p>NCBI BioProject number</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
52719
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/84e1ef5d-17ca-46c9-82cd-3a28d66a3b2b/content
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https://doi.org/10.26008/1912/bco-dmo.936856.1
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dataset
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px">Samples were selected from the NES-LTER transect and various time series sites in <span style="color:rgb(0, 0, 0)">Narragansett Bay, Rhode Island (</span>NB</span>) during winter and summer periods from January 2018 through February 2023 to compare seasonal and regional patterns of <em>Pseudo-nitzschia</em> species composition and DA, as well as environmental drivers. NB and NES will henceforth be referred to as subregions of the larger Northeast U.S. Continental Shelf region, with NES specifically referring to the area spanned by the NES-LTER transect. Samples were collected on NES-LTER cruises (<em>R/V</em> Endeavor, <em>R/V</em> Atlantis) from 11 stations along a 150 km transect (n=77) each winter (January-February) and summer (July-August). Samples from three to four stations per cruise were used in this dataset spanning innershelf (L1), midshelf (L3, L4) and outershelf (L7, L8, L10) sections of the transect. The northernmost station, L1, is about 50 km from the mouth of NB. To collect plankton biomass for nucleic acid isolation, CTD rosette seawater from the surface and subsurface chlorophyll maximum (SCM) were passed via peristaltic pump over 25 mm 5 µm pore size filters (Sterlitech, Kent, WA, USA). Biomass filters were either flash frozen in liquid nitrogen (2018-2022) or placed in DNA/RNA shield (winter 2023; Zymo Research, Irvine, CA, USA) and stored in a -80°C freezer. The SCM depth varied as observed by <em>in situ</em> chlorophyll fluorescence, with a median depth of 28 m for summer and 19 m for winter samples. In cases where the SCM was not well defined due to water column mixing that typically took place in winter at nearshore stations, a sampling depth between 20 and 30 m was targeted.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">In NB, surface seawater samples were collected from various sites in the East and West Passages including the Narragansett Bay Long-Term Plankton Time Series (NBPTS) site, Whale Rock (WR), Castle Hill Beach (CHB), East Passage (EP), and University of Rhode Island Graduate School of Oceanography (GSO) dock. Seawater was transported back to the laboratory and passed over 25 mm 5 µm pore size filters (Sterlitech, Kent, WA, USA) using a peristaltic pump before flash freezing in liquid nitrogen and storage at -80°C. To fill in several missing dates from this time series, six samples collected separately in the NBPTS (https://web.uri.edu/gso/research/plankton/) sampling program were used. These samples differed in collection methodology only by the filter pore size used (0.22 µm, Express Plus, Millipore Sigma) and vacuum as opposed to peristaltic filtration.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">DNA was extracted from most NB and NES samples (n=219) using a modified version of the DNeasy Plant Kit (Qiagen, Germantown, MD, USA) that included a 1-minute bead beating step (0.1 mm and 0.5 mm Zirconia/Silica beads, BioSpec Products, Bartlesville, OK, USA) and two part elution into a total of 45 µL Buffer AE. Similarly, the six NBPTS samples were extracted using a modified version of the DNeasy Blood &amp; Tissue kit (Qiagen, Germantown, MD, USA) with a 1-minute bead beating step and final elution into 50 µL Buffer AE. Some NES samples (n=18) were extracted using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) with a 1-minute bead beating step (0.4 mm Zirconium Beads, OPS Diagnostics, Lebanon, NJ, USA) and final elution into 50 µL nuclease-free water. DNA from each sample was amplified with a primer set that targets the eukaryotic internal transcribed spacer region 1 (ITS1) and effectively distinguishes <em>Pseudo-nitzschia</em> species (White et al., 1990; Sterling et al., 2022). Briefly, DNA was diluted to 1-4 ng/µL and 2 µL of template was added to 25 µL PCR reactions with Phusion Hot Start High-Fidelity Master Mix (Thermo Fisher Scientific Inc., Waltham, MA, USA) and HPLC-purified forward and reverse primers at 0.5 µM concentration with Illumina MiSeq adapters (Integrated DNA Technologies, Coralville, IA, USA). A stepwise thermocycle was used as described in Sterling et al. (2022).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">DNA amplicons were sequenced at the Rhode Island-INBRE Molecular Informatics Core on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA, USA). There, libraries were prepared by cleaning ITS1 PCR products with KAPA pure beads (KAPA Biosystems, Woburn, MA, USA) and attaching sequencing indices and adapters using PCR. This amplification was performed with the Illumina Nextera XT Index Kit (Illumina, San Diego, CA, USA) and Phusion High Fidelity Master Mix, followed by a second round of cleaning with KAPA pure beads and visualization with gel electrophoresis. The quality of select samples was assessed on a Bioanalyzer DNA1000 chip (Agilent Technologies, Santa Clara, CA, USA) and all samples were quantified on a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA). The final library was pooled, quantified with qPCR on a LightCycler480 (Roche, Pleasanton, CA, USA) using a KAPA Biosystems Illumina Kit (KAPA Biosystems, Woburn, MA, USA), and sequenced on the Illumina MiSeq using v3 chemistry and 2x250 paired-end reads. Samples were sequenced across five separate MiSeq runs using identical methods and negative controls.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">Various biological, chemical, and physical data were collected during each sampling event. In NB, surface temperature and salinity were measured using multiparameter sondes (6920 V2 for samples collected at NBPTS and WR; ProDSS for samples collected at CHB and GSO dock; YSI, Yellow Springs, Ohio, USA). During NES sampling, temperature and salinity were measured using two SBE911 CTD sensors (Sea Bird Electronics, Bellevue, WA, USA) and the mean of the two measurements was used in the final analysis. Dissolved macronutrient samples were collected by freezing 0.2 µm seawater filtrate at -20°C. NB site nutrients were analyzed at the University of Rhode Island Marine Science Research Facility (URI MSRF, Narragansett, RI, USA) on a QuickChem 8500 (Lachat, Milwaukee, WI, USA) while NES samples were measured at the Woods Hole Oceanographic Institution’s Nutrient Analytical Facility (Woods Hole, MA, USA) on a four-channel segmented flow AA3 HR Autoanalyzer (SEAL Analytical, Mequon, WI, USA). Both instruments measured nitrite + nitrate, ammonium, silicate, and phosphate. Nitrite + nitrate and ammonium values were summed and used in the analysis as dissolved inorganic nitrogen (DIN). Any measurements below each instrument’s limit of detection for each nutrient type were replaced with zero.</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif">Biomass for particle-associated DA analysis was collected, extracted, and analyzed via liquid chromatography with tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring. All samples were chromatographically separated in an identical fashion to Sterling et al. (2022), and the majority of samples (n=167) were analyzed using a 4500 QTRAP mass spectrometer (SCIEX, Framingham, MA, USA). A subset of samples (n=42) were measured using a 1290 Infinity II UHPLC system coupled to a 6470 Triple Quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA, USA). The peak of DA eluted at 10.41 min. Analysis was carried out in positive mode, and three transitions from the protonated DA molecule were used and optimized for quantification: <em>m/z</em> 312 → 266, <em>m/z</em> 312 → 161, and <em>m/z</em> 312 → 105 determined by MassHunter Optimizer (Agilent, Santa Clara, CA, USA) including the optimized fragmentor (112), collision energy (20, 28, 48), and cell accelerator voltage (4) settings. The <em>m/z</em> 312 → 266 transition was used for quantification following acquisition from both mass spectrometry instruments. Particle-associated DA was quantified to ng particulate DA L<sup>-1</sup> of filtered seawater using an external calibration curve created with pure DA standards of increasing concentrations included in each analysis (DA Certified Reference Material, National Research Council Canada, Halifax, Nova Scotia).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif"><em>Pseudo-nitzschia </em>spp. abundance was quantified using light microscopy cell counts of live (NBPTS site) and preserved (all other sites) samples. For preserved samples, acidic Lugol’s solution was added to whole seawater for a final concentration of 1% Lugol’s and stored at 4°C until enumeration. A Sedgewick-Rafter counting chamber (Science First/Wildco, Yulee, FL, USA) and a BX40 light microscope (Olympus, Tokyo, Japan) were used to identify and enumerate cells at the genus level, since many <em>Pseudo-nitzschia</em> species are morphologically cryptic under light microscopy (Bates et al., 2018).</span></p>
<p>&nbsp;</p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px">Sampling Locations</span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Narragansett Bay sites: </span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Narragansett Bay Long Term Plankton Time Series (41.57 N -71.39 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Whale Rock (41.43 N -71.42 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">East Passage (41.45 N -71.38 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Castle Hill Beach (41.46 N -71.36 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">Graduate School of Oceanography dock (41.49 N -71.42 W)</span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">NES stations: </span></span></span></p>
<p><span style="font-family:arial,helvetica,sans-serif"><span style="font-size:14px"><span style="color:rgb(0, 0, 0)">L1 (41.20 N -70.88 W), L3 (40.86 N -70.88 W), L4 (40.70 N -70.88 W), L7 (40.23 N -70.88 W), L8 (40.14 N -70.77 W), L10 (39.93 N -70.88 W)</span></span></span></p>
Specified by the Principal Investigator(s)
<p>Raw sequencing read quality was assessed using FastQC and MultiQC (v.0.11.9, v1.11) before and after primer and adapter trimming in Cutadapt (v3.2). The Divisive Amplicon Denoising Algorithm (DADA2) was used in R to estimate sequencing error and identify distinct amplicon sequence variants (ASVs) (v1.20.0). DADA2 was run separately for each sequencing run because it is designed to account for run-specific error. Taxonomy was assigned to ASVs from all sequencing runs using a dual approach to maximize the number of ASVs identified to the species level and enhance confidence. First, the scikit-learn naïve Bayes machine learning classifier in QIIME2 (v2022.11) and a curated reference database were used to assign taxonomy with a confidence threshold of 0.8. This curated database from Roche et al. (2022) included 302 unique <em>Pseudo-nitzschia </em>spp. ITS1 sequences from the National Center for Biotechnology Information (NCBI) GenBank with 51 different species represented (retrieved June 1, 2021). Next, to ensure that relevant <em>Pseudo-nitzschia </em>spp<em>.</em> ITS1 taxonomy was not omitted from the curated database, a megablast search was performed using the entire BLAST nt database. Additional ASVs classified by megablast were retained if there was &gt;99% identity and &gt;99% query cover to NCBI <em>Pseudo-nitzschia</em> species. If QIIME2 and megablast taxonomic assignment did not match for a particular ASV, no species-level taxonomy was assigned. Samples containing no reads identified to the <em>Pseudo-nitzschia</em> species level were removed from the analysis (n=15). To avoid potentially falsely detected taxa, ASVs classified as a species that appeared in only one sample across the dataset were discarded (n=6).</p>
Specified by the Principal Investigator(s)
1) Processed the submitted file named DATASET02_env_metadata_species_presence_v2.csv, which contains environmental data and indications of the presence and absence of species, with the BCO-DMO tool Laminar.
Renamed parameters according to BCO-DMO naming conventions. Replaced all periods in the parameter names with underscores and removed units from names.
Converted the format of the sample date parameter 'Sample_Date' from %m/%d/%y to and ISO 8601 standard format of %Y-%m-%d.
Saved the modified dataset to the file 936856_v1_pseudo_nitzschia_environmental.csv
2) Processed the submitted file named DATASET02_env_metadata_species_presence_v2.csv with Laminar to create an unpivoted format.
Renamed parameters according to BCO-DMO naming conventions. Replaced all periods in the parameter names with underscores and removed units from names.
Converted the format of the sample date parameter 'Sample_Date' from %m/%d/%y to and ISO 8601 standard format of %Y-%m-%d.
Unpivoted the dataset on the species parameters to produce two columns named species and present. The column 'species' lists all the species parameter names and the column 'present' is a flag representing 1 if a species is present and 0 if a species is absent.
The values in the species column were modified to replace underscores with spaces, add a period after var, and add a hyphen between Pseudo and nitzschia to get Pseudo-nitzschia.
Saved the modified dataset to the file unpivoted_pseudo_nitzschia_environmental.csv.
3) Renamed the submitted file Supp_DATASET_PNspecies_presence_absence.csv, which contains indications of the presence and absence of species, to pseudo_nitzschia_presence_absence.csv.
4) Created a taxonomy table using the species names in the dataset and getting taxonomy values using the World Register of Marine Species (WoRMS) website and saved it to the file species_taxonomy.csv.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina MiSeq Platform
Illumina MiSeq Platform
PI Supplied Instrument Name: Illumina MiSeq Platform PI Supplied Instrument Description:Manufactured by Illumina, Inc., San Diego, CA, USA Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
SBE911 CTD sensors
SBE911 CTD sensors
PI Supplied Instrument Name: SBE911 CTD sensors PI Supplied Instrument Description:Manufactured by Sea Bird Electronics, Bellevue, WA, USA Instrument Name: CTD Sea-Bird 911 Instrument Short Name:CTD SBE 911 Instrument Description: The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0035/
Lachat QuickChem 8500
Lachat QuickChem 8500
PI Supplied Instrument Name: Lachat QuickChem 8500 PI Supplied Instrument Description:Manufactured by Hach, Loveland, CO, USA Instrument Name: Lachat QuikChem 8500 flow injection analysis system Instrument Short Name:QuikChem 8500 Instrument Description: The Lachat QuikChem 8500 Series 2 Flow Injection Analysis System features high sample throughput and simple, but rapid, method changeover. The QuikChem 8500 Series 2 system maximises productivity in determining ionic species in a variety of sample types, from sub-ppb to percent concentrations. Analysis takes 20 to 60 seconds, with a sample throughput of 60 to 120 samples per hour.
6470 Triple Quadrupole mass spectrometer
6470 Triple Quadrupole mass spectrometer
PI Supplied Instrument Name: 6470 Triple Quadrupole mass spectrometer PI Supplied Instrument Description:Manufactured by Agilent Technologies, Santa Clara, CA, USA Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
SCIEX 4500 Qtrap mass spectrometer
SCIEX 4500 Qtrap mass spectrometer
PI Supplied Instrument Name: SCIEX 4500 Qtrap mass spectrometer PI Supplied Instrument Description:Manufactured by Sciex, Framingham, MA, USA Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
BX40 light microscope
BX40 light microscope
PI Supplied Instrument Name: BX40 light microscope PI Supplied Instrument Description:Manufactured by Olympus, Tokyo, Japan Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
AA3 HR Autoanalyzer
AA3 HR Autoanalyzer
PI Supplied Instrument Name: AA3 HR Autoanalyzer PI Supplied Instrument Description:Manufactured by SEAL Analytical, Mequon, WI, USA Instrument Name: Seal Analytical AutoAnalyser 3HR Instrument Short Name:Seal Analytical AutoAnalyser 3HR Instrument Description: A fully automated Segmented Flow Analysis (SFA) system, ideal for water and seawater analysis. It comprises a modular system which integrates an autosampler, peristaltic pump, chemistry manifold and detector. The sample and reagents are pumped continuously through the chemistry manifold, and air bubbles are introduced at regular intervals forming reaction segments which are mixed using glass coils. The AA3 uses segmented flow analysis principles to reduce inter-sample dispersion, and can analyse up to 100 samples per hour using stable LED light sources.
Sedgewick Rafter Counting Chamber
Sedgewick Rafter Counting Chamber
PI Supplied Instrument Name: Sedgewick Rafter Counting Chamber PI Supplied Instrument Description:Manufactured by Science First/Wildco, Yulee, FL, USA Instrument Name: Sedgewick Rafter Counting Chamber Instrument Short Name: Instrument Description: Sedgewick Rafter Counting Chambers are transparent slides widely water analysis, culture inspection, and for other applications where particles per unit volume in fluid must be determined. The slide has a base that is ruled in one-thousand 1-millimeter squares. When a liquid is held in the cell by a coverglass, the grid subdivides 1 milliliter of liquid into 1 microliter volume.
Eppendorf Mastercycler EP Thermal Cycler Series
Eppendorf Mastercycler EP Thermal Cycler Series
PI Supplied Instrument Name: Eppendorf Mastercycler EP Thermal Cycler Series Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
1290 Infinity II UHPLC system
1290 Infinity II UHPLC system
PI Supplied Instrument Name: 1290 Infinity II UHPLC system PI Supplied Instrument Description:Manufactured by Agilent Technologies, Santa Clara, CA, USA Instrument Name: Ultra-high-performance liquid chromatography Instrument Short Name:UHPLC Instrument Description: Ultra high-performance liquid chromatography: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small (< 2 microm) particles and the inlet pressure is relatively high.
YSI ProDSS multiparameter meter
YSI ProDSS multiparameter meter
PI Supplied Instrument Name: YSI ProDSS multiparameter meter PI Supplied Instrument Description:Manufactured by YSI Inc. / Xylem Inc., Yellow Springs, OH, USA Instrument Name: YSI Professional Plus Multi-Parameter Probe Instrument Short Name:YSI ProPlus Instrument Description: The YSI Professional Plus handheld multiparameter meter provides for the measurement of a variety of combinations for dissolved oxygen, conductivity, specific conductance, salinity, resistivity, total dissolved solids (TDS), pH, ORP, pH/ORP combination, ammonium (ammonia), nitrate, chloride and temperature. More information from the manufacturer.
Cruise: EN608
EN608
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN608
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN617
EN617
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN617
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN627
EN627
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN627
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN644
EN644
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN644
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN649
EN649
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN649
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN655
EN655
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN655
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN661
EN661
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN661
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN668
EN668
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN668
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: AT46
AT46
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT46
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN687
EN687
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN687
Heidi M. Sosik
Woods Hole Oceanographic Institution
Cruise: EN695
EN695
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN695
Heidi M. Sosik
Woods Hole Oceanographic Institution
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel