http://lod.bco-dmo.org/id/dataset/814424
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
2020-06-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Environmental measurements and high throughput sequencing data from samples collected at Martha's Vineyard Coastal Observation (MVCO) from 2013-2017
2020-06-05
publication
2020-06-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-06-08
publication
https://doi.org/10.26008/1912/bco-dmo.814424.1
Rebecca J. Gast
Woods Hole Oceanographic Institution
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: Gast, R. (2020) Environmental measurements and high throughput sequencing data from samples collected at Martha's Vineyard Coastal Observation (MVCO) from 2013-2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-06-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.814424.1 [access date]
Links to high throughput sequencing data and associated MVCO environmental measurements Dataset Description: <p>This dataset contains environmental measurements from Martha's Vineyard Coastal Observatory (MVCO) made from 2013-2017. Related&nbsp;high throughput sequencing data are available from NCBI. These are described below and cited under "Related Datasets".</p> Methods and Sampling: <p>Surface water samples were collected at approximately 2m depth using a Niskin bottle or a bucket near the Martha’s Vineyard Coastal Observatory (MVCO) offshore tower (41 19.500' N, 70 34.0' W). Sampling was accomplished from February 2013 – August 2017 about every 1-2 months, and usually twice monthly April – November, for a total of 62 samples. Water was kept cool and in the dark for transport back to the laboratory (about 1.5 hours).&nbsp;</p>
<p><strong>Environmental data:</strong><br />
Reported temperature data are from the CTD rosette aboard the R/V Tioga. Chlorophyll and&nbsp;phaeo were collected and analyzed in the Sosik lab at WHOI using a Turner Designs Aquafluor Handheld 800446 extracted in 90% acetone.</p>
<p>Nutrients were analyzed at WHOI's Nutrient Facility. The official protocol summary can be found in the NES-LTER EDI data submission: <a href="https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-nes.1.2" target="_blank">https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-nes.1.2</a></p>
<p>HPLC were analyzed at Horn Point Lab, as per NASA protocol. The summary protocol for HPLC and chl is available from Seabass: <a href="https://seabass.gsfc.nasa.gov/archive/WHOI/MVCO/documents" target="_blank">https://seabass.gsfc.nasa.gov/archive/WHOI/MVCO/documents</a><br />
<br />
<strong>Sequencing data:</strong><br />
Volumes of water ranging from 0.75 to 2.5L were filtered in duplicate onto 45mm 0.22 µm Durapore GV filters under gentle vacuum. Filters were cut in half, placed into sterile 1.5 ml microfuge tubes, and stored at -80C until extraction.</p>
<p>Nucleic acids were extracted using the Zymo Research Fungal/Bacterial DNA MicroPrep Kit (Zymo Research Products). One half filter for each sample was transferred to a 2 ml microcentrifuge tube with silica beads and lysis buffer, and then shaken using a vortex adapter for 5 minutes. The extraction was then processed following the kit instructions and the eluted DNA frozen at -20C.</p>
<p>The eukaryotic ribosomal RNA gene V4 region was targeted for amplification and sequencing using 574V4F (5' [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]CGGTAAYTCCAGCTCYV) and 1132V4R (5' [GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG]CCGTCAATTHCTTYAART), described in Hugerth et al. (2014) and modified to include 5' adapter sequences for Illumina MiSeq (in square brackets). PCR reactions were accomplished in triplicate for each sample using 1 µl template DNA, 1.25 units AmpliTaq GoldR 360 DNA polymerase, 2mM MgCl2, 2 µl 2.5 µM dNTPs, and 2.5 µl 10X reaction buffer (25 µl total volume) with the conditions: 95C for 8 minutes; 40 cycles of 95C for 30 seconds, 58C for 30 seconds, 72C for 90 seconds; 72C for 5 minutes; 4C hold. No template negative controls were included with every set of PCRs. Each sample reaction was examined to confirm the correct product size of approximately 500 bp. Triplicate reactions were pooled and purified using either DNA Clean and Concentrator – 5 kit (Zymo Research) or AMPure XP beads. The samples were sent to the University of Rhode Island Genomics and Sequencing Center for library preparation and Illumina MiSeq (250 bp paired end; 500 cycle kit V2) sequencing. Samples 1-27 and 28-62 were sequenced in separate runs about a year apart.</p>
<p>Ciliate-specific amplicons were generated by amplifying the region between 152-528 bp of the 18S ribosomal RNA gene. The primers used for amplification are from Doherty et al 2007 (Aquatic Microbial Ecology). Primers were modified to carry 5' adapter sequences as noted above. AmpliTaq Gold 360 was used for amplification, and triplicate reactions were accomplished for each sample. Replicates were combined and purified using Agencourt AMPure XP. Products were sent to URI Genomics and Sequencing Center for Illumina MiSeq.</p>
<p>V4 amplicon raw reads are available at NCBI SRA project PRJNA504617. Ciliate amplicon raw reads are available at NCBI SRA project PRJNA626352. The Imaging FlowCytobot Dashboard for shared access to image data and data products, including MVCO time series, is available at <a href="https://ifcb-data.whoi.edu/mvco" target="_blank">https://ifcb-data.whoi.edu/mvco</a> and the WHOI dock time series is available at <a href="https://ifcb-data.whoi.edu/WHOI_dock" target="_blank">https://ifcb-data.whoi.edu/WHOI_dock</a>.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1434440 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1434440
completed
Rebecca J. Gast
Woods Hole Oceanographic Institution
508-289-3209
266 Woods Hole Rd. MS #32
Woods Hole
MA
02543
USA
rgast@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Start_Date
Event_Number
Temperature
Chl
Phaeo
NO2_NO3
NH4
SiO2
PO43
HPLC_Total_Chl_a
HPLC_Total_Chl_b
HPLC_Total_Chl_c
HPLC_Carotene
HPLC_But_Fucoxanthin
HPLC_Hex_Fucoxanthin
HPLC_Alloxanthin
HPLC_Diadinoxanthin
HPLC_Diatoxanthin
HPLC_Fucoxanthin
HPLC_Peridinin
HPLC_Zeaxanthin
bucket
CTD
Turner Designs Aquafluor Handheld 800446
theme
None, User defined
date
event
water temperature at measurement depth
chl_tot
total phaeopigment
nitrate plus nitrite
Ammonium
Silicon
reactive phosphorus (PO4)
chlorophyll a
chlorophyll b
chlorophyll c total
carotene
19-prime-butanoyloxyfucoxanthin
19-prime-hexanoyloxyfucoxanthin
alloxanthin
diadinoxanthin
diatoxanthin
fucoxanthin
peridinin
zeaxanthin
featureType
BCO-DMO Standard Parameters
bucket
CTD Sea-Bird
Fluorometer
Niskin bottle
Thermal Cycler
instrument
BCO-DMO Standard Instruments
MVCO
service
Deployment Activity
41 19.500' N, 70 34.0' W
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.
Dynamics of Protistan Grazers: Diversity, Abundance and Prey Relations
https://osprey.bco-dmo.org/project/564653
Dynamics of Protistan Grazers: Diversity, Abundance and Prey Relations
<p><em>Description from NSF award abstract:</em><br />
Some of the most important primary producers and consumers in aquatic ecosystems are protists, or single-celled eukaryotes. It is well established that protistan predation can be a significant source of mortality for bacteria and phytoplankton. Grazing protists in turn serve as prey for zooplankton (copepods), and through the excretion of nitrogen and phosphorus compounds, they play a major role in the release of regenerated nutrients. Despite decades of studies on protistan grazing, knowledge gaps still exist with respect to their abundance, distribution, seasonality, prey selectivity, and co-occurrence patterns. The results from this project will advance the understanding of grazing communities in situ and how they respond to environmental conditions and prey communities. This will be one of very few studies of grazers that is unbiased by artificial prey and containment, and will yield both morphologic and genetic information about the organisms present and the distribution patterns of particular grazer populations.</p>
<p>This project examines whether the persistence of a group of protistan grazers is determined by its feeding strategy (grazers with specialist feeding strategies are more ephemeral than generalists), and whether certain morphotypes exhibiting generalist feeding strategies have underlying genotypic diversity that maps to specialist feeding strategies. It builds upon an ongoing time series (with hourly resolution since 2006) of automated, high-resolution, measurements of the phytoplankton community by the Imaging FlowCytobot at the Martha's Vineyard Coastal Observatory. These measurements have led to the observation that, in addition to shifts from pico- and small nanoplankton during the summer to larger microplankton in the fall and winter, particular species (especially among the diatoms) exhibit distinct and recurring seasonal patterns. The instrument will be modified to also conduct automated measurements of grazer communities in situ. Links between selected grazer taxa (chosen based on the image time series) and phytoplankton prey will be provided through genetic analyses of individual cells (with their ingested prey). These cells will be obtained by use of a recently developed cell sorter that also captures an image of each sorted cell. In addition to providing predator/prey links, the genetic information will allow the investigators to determine whether a grazer morphotype represents multiple species. A third approach, high throughput sequencing and quantitative PCR analysis of whole water samples, will be applied to investigate abundance patterns of species whose morphology does not reliably map to genotype.</p>
Staining IFCB
largerWorkCitation
project
eng; USA
oceans
41 19.500' N, 70 34.0' W
-70.5667
-70.5667
41.325
41.325
2013-02-14
2017-08-02
Martha’s Vineyard Coastal Observatory, WHOI Dock
0
BCO-DMO catalogue of parameters from Environmental measurements and high throughput sequencing data from samples collected at Martha's Vineyard Coastal Observation (MVCO) from 2013-2017
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/814437.rdf
Name: Start_Date
Units: unitless
Description: <p>Date sampled; format: yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/814438.rdf
Name: Event_Number
Units: unitless
Description: <p>MVCO event number</p>
http://lod.bco-dmo.org/id/dataset-parameter/814439.rdf
Name: Temperature
Units: degress Celsius
Description: <p>water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/814440.rdf
Name: Chl
Units: micrograms per liter (ug per liter)
Description: <p>total chlorophyll</p>
http://lod.bco-dmo.org/id/dataset-parameter/814441.rdf
Name: Phaeo
Units: ug per liter
Description: <p>total phaeo pigment</p>
http://lod.bco-dmo.org/id/dataset-parameter/814442.rdf
Name: NO2_NO3
Units: micromolar
Description: <p>nitrate and nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/814443.rdf
Name: NH4
Units: micromolar
Description: <p>ammonia</p>
http://lod.bco-dmo.org/id/dataset-parameter/814444.rdf
Name: SiO2
Units: micromolar
Description: <p>silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814445.rdf
Name: PO43
Units: micromolar
Description: <p>phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/814446.rdf
Name: HPLC_Total_Chl_a
Units: ug per liter
Description: <p>HPLC determined chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/814447.rdf
Name: HPLC_Total_Chl_b
Units: ug per liter
Description: <p>HPLC determined chlorophyll b</p>
http://lod.bco-dmo.org/id/dataset-parameter/814448.rdf
Name: HPLC_Total_Chl_c
Units: ug per liter
Description: <p>HPLC determined chlorophyll c</p>
http://lod.bco-dmo.org/id/dataset-parameter/814449.rdf
Name: HPLC_Carotene
Units: ug per liter
Description: <p>HPLC determined carotene</p>
http://lod.bco-dmo.org/id/dataset-parameter/814450.rdf
Name: HPLC_But_Fucoxanthin
Units: ug per liter
Description: <p>HPLC determined 19'-butanolyloxyfucoxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814451.rdf
Name: HPLC_Hex_Fucoxanthin
Units: ug per liter
Description: <p>HPLC determined 19'-hexanoyloxyfucoxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814452.rdf
Name: HPLC_Alloxanthin
Units: ug per liter
Description: <p>HPLC determined alloxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814453.rdf
Name: HPLC_Diadinoxanthin
Units: ug per liter
Description: <p>HPLC determined Diadinoxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814454.rdf
Name: HPLC_Diatoxanthin
Units: ug per liter
Description: <p>HPLC determined Diatoxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814455.rdf
Name: HPLC_Fucoxanthin
Units: ug per liter
Description: <p>HPLC determined Fucoxanthin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814456.rdf
Name: HPLC_Peridinin
Units: ug per liter
Description: <p>HPLC determined Peridinin</p>
http://lod.bco-dmo.org/id/dataset-parameter/814457.rdf
Name: HPLC_Zeaxanthin
Units: ug per liter
Description: <p>HPLC determined Zeaxanthin</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
10317
https://darchive.mblwhoilibrary.org/bitstream/1912/25827/1/dataset-814424_mvco-environmental-measurements-and-high-throughput-sequencing__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.814424.1
download
onLine
dataset
<p>Surface water samples were collected at approximately 2m depth using a Niskin bottle or a bucket near the Martha’s Vineyard Coastal Observatory (MVCO) offshore tower (41 19.500' N, 70 34.0' W). Sampling was accomplished from February 2013 – August 2017 about every 1-2 months, and usually twice monthly April – November, for a total of 62 samples. Water was kept cool and in the dark for transport back to the laboratory (about 1.5 hours).&nbsp;</p>
<p><strong>Environmental data:</strong><br />
Reported temperature data are from the CTD rosette aboard the R/V Tioga. Chlorophyll and&nbsp;phaeo were collected and analyzed in the Sosik lab at WHOI using a Turner Designs Aquafluor Handheld 800446 extracted in 90% acetone.</p>
<p>Nutrients were analyzed at WHOI's Nutrient Facility. The official protocol summary can be found in the NES-LTER EDI data submission: <a href="https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-nes.1.2" target="_blank">https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-nes.1.2</a></p>
<p>HPLC were analyzed at Horn Point Lab, as per NASA protocol. The summary protocol for HPLC and chl is available from Seabass: <a href="https://seabass.gsfc.nasa.gov/archive/WHOI/MVCO/documents" target="_blank">https://seabass.gsfc.nasa.gov/archive/WHOI/MVCO/documents</a><br />
<br />
<strong>Sequencing data:</strong><br />
Volumes of water ranging from 0.75 to 2.5L were filtered in duplicate onto 45mm 0.22 µm Durapore GV filters under gentle vacuum. Filters were cut in half, placed into sterile 1.5 ml microfuge tubes, and stored at -80C until extraction.</p>
<p>Nucleic acids were extracted using the Zymo Research Fungal/Bacterial DNA MicroPrep Kit (Zymo Research Products). One half filter for each sample was transferred to a 2 ml microcentrifuge tube with silica beads and lysis buffer, and then shaken using a vortex adapter for 5 minutes. The extraction was then processed following the kit instructions and the eluted DNA frozen at -20C.</p>
<p>The eukaryotic ribosomal RNA gene V4 region was targeted for amplification and sequencing using 574V4F (5' [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]CGGTAAYTCCAGCTCYV) and 1132V4R (5' [GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG]CCGTCAATTHCTTYAART), described in Hugerth et al. (2014) and modified to include 5' adapter sequences for Illumina MiSeq (in square brackets). PCR reactions were accomplished in triplicate for each sample using 1 µl template DNA, 1.25 units AmpliTaq GoldR 360 DNA polymerase, 2mM MgCl2, 2 µl 2.5 µM dNTPs, and 2.5 µl 10X reaction buffer (25 µl total volume) with the conditions: 95C for 8 minutes; 40 cycles of 95C for 30 seconds, 58C for 30 seconds, 72C for 90 seconds; 72C for 5 minutes; 4C hold. No template negative controls were included with every set of PCRs. Each sample reaction was examined to confirm the correct product size of approximately 500 bp. Triplicate reactions were pooled and purified using either DNA Clean and Concentrator – 5 kit (Zymo Research) or AMPure XP beads. The samples were sent to the University of Rhode Island Genomics and Sequencing Center for library preparation and Illumina MiSeq (250 bp paired end; 500 cycle kit V2) sequencing. Samples 1-27 and 28-62 were sequenced in separate runs about a year apart.</p>
<p>Ciliate-specific amplicons were generated by amplifying the region between 152-528 bp of the 18S ribosomal RNA gene. The primers used for amplification are from Doherty et al 2007 (Aquatic Microbial Ecology). Primers were modified to carry 5' adapter sequences as noted above. AmpliTaq Gold 360 was used for amplification, and triplicate reactions were accomplished for each sample. Replicates were combined and purified using Agencourt AMPure XP. Products were sent to URI Genomics and Sequencing Center for Illumina MiSeq.</p>
<p>V4 amplicon raw reads are available at NCBI SRA project PRJNA504617. Ciliate amplicon raw reads are available at NCBI SRA project PRJNA626352. The Imaging FlowCytobot Dashboard for shared access to image data and data products, including MVCO time series, is available at <a href="https://ifcb-data.whoi.edu/mvco" target="_blank">https://ifcb-data.whoi.edu/mvco</a> and the WHOI dock time series is available at <a href="https://ifcb-data.whoi.edu/WHOI_dock" target="_blank">https://ifcb-data.whoi.edu/WHOI_dock</a>.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
- renamed fields;<br />
- converted date to YYYY-MM-DD format;<br />
- changed missing data identifiers from "NaN" to "nd".</p>
Specified by the Principal Investigator(s)
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
bucket
bucket
PI Supplied Instrument Name: bucket Instrument Name: bucket Instrument Short Name:bucket Instrument Description: A bucket used to collect surface sea water samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0536/
CTD
CTD
PI Supplied Instrument Name: CTD Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Turner Designs Aquafluor Handheld 800446
Turner Designs Aquafluor Handheld 800446
PI Supplied Instrument Name: Turner Designs Aquafluor Handheld 800446 Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
PI Supplied Instrument Name: 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)
Deployment: MVCO
MVCO
Martha's Vineyard Coastal Observatory
Martha's Vineyard Coastal Observatory
mooring
Martha's Vineyard Coastal Observatory
Martha's Vineyard Coastal Observatory
mooring