http://lod.bco-dmo.org/id/dataset/897547
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
2023-06-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Relative abundances of different Syndiniales groups from surface water samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly between 2013 and 2021
2023-06-14
publication
2023-06-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-10-31
publication
https://doi.org/10.26008/1912/bco-dmo.897547.1
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. J. (2023) Relative abundances of different Syndiniales groups from surface water samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly between 2013 and 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.897547.1 [access date]
MVCO Syndiniales amplicon ASV counts Dataset Description: Methods and Sampling: <p>Water samples were collected monthly or bimonthly (September 2019 to October 2020) at the Martha's Vineyard Coastal Observatory (MVCO) from about 2 meters below the surface using bucket casts or a CTD deployed from R/V Tioga. Samples were transferred to a carboy in a cooler for transport back to the laboratory. Water was processed within 2 hours of collection. One liter of whole seawater was collected onto 47-millimeter (mm) 0.2-micrometer (µm) Millpore Isopore filters and stored at -20 degrees Celsius (°C) for DNA extraction and amplicon sequencing. Nucleic acids were extracted from half of a 47mm filter that was cut into small pieces using scissors and cleaned with alcohol in between samples. The lysis method followed a hot detergent plus bead disruption protocol (Gast et al., 2004). Filter pieces were placed in a sterile 2-milliliter (ml) microfuge tube and 2 x lysis buffer was added, along with approximately 50 microliters (µl) of beads. The tubes were vortexed for 30 seconds and then placed at 65°C for 5 minutes, followed by two cycles of vortex and heat incubation. Sodium chloride and CTAB were added, and the samples were incubated at 70°C for 10 minutes. Following extraction with an equal volume of chloroform, the aqueous phase was removed and precipitated overnight at -20°C with 0.6 volume of isopropanol. The recovered DNA pellet was resuspended in 20 µl of sterile water.</p>
<p>Amplification of the V4 region of the 18S ribosomal RNA gene was accomplished using the primers 574V4F (5’ [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]CGGTAAYTCCAGCTCYV) and 1132V4R (5’ [GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG]CCGTCAATTHCTTYAART), described in Hugerth et al. (2014) and modified to include 5’ adapter sequences (indicated by square brackets). PCR reactions were performed in triplicate for each sample using 1 µl template DNA, 1.25 units AmpliTaq DNA polymerase, 2 millimoles (mM) MgCl2, 2 µl 2.5 µM dNTPs, and 2.5 µl 10X reaction buffer (25 µl total volume) with the conditions: 95°C for 5 minutes; 35 cycles of 95°C for 30 seconds, 58°C for 30 seconds, 72°C for 90 seconds; 72°C for 5 minutes; 4°C hold. No template negative controls were included. Each sample reaction was examined to confirm the correct product size of approximately 500 base pairs (bp). Triplicate reactions were pooled and sent to the RI-INBRE Molecular Informatics Core for library preparation and Illumina MiSeq (250 bp paired end; 500 cycle kit V2) sequencing.</p>
<p>Amplicon data collected in this work was combined with other MVCO time series amplicon data to examine the temporal variation in Syndiniales types. The prior sequencing effort covered samples collected between 2013-2019 and 2020-2021, and used the same primer set reported here. Trimmed and demultiplexed raw reads were imported into qiime2 and the forward reads were analyzed for high quality (Q value 30 over 90% of read), removal of chimeric sequences, identification of amplicon sequence variants (ASVs) at 100% similarity, removal of ASVs that occurred in fewer than 2 samples, and assignment of taxonomy using PR2 database.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851012 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851012
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
latitude
longitude
taxon
date
counts
bucket
CTD
PCR
theme
None, User defined
latitude
longitude
taxon
date
count
featureType
BCO-DMO Standard Parameters
bucket
CTD - profiler
Thermal Cycler
instrument
BCO-DMO Standard Instruments
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.
Trojan Horses in the Marine Realm: Protist Parasite-host Dynamics in Coastal Waters
https://osprey.bco-dmo.org/project/786261
Trojan Horses in the Marine Realm: Protist Parasite-host Dynamics in Coastal Waters
<p><em>NSF Award Abstract:</em><br />
The ecological importance of parasitic dinoflagellates has been recognized for some time, particularly during epidemic outbreaks that cause mass mortality of their hosts, damage to aquaculture, and render commercially valuable Crustacea unpalatable. The dominate parasitic dinoflagellate group found in international global ocean surveys is referred to as MALV II Syndiniales. In the planktonic environment, the MALV II Syndiniales group not only exerts top-down controls on their prey populations, but based on their apparent ubiquity and abundance, they likely shape the pools of nutrients in marine water columns. Data on cultured samples reveals this hyper-diverse group can infect a wide range of protist hosts, as well as copepods, and fish larvae. Gaps in knowledge of the specificity and dynamics of the host-parasite interactions contribute to difficulties in estimating the impacts on the coastal ecosystems. In this project, researchers combine novel methods in microscopy, genomics, and chemistry to track host-parasite dynamics at a coastal site over an annual cycle followed by modeling to assess the impacts on microbial ecosystem dynamics. The researchers will engage undergraduate and high school students in field and laboratory research activities. In addition, support for a graduate student is included along with plans to disseminate the research results more broadly through publications and presentations.</p>
<p>Syndiniales parasitism is a widespread, albeit under-studied symbiotic interaction in the marine environment and little is known about regulation of protist populations by these parasites. In spite of their cosmopolitan distribution in the global ocean and their apparent abundance in molecular datasets of protist marker genes, little is known about the ecology of these parasites and almost no genomic data exists for them. In this project, the researchers combine high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, single cell genomics, and modeling to produce the first focused assessment of host-MALVII parasite dynamics and ecology at the community level in a coastal marine ecosystem. The researchers will evaluate temporal dynamics of host and parasite diversity and will examine temporal variation in levels of infection of the protist community and host-parasite specificity using high-resolution sampling in Salt Pond, Falmouth, MA, and in situ hybridization microscopy. Molecular approaches include amplicon tag high throughput sequencing, leveraging the emerging third generation sequencing technology, Oxford Nanopore's MinION to elucidate host-parasite identities. The researchers will also apply advances in single-cell genome sequencing to inform on strain-specific genome content, including the molecular mechanisms underpinning protist parasitism. Contributions to pools of particulate and dissolved organic matter will be estimated for several of the most commonly infected host taxa in Salt Pond using laboratory experiments, providing the first set of values for modeling impacts of Syndiniales parasitism on pools of organic and inorganic nutrients.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Coastal Parasites
largerWorkCitation
project
eng; USA
oceans
-70.5667
-70.5667
41.325
41.325
2013-02-14
2021-12-20
Salt Pond, Falmouth, MA
0
BCO-DMO catalogue of parameters from Relative abundances of different Syndiniales groups from surface water samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly between 2013 and 2021
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/897592.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude of Martha's Vineyard Coastal Observatory (MVCO); positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/897593.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude of Martha's Vineyard Coastal Observatory (MVCO); negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/897594.rdf
Name: taxon
Units: unitless
Description: <p>taxon</p>
http://lod.bco-dmo.org/id/dataset-parameter/897595.rdf
Name: date
Units: unitless
Description: <p>date when water samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/897596.rdf
Name: counts
Units: unitless
Description: <p>amplicon sequence variant (ASV) count</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
970684
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/752b43f4-2627-4f9e-a429-4edecb94afc2/content
download
https://doi.org/10.26008/1912/bco-dmo.897547.1
download
onLine
dataset
<p>Water samples were collected monthly or bimonthly (September 2019 to October 2020) at the Martha's Vineyard Coastal Observatory (MVCO) from about 2 meters below the surface using bucket casts or a CTD deployed from R/V Tioga. Samples were transferred to a carboy in a cooler for transport back to the laboratory. Water was processed within 2 hours of collection. One liter of whole seawater was collected onto 47-millimeter (mm) 0.2-micrometer (µm) Millpore Isopore filters and stored at -20 degrees Celsius (°C) for DNA extraction and amplicon sequencing. Nucleic acids were extracted from half of a 47mm filter that was cut into small pieces using scissors and cleaned with alcohol in between samples. The lysis method followed a hot detergent plus bead disruption protocol (Gast et al., 2004). Filter pieces were placed in a sterile 2-milliliter (ml) microfuge tube and 2 x lysis buffer was added, along with approximately 50 microliters (µl) of beads. The tubes were vortexed for 30 seconds and then placed at 65°C for 5 minutes, followed by two cycles of vortex and heat incubation. Sodium chloride and CTAB were added, and the samples were incubated at 70°C for 10 minutes. Following extraction with an equal volume of chloroform, the aqueous phase was removed and precipitated overnight at -20°C with 0.6 volume of isopropanol. The recovered DNA pellet was resuspended in 20 µl of sterile water.</p>
<p>Amplification of the V4 region of the 18S ribosomal RNA gene was accomplished using the primers 574V4F (5’ [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]CGGTAAYTCCAGCTCYV) and 1132V4R (5’ [GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG]CCGTCAATTHCTTYAART), described in Hugerth et al. (2014) and modified to include 5’ adapter sequences (indicated by square brackets). PCR reactions were performed in triplicate for each sample using 1 µl template DNA, 1.25 units AmpliTaq DNA polymerase, 2 millimoles (mM) MgCl2, 2 µl 2.5 µM dNTPs, and 2.5 µl 10X reaction buffer (25 µl total volume) with the conditions: 95°C for 5 minutes; 35 cycles of 95°C for 30 seconds, 58°C for 30 seconds, 72°C for 90 seconds; 72°C for 5 minutes; 4°C hold. No template negative controls were included. Each sample reaction was examined to confirm the correct product size of approximately 500 base pairs (bp). Triplicate reactions were pooled and sent to the RI-INBRE Molecular Informatics Core for library preparation and Illumina MiSeq (250 bp paired end; 500 cycle kit V2) sequencing.</p>
<p>Amplicon data collected in this work was combined with other MVCO time series amplicon data to examine the temporal variation in Syndiniales types. The prior sequencing effort covered samples collected between 2013-2019 and 2020-2021, and used the same primer set reported here. Trimmed and demultiplexed raw reads were imported into qiime2 and the forward reads were analyzed for high quality (Q value 30 over 90% of read), removal of chimeric sequences, identification of amplicon sequence variants (ASVs) at 100% similarity, removal of ASVs that occurred in fewer than 2 samples, and assignment of taxonomy using PR2 database.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
qiime2 was used to process the amplicon sequence data.</p>
<p><em><strong>Demultiplex</strong></em></p>
<p>qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path &lt;manifest file name&gt; --output-path &lt;name.qza&gt; --input-format PairedEndFastqManifestPhred33V2</p>
<p>qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path &lt;manifest file name&gt; --output-path &lt;name.qza&gt; --input-format SingleEndFastqManifestPhred33V2</p>
<p>To evaluate the sequences qiime demux summarize --i-data name.qza --o-visualization name.qzv</p>
<p><em><strong>Denoise, dereplicate, quality filter &amp; remove chimeras</strong></em></p>
<p>qiime dada2 denoise-single --i-demultiplexed-seqs &lt;.qza file from above&gt; --p-trim-left 10 --p-trunc-len 290 --p-chimera-method pooled --o-table &lt;name.qza&gt; --o-representative-sequences &lt;name.qza&gt; --o-denoising-stats &lt;name.qza&gt;</p>
<p><em><strong>Remove singletons</strong></em></p>
<p>qiime feature-table filter-features --i-table &lt;name of table generated in prior step&gt; --p-min-frequency 2 --o-filtered-table &lt;new table name .qza&gt;</p>
<p>qiime feature-table filter-seqs --i-data &lt;name of rep seq file created in prior step&gt; --i-table &lt;name of filtered table&gt; --o-filtered-data &lt;new repseq file .qza&gt;</p>
<p><em><strong>Cluster sequences based upon identity</strong></em></p>
<p>qiime vsearch cluster-features-de-novo --i-table &lt;name.qza&gt; (filtered table) --i-sequences &lt;name.qza&gt; (filtered rep-seqs file) --p-perc-identity 1.0 --o-clustered-table &lt;name.qza&gt; (this is a biom table that has abundances of each cluster) --o-clustered-sequences &lt;name.qza&gt; (this is a new rep-set of sequences - your ASVs)</p>
<p><em><strong>Assign taxonomy</strong></em></p>
<p>qiime feature-classifier classify-consensus-vsearch --i-query &lt;name.qza&gt; (this is the rep-set of sequences just created by cluster) --i-reference-reads pr2_4.12.0_18S.qza (this is the PR2 reference set of sequences) --i-reference-taxonomy pr2_4.12.0_18S_tax.qza (this is the corresponding PR2 taxonomy) --p-maxaccepts 1 --o-classification &lt;name.qza&gt; (this is your rep-set sequences and their taxonomy)</p>
<p><strong>BCO-DMO Processing:</strong><br />
- added columns for the latitude and longitude of the sampling locations;<br />
- converted the date field to YYYY-MM-DD format.</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 PI Supplied Instrument Description:Samples were collected from about 2 meters below the surface using bucket casts or a CTD. 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 PI Supplied Instrument Description:Samples were collected from about 2 meters below the surface using bucket casts or a CTD. Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PCR
PCR
PI Supplied Instrument Name: PCR 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)