http://lod.bco-dmo.org/id/dataset/897734
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
2023-06-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Group II Syndiniales infected host and dinospore counts determined from CARD-FISH hybridization carried out on samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly from September 2019 to October 2020
2023-06-21
publication
2023-06-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-10-31
publication
https://doi.org/10.26008/1912/bco-dmo.897734.1
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) Group II Syndiniales infected host and dinospore counts determined from CARD-FISH hybridization carried out on samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly from September 2019 to October 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.897734.1 [access date]
MVCO CARD-FISH hybridization count results 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. 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. For in situ hybridization, variable amounts of whole water were collected by gentle filtration onto 47mm 3 µm Millipore Isopore filters for detection of infected hosts, and onto 47mm 0.2 µm Millipore Isopore filters (black) for the detection of free dinospores (see Supplemental File "MVCO_water_amt.csv"). Filtration was stopped when about 20 milliliters (ml) of water remained in the filter tower, and 20 ml of 8% formaldehyde (in filter sterile seawater) was added to fix the cells. After an hour, the solution was filtered, and the samples were rinsed three times with 20 ml of phosphate buffered saline (1x PBS). Filters were stored at -20°C until in situ hybridization.</p>
<p>The detailed hybridization method can be found at protocols.io at doi: <a href="http://dx.doi.org/10.17504/protocols.io.bsxmnfk6" target="_blank">10.17504/protocols.io.bsxmnfk6</a>. A one-eighth pie-shaped section was cut from each filter and placed on a glass slide. 20 µl of hybridization buffer (40% formamide) containing the horseradish peroxidase labeled probe (ALV01; 5’-GCC TGC CGT GAA CAC TCT-3’; Chambouvet el al. 2008) in a 9:1 ratio (final probe concentration 50 nanograms per microliter (ng µl-1)) was placed on the filter slice. Slides were put into 50ml centrifuge tubes containing a hybridization buffer saturated paper towel and incubated overnight at 37°C. Filter pieces were washed twice in 3 ml of wash solution at 46°C, then allowed to soak in 3 ml of TNT buffer at room temperature. Filters were placed on a new glass slide and the fluorescence signal was amplified using a tyramide signal amplification kit (Akoya Biosciences TSA Plus Fluorescein; NEL741001KT). After signal amplification, filters were washed twice in 3 ml of TNT buffer at 55°C to neutralize any residual fluorescein. Filter pieces were transferred to new glass slides and cellulose was stained using 20 µl of Calcofluor White for 7 minutes. Filter pieces were washed twice in 3 ml of water, then placed on new glass slides for counterstaining and mounting with a mixture of propidium iodide and Citiflour media (20 µl per slide). Hybridized filters were held overnight at 4°C, and then at -20°C for long-term storage.</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
date
percent_infected_hosts
GrpII_dinospores_per_L
avg_cells_per_L
latitude
longitude
CTD
Imaging Flow CytoBot (IFCB)
Zeiss Axioskop S-100
theme
None, User defined
date
abundance
latitude
longitude
featureType
BCO-DMO Standard Parameters
bucket
CTD - profiler
Imaging FlowCytobot
Inverted Microscope
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
2019-09-16
2020-10-15
Salt Pond, Falmouth, MA
0
BCO-DMO catalogue of parameters from Group II Syndiniales infected host and dinospore counts determined from CARD-FISH hybridization carried out on samples collected at the Martha's Vineyard Coastal Observatory (MVCO) monthly or bimonthly from September 2019 to October 2020
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/897747.rdf
Name: date
Units: unitless
Description: <p>sample date</p>
http://lod.bco-dmo.org/id/dataset-parameter/897748.rdf
Name: percent_infected_hosts
Units: unitless (percent)
Description: <p>percent infected hosts (by GrpII Syndiniales)</p>
http://lod.bco-dmo.org/id/dataset-parameter/897749.rdf
Name: GrpII_dinospores_per_L
Units: per liter
Description: <p>GrpII dinospores per liter</p>
http://lod.bco-dmo.org/id/dataset-parameter/897750.rdf
Name: avg_cells_per_L
Units: per liter
Description: <p>average number of cells per liter</p>
http://lod.bco-dmo.org/id/dataset-parameter/897753.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/897755.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude of Martha's Vineyard Coastal Observatory (MVCO); negative values = West</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
988
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/0faa80e6-8d4e-45ae-963e-9e628349c5b6/content
download
https://doi.org/10.26008/1912/bco-dmo.897734.1
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. 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. For in situ hybridization, variable amounts of whole water were collected by gentle filtration onto 47mm 3 µm Millipore Isopore filters for detection of infected hosts, and onto 47mm 0.2 µm Millipore Isopore filters (black) for the detection of free dinospores (see Supplemental File "MVCO_water_amt.csv"). Filtration was stopped when about 20 milliliters (ml) of water remained in the filter tower, and 20 ml of 8% formaldehyde (in filter sterile seawater) was added to fix the cells. After an hour, the solution was filtered, and the samples were rinsed three times with 20 ml of phosphate buffered saline (1x PBS). Filters were stored at -20°C until in situ hybridization.</p>
<p>The detailed hybridization method can be found at protocols.io at doi: <a href="http://dx.doi.org/10.17504/protocols.io.bsxmnfk6" target="_blank">10.17504/protocols.io.bsxmnfk6</a>. A one-eighth pie-shaped section was cut from each filter and placed on a glass slide. 20 µl of hybridization buffer (40% formamide) containing the horseradish peroxidase labeled probe (ALV01; 5’-GCC TGC CGT GAA CAC TCT-3’; Chambouvet el al. 2008) in a 9:1 ratio (final probe concentration 50 nanograms per microliter (ng µl-1)) was placed on the filter slice. Slides were put into 50ml centrifuge tubes containing a hybridization buffer saturated paper towel and incubated overnight at 37°C. Filter pieces were washed twice in 3 ml of wash solution at 46°C, then allowed to soak in 3 ml of TNT buffer at room temperature. Filters were placed on a new glass slide and the fluorescence signal was amplified using a tyramide signal amplification kit (Akoya Biosciences TSA Plus Fluorescein; NEL741001KT). After signal amplification, filters were washed twice in 3 ml of TNT buffer at 55°C to neutralize any residual fluorescein. Filter pieces were transferred to new glass slides and cellulose was stained using 20 µl of Calcofluor White for 7 minutes. Filter pieces were washed twice in 3 ml of water, then placed on new glass slides for counterstaining and mounting with a mixture of propidium iodide and Citiflour media (20 µl per slide). Hybridized filters were held overnight at 4°C, and then at -20°C for long-term storage.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
The filters were viewed using FITC, which allowed visualization of the CARD-FISH fluorescein stain and the red propidium iodide staining of the nuclei. Infected hosts were enumerated under 630X magnification by counting 30 random fields that covered the entire filter piece. Free dinospores were counted at 630X, again covering the whole filter piece in 30 random fields of view. The average number of cells per field was calculated and then multiplied by 8 to represent the whole filter area. This was then converted to cells per liter using correction factors calculated using a stage micrometer and the filtration region diameter.</p>
<p>Cells per ml = (avg COUNT per field)*8 / ml filtered) x CF</p>
<p>CF = area of funnel um²/ area of microscope field um²</p>
<p>For Zeiss S100 with 47 mm filter at 63X/40X, CF = 1.01736 x 10⁹/7.7644 x 10⁴ (13103), 1.94638 x 10⁵ (5226)</p>
<p>Calculation of the percent total infected protistan cells was accomplished using estimations of total eukaryote abundances from the Imaging Flow CytoBot (IFCB). The total number of cells was estimated as the average of all automated counts collected on the same day of sampling, or on a set of days near the day of sampling. IFCB counts are based upon an automated classifier, and objects binned as detritus or other non-plankton cells were excluded from the final estimates. All cell abundances were expressed as per liter.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to comply with BCO-DMO naming conventions;<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
PI Supplied Instrument Name: 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/
Imaging Flow CytoBot (IFCB)
Imaging Flow CytoBot (IFCB)
PI Supplied Instrument Name: Imaging Flow CytoBot (IFCB) PI Supplied Instrument Description:Calculation of the percent total infected protistan cells was accomplished using estimations of total eukaryote abundances from the Imaging Flow CytoBot (IFCB). Instrument Name: Imaging FlowCytobot Instrument Short Name:IFCB Instrument Description: The Imaging FlowCytobot (IFCB) is an in-situ automated submersible imaging flow cytometer that generates images of particles in-flow taken from the aquatic environment. https://mclanelabs.com/imaging-flowcytobot/
Zeiss Axioskop S-100
Zeiss Axioskop S-100
PI Supplied Instrument Name: Zeiss Axioskop S-100 PI Supplied Instrument Description:Hybridized filters were counted on a Zeiss Axioskop S-100 with epifluorescence. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/