http://lod.bco-dmo.org/id/dataset/905060
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
2023-07-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Epifluorescence Microscopy Water Column Samples from R/V Tangaroa TAN1810 in the Chatham Rise (Subtropical and Sub-Antarctic waters off of New Zealand) from October to November 2018 (Salp Food Web Ecology project)
2023-07-24
publication
2023-07-24
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-02-11
publication
https://doi.org/10.26008/1912/bco-dmo.905060.1
Natalia Yingling
Florida State University
principalInvestigator
Karen E. Selph
University of Hawai'i
principalInvestigator
Michael R. Stukel
Florida State University
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: Yingling, N., Selph, K. E., Stukel, M. R. (2026) Epifluorescence Microscopy Water Column Samples from R/V Tangaroa TAN1810 in the Chatham Rise (Subtropical and Sub-Antarctic waters off of New Zealand) from October to November 2018 (Salp Food Web Ecology project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-07-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.905060.1 [access date]
Epifluorescence Microscopy Water Column Samples from Subtropical and Subantarctic Waters East of New Zealand Dataset Description: Methods and Sampling: <p><strong>Field Collection</strong></p>
<p>Data was collected in the Chatham Rise section of the Southern Ocean, located east of Aotearoa New Zealand, as part of the SALPOOP (‘Salp Particle expOrt and Ocean Production’) voyage during October to November 2018.&nbsp;). We conducted five Lagrangian experiments (hereafter referred to as “cycles”) that lasted four to eight days&nbsp;(Décima et al., 2023).&nbsp;There were three cycles that were sampled in SA waters (1, 2 and 5) and two cycles in ST waters (3 and 4) while salps were only present in three cycles (1, 2 and 4).&nbsp;Six depths were chosen to span the euphotic zone (based on chlorophyll fluorescence measured during the conductivity-temperature-depth (CTD) downcast profiles).</p>
<p>&nbsp;</p>
<p><strong>Epifluorescence Microscopy Sampling</strong></p>
<p>From each depth, two different volumes of water were sampled: 50 mL for nanoplankton- epifluorescence microscopy (filtered through a 0.8-µm pore-size black polycarbonate filter) and 400 mL for microplankton epifluorescence microscopy (filtered through an 8-µm pore-size filter). Utilizing two different sized filters and sampling volumes allowed for appropriate, adjustable filtered volumes and avoid overlapping cells on the slides.&nbsp;20&nbsp;µm&nbsp;backing filters were utilized as data has indicated that they support the membrane filters and ensure even dispersal of sample on the filter&nbsp;(Kemp et al., 1993; Taylor et al., 2015).&nbsp;The samples were preserved&nbsp;using buffered formalin, alkaline Lugol’s solution, and sodium thiosulfate then stained using proflavine and 4’, 6-diamidino-2phenylindole (DAPI) (modified protocol from Sherr and Sherr, 1993 in&nbsp;Kemp et al. 1993). During and immediately after filtration, filters were covered with tin foil to prevent photochemical quenching. Filters were mounted onto a glass slide and frozen in a -80º C freezer for later analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756465 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756465
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756610 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756610
completed
Natalia Yingling
Florida State University
1011 Academic Way
Tallahassee
FL
USA
ny18b@fsu.edu
pointOfContact
Karen E. Selph
University of Hawai'i
808-956-7941
Department of Oceanography 1000 Pope Road, MSB 205
Honolulu
HI
96822
USA
selph@hawaii.edu
pointOfContact
Michael R. Stukel
Florida State University
815-258-3875
Earth, Ocean, and Atmos. Science Building (EOA) Rm. 6089 1011 Academic Way
Tallahassee
FL
32306
USA
mstukel@fsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
ID
Cycle
Cast
Image_Number
Particle_Number
Filter_Pore_Size
Volume_Filtered
Depth
Long
Lat
Date
Area
Width
Feret_Length
Conversion_Ratio
Calculated_Width
Biovolume
ESD
Biomass
Final_Biomass
Diatoms
Olympus DP72 camera
Epifluorescence microscope: Olympus BX51 microscope with a Olympus DP72 camera and Exfo X-cite Series 120 mercury bulb with a FITC filter for green fluroescence
theme
None, User defined
sample identification
experiment id
cast
sample description
number
filter_size
volume
depth
longitude
latitude
date
area_measured
width
length
ratio
biovolume
ESD (Equivalent spherical diameter)
wet_weight_biomass
diatom abundance
featureType
BCO-DMO Standard Parameters
Camera
Fluorescence Microscope
instrument
BCO-DMO Standard Instruments
TAN1810
service
Deployment Activity
Chatham Rise (Subtropical and Sub-Antarctic waters off of New Zealand)
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.
Collaborative Research: Quantifying trophic roles and food web ecology of salp blooms of the Chatham Rise
https://osprey.bco-dmo.org/project/754878
Collaborative Research: Quantifying trophic roles and food web ecology of salp blooms of the Chatham Rise
<p><em>NSF Award Abstract:</em><br />
Salps are unique open-ocean animals that range in size from a few millimeters to greater than twenty centimeters, have a gelatinous (jelly-like) body, and can form long chains of many connected individuals. These oceanic organisms act as oceanic vacuum cleaners, having incredibly high feeding rates on phytoplankton and, unusual for consumers of their size, smaller bacteria-sized prey. This rapid feeding and the salps' tendency to form dense blooms, allows them move substantial amounts of prey carbon from the surface into the deep ocean, leading to carbon dioxide removal from the atmosphere. However, salps are often considered a trophic dead-end, rather than a link, in the food web due to the assumption that they themselves are not consumed, since their gelatinous bodies are less nutritious than co-occurring crustacean prey. Along with this, salp populations are hypothesized to be increasing due to climate change. This proposal addresses these questions: 1) Do salps compete primarily with crustaceans (as in the prevailing paradigm) or are they competitors of single-celled protists, which are the dominant grazers of small phytoplankton? 2) Do salp blooms increase the efficiency of food-web pathways from tiny phytoplankton to fisheries production in nutrient-poor ocean regions?</p>
<p>This project will support the interdisciplinary education of a graduate student who will learn modeling and laboratory techniques in the fields of biological and chemical oceanography and stimulate international collaborations between scientists in the United States and New Zealand. Additionally, several Education and Outreach initiatives are planned, including development of a week-long immersive high school class in biological oceanography, and education modules that will serve the "scientists-in-the schools" program in Tallahassee, FL.</p>
<p>It is commonly assumed that salps are a trophic sink. However, this idea was developed before the discovery that protists (rather than crustaceans) are the dominant grazers in the open ocean and was biased by the difficulty of recognizing gelatinous salps in fish guts. More recent studies show that salps are found in guts of a diverse group of fish and seabirds and are a readily available prey source when crustacean abundance is low. This proposal seeks to quantify food web flows through contrasting salp-dominated and salp-absent water parcels near the Chatham Rise off western New Zealand where salp blooms are a predictable phenomenon. The proposal will leverage previously obtained data on salp abundance, bulk grazing impact, and biogeochemical significance during Lagrangian experiments conducted by New Zealand-based collaborators. The proposal will determine 1) taxon- and size-specific phytoplankton growth rate measurements, 2) taxon- and size-specific protozoan and salp grazing rate measurements, 3) compound specific isotopic analysis of the amino acids of mesozooplankton to quantify the trophic position of salps, hyperiid amphipods, and other crustaceans, 4) sediment traps to quantify zooplankton carcass sinking rates, and 5) linear inverse ecosystem modeling syntheses. Secondary production and trophic flows from this well-constrained ecosystem model will be compared to crustacean-dominated and microbial loop-dominated ecosystems in similarly characterized regions (California Current, Costa Rica Dome, and Gulf of Mexico).</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>
Salp Food Web Ecology
largerWorkCitation
project
eng; USA
oceans
Chatham Rise (Subtropical and Sub-Antarctic waters off of New Zealand)
174
180
-45
-42
2018-10-25
2018-11-18
East of New Zealand, Chatham Rise area
0
BCO-DMO catalogue of parameters from Epifluorescence Microscopy Water Column Samples from R/V Tangaroa TAN1810 in the Chatham Rise (Subtropical and Sub-Antarctic waters off of New Zealand) from October to November 2018 (Salp Food Web Ecology 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
http://lod.bco-dmo.org/id/dataset-parameter/905126.rdf
Name: ID
Units: unitless
Description: <p>Unique number given to each individual cell measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/905127.rdf
Name: Cycle
Units: unitless
Description: <p>Lagrangian experiment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/905128.rdf
Name: Cast
Units: unitless
Description: <p>CTD deployment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/993729.rdf
Name: Image_Number
Units: unitless
Description: <p>Identifier for one of 20 images taken per slide</p>
http://lod.bco-dmo.org/id/dataset-parameter/905129.rdf
Name: Particle_Number
Units: unitless
Description: <p>Number assigned to each particle imaged in a particular image</p>
http://lod.bco-dmo.org/id/dataset-parameter/905130.rdf
Name: Filter_Pore_Size
Units: microns (µm)
Description: <p>Pore size of filters that were used to filter the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/905131.rdf
Name: Volume_Filtered
Units: mL
Description: <p>Volume of water filtered for that slide in mL</p>
http://lod.bco-dmo.org/id/dataset-parameter/905132.rdf
Name: Depth
Units: meters
Description: <p>Depth the sample originated in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/905134.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude of sample location in decimal degrees; a positive value indicates an Eastern coordinate</p>
http://lod.bco-dmo.org/id/dataset-parameter/905133.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of sample location in decimal degrees; negative values indicates a Northern coordinate</p>
http://lod.bco-dmo.org/id/dataset-parameter/905135.rdf
Name: Date
Units: unitless
Description: <p>Date in New Zealand Standard Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/905136.rdf
Name: Area
Units: microns squared (µm^2)
Description: <p>Area of the cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/905137.rdf
Name: Width
Units: microns (µm)
Description: <p>Width of the cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/905138.rdf
Name: Feret_Length
Units: microns (µm)
Description: <p>Feret lenth of the cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/905139.rdf
Name: Conversion_Ratio
Units: unitless
Description: <p>Conversation ratio that incorporates area of the image taken and provides a single value for the ratio of cells actually counted (note: this value changes based on pore size of the filter)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905140.rdf
Name: Calculated_Width
Units: microns (µm)
Description: <p>Calculated width (equation one found within the data processing description of this metadata page)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905141.rdf
Name: Biovolume
Units: µm^3
Description: <p>calculated biovolume (equation two found within the data processing description of this metadata page)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905142.rdf
Name: ESD
Units: microns (µm)
Description: <p>Equivalent Spherical diameter (equation three found within the data processing description of this metadata page) in µm</p>
http://lod.bco-dmo.org/id/dataset-parameter/905143.rdf
Name: Biomass
Units: picogram of carbon per cell (pg C cell^-1)
Description: <p>Biomass in units of pg C (If a non-diatom, use equation four found within the data processing description of this metadata page; if diatom, use equation 5)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905144.rdf
Name: Final_Biomass
Units: picogram of carbon per mL (pg C/mL)
Description: <p>Biomass in units of pg C/mL (note: this value is the biomass (pg C) divided by the volume filtered (mL) and the conversion ratio)</p>
http://lod.bco-dmo.org/id/dataset-parameter/905145.rdf
Name: Diatoms
Units: unitless
Description: <p>0 represents that this cell is not a diatom, 1 represents this cell is a diatom</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
https://doi.org/10.26008/1912/bco-dmo.905060.1
download
onLine
dataset
<p><strong>Field Collection</strong></p>
<p>Data was collected in the Chatham Rise section of the Southern Ocean, located east of Aotearoa New Zealand, as part of the SALPOOP (‘Salp Particle expOrt and Ocean Production’) voyage during October to November 2018.&nbsp;). We conducted five Lagrangian experiments (hereafter referred to as “cycles”) that lasted four to eight days&nbsp;(Décima et al., 2023).&nbsp;There were three cycles that were sampled in SA waters (1, 2 and 5) and two cycles in ST waters (3 and 4) while salps were only present in three cycles (1, 2 and 4).&nbsp;Six depths were chosen to span the euphotic zone (based on chlorophyll fluorescence measured during the conductivity-temperature-depth (CTD) downcast profiles).</p>
<p>&nbsp;</p>
<p><strong>Epifluorescence Microscopy Sampling</strong></p>
<p>From each depth, two different volumes of water were sampled: 50 mL for nanoplankton- epifluorescence microscopy (filtered through a 0.8-µm pore-size black polycarbonate filter) and 400 mL for microplankton epifluorescence microscopy (filtered through an 8-µm pore-size filter). Utilizing two different sized filters and sampling volumes allowed for appropriate, adjustable filtered volumes and avoid overlapping cells on the slides.&nbsp;20&nbsp;µm&nbsp;backing filters were utilized as data has indicated that they support the membrane filters and ensure even dispersal of sample on the filter&nbsp;(Kemp et al., 1993; Taylor et al., 2015).&nbsp;The samples were preserved&nbsp;using buffered formalin, alkaline Lugol’s solution, and sodium thiosulfate then stained using proflavine and 4’, 6-diamidino-2phenylindole (DAPI) (modified protocol from Sherr and Sherr, 1993 in&nbsp;Kemp et al. 1993). During and immediately after filtration, filters were covered with tin foil to prevent photochemical quenching. Filters were mounted onto a glass slide and frozen in a -80º C freezer for later analysis.</p>
Specified by the Principal Investigator(s)
<p><strong>Processing Notes from Researcher:</strong></p>
<p><u>Epifluorescence Microscopy Analysis</u></p>
<p>Phytoplankton images were captured with an&nbsp;Olympus Microscope DP72 Camera&nbsp;using an&nbsp;Olympus BX51&nbsp;fluorescence microscope. 20 images were taken under the fluorescence of FITC (green fluorescence)&nbsp;n order to capture the fluorescence of cell proteins. Proflavine overstained cells to the point that we were not able to confidently differentiate heterotrophic cells from autotrophic cells, therefore only biomass and abundance values were able to be calculated. A 60x magnification lens was used to image slides with 0.8&nbsp;µm filters&nbsp;while 20x magnification was used to image slides with 8&nbsp;µm filters.&nbsp;Images were then processed using the ImageJ image analysis software (v 1.52a or 1.53c). Cells were manually outlined using the freehand tool and approximate feret cell length and cell area were calculated by ImageJ in pixels and then converted to microns using a calibration scale. To avoid biasing the examined cell size, cells that were roughly greater than 50% out of frame and cells that were broken or fragmented were not included in analysis. Conversions factors were applied to account for volume filtered and percentage of the filter area analyzed. To determine the true filtration diameter, a light microscope was used to examine a 25 mm glass fiber filter (GF/F) filter that had a small amount of dyed water filtered through. It was discovered that the filter funnel blocks roughly 12% of the 25-mm filter and the filtered region had a diameter of 22 mm. Equations 1-5 show the equations used to calculate cell width, biovolume, ESD (equivalent spherical diameter) and biomass, where * implies we assumed that cell height = cell width/2. ESD was used as a consistent measure of mean cell size since many plankton have an irregular shape. The height of a cell was assumed to be roughly equivalent to half of the cell width since cells are often flattened during filtration&nbsp;(Taylor et al., 2011)&nbsp;with the exception of diatoms. The biomass of diatoms (which were the only taxon we could conclusively identify) was estimated allometrically&nbsp;using equation 5 while all other cell biomass (non-diatoms) was estimated allometrically using equation 4.&nbsp;(Menden-Deuer and Lessard, 2000).&nbsp;</p>
<p>&nbsp;</p>
<p>Equation 1: Cell width = (4/π) x (Area of the cell/Feret length of the cell)</p>
<p>Equation 2: Biovolume = (4/3)(π) x (Feret Length/2) x (Cell Width/2) x (Cell Height*/2)</p>
<p>Equation 3: ESD = 2 x (3 x Biovolume/4π)^(1/3)</p>
<p>Equation 4: Biomass (non-diatoms) = 0.216 x Biovolume^0.939</p>
<p>Equation 5: Biomass (diatoms) = 0.288 x Biovolume^0.811</p>
Specified by the Principal Investigator(s)
* Spaces in column name headers replaced by underscores ("_").
* Dates converted from %m/%d/%y format to %Y-%m-%d format.
* Latitude and longitude coordinates rounded to 6 decimal places.
* Latitude and longitude values headers have been corrected in the published primary data file (905060_v1_epifluorescence_microscopy.csv); originally, the submitted file contained swapped header names.
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
Olympus DP72 camera
Olympus DP72 camera
PI Supplied Instrument Name: Olympus DP72 camera PI Supplied Instrument Description:Slides were calibrated from pixels to microns for both 0.8 µm and 8 µm to determine what length of pixels equates to µm thus only micron area, width and feret length are show in the raw datasheet. Our data also includes conversation ratios in the raw excel sheet. This ratio should be included when determining biomass in units of pg C/mL or abundance in #/mL, along with volume filter, as this ratio incorporates the area of the images taken and gives a value that states the ratio of the cells that were actually counted for 0.8 µm and 8 µm samples. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Epifluorescence microscope: Olympus BX51 microscope with a Olympus DP72 camera and Exfo X-cite Series 120 mercury bulb with a FITC filter for green fluroescence
Epifluorescence microscope: Olympus BX51 microscope with a Olympus DP72 camera and Exfo X-cite Series 120 mercury bulb with a FITC filter for green fluroescence
PI Supplied Instrument Name: Epifluorescence microscope: Olympus BX51 microscope with a Olympus DP72 camera and Exfo X-cite Series 120 mercury bulb with a FITC filter for green fluroescence PI Supplied Instrument Description:Slides were calibrated from pixels to microns for both 0.8 µm and 8 µm to determine what length of pixels equates to µm thus only micron area, width and feret length are show in the raw datasheet. Our data also includes conversation ratios in the raw excel sheet. This ratio should be included when determining biomass in units of pg C/mL or abundance in #/mL, along with volume filter, as this ratio incorporates the area of the images taken and gives a value that states the ratio of the cells that were actually counted for 0.8 µm and 8 µm samples. Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Cruise: TAN1810
TAN1810
Community Standard Description
International Council for the Exploration of the Sea
R/V Tangaroa
vessel
TAN1810
Moira Decima
New Zealand National Institute of Water and Atmospheric Research
Community Standard Description
International Council for the Exploration of the Sea
R/V Tangaroa
vessel