http://lod.bco-dmo.org/id/dataset/881563
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
2022-09-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Particle size, volume, and converted biomass from FlowCam runs on the "SalpPOOP" cruise on R/V Tangaroa during October and November 2018
2023-05-09
publication
2023-05-09
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-05-11
publication
https://doi.org/10.26008/1912/bco-dmo.881563.1
Christian Fender
Florida State University
principalInvestigator
Karen E. Selph
University of Hawaiʻi at Mānoa
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: Fender, C., Selph, K. E., Stukel, M. (2023) Particle size, volume, and converted biomass from FlowCam runs on the "SalpPOOP" cruise on R/V Tangaroa during October and November 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-05-09 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.881563.1 [access date]
FlowCam Particle Sizes Dataset Description: <p>Note: A more condensed dataset containing the average abundance and biomass contribution of each particle size class is also available in the related dataset "FlowCam Particle Carbon Content" (<a href="https://www.bco-dmo.org/dataset/881656" target="_blank">https://www.bco-dmo.org/dataset/881656</a>).</p> Methods and Sampling: <p>Samples were collected during October and November 2018 on R/V Tangaroa cruise TAN1810 ("SalpPOOP" cruise) in the Chatham Rise (subtropical and subantarctic waters off the coast of New Zealand). Samples were collected from Niskin bottles of CTD deployments to the base of the mixed layer and the deep chlorophyll maximum. 250 mL subsamples were concentrated by gravity filtration to 10 mL over a 2 µm 47 mm filter, and 2 mL of this concentrate was imaged using a FlowCam's 10X objective lens to quantify the larger (&gt;3 µm) phytoplankton (Sieracki et al. 1998).</p>
<p>FlowCam image analyses were conducted using FlowCam's dedicated classification software VisualSpreadsheet (v. 4.18.5). First, duplicate images resulting from parabolic flow within the flow cell were manually removed. The particles within the remaining images were then classified based on the quality with which VisualSpreadsheet detected their outlines. For particles where the outline appeared to provide good estimates of length and width (classes "Other", "Pennates", "Chaeto", and "Ciliate"), size was calculated for a prolate spheroid using the minimum feret as width and maximum feret as length.</p>
<p>Four categories of particles imaged by the FlowCam proved problematic due to poorer outline quality and had to be treated specially. For such pennate diatoms (class "BadPen"), we manually measured the caliper width of every such pennate diatom in the first CTD cast of each of the four cycles to derive the average pennate width for that cast, and applied this average retroactively to all poorly detected pennates within that cycle. Equivalent spherical diameter (ESD) and biovolume (BV) for the resulting prolate spheroid were then calculated as normal. For semi-transparent dinoflagellates (class "ClearDino"), we recalculated the width using the recorded length and mean aspect ratio for well-detected dinoflagellates in the first CTD cast of each cycle and then calculated ESD and BV normally. For <em>Chaetoceros</em> (class "BadChaeto") we recalculated the length and width of these particles using the recorded aspect ratio and area. Each <em>Asterionelopsis</em> colony (class "Aster") was saved as an individual image file, and representative single cells within a colony that were parallel to the camera’s field of view were manually analyzed using ImageJ (v. 1.52a). This procedure was repeated for all colonies in the first cast of each cycle and the mean width and length taken to produce an "average" <em>Asterionelopsis</em> cell. We then manually counted the number of individual cells present in each image and applied them to the averaged cell sizes to estimate the total biovolume.</p>
<p>The biomass of ciliates (class "Ciliate") was estimated as 0.19 pg C µm⁻³ Putt and Stoecker 1989). The biomass of diatoms (classes "Chaeto", "BadChaeto","Pennate", "BadPen", and "Aster") was estimated allometrically as 0.288*Biovolume^0.811 while other protists and unidentified particles (classes "Other" and "ClearDino") were estimated using 0.216*Biovolume^0.939 (Menden-Deuer and Lessard 2000).</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
Christian Fender
Florida State University
864-992-3182
Earth, Ocean, and Atmos. Science Building (EOA) Rm. 5039 1011 Academic Way
Tallahassee
FL
32306-4520
USA
ckf18b@fsu.edu
pointOfContact
Karen E. Selph
University of Hawaiʻi at Mānoa
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
Particle_ID
Class
Cycle
Cast
Depth
Rep
Lat
Lon
Date
Length
Width
Aspect_Ratio
BV
ESD
Biomass
Yokogawa Fluid Imaging Technologies FlowCam Model VS-IV
theme
None, User defined
sample identification
taxon
experiment id
cast
depth
replicate
latitude
longitude
date
length
width
ratio
biovolume
ESD (Equivalent spherical diameter)
wet_weight_biomass
featureType
BCO-DMO Standard Parameters
CTD - profiler
Niskin bottle
Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system
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)
174.095
-179.812
-44.6358
-42.6622
2018-10-24
2018-11-14
East of New Zealand, Chatham Rise area
0
BCO-DMO catalogue of parameters from Particle size, volume, and converted biomass from FlowCam runs on the "SalpPOOP" cruise on R/V Tangaroa during October and November 2018
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/881607.rdf
Name: Particle_ID
Units: unitless
Description: <p>Running particle identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/881608.rdf
Name: Class
Units: unitless
Description: <p>Classification used to determine processing method (see Acquisition Description)</p>
http://lod.bco-dmo.org/id/dataset-parameter/881609.rdf
Name: Cycle
Units: unitless
Description: <p>Lagrangian experiment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/881610.rdf
Name: Cast
Units: unitless
Description: <p>CTD deployment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/881611.rdf
Name: Depth
Units: meters (m)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/881612.rdf
Name: Rep
Units: unitless
Description: <p>Replicate run</p>
http://lod.bco-dmo.org/id/dataset-parameter/881613.rdf
Name: Lat
Units: decimal degrees North
Description: <p>Latitude; negative values = South</p>
http://lod.bco-dmo.org/id/dataset-parameter/881614.rdf
Name: Lon
Units: decimal degrees East
Description: <p>Longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/881615.rdf
Name: Date
Units: unitless
Description: <p>Date in NZST time zone</p>
http://lod.bco-dmo.org/id/dataset-parameter/881616.rdf
Name: Length
Units: micrometers (um)
Description: <p>Maximum caliper distance</p>
http://lod.bco-dmo.org/id/dataset-parameter/881617.rdf
Name: Width
Units: micrometers (um)
Description: <p>Minimum caliper distance</p>
http://lod.bco-dmo.org/id/dataset-parameter/881618.rdf
Name: Aspect_Ratio
Units: unitless
Description: <p>Ratio of width to length</p>
http://lod.bco-dmo.org/id/dataset-parameter/881619.rdf
Name: BV
Units: cubic micrometers (um^3)
Description: <p>Volume of the particle (biovolume)</p>
http://lod.bco-dmo.org/id/dataset-parameter/881620.rdf
Name: ESD
Units: micrometers (um)
Description: <p>Equivalent spherical diameter</p>
http://lod.bco-dmo.org/id/dataset-parameter/881621.rdf
Name: Biomass
Units: picograms Carbon (pg C)
Description: <p>Converted carbon biomass</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
27124309
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/d66e14c1-83e3-4b92-a213-deac41382f26/content
download
https://doi.org/10.26008/1912/bco-dmo.881563.1
download
onLine
dataset
<p>Samples were collected during October and November 2018 on R/V Tangaroa cruise TAN1810 ("SalpPOOP" cruise) in the Chatham Rise (subtropical and subantarctic waters off the coast of New Zealand). Samples were collected from Niskin bottles of CTD deployments to the base of the mixed layer and the deep chlorophyll maximum. 250 mL subsamples were concentrated by gravity filtration to 10 mL over a 2 µm 47 mm filter, and 2 mL of this concentrate was imaged using a FlowCam's 10X objective lens to quantify the larger (&gt;3 µm) phytoplankton (Sieracki et al. 1998).</p>
<p>FlowCam image analyses were conducted using FlowCam's dedicated classification software VisualSpreadsheet (v. 4.18.5). First, duplicate images resulting from parabolic flow within the flow cell were manually removed. The particles within the remaining images were then classified based on the quality with which VisualSpreadsheet detected their outlines. For particles where the outline appeared to provide good estimates of length and width (classes "Other", "Pennates", "Chaeto", and "Ciliate"), size was calculated for a prolate spheroid using the minimum feret as width and maximum feret as length.</p>
<p>Four categories of particles imaged by the FlowCam proved problematic due to poorer outline quality and had to be treated specially. For such pennate diatoms (class "BadPen"), we manually measured the caliper width of every such pennate diatom in the first CTD cast of each of the four cycles to derive the average pennate width for that cast, and applied this average retroactively to all poorly detected pennates within that cycle. Equivalent spherical diameter (ESD) and biovolume (BV) for the resulting prolate spheroid were then calculated as normal. For semi-transparent dinoflagellates (class "ClearDino"), we recalculated the width using the recorded length and mean aspect ratio for well-detected dinoflagellates in the first CTD cast of each cycle and then calculated ESD and BV normally. For <em>Chaetoceros</em> (class "BadChaeto") we recalculated the length and width of these particles using the recorded aspect ratio and area. Each <em>Asterionelopsis</em> colony (class "Aster") was saved as an individual image file, and representative single cells within a colony that were parallel to the camera’s field of view were manually analyzed using ImageJ (v. 1.52a). This procedure was repeated for all colonies in the first cast of each cycle and the mean width and length taken to produce an "average" <em>Asterionelopsis</em> cell. We then manually counted the number of individual cells present in each image and applied them to the averaged cell sizes to estimate the total biovolume.</p>
<p>The biomass of ciliates (class "Ciliate") was estimated as 0.19 pg C µm⁻³ Putt and Stoecker 1989). The biomass of diatoms (classes "Chaeto", "BadChaeto","Pennate", "BadPen", and "Aster") was estimated allometrically as 0.288*Biovolume^0.811 while other protists and unidentified particles (classes "Other" and "ClearDino") were estimated using 0.216*Biovolume^0.939 (Menden-Deuer and Lessard 2000).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- started with file named "FlowCam_RawV2.xlsx" received February 2023;<br />
- converted Date field to YYYY-MM-DD format;<br />
- renamed fields to comply with BCO-DMO naming conventions;<br />
- rounded Lat and Lon fields to 4 decimal places.</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: 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/
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/
Yokogawa Fluid Imaging Technologies FlowCam Model VS-IV
Yokogawa Fluid Imaging Technologies FlowCam Model VS-IV
PI Supplied Instrument Name: Yokogawa Fluid Imaging Technologies FlowCam Model VS-IV Instrument Name: Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system Instrument Short Name:FlowCAM Instrument Description: Imaging cytometers are automated instruments that quantify properties of single cells, one cell at a time. They combine some aspects of flow cytometry with particle imaging capabilities in an automated device to classify small particles, including phytoplankton and protozoa. They can measure a variety of properties: cell size, cell granularity, cell aspect ratio, equivalent spherical diameter (ESD) and area-based diameter (ABD) [to estimate bio-volume, which is used to estimate cell carbon biomass]. Particle images are digitally recorded and sorted into different classes according to training libraries using a support vector machine (supervised learning methods). The instruments particle-size is calibrated using different sizes of latex beads.
The FlowCam VS series are automated imaging-in-flow instruments that generate high-resolution digital images for measuring size and shape of microscopic particles. The sample introduced in the system is attracted by a peristaltic or a syringe pump into a flow cell (or flow chamber) with known dimensions, located in front of a microscope objective which is connected to a camera video. The benchtop model is ideally suited to a typical laboratory environment with applications in oceanographic research, municipal water, biopharmaceutical formulations, chemicals, oil and gas, biofuels, and many other markets. FlowCam VS is available in four models, from the imaging-only VS-I (i.e. without excitation wavelength or fluorescence emission wavelengths) to the top-of-the-line VS-IV with two channels of fluorescence measurement and scatter triggering capabilities. The instrument can measure particles between 2µm and 2mm; can analyse in vivo or fixed samples; has a flow rate between 0.005 ml/minute and 250 ml/minute (dependant upon magnification, flow cell depth, camera frame rate, efficiency desired, etc.). It can produce either 8-bit Grayscale (Monochrome Camera) or 24-bit Colour (Colour Camera) images, depending on the model.
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