http://lod.bco-dmo.org/id/dataset/546610
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
2015-02-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Laboratory results on Copepod gut fullness using two tintinnid diets from San Francisco State University in 2013 (Food Limitation in Copepod nauplii project)
2015-01-15
publication
2015-01-15
revision
BCO-DMO Linked Data URI
2015-01-15
creation
http://lod.bco-dmo.org/id/dataset/546610
William Kimmerer
San Francisco State University
principalInvestigator
Sarah Cohen
San Francisco 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: Kimmerer, W., Cohen, S. (2015) Laboratory results on Copepod gut fullness using two tintinnid diets from San Francisco State University in 2013 (Food Limitation in Copepod nauplii project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-01-15) Version Date 2015-01-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546610 [access date]
Copepod gut fullness on two tintinnid diets Dataset Description: <p>Adult and naupliar <em>P. marinus</em> gut fullness on two Tintinnid diets.&nbsp;Gut&nbsp;fullness index&nbsp;of adult and naupliar&nbsp;<em>Pseudodiaptomus marinus</em>&nbsp;fed two different prey items,&nbsp;measured by image pixels and epifluorescent microscopy.</p>
<p><strong>Related Reference:</strong></p>
<p>Kamiyama, T. (2000). Application of a vital staining method to measure feeding rates of field ciliate assemblages on a harmful alga. Marine Ecology Progress Series</p>
<p>Li, A., et al. (1996). Ingestion of fluorescently labeled and phycoerythrin-containing prey by mixotrophic dinoflagellates." Aquatic Microbial Ecology 10(2): 139-147.</p>
<p>Merrell, J. R. and D. K. Stoecker (1998). Differential grazing on protozoan microplankton by developmental stages of the calanoid copepod Eurytemora affinis Poppe. Journal of Plankton Research 20(2): 289-304.</p>
<p>Vogt, R.A., T.R. Ignoffo, L.J. Sullivan, J. Herndon, J.H. Stillman, and W. Kimmerer. 2013. Feeding capabilities and limitations in the nauplii of two pelagic estuarine copepods, <em>Pseudodiaptomus marinus</em> and <em>Oithona davisae</em>. Limnology and Oceanography 58: 2145-2157</p> Methods and Sampling: <p>Adult and naupliar&nbsp;<em>P. marinus</em> were incubated with either&nbsp;<em>Codonellopsis </em>or <em>Favella&nbsp;</em>for 1 hour. Incubations were terminated by gently pouring the&nbsp;contents of incubation bottles through a 53 mm sieve, then&nbsp;rinsing the copepods into a petri dish with GF/F filtered&nbsp;water. A total of 12 copepods were sampled from each&nbsp;stage for each phytoplankton and for the controls.</p>
<p>Copepods were sorted under a dissecting microscope and&nbsp;immediately transferred to glass microscope slides. Excess&nbsp;water was removed with a fine-tipped Pasteur pipette to&nbsp;immobilize the copepod for optimal viewing. To minimize&nbsp;pigment degradation, slides containing the copepods were&nbsp;transferred to the microscope as quickly as possible, always&nbsp;within 2 min of sorting.</p>
<p>A Nikon model E400 epifluorescence microscope at 20X magnification, outfitted with a Nikon B-2A long-pass filter cube (470EX/515LP, Nikon) and a custom band-pass filter cube (430EX/680EM, Omega Optical) was used. The longpass filter pair provided a brighter overall image than the band-pass filter pair and also fluoresced non-chlorophyll structures (e.g., the copepod exoskeleton fluoresces green with blue excitation). The band-pass filter cube showed fluorescence from only chlorophyll and phaeopigments. Photographs of the copepods were taken at each filter setting using a Canon Digital model T3i single-lens reflex camera (ISO 6400, F 1/15) remotely controlled with the Canon Electro-Optical System Utility software to produce clear images of the epifluorescence (Vogt, 2013,Fig. 1).</p>
<p>Images were processed with Photoshop CS6 (Adobe). Total gut area was manually digitized using the lasso and measurement tools on the long-pass-filtered images. The mean gut area of 12 individuals for each copepod species and stage was used for calculations. The threshold tool was used to select areas of the long-pass-filtered images containing pigment (gut pigment area) that exceeded baseline fluorescence. Signal intensity was not used in the calculation of the GPI (Gut Pigment Index) because pigment content and composition differed among phytoplankton taxa. Pixels of the band-pass-filtered images exceeding the threshold value were selected and their area estimated using the measurement tool. The gut-pigment area was then divided by the total gut area, yielding a relative GPI for each copepod. The same procedure was used to process images of copepods sampled from the control bottles. Copepods with &lt;5% GPI were assumed not to have fed, as the GPI values in those samples were within the range of indices estimated from the controls.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0929075 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0929075
completed
William Kimmerer
San Francisco State University
(415) 338-3515
San Francisco State University / Romberg Tiburon Center 3152 Paradise Drive
Tiburon
CA
94920
kimmerer@sfsu.edu
pointOfContact
Sarah Cohen
San Francisco State University
415-338-3750
Romberg Tiburon Center 3152 Paradise Drive
Tiburon
CA
94920
USA
sarahcoh@sfsu.edu
pointOfContact
asNeeded
Dataset Version: 2015-01-15
Unknown
pcent_full_bin
prey
stage
count
camera
Epifluorescence Microscope
theme
None, User defined
No BCO-DMO term
stage
count
featureType
BCO-DMO Standard Parameters
Camera
Fluorescence Microscope
instrument
BCO-DMO Standard Instruments
Kimmerer_2013
service
Deployment Activity
San Francisco State University lab
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.
Feeding and food limitation in copepod nauplii, the neglected life stage
https://osprey.bco-dmo.org/project/546027
Feeding and food limitation in copepod nauplii, the neglected life stage
<p>This project will investigate feeding by copepod nauplius larvae, the most abundant metazoans in the sea. It will answer three questions: 1) How does food selection by adults and nauplii differ when they are fed multiple prey species in the laboratory? 2) How does food selection by adults and nauplii differ when they are feeding on natural prey assemblages? and, 3) How do growth, development, and survival differ between copepodites and nauplii when their growth is food limited? Comparative experiments and field-based measurements will contrast the food consumed, and the effects of food limitation, between nauplii and later life stages. This contrast will include attributes of food such as size, taxon, and motility, and will include experiments with cultured prey offered singly or in a mixture, and natural prey, and apply genetic techniques to determine prey consumption by a predatory copepod. Copepods will be collected from the San Francisco Estuary, with four species selected for experiments to span taxonomic groups, sizes, salinity ranges, and general feeding behavior. A variety of techniques will be applied to account for the inevitable biases and limitations of each; all but one have previously been applied in our laboratories. These will include laboratory feeding experiments using cultured prey individually and in mixtures, and experiments using natural prey. Consumption of prey in experimental bottles will be measured as chlorophyll concentration and through particle counts by microscopy and flow cytometry. Radioactively labeled prey will be used in short incubations to determine feeding on particular prey types. Samples from the field will be examined for gut fluorescence. Separate experiments will determine how nauplii and copepodites survive and grow at different concentrations of food. Investigations of feeding by a predatory copepod (Tortanus dextrilobatus) will use molecular techniques to identify mitochondrial and nuclear DNA from diverse suspected prey species. Specific primers will be developed for common zooplankton species consumed by T. dextrilobatus in the laboratory. General primers and screening protocols developed here will be useful for identifying food web interactions in other estuarine communities.</p>
<p>Copepod nauplii are important both in their diverse trophic roles in ocean foodwebs and in the population dynamics of copepods. Nauplii have a completely different feeding apparatus from later stages, and the first feeding stage can be very sensitive to starvation, making these life stages critical to population dynamics. Yet extant copepod population models treat nauplii as miniature adults. This work will provide valuable input to the growing efforts at modeling ocean ecosystems. </p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Project_further_details_Kimmerer_copepod_naup_feeding.pdf" target="_blank">Further details from final report (pdf)</a></p>
food limitation in copepod nauplii
largerWorkCitation
project
eng; USA
biota
oceans
San Francisco State University lab
2015-01-15
San Francisco Estuary
0
BCO-DMO catalogue of parameters from Laboratory results on Copepod gut fullness using two tintinnid diets from San Francisco State University in 2013 (Food Limitation in Copepod nauplii 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/546619.rdf
Name: pcent_full_bin
Units: percent
Description: <p>gut fullness in 20% intervals</p>
http://lod.bco-dmo.org/id/dataset-parameter/546620.rdf
Name: prey
Units: unitless
Description: <p>food item name</p>
http://lod.bco-dmo.org/id/dataset-parameter/546621.rdf
Name: stage
Units: unitless
Description: <p>copepod life stage: N=nauplius</p>
http://lod.bco-dmo.org/id/dataset-parameter/546622.rdf
Name: count
Units: prey
Description: <p>number of prey items in gut</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
564
https://datadocs.bco-dmo.org/file/QAAXxY8FkV9L8N/fullness_diet.csv
fullness_diet.csv
Primary data file for dataset ID 546610
download
https://osprey.bco-dmo.org/dataset/546610/data/download
download
onLine
dataset
<p>Adult and naupliar&nbsp;<em>P. marinus</em> were incubated with either&nbsp;<em>Codonellopsis </em>or <em>Favella&nbsp;</em>for 1 hour. Incubations were terminated by gently pouring the&nbsp;contents of incubation bottles through a 53 mm sieve, then&nbsp;rinsing the copepods into a petri dish with GF/F filtered&nbsp;water. A total of 12 copepods were sampled from each&nbsp;stage for each phytoplankton and for the controls.</p>
<p>Copepods were sorted under a dissecting microscope and&nbsp;immediately transferred to glass microscope slides. Excess&nbsp;water was removed with a fine-tipped Pasteur pipette to&nbsp;immobilize the copepod for optimal viewing. To minimize&nbsp;pigment degradation, slides containing the copepods were&nbsp;transferred to the microscope as quickly as possible, always&nbsp;within 2 min of sorting.</p>
<p>A Nikon model E400 epifluorescence microscope at 20X magnification, outfitted with a Nikon B-2A long-pass filter cube (470EX/515LP, Nikon) and a custom band-pass filter cube (430EX/680EM, Omega Optical) was used. The longpass filter pair provided a brighter overall image than the band-pass filter pair and also fluoresced non-chlorophyll structures (e.g., the copepod exoskeleton fluoresces green with blue excitation). The band-pass filter cube showed fluorescence from only chlorophyll and phaeopigments. Photographs of the copepods were taken at each filter setting using a Canon Digital model T3i single-lens reflex camera (ISO 6400, F 1/15) remotely controlled with the Canon Electro-Optical System Utility software to produce clear images of the epifluorescence (Vogt, 2013,Fig. 1).</p>
<p>Images were processed with Photoshop CS6 (Adobe). Total gut area was manually digitized using the lasso and measurement tools on the long-pass-filtered images. The mean gut area of 12 individuals for each copepod species and stage was used for calculations. The threshold tool was used to select areas of the long-pass-filtered images containing pigment (gut pigment area) that exceeded baseline fluorescence. Signal intensity was not used in the calculation of the GPI (Gut Pigment Index) because pigment content and composition differed among phytoplankton taxa. Pixels of the band-pass-filtered images exceeding the threshold value were selected and their area estimated using the measurement tool. The gut-pigment area was then divided by the total gut area, yielding a relative GPI for each copepod. The same procedure was used to process images of copepods sampled from the control bottles. Copepods with &lt;5% GPI were assumed not to have fed, as the GPI values in those samples were within the range of indices estimated from the controls.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
-&nbsp;reformatted data rows and columns</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
camera
camera
PI Supplied Instrument Name: camera PI Supplied Instrument Description:Canon® Digital model T3i single lens reflex (SLR) camera (ISO 6400, F 1/15) remotely controlled with the Canon Electro-Optical System (EOS) Utility software. 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
Epifluorescence Microscope
PI Supplied Instrument Name: Epifluorescence Microscope PI Supplied Instrument Description:Nikon model E400 epifluorescence microscope at 20X magnification, outfitted with a Nikon B-2A longpass filter cube (470EX/515LP, Nikon) and a custom bandpass filter cube (430EX/680EM, Omega Optical). 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/
Deployment: Kimmerer_2013
Kimmerer_2013
SFSU RTC
laboratory
Kimmerer_2013
William Kimmerer
San Francisco State University
SFSU RTC
laboratory