http://lod.bco-dmo.org/id/dataset/546723
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)
Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project)
2021-06-10
publication
2021-06-10
revision
BCO-DMO Linked Data URI
2021-06-10
creation
http://lod.bco-dmo.org/id/dataset/546723
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. (2021) Identification of copepod gut contents analyzed at San Francisco State University in 2013 (Food Limitation in Copepod nauplii project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546723 [access date]
Identification of copepod gut contents Dataset Description: <p>Field collected copepod gut content sequences were identified&nbsp;either by comparison to our sequence library of local copepod species or using a sequence similarity approach. Sequences were Blasted using NCBI’s web_blast.pl script (http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl). The Blast output was manipulated with perl scripts we wrote to isolate the accession numbers for the BLAST hits, use the accession numbers to get the full records using NCBI’s Batch Entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez), and get the taxonomic information from the full records. See <a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/nauplii_gutcontent_sequence.pdf" target="_blank">nauplii_gutcontent_sequence.pdf</a> for the output of these programs. We then compared the taxonomic information among the top 10% BLAST scores to assign the sequence to the lowest, taxonomic level shared by the top scoring hits.</p>
<p><strong>Related Reference:</strong></p>
<p>* Craig, Carrie, Wim J. Kimmerer, and C. Sarah Cohen. 2014. A DNA-based method for investigating feeding by copepod nauplii. Journal of Plankton Research 36 (1): 271-275</p> Methods and Sampling: <p>See <a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Kimmerer_genetics_methodology.pdf" target="_blank">Methodology</a> (pdf).</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: 2
Unknown
station
date
contig_name
sequence_id
stage
copepod_sp
taxon_Perl
taxon_level_Perl
taxon_Claident
taxon_level_Claident
taxon_notes_Claident
min_identity_SAP
posterior_prob_100_SAP
taxon_level_100_SAP
posterior_prob_95_100_SAP
taxon_level_95_100_SAP
probability
warning_comment
Automated Sequencer
HPLC
Plankton Net
Thermal Cycler
theme
None, User defined
station
date
No BCO-DMO term
sample identification
stage
taxon
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
High-Performance Liquid Chromatograph
Plankton Net
Thermal Cycler
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
2021-06-10
San Francisco Estuary
0
BCO-DMO catalogue of parameters from Identification of copepod gut contents analyzed at 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/546734.rdf
Name: station
Units: unitless
Description: <p>tow location</p>
http://lod.bco-dmo.org/id/dataset-parameter/546735.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>tow date</p>
http://lod.bco-dmo.org/id/dataset-parameter/546736.rdf
Name: contig_name
Units: unitless
Description: <p>??</p>
http://lod.bco-dmo.org/id/dataset-parameter/546737.rdf
Name: sequence_id
Units: unitless
Description: <p>squence identification: sample name followed by sequence number. TDF=adult; TDN = nauplii</p>
http://lod.bco-dmo.org/id/dataset-parameter/546738.rdf
Name: stage
Units: unitless
Description: <p>copepod life stage: N=nauplius</p>
http://lod.bco-dmo.org/id/dataset-parameter/546739.rdf
Name: copepod_sp
Units: unitless
Description: <p>copepod species - id from SF barcode library</p>
http://lod.bco-dmo.org/id/dataset-parameter/546740.rdf
Name: taxon_Perl
Units: unitless
Description: <p>taxonomic id of prey item in gut using Perl program with 10% cut-off</p>
http://lod.bco-dmo.org/id/dataset-parameter/546741.rdf
Name: taxon_level_Perl
Units: unitless
Description: <p>taxonomic level of tax id'd from Perl</p>
http://lod.bco-dmo.org/id/dataset-parameter/546742.rdf
Name: taxon_Claident
Units: unitless
Description: <p>taxonomic id of prey items in gut using Claident with default settings against SSU_genus database</p>
http://lod.bco-dmo.org/id/dataset-parameter/546743.rdf
Name: taxon_level_Claident
Units: unitless
Description: <p>taxonomic level of taxon id'd with Claident</p>
http://lod.bco-dmo.org/id/dataset-parameter/546744.rdf
Name: taxon_notes_Claident
Units: unitless
Description: <p>comments on identity matching success</p>
http://lod.bco-dmo.org/id/dataset-parameter/546745.rdf
Name: min_identity_SAP
Units: proportion
Description: <p>minimum identity probability of prey items in gut using SAP (Statistical Assignment Program) <a href="http://ib.berkeley.edu/labs/slatkin/munch/StatisticalAssignmentPackage.html">http://ib.berkeley.edu/labs/slatkin/munch/StatisticalAssignmentPackage.html</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/546746.rdf
Name: posterior_prob_100_SAP
Units: unitless
Description: <p>taxonomic name of SAP results for exact match</p>
http://lod.bco-dmo.org/id/dataset-parameter/546747.rdf
Name: taxon_level_100_SAP
Units: unitless
Description: <p>taxonomic level of taxon id'd with SAP and 100% probability</p>
http://lod.bco-dmo.org/id/dataset-parameter/546748.rdf
Name: posterior_prob_95_100_SAP
Units: unitless
Description: <p>taxonomic name of SAP results for identity probability at 95-100%</p>
http://lod.bco-dmo.org/id/dataset-parameter/546749.rdf
Name: taxon_level_95_100_SAP
Units: unitless
Description: <p>taxonomic level of taxon id'd with SAP and identity probability at 95-100%</p>
http://lod.bco-dmo.org/id/dataset-parameter/546750.rdf
Name: probability
Units: percent
Description: <p>SAP probability</p>
http://lod.bco-dmo.org/id/dataset-parameter/546751.rdf
Name: warning_comment
Units: unitless
Description: <p>warnings and comments from SAP run</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
213795
https://datadocs.bco-dmo.org/file/p99nDNWUAPq9w6/molec_gut_content.csv
molec_gut_content.csv
Primary data file for dataset ID 546723
download
https://osprey.bco-dmo.org/dataset/546723/data/download
download
onLine
dataset
<p>See <a href="http://dmoserv3.bco-dmo.org/data_docs/Food_limits_copepod_nauplii/Kimmerer_genetics_methodology.pdf" target="_blank">Methodology</a> (pdf).</p>
Specified by the Principal Investigator(s)
BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- replaced blanks with underscores
- Oithona davisae + other -->' changed to 'Oithona_davisae_and_other
- reformated date from mmm/dd/yyyy to yyyy-mm-dd
- removed commas and apostrophes
BCO-DMO data manager processing notes
* Version 2 (2021-06-10) replaces version 1 (2015-01-15). There was an unsupported character in the source file in comment "Rust_pulls_it_out_of_Fungi…". Converted to utf-8.
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
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:ABI 3130 Genetic Analyzer Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
HPLC
HPLC
PI Supplied Instrument Name: HPLC Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
Plankton Net
Plankton Net
PI Supplied Instrument Name: Plankton Net PI Supplied Instrument Description:Mesh size 100 microns or 150 microns Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler 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)
Deployment: Kimmerer_2013
Kimmerer_2013
SFSU RTC
laboratory
Kimmerer_2013
William Kimmerer
San Francisco State University
SFSU RTC
laboratory