| Contributors | Affiliation | Role |
|---|---|---|
| Kimmerer, William | San Francisco State University (SFSU) | Principal Investigator |
| Cohen, Sarah | San Francisco State University (SFSU) | Co-Principal Investigator |
| Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Field collected copepod nauplii gut content sequences were identified using the BLASTN algorithm on GenBank or by comparison to a sequence library of local copepod species constructed for this project. Blast searches of the GenBank database were conducted on May 16, 2013. BLASTed sequences were identified to the taxonomic level at which there was consensus among matches within 10% of the best score.
Related Reference:
* 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
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, Pseudodiaptomus marinus and Oithona davisae. Limnology and Oceanography 58: 2145-2157.
See Methodology (pdf).
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
- moved sequence id's to separate column
- replaced '?' with '_maybe'
- changed Pseudodioptamus to Pseudodiaptomus
| File |
|---|
naup_blast.csv (Comma Separated Values (.csv), 2.12 MB) MD5:507a8ae381af8b3e6367d14fdf0e1c65 Primary data file for dataset ID 546671 |
| Parameter | Description | Units |
| sequence_id | squence identification: sample name followed by sequence number. TDF=adult; TDN = nauplii | unitless |
| GenBank_id | GenBank accession number of BLAST hit | unitless |
| BLAST_score | BLAST score: statistical significance of sequence matches to GenBank database | unitless |
| domain | taxonomic domain: Bacteria or Eukaryota | unitless |
| tax_rank_1 | highest taxonomic name | unitless |
| tax_rank_2 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_3 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_4 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_5 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_6 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_7 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_8 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_9 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_10 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_11 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_12 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_13 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_14 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_15 | taxonomic name; more specific than preceeding | unitless |
| tax_rank_16 | taxonomic name; more specific than preceeding | unitless |
| Dataset-specific Instrument Name | Automated Sequencer |
| Generic Instrument Name | Automated DNA Sequencer |
| Dataset-specific Description | ABI 3130 Genetic Analyzer |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
| Dataset-specific Instrument Name | HPLC |
| Generic Instrument Name | High-Performance Liquid Chromatograph |
| Generic 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. |
| Dataset-specific Instrument Name | Plankton Net |
| Generic Instrument Name | Plankton Net |
| Dataset-specific Description | Mesh size 100 microns or 150 microns |
| Generic 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. |
| Dataset-specific Instrument Name | Thermal Cycler |
| Generic Instrument Name | Thermal Cycler |
| Generic 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) |
| Website | |
| Platform | SFSU RTC |
| Start Date | 2009-09-01 |
| End Date | 2014-08-31 |
| Description | Copepod feeding studies |
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.
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.
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |