Rockefeller University

Program for the Human Environment

The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

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Revealing krill diets with DNA

Krill swarm under Antarctic ice, Boston UniversityKrill are shrimp-like crustaceans found throughout the world’s oceans. The Antarctic krill, Euphasia superba, is thought to be the most abundant species on the planet in terms of biomass (500 million metric tonnes corresponding to 5 x 10^14 individuals), is a primary food source for whales, seals, and oceanic birds, and functions as a major planetary carbon sink by excreting waste that sinks to ocean floor. What does this very abundant, central-to-food-web species eat? For many animals, observation of eating behavior is impractical, and analysis of stomach contents or feces may be the only way to determine diet. However, such material may be morphologically unrecognizable. 

Antarctic krill filtering for prey, Rutgers UniversityIn August 2006 Marine Biotech 8:686, researchers from University of Tasmania and Department of Environment, Tasmania, compare DNA sequencing and light microscopy in identifying prey in stomach contents of E. superba. Passmore et al isolated DNA from stomach contents of 6 ethanol preserved krill and, using diatom-specific primers, amplified a 103 bp portion of nuclear small subunit RNA (ssRNA). ssRNA was used because at present it has the best taxonomic representation in GenBank for krill prey species. The researchers sequenced at least 50 clones from each individual krill and found 14 OTUs (operational taxonomic units), with 86% to 100% match to GenBank sequences. These results were compared to microscopic identification of diatom silica skeleton fragments in stomach contents, which involved counting 1000-3000 fragments per individual. Results were similar, although DNA analysis and light microscopy each appeared more sensitive for certain species. This study might be a best case for light microscopy because silica-skeletoned diatoms are not easily digested. As the authors point out, krill also consume a range of protozoa and small zooplankton, and the importance of these sources may be underappreciated.The authors conclude “the application of DNA diet analysis to krill warrants further investigation, particularly for prey that are difficult to study using other methods“.

This work shows the essential need for a comprehensive reference library, so far lacking. A study underway is examining mitochondrial and nuclear genes as barcodes for phytoplankton. Looking ahead, a “massively parallel” pyrosequencing approach could enable rapid and representative analysis of mixed environmental samples, such as stomach contents, without biases resulting from amplification and cloning. 

This entry was posted on Saturday, January 27th, 2007 at 11:38 pm and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

One Response to “Revealing krill diets with DNA”

  1. Jonathan D Says:
    December 16th, 2015 at 11:32 pm

    Interesting study. Perhaps modern methods could be used to more quickly and cheaply identify the matching DNA between the stomach contents of krill and the range of protozoa and small zooplankton. It would be interesting to track how environmental changes might affect these species.

Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.