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 tiny food webs

As Bruegel the Elder recognized in 1557, “big fish eat little fish”. Determining exactly what eats what remains a fundamental question in modern ecology and this task is particularly challenging for biologists studying small organisms, which make up the bulk of the biomass in ecosystems. To add interest, a number of these tiny creatures with unknown diets are medically and/or economically important disease vectors.

The Metropolitan Museum of Art www.metmuseum.org

In Mol Ecol Resources May 2008 researchers from University of California, Irvine, Kenya Medical Research Insitute, and Kanazawa University, Japan, apply DNA analysis identify gut contents of larval Anopheles gambiae complex mosquitoes, the major malaria vector in Africa. 

Photo Richard C. RussellAuthors Garros, Ngugi, Githeko, Tuno, and Yan collected anopheline larva near Kisumu in western Kenya, dissected stomach contents of third and fourth instar forms, extracted DNA, and amplified an 800 bp fragment of nuclear 18s rRNA. A separate PCR assay was used to confirm species identity (five were A. gambiae s.s. and 68 were sister species A. arabiensis). According to authors, 18s rRNA was analyzed rather than COI because “more sequences are available [for 18s than for COI] in databases for plants, fungi, and protists”. I note there are now many research groups working on “plants, fungi, and protists” so it should be possible to achieve greater resolution in this sort of study as the DNA barcode libraries are built up.

The PCR products from gut contents were first screened with a restriction endonuclease known to digest mosquito but not algal 18s.  355 PCR products from eight randomly selected larvae were screened, yielding 14 unique non-mosquito sequences. Best matches in GenBank blast results clustered into 3 main clades: green algae (7), fungi (5), and unknown eukaryotes (2). The authors conclude “the method presented in this study may be a promising tool to investigate natural diets of [anopheline] larvae”. Looking ahead, “such studies will not only improve our understanding of Anopheles larval ecology, but also provide fundamental information to facilitate the develpment of novel larval control tools.”

This study is one demonstration of how routine DNA analysis combined with expanding DNA barcode libraries will help reveal and monitor changes in a multiplicity of tiny food webs. More generally, routine DNA analysis combined with reliable DNA reference libraries opens wide avenues for rapid progress in understanding how the diversity of organisms interact, with benefits to society and science. Continued development of robust, inexpensive methods for analyzing DNA from the various types of biological samples and methods of matching the results to well-curated DNA reference libraries will speed this along.   

This entry was posted on Wednesday, May 7th, 2008 at 10:16 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.

2 Responses to “Revealing tiny food webs”

  1. Rachel Says:
    June 6th, 2008 at 7:18 am

    Though DNA bar coding is in its early stages, i expect it to bring revolutionary changes around us. In future it will also help in identifying alien species to native species also in a big way. DNA bar coding will determine the landscapes and also what food we take.

  2. Marlenna Says:
    July 4th, 2008 at 5:59 pm

    DNA reference libraries opens wide avenues for rapid progress in understanding how the diversity of organisms interact and that is two way street. Plenty of knowledge can emerge from this.

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.