Research Areas > Contaminants > Sediment Quality Assessment > Benthic Assessment Methods > DNA Barcoding

Project: DNA Barcoding

Background and Objectives

Assemblages of benthic invertebrate species are often used to assess sediment condition. However, traditional methods for gathering data on benthic infauna communities can be time-consuming and labor-intensive. Samples are traditionally processed by trained taxonomists, who must identify and count each organism by hand. This project examines a new molecular tool for rapidly identifying the species found within benthic community assemblages. DNA barcoding espouses the idea that all biological species can be identified using a short gene sequence from a standardized position in the genome – a “DNA barcode” – analogous to the black stripes of the Universal Product Code used to distinguish commercial products.

Building a barcode reference library of DNA sequences from known voucher specimens is the first step in being able to use DNA barcoding for sample processing. With a reference library, unknown specimens could be identified by ‘looking up’ their sequences. Barcoding data could then be interpreted to correspond with other benthic indices. Additionally, examination of barcode data will likely reveal instances where a reassessment of morphologically-defined species is warranted. For instance, cryptic (previously unrecognized) species may be discovered, or a merger of groups previously believed to be separate species may be indicated. Thus, one short-term benefit of DNA barcoding research will be clarification of the catalog of benthic invertebrate species taxonomy for southern California.

The goal of this project is to assess the efficacy of barcoding for rapidly identifying freshwater and marine benthic invertebrate species in environmental condition assessments of the Southern California Bight.

Status

This project was initiated in 2009, with anticipated completion in 2012.

Methods

The project will involve four steps. The first is to establish a DNA barcode reference library of voucher specimens for southern California. To sequence a specimen’s DNA barcode, DNA is first extracted from the tissue using standard and widely available tools of molecular biology. The barcode region is then isolated, replicated by PCR amplification, and sequenced. The barcode region must consistently identify all members of the species, while excluding closely related species.

Secondly, researchers must develop modified protocols for sample processing that accommodate examination by molecular methods. Current methods for preserving benthic invertebrates rely on formalin as a fixative, which renders the samples unsuitable for molecular processing.

The third task is to investigate the relationship between barcode-based taxonomy and traditional morphology-based taxonomy, and demonstrate how barcoding can expand our ability to assess species composition and identify cryptic species.

The fourth effort will involve determining how to convert barcode data to usable environmental indices. Current benthic indices are based on abundance and diversity of individual species. Barcode data will elicit the diversity of species, but may not provide an accurate count of the number of individual organisms in the sample.

Partners

This project is being conducted in collaboration with the US Environmental Protection Agency, Canadian Centre for DNA Barcoding, Stroud Water Research Center, and SCCWRP’s member agencies.

Presentations

• DNA barcoding of southern California freshwater macroinvertebrates - January 2011 presentation to SCCWRP member agencies sharing findings from DNA barcoding analysis of benthic samples from freshwater streams.

• Adaptation of the Benthic Response Index to utilize DNA barcoding data - January 2011 presentation to SCCWRP member agencies describing a method to correlate DNA barcoding data with a traditional benthic community assessment method.

• DNA barcoding: A new approach for rapidly identifying species (Video) - January 2010 presentation to SCCWRP member agencies describing research to develop DNA barcoding for benthic community assessment.