By Erik Pilgrim

from GeneWatch 26-5
Nov-Dec 2013

At the U.S. EPA, several projects in the Office of Research and Development have been investigating the use of DNA barcoding for identifying various aquatic organisms to species. One of the main areas of research is in determining the utility of DNA barcoding for environmental bioassessment - evaluating the environmental health and condition of a site based on the organisms found living there. Standard bioassessment relies on identification of biota, typically benthic invertebrates, using morphological characters. These morphological IDs are done by highly trained taxonomists, which can take many months or even a year to complete. Our work at EPA, along with collaborators outside the agency, seeks to capitalize on the potential speed and cost savings associated with identifying these benthic organisms through DNA barcode data.

The use of DNA barcoding for environmental bioassessment potentially has several significant advantages:

1) Identification by high-throughput molecular techniques is considerably faster than current morphological techniques, with samples being processed in weeks to 1-2 months, as opposed to 6-18 months.

2) With continued cost declines for molecular work, DNA barcoding for bioassessment is comparable in cost or even cheaper than standard morphological methods.

3) Identifications based on DNA barcodes are at the species level, but morphological identifications, because many benthic organisms are small or are juvenile life stages, are often at the family or genus level, especially for freshwater ecosystems where accurate bioassessment is the most critical.

4) DNA sequence identifications are not subjective in that no matter how many times the same sequence is queried against the database, the identification will always be the same, whereas morphological IDs performed by different taxonomists or laboratories are known to raise disagreements over IDs.

5) DNA-based identification can be applied to all biota, including groups normally omitted from standard bioassessment because of their small size (less than 0.5 mm) or extreme difficulty in identification (e.g nematodes).

Current and past EPA research into DNA barcoding has shown several interesting results. Our previous research has shown that DNA barcoding of benthic invertebrates at a large scale is feasible, and that the largest impediment to successful DNA work is in proper preservation of samples as opposed to any of the molecular genetic techniques. Our current collaborative work with research groups like the Southern California Coastal Water Research Project (SCCWRP) and Stroud Water Research Center has helped develop new protocols for the collection and storage of benthic invertebrates for molecular genetic workflows, and has shown that DNA barcoding identification of freshwater benthic invertebrates provides more information than standard IDs and that this information has value for assessing environmental condition.

Ongoing research at EPA has moved into the use of Next Generation DNA Sequencing for bulk processing of samples. The development of Next Generation Sequencing techniques for environmental bioassessment has the potential to speed aquatic community identification and lower costs even more through DNA extraction, PCR, and DNA sequencing of bulk, unprocessed benthic samples. Current research investigates these NGS applications for stream, lake, and coastal marine samples. Our lab is working to develop techniques and workflows to generate the most useful data in the most cost-effective manner while also working to be user friendly for end users and decision makers. Toward these goals, we continue to collaborate with non-agency research groups such as SCCWRP, as well as maintaining strong relationships with international researchers in this field such as the Canadian Centre for DNA Barcoding and CSIRO-Australia.

Several challenges lie ahead for the development of DNA barcoding for bioassessment. Our first challenge is to foster better communication between molecular genetic researchers and environmental scientists, to ensure that the work is collaborative instead of confrontational. Second, the data generated through DNA-based identification is different from standard bioassessment, and molecular geneticists and environmental researchers need to work together to determine the most appropriate uses and analyses of this new data. Lastly, this molecular work will generate much more data than has ever been possible for bioassessment, so methods must be developed to handle such large amounts of data while providing the most useful outputs for making determinations of environmental health.

This is an exciting time for both DNA barcoding and environmental bioassessment. These molecular genetic applications could be a transformative technology for the field of bioassessment. Our ultimate goal is to provide better information in a timely, cost-effective manner, in order to provide decision makers with best methods for assessing aquatic environmental health and condition. 


Erik Pilgrim, PhD, is a Research Scientist at the U.S. Environmental Protection Agency, where he applies DNA barcoding to bioassessment and invasive species monitoring and detection.

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