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About the Authors:
Eric D. Stein
* E-mail: [email protected]
Affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America
Bryan P. White
Affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America
Raphael D. Mazor
Affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America
Peter E. Miller
Affiliation: Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
Erik M. Pilgrim
Affiliation: United States Environmental Protection Agency, National Exposure Research Laboratory, Cincinnati, Ohio, United States of America
Introduction
Molecular methods such as DNA barcoding are emerging as a new tool for species identification [1] and, more recently, environmental biomonitoring [2]–[4]. Biomonitoring (often called bioassessment) is the process of evaluating the overall ecological health of an aquatic environment (such as streams or wetlands) based on the composition and structure of the benthic (bottom dwelling) community. Most often, benthic invertebrate (insect larvae) or instream algal (diatoms or soft-bodied algae) communities are used as the basis of these assessments. Changes in the type or number of organisms, relative to a reference condition, is used to indicate detrimental effects associated with changes in water quality, flow, or physical habitat. Biomonitoring results are commonly used in water quality protection programs as part of ambient monitoring or permit-required compliance assessments.
Routine application of molecular methods to support species identification for biomonitoring will require that each step of sample collection, handling and processing be considered in terms of its potential to affect DNA integrity. Advantages of molecular methods in biomonitoring include the potential to increase the speed, accuracy and resolution of species identification and thereby support effective biomonitoring programs [5]–[9]. Barcoding involves identifying species based on a short DNA sequence from a standardized genetic locus, such as the mitochondrial gene cytochrome c oxidase I (COI) for most metazoans. Using standard molecular methods, DNA is extracted from specimen tissue and sequenced for the 650-bp barcoding region of COI [1]. DNA from unknown specimens collected in benthic samples can be identified by comparing their barcode sequences to a reference library, such as the Barcode of Life Data Systems (BOLD) [10].
The implications of different preservation methods on DNA quality have not been well studied in the context...