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Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).
PLoS One. 2014; 9(12):e114329.Plos

Abstract

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Authors+Show Affiliations

Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America.Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

25474207

Citation

Turner, Cameron R., et al. "Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA From Asian Bigheaded Carp (Hypophthalmichthys Spp.)." PloS One, vol. 9, no. 12, 2014, pp. e114329.
Turner CR, Miller DJ, Coyne KJ, et al. Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.). PLoS One. 2014;9(12):e114329.
Turner, C. R., Miller, D. J., Coyne, K. J., & Corush, J. (2014). Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.). PloS One, 9(12), e114329. https://doi.org/10.1371/journal.pone.0114329
Turner CR, et al. Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA From Asian Bigheaded Carp (Hypophthalmichthys Spp.). PLoS One. 2014;9(12):e114329. PubMed PMID: 25474207.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.). AU - Turner,Cameron R, AU - Miller,Derryl J, AU - Coyne,Kathryn J, AU - Corush,Joel, Y1 - 2014/12/04/ PY - 2014/02/22/received PY - 2014/11/06/accepted PY - 2014/12/5/entrez PY - 2014/12/5/pubmed PY - 2015/12/15/medline SP - e114329 EP - e114329 JF - PloS one JO - PLoS One VL - 9 IS - 12 N2 - Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/25474207/Improved_methods_for_capture_extraction_and_quantitative_assay_of_environmental_DNA_from_Asian_bigheaded_carp__Hypophthalmichthys_spp___ L2 - https://dx.plos.org/10.1371/journal.pone.0114329 DB - PRIME DP - Unbound Medicine ER -
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