Comparison of the efficiency of three methods of isolating fish DNA from environmental samples

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dc.contributor.authorBanks, Jonathan C.en_NZ
dc.contributor.authorWatson, Nathanen_NZ
dc.contributor.authorHogg, Ian D.en_NZ
dc.date.accessioned2016-06-10T01:36:50Z
dc.date.available2014en_NZ
dc.date.available2016-06-10T01:36:50Z
dc.date.issued2014en_NZ
dc.description.abstractThe Lake Ecosystem Restoration New Zealand (LERNZ) project was initiated to restore indigenous biodiversity in lakes in part by developing new pest fish management and control technologies. One objective of the management of pest fish was to develop genetic based assays to detect pest fish from environmental samples such as water, and to assess the feasibility of using these methods in the field. This report compares three methods (the Piscitron II, Piscitron III and a pH adjusted method) of isolating DNA for two species of exotic fish from water samples. We compared DNA isolation efficiency using newly developed qPCR assays for koi carp, Cyprinus carpio and goldfish, Carassius auratus , and present the primer and hydrolysis probe sequences for the assays, and assay thermal conditions. Minimum levels of detectable fish biomass are reported for koi carp water collected from a 6800 L tank at ambient temperature containing a 1.6 kg koi carp. The koi carp and goldfish assays were also tested on Waikato River water collected next to Hammond Park, Hamilton, New Zealand, an area of river known to contain koi carp and goldfish. We found that the Piscitron II and Piscitron III methods, which filtered water through glass fibre filters or glass wool aquarium filters, respectively, performed equally well in terms of DNA extraction but considerably better than the pH adjusted method. Minimum detectable amounts of koi carp DNA were calculated by producing serial dilutions of the tank water containing 2.35* 10⁻⁴ kg of koi carp/L. Because fish densities tend to be reported as kg/m² of lake surface, we converted our minimum detectable amount from a weight per volume to a weight per area by assuming an average lake depth of 1.5 m (a typical Waikato lake depth) which resulted in a minimum detectable amount of 0.35 kg carp/m² of water surface area. We also produced serial dilutions of DNA extracted from the koi carp tank and the minimum detectable amount of koi carp biomass was much lower at 0.0035 kg/m² which is less than the range of carp densities (0.005-0.0768 kg/m²) reported for Waikato lakes and rivers.
dc.format.mimetypeapplication/pdf
dc.identifier.citationBanks, J. C., Watson, N., & Hogg, I. D. (2014). Comparison of the efficiency of three methods of isolating fish DNA from environmental samples (ERI report No 45). Client report prepared for Lake Ecosystem Restoration New Zealand. Hamilton, New Zealand: Environmental Research Institute, Faculty of Science and Engineering, University of Waikato.en
dc.identifier.issn2350-3432en_NZ
dc.identifier.urihttps://hdl.handle.net/10289/10303
dc.language.isoen
dc.publisherEnvironmental Research Institute, Faculty of Science and Engineering, University of Waikatoen_NZ
dc.relation.isPartOfComparison of the efficiency of three methods of isolating fish DNA from environmental samplesen_NZ
dc.relation.ispartofseriesERI report
dc.rights© 2014 copyright with the author
dc.titleComparison of the efficiency of three methods of isolating fish DNA from environmental samplesen_NZ
dc.typeReport
pubs.commissioning-bodyLake Ecosystem Restoration New Zealand (LERNZ)en_NZ
pubs.confidentialfalseen_NZ
pubs.elements-id129983
pubs.organisational-group/Waikato
pubs.organisational-group/Waikato/FSEN
pubs.organisational-group/Waikato/FSEN/School of Science
pubs.place-of-publicationHamilton, New Zealand
pubs.publisher-urlhttp://www.waikato.ac.nz/eri/research/publicationsen_NZ
uow.relation.series45
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