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A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA) : a lab and field evaluation

(2018) ECOLOGICAL INDICATORS. 84. p.564-572
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Abstract
Environmental DNA (eDNA) techniques are becoming increasingly popular in conservation and invasion biology, especially for monitoring and early detection of rare, endangered or invasive species. An exponential increase in varying methods regarding eDNA collection and analysis has been observed, which leads to mixed success in detection efficiency in studies on aquatic invertebrates. In this study, we tested and compared three sampling and three DNA extraction methods using the crayfish Procambarus clarkii as model species. Based on existing and newly developed primers, we were able to identify this species from tissue DNA and filtered eDNA samples from water of aquaria kept in the laboratory as well as water from natural ponds. The species could be positively identified in field and laboratory samples, though effectiveness differed greatly. Results in our study seemed to be highly dependent on primer choice, DNA extraction method, and the type of sample (tissue or filter). Our results showed that both an adapted phenol:chlorophorm:isoamyl alcohol protocol and a MasterPure extraction kit provided the most reliable results to detect the species based on tissue and filtered eDNA samples. The results are promising, but also highlight the necessity for a standardized protocol for each step of the eDNA-based monitoring process. These protocols will need to be optimized individually for target groups or species.
Keywords
Environmental DNA, Crayfish, Procambarus clarkii, Invasive species, RED-SWAMP CRAYFISH, PROCAMBARUS-CLARKII GIRARD, PACIFASTACUS-LENIUSCULUS, SPECIES DETECTION, FLANDERS BELGIUM, SURVEY TOOL, WATER, SAMPLES, EXTRACTION, INDICATOR

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Citation

Please use this url to cite or link to this publication:

Chicago
Geerts, Aurora N, Pieter Boets, Stef Van den Heede, Peter Goethals, and Christine Van der heyden. 2018. “A Search for Standardized Protocols to Detect Alien Invasive Crayfish Based on Environmental DNA (eDNA) : a Lab and Field Evaluation.” Ecological Indicators 84: 564–572.
APA
Geerts, A. N., Boets, P., Van den Heede, S., Goethals, P., & Van der heyden, C. (2018). A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA) : a lab and field evaluation. ECOLOGICAL INDICATORS, 84, 564–572.
Vancouver
1.
Geerts AN, Boets P, Van den Heede S, Goethals P, Van der heyden C. A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA) : a lab and field evaluation. ECOLOGICAL INDICATORS. 2018;84:564–72.
MLA
Geerts, Aurora N, Pieter Boets, Stef Van den Heede, et al. “A Search for Standardized Protocols to Detect Alien Invasive Crayfish Based on Environmental DNA (eDNA) : a Lab and Field Evaluation.” ECOLOGICAL INDICATORS 84 (2018): 564–572. Print.
@article{8566882,
  abstract     = {Environmental DNA (eDNA) techniques are becoming increasingly popular in conservation and invasion biology, especially for monitoring and early detection of rare, endangered or invasive species. An exponential increase in varying methods regarding eDNA collection and analysis has been observed, which leads to mixed success in detection efficiency in studies on aquatic invertebrates. In this study, we tested and compared three sampling and three DNA extraction methods using the crayfish Procambarus clarkii as model species. Based on existing and newly developed primers, we were able to identify this species from tissue DNA and filtered eDNA samples from water of aquaria kept in the laboratory as well as water from natural ponds. The species could be positively identified in field and laboratory samples, though effectiveness differed greatly. Results in our study seemed to be highly dependent on primer choice, DNA extraction method, and the type of sample (tissue or filter). Our results showed that both an adapted phenol:chlorophorm:isoamyl alcohol protocol and a MasterPure extraction kit provided the most reliable results to detect the species based on tissue and filtered eDNA samples. The results are promising, but also highlight the necessity for a standardized protocol for each step of the eDNA-based monitoring process. These protocols will need to be optimized individually for target groups or species.},
  author       = {Geerts, Aurora N and Boets, Pieter and Van den Heede, Stef and Goethals, Peter and Van der heyden, Christine},
  issn         = {1470-160X},
  journal      = {ECOLOGICAL INDICATORS},
  keyword      = {Environmental DNA,Crayfish,Procambarus clarkii,Invasive species,RED-SWAMP CRAYFISH,PROCAMBARUS-CLARKII GIRARD,PACIFASTACUS-LENIUSCULUS,SPECIES DETECTION,FLANDERS BELGIUM,SURVEY TOOL,WATER,SAMPLES,EXTRACTION,INDICATOR},
  language     = {eng},
  pages        = {564--572},
  title        = {A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA) : a lab and field evaluation},
  url          = {http://dx.doi.org/10.1016/j.ecolind.2017.08.068},
  volume       = {84},
  year         = {2018},
}

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