Early detection of a highly invasive bivalve based on environmental DNA (eDNA)

  • Zhiqiang Xia
  • Aibin Zhan
  • Yangchun Gao
  • Lei Zhang
  • G. Douglas Haffner
  • Hugh J. MacIsaac
Original Paper

Abstract

Management of non-indigenous invasive species (NIS) is challenging owing in part to limitations of early detection and identification. The advent of environmental DNA (eDNA) techniques provides an efficient way to detect NIS when their abundance is extremely low. However, eDNA-based methods often suffer from uncertain detection sensitivity, which requires detailed testing before applying these methods in the field. Here we developed an eDNA tool for early detection of the highly invasive golden mussel, Limnoperna fortunei, based on the mitochondrial cytochrome c oxidase subunit I gene (COI). Further, we tested technical issues, including sampling strategy and detection sensitivity, based on a laboratory experiment. We then applied the method to field samples collected from water bodies in China where this mussel has or is expected to colonize. Results showed that the detection limit varied extensively among our newly developed primer pairs, ranging from 4 × 10−2 to 4 × 10−6 ng of total genomic DNA. Laboratory detection was affected by the availability of eDNA (i.e., both mussel abundance and incubation time). Detection capacity was higher in laboratory samples containing re-suspended matter from the bottom layer versus that collected from the surface. Among 25 field sites, detection was 100% at sites with high mussel abundance and as low as 40% at sites with low abundance when tested using our most sensitive primer pair. Early detection of NIS present at low abundance in nature requires not only sensitive primers, but also an optimized sampling strategy to reduce the occurrence of false negatives. Careful selection and detailed testing of primer pairs ensures effective eDNA-based species detection in surveillance and management programs.

Keywords

eDNA Golden mussel Invasive species Limnoperna fortunei Primer sensitivity Sampling strategy 

Supplementary material

10530_2017_1545_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 14 kb)

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Zhiqiang Xia
    • 1
    • 2
    • 3
  • Aibin Zhan
    • 3
    • 4
  • Yangchun Gao
    • 3
    • 4
  • Lei Zhang
    • 2
    • 5
  • G. Douglas Haffner
    • 1
    • 2
    • 5
  • Hugh J. MacIsaac
    • 1
    • 6
  1. 1.Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorCanada
  2. 2.International S&T Collaborative Base for Water Environment Monitoring and Simulation in Three Gorges Reservoir RegionChongqingChina
  3. 3.Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijingChina
  4. 4.University of Chinese Academy of SciencesBeijingChina
  5. 5.College of Resources and EnvironmentSouthwest UniversityChongqingChina
  6. 6.Yunnan UniversityKunmingChina

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