Meta-genomic surveillance of invasive species in the bait trade

Abstract

There are a number of different pathways by which invasive species can enter aquatic ecosystems, including the relatively unstudied live bait trade. Through contaminated stocks, the bait trade vector has the potential to distribute species widely, and unknowingly, across a wide geographic area. These introductions can have large implications for the conservation of native biodiversity and habitats. Reliable techniques for monitoring for invasive species remains challenging, particularly due to a lack of taxonomic expertise by those using live bait. Here, we show that non-target species (i.e., rare; not intended to be purchased) can be detected based on environmental DNA (eDNA) collected in water samples from commercial bait vendors. Utilizing high-throughput DNA sequencing, we analyzed water samples collected from six different commercial bait shops, screening the resulting sequence data for presence of non-target, and potentially invasive species of fish. Our findings show that DNA from multiple non-target species was present in the collected samples, including DNA from at least one potentially harmful invasive species. Additionally, this work supports the use of eDNA surveillance for screening the bait shop vector for rare and potentially harmful aquatic invasive species.

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. Ficetola GF, Bonin A, Miaud C (2008) Population genetics reveals origin and number of founders in a biological invasion. Mol Ecol 17:773–782. doi:10.1111/j.1365-294X.2007.03622.x

    CAS  PubMed  Article  Google Scholar 

  2. Frazier M, Miller AW, Lee H II (2013) Counting at low concentrations: the statistical challenges of verifying ballast water discharge standards. Ecol Appl 23(2):1–13

  3. Holeck KT, Mills EL, MacIsaac HJ et al (2004) Bridging troubled waters: biological invasions, transoceanic shipping, and the Laurentian Great Lakes. Bioscience 54:919–929

    Article  Google Scholar 

  4. Hulme PE, Bacher S, Kenis M et al (2008) Grasping at the routes of biological invasions: a framework for integrating pathways into policy. J Appl Ecol 45:403–414. doi:10.1111/j.1365-2664.2007.01442.x

    Article  Google Scholar 

  5. Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4:150–157. doi:10.1111/j.1755-263X.2010.00158.x

    Article  Google Scholar 

  6. Jerde CL, Chadderton WL, Mahon AR et al (2013) Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program. Can J Fish Aquat Sci 70:522–526. doi:10.1139/cjfas-2012-0478

    CAS  Article  Google Scholar 

  7. Kelly DW (2007) Vectors and pathways for nonindigenous aquatic species in the Great Lakes. Transportation Research Board Special Report

  8. Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS One 9:e86175. doi:10.1371/journal.pone.0086175.s007

    PubMed Central  PubMed  Article  Google Scholar 

  9. Krause L, Diaz NN, Bartels D et al (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics 22:e281–e289. doi:10.1093/bioinformatics/btl247

    CAS  PubMed  Article  Google Scholar 

  10. Leung B, Lodge DM, Finnoff D et al (2002) An ounce of prevention or a pound of cure: bioeconomic risk analysis of invasive species. Proc R Soc Lond B Biol Sci 269:2407–2413. doi:10.1098/rspb.2002.2179

    Article  Google Scholar 

  11. Lodge DM, Williams S, MacIsaac HJ et al (2006) Biological invasions: recommendations for US policy and management. Ecol Appl 16:2035–2054. doi:10.1890/1051-0761(2006)016[2035:BIRFUP]2.0.CO;2

    PubMed  Article  Google Scholar 

  12. Lodge DM, Turner CR, Jerde CL et al (2012) Perspective: conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol 23:2555–2558

    Article  Google Scholar 

  13. Mahon AR, Rohly A, Budny M et al (2010) Environmental DNA monitoring and surveillance: standard operation procedures. Report to the United States Army Corps of Engineers Environmental Laboratories, Cooperative Environmental Studies Unit, Vicksburg, Mississippi. CESU agreement #W912HZ-08-2-0014, modification P00007

  14. Mahon AR, Jerde CL, Galaska M et al (2013) Validation of eDNA surveillance sensitivity for detection of asian carps in controlled and field experiments. PLoS One 8:e58316. doi:10.1371/journal.pone.0058316.t002

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  15. Mills EL, Dermott RM, Roseman E et al (1993) Colonization, ecology, and population-structure of the quagga mussel (Bivalvia, Dreissenidae) in the Lower Great-Lakes. Can J Fish Aquat Sci 50:2305–2314

    Article  Google Scholar 

  16. Moy PB, Polls I, Dettmers JM (2011) The Chicago sanitary and ship canal aquatic nuisance species dispersal barrier. Invasive Asian Carps in North America. Am Fish Soc 74:121–137

  17. Rahel FJ (2004) Unauthorized fish introductions: fisheries management of the people, for the people, or by the people? American Fisheries Society Symposium

  18. Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805. doi:10.1111/j.1365-294X.2012.05538.x

    CAS  PubMed  Article  Google Scholar 

  19. Thomsen PF, Kielgast J, Iversen LL et al (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573. doi:10.1111/j.1365-294X.2011.05418.x

    CAS  PubMed  Article  Google Scholar 

  20. Wilcox TM, McKelvey KS, Young MK et al (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 8:e59520. doi:10.1371/journal.pone.0059520.t003

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  21. Wommack KE, Bhavsar J, Ravel J (2008) Metagenomics: read length matters. Appl Environ Microbiol 74:1453–1463. doi:10.1128/AEM.02181-07

    CAS  PubMed Central  PubMed  Article  Google Scholar 

Download references

Acknowledgements

People (M. Hensen, M. Budny, J. Bergner). We also thank state Department of Natural Resources groups in Michigan, Wisconsin, Ohio, and Illinois. This project was funded in part by a grant to ARM and CLJ from the U.S. Environmental Protection Agency’s Great Lake Restoration Initiative. Additional funding to CLJ was from CSCOR, GLRI eDNA surveillance, Great Lakes Fisheries Trust, SERDP. Additional support for ARM was from Central Michigan University’s College of Science and Technology and Dept. of Biology (L. Nathan RA fellowship support).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Andrew R. Mahon.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 43 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Mahon, A.R., Nathan, L.R. & Jerde, C.L. Meta-genomic surveillance of invasive species in the bait trade. Conservation Genet Resour 6, 563–567 (2014). https://doi.org/10.1007/s12686-014-0213-9

Download citation

Keywords

  • Invasive species
  • Bait shop
  • Genomics
  • Great Lakes
  • Environmental DNA