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Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity

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Abstract

Protecting plants from new pathogen incursions requires effective surveillance practices. Environmental DNA (eDNA) metabarcoding shows considerable promise for detecting invasive organisms in terrestrial and aquatic ecosystems. Metabarcoding is widely used to characterise plant microbiotas and is beginning to be applied to plant biosecurity. However, diagnostic assays for biosecurity must fit within internationally agreed frameworks. Development of new gene targets to improve taxonomic resolution, improved reference databases and simplified bioinformatics platforms are required before phytopathogenic bacteria and fungi can be routinely detected by metabarcoding. Building biodiversity maps from accumulated metabarcoding data represents an important opportunity to define organism presence/absence in New Zealand and Australia and thus to enhance biosecurity decision making. Advances in sequencing technologies and infrastructure promise the creation of eDNA biosecurity surveillance networks from substrates including soil, trapped spores and insects.

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Acknowledgements

This review contributes to a key aim of New Zealand’s Biological Heritage National Science Challenge (NSC). SB and GL have received direct NSC financial support. Better Border Biosecurity (B3) funding underpins ongoing collaboration with staff at the Ministry for Primary Industries. We thank Andy Pitman and an anonymous reviewer for comments that improved this manuscript.

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Authors and Affiliations

  1. The New Zealand Institute for Plant & Food Research Ltd., Lincoln, New Zealand

    S. R. Bulman

  2. Better Border Biosecurity (B3), Lincoln, New Zealand

    S. R. Bulman

  3. Scion, New Zealand Forest Research Institute Ltd., Rotorua, 3046, New Zealand

    R. L. McDougal

  4. SARDI Sustainable Systems, Adelaide, SA 5001, Australia

    K. Hill

  5. School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Lincoln, SA 5064, Australia

    K. Hill

  6. School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand

    G. Lear

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  3. K. Hill
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  4. G. Lear
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Correspondence to S. R. Bulman.

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Bulman, S.R., McDougal, R.L., Hill, K. et al. Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity. Australasian Plant Pathol. 47, 467–474 (2018). https://doi.org/10.1007/s13313-018-0579-3

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