PAPER: DNA metabarcoding to assess biodiversity

Using DNA metabarcoding to assess New Zealand's terrestrial biodiversity.

May 2017

Holdaway RJ, Wood JR, Dickie IA, Orwin KH, Bellingham PJ, Richardson SJ, Lyver PO, Timoti P, Buckley TR 2017. Using DNA metabarcoding to assess New Zealand's terrestrial biodiversity. New Zealand Journal of Ecology 41(2): 251-262.

ABSTRACT

High throughput DNA sequencing technology has enabled entire biological communities to be characterised from DNA derived from pools of organisms, such as bulk-collected invertebrates, or DNA extracted from environmental samples (e.g. soil). These DNA-based techniques have the potential to revolutionise biodiversity monitoring. One approach in particular, DNA metabarcoding, can provide unprecedented taxonomic breadth at a scale not practically achievable through the morphological identification of individual organisms. Here, we assess the current strengths and weaknesses of DNA metabarcoding techniques for biodiversity assessment. We argue that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data. We present a conceptual framework for how this might be done, explore potential applications within national biodiversity assessment frameworks, Māori biodiversity monitoring and the primary sector, and highlight areas of current uncertainty and future research directions. Rapid developments in DNA sequencing technology and bioinformatics will make DNA-based community data increasingly accessible to ecologists, and there needs to be a corresponding shift in research focus from DNA metabarcoding method development and evaluation to real-world applications that provide rich information for a range of purposes, including conservation planning and land management decisions.

KEYWORDS

biodiversity monitoring; bioinformatics; biosecurity; cultural indicators; ecosystem function; environmental DNA; national framework; species detection; te ao maori; uncertainty; soil food-web; environmental DNA; microbial communities; ancient DNA; conservation; diversity; identification; sequences; accuracy; patterns;