Dr Louise Weaver1, Dr Shaun Wilkinson2, Dr Annette Bolton1, Ms Judith Webber1, Dr Brian Smith3, Ms Prudence Gowo4, Dr Aimee van der Reis5, Dr Kim Handley4, Dr Libby Liggins4, Dr Murray Close1, Dr Andy Hicks6
1ESR, Christchurch, New Zealand, 2Wilderlab NZ Ltd, Miramar, New Zealand, 3NIWA, Hamilton, New Zealand, 4University of Auckland, Auckland, New Zealand, 5Massey University, Palmerston North, New Zealand, 6Ministry for the Environment, Wellington, New Zealand
Biography:
Louise Weaver is the technical lead for ESR's Environmental Microbial Solutions group. Louise leads research to investigate the diversity of groundwater systems, from micro- to macro-scale, to improve the understanding of the biological function of groundwater to remove contaminants. Louise's team use a multi-disciplinary approach, including next-generation molecular tools to improve understanding of groundwater ecosystems and develop novel stress markers. Her research specifically aims to protect source water for our drinking water now and in the face of climate change stress.
Abstract:
Groundwater ecosystems are important water sources with a unique diversity of macrofauna known as stygofauna. Stygofauna are sensitive to pollutants, and their presence (or lack thereof) can help predict if contamination exists. Traditionally, stygofauna species are identified using external morphological characteristics and taxonomic keys, but this method has limited use in groundwater ecosystems where intact specimen collection is difficult. Environmental DNA (eDNA) has been demonstrated as an effective tool for identifying stygofauna species in groundwater. However, extracting high-quality DNA from stygofauna is inherently difficult, and more molecular reference sequences (barcodes) are needed to identify these organisms accurately.
This project, therefore, evaluated and optimised different extraction methods to obtain high-quality and quantity DNA from stygofauna. The DNA was then used to generate new COI reference barcodes and produce a mega barcode suitable for GridION sequencing.
The QIAmp DNA microextraction kit was the best method for obtaining stygofauna DNA. Variations in the quality and quantity of the DNA extracted occurred and may be attributed to multiple factors, including specimen age, type, size, and possibly preservation solution. New COI barcodes were produced, but the success rate varied, with some stygofauna specimens failing to produce COI barcodes despite adequate DNA quality and quantity.
Continuing to optimise DNA extraction from stygofauna and investigating the factors that may influence the quality and quantity of DNA and the success of reference sequences is not just important but urgent. This research is pivotal to using stygofauna species to indicate pollution in groundwater ecosystems.