Using eDNA to examine eukaryotic communities in shallow groundwater of a tropical sandy creek

Lisa Chandler^1,2, Dr Andrew  Harford², Professor Grant Hose³, Dr Chris Humphrey², Dr  Anthony Chariton³, Mr Paul Greenfield⁴, Professor  Jenny Davis¹

¹Research Institute for the Environment and Livelihoods, College of Engineering, IT & Environment, Charles Darwin University, Casuarina, Australia, ²Australia Department of Agriculture Water and the Environment, Supervising Scientist Branch, Eaton, Australia, ³Macquarie University Faculty of Science and Engineering, Department of Biological Sciences, Macquarie Park, Australia, ⁴Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australia

Abstract:

Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to relatively stable environmental conditions and have a narrow spatial distribution. Characterising these communities using traditional methods is generally limited to a small proportion of the whole community because taxonomic information is often limited, morphological identification is often time consuming, and many microeukaryote taxa are difficult to isolate and culture. In this study we examined eukaryotic community composition in shallow sand bed aquifer in a wet-dry tropical environment, using traditional stygofauna sampling methods and environmental DNA (eDNA), as part of a broader ecological risk assessment for shallow groundwater communities exposed to mine-water impacts. The aquifer had a gradient of contamination from Mg- and SO₄-dominated, saline mine-water. Sampling occurred during the dry-season when only subsurface water was present. Groundwaters were collected from piezometers (approximately 2m in depth), located in the creek channel upstream and downstream of the mine-water influence. Traditional morphological assessment (from net samples) and next generation sequencing of eDNA was used to analyse the eukaryote assemblages. With the molecular data we observed significant changes in community composition with exposure to mine-waters, however this was not reflected in the data from the stygofauna sampling. The changes in eDNA-based assemblage data were most strongly correlated with concentrations of SO₄, Mg and Na, as well as water table level. These findings indicate that studies based only on traditional stygofauna sampling methods may be limited in their ability to detect community changes for impact assessments.

Biography:

Lisa Chandler is a PhD student at Charles Darwin University and also works with the Supervising Scientist Branch of the Department of Agriculture Water and the Environment. She has over eighteen years’ experience in aquatic ecology research and monitoring, specialising in freshwater invertebrates, in both government and private sectors. Lisa completed a Bachelor of Science at Flinders University majoring in marine biology, then completed her Honours year at the University of Western Australia examining growth and recruitment of a seagrass species in response to disturbance.