Using metagenomic approaches to understand impacts of coal seam gas and coal mining to stygofaunal assemblages

Many of the ecosystem services provided by groundwater are facilitated or mediated by phreatic microbes and possibly invertebrates (stygofauna). Coal mining and coal seam gas (CSG) activities typically influence groundwater hydrology (e.g. drawdown, altered groundwater pressures) and may also change physical and chemical aspects of groundwater via pathways such as leaching of contaminants from storages, seepage of saline or contaminated water from voids, and accidental chemical spills. The implications of these alterations of groundwater hydrology and groundwater quality on phreatic ecological functions (e.g. organic matter decomposition, nutrient cycling) and their associated ecosystem services are poorly known.

One major challenge is sampling and identifying groundwater microbial assemblages and stygofauna. Environmental Impact Statements (EISs) seldom acknowledge the risks of coal mining or CSG activities to the ecological integrity or functioning of groundwater microbial assemblages. Despite the likely central roles in biogeochemical processes played by microbes in most groundwater ecosystems (Griebler and Lueders 2009), phreatic microbial assemblages are never assessed in EISs.

The analysis of DNA shed in the environment, termed ‘environmental DNA’ (eDNA), is a powerful, rapid, non-invasive and potentially cost-efficient tool for addressing many of these challenges. Recent advances in metagenomics (eDNA) technology have yielded rapid and cost-effective genetic approaches for assessing structure and biodiversity of groundwater biota. Coupling eDNA techniques with high-throughput sequencing enables detection of DNA from many different species within a single environmental sample (eDNA metabarcoding). This approach allows the characterization of entire ecological communities (eukaryotes and prokaryotes) and, combined with bioinformatics, greatly increases our ability to predict biotic functions within ecosystems (reviews in Deiner et al. 2017; Ruppert et al. 2019).