Environmental DNA reveals temporal and spatial variability of invertebrate communities in arid-lands ephemeral water bodies

Context: Throughout semi-arid and arid Australia surface freshwater is rare, and where it does occur, it is often ephemeral. This is the case for freshwater granite rock-holes throughout much of southern Australia. Rock-holes support freshwater invertebrate communities, but the ongoing threat of climate change means that this ecosystem is likely to experience hydrological disruptions. Rock-holes are also likely to be heavily affected by invasive vertebrates such as feral goats, leading to declining water quality. However, the ecology of this ecosystem is poorly understood despite its relative ecological significance and the extent of its associated threats. Aims: To provide a baseline ecological understanding of this ecosystem, we documented species richness and variability at a series of rock-holes in the Gawler bioregion in South Australia. Methods: We targeted invertebrate taxa present in seven rock-holes, using an environmental DNA approach. Freshwater samples were extracted and sequenced using COI insect–mollusc primers and 16S rRNA crustacean primers. Key results: Metabarcoding recorded invertebrates from 22 orders and 45 families. Community composition varied among rock-holes and throughout the year, with a peak in species richness in winter. Conclusions: Our findings demonstrate the importance of these ecosystems to a range of endemic taxa, and the validity of environmental DNA metabarcoding as an approach for assessing the community composition of rock-hole invertebrates. Implications: We propose establishment of monitoring programs, development of custom barcode reference libraries for the rock-hole ecosystem, and future research into the likely impacts of climate change on the communities associated with them.