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The influence of climate change and anthropogenic activities (e.g., water withdrawals) on groundwater basins has gained attention recently across the globe. However, the understanding of hydrological stores (e.g., groundwater storage) in one of the largest and deepest artesian basins, the Great Artesian Basin (GAB) is limited due to the poor distribution of groundwater monitoring bores. In this study, Gravity Recovery and Climate Experiment (GRACE) satellite and ancillary data from observations and models (soil moisture, rainfall, and evapotranspiration (ET)) were used to assess changes in terrestrial water storage and groundwater storage (GWS) variations across the GAB and its sub-basins (Carpentaria, Surat, Western Eromanga, and Central Eromanga). Results show that there is strong relationship of GWS variation with rainfall (r = 0.9) and ET (r = 0.9 to 1) in the Surat and some parts of the Carpentaria sub-basin in the GAB (2002–2017). Using multi-variate methods, we found that variation in GWS is primarily driven by rainfall in the Carpentaria sub-basin. While changes in rainfall account for much of the observed spatio-temporal distribution of water storage changes in Carpentaria and some parts of the Surat sub-basin (r = 0.90 at 0–2 months lag), the relationship of GWS with rainfall and ET in Central Eromanga sub-basin (r = 0.10–0.30 at more than 12 months lag) suggest the effects of human water extraction in the GAB.

Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.

Aim: Spring wetlands in arid regions of Australia provide habitat for many highly endemic organisms, including fish, molluscs, crustaceans and plants, but these unique ecosystems have been under pressure since the arrival of Europeans about 250 years ago. Arguments over whether particular plant species are long-term spring inhabitants or recent immigrants are confounding efforts to conserve spring flora. One such example is the swamp foxtail, Cenchrus purpurascens, a grass that is variably listed in the literature as being native to Australian wetlands or as being an introduced weedy species from Asia. Location: Australia, China and Korea. Methods: We use DNA sequences of the nuclear ITS and the chloroplast DNA regions trnL-F and matK, complemented with newly designed simple sequence repeat (SSR) markers, to assess the native status of C. purpurascens in Australia and determine whether there is genetic differentiation among spring populations. Results: We find that, although there has been gene flow between Asia and Australia in the geological past, the populations are now strongly differentiated: C. purpurascens has probably been present in Australia through the Pleistocene. In Australia, there is also strong genetic differentiation among populations from different springs, and between springs and non-springs populations, indicating long-term occupancy of some springs sites. Main conclusions: Cenchrus purpurascens was present in Australia well before European colonization of the continent. The level of genetic differentiation among populations enhances the existing conservation values of Elizabeth Springs, Edgbaston, Doongmabulla and Carnarvon Gorge springs complexes within the Great Artesian Basin.

The Great Artesian Basin of Australia represents one of the largest and deepest basins of freshwater on Earth. Thousands of springs fed by the Basin are scattered across Australia’s arid zone, often representing the sole sources of freshwater for thousands of kilometers. As “islands” in the desert, the springs support endemic fauna and flora that have undergone millions of years of evolution in almost total isolation. Here, we review the current body of knowledge surrounding Great Artesian Basin springs and their significance from ecological, evolutionary, and cultural perspectives using South Australian spring wetlands as a case study. We begin by identifying the status of these springs as critical sources of groundwater, the unique biodiversity they support, and their cultural significance to the Arabana people as Traditional Custodians of the land. We then summarize known threats to the springs and their biota, both exogenous and endogenous, and the potential impacts of such processes. Finally, considering the status of these at-risk habitats as time capsules of biodiversity, we discuss lessons that can be learnt from current conservation and management practices in South Australia. We propose key recommendations for improved biodiversity assessment and monitoring of Great Artesian Basin springs nationwide, including 1) enhanced legal protections for spring biota; 2) increased taxonomic funding and capacity; 3) improved biodiversity monitoring methods, and 4) opportunities for reciprocal knowledge-sharing with Aboriginal peoples when conducting biodiversity research.

Aim: We investigate the phylogeographical history and determine the time-scale of population divergence of hydrobiid freshwater snails (genus Trochidrobia) inhabiting groundwater springs in the Australian desert. We test the hypothesis that divergence between geographically distinct snail populations occurred simultaneously due to their isolation in hydrologically discrete spring systems, i.e. 'trapped in desert springs'. Location: Groundwater springs of the Great Artesian Basin (GAB) in central Australia. Methods: DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene and the nuclear 28S and internal transcribed spacer rRNA genes were used to reconstruct phylogenetic relationships within and among three species of Trochidrobia (Hydrobiidae): T. punicea (13 spring groups, n = 90), T. smithi (12 spring groups, n = 62) and T. minuta (2 spring groups, n = 4). Bayesian relaxed molecular clock analyses and approximate Bayesian computation were used to date lineage divergence and distinguish between alternative biogeographical scenarios. Results: The diversification of the three Trochidrobia species probably occurred between 2.54 and 9.3 Ma, prior to the formation of the springs c. 1 Ma. Intraspecific divergences within the two widespread species occurred after the formation and colonization of the springs. Coalescent modelling and molecular clock analyses supported a simultaneous radiation of five allopatric intraspecific snail lineages within T. punicea (two lineages) and T. smithi (three lineages) across the GAB springs examined. Main conclusions: The analyses support the 'trapped in desert springs' hypothesis for the diversification of intraspecific lineages within the species T. punicea and T. smithi. This hypothesis suggests that the formation of deserts around Lake Eyre in the early Pleistocene led to the hydrological isolation of spring complexes in the GAB, resulting in significant molecular divergence, but no morphological divergence, of Trochidrobia snail populations.

The production of coalbed methane, or coal seam gas (CSG) in Australia increased 250-fold since the 1990s to around 1502 petajoules in 2019 and continues to expand. Groundwater flow in the aquifers intersected by gas wells could potentially facilitate a transport pathway for migration of contaminants or poorer quality water from deeper formations. While regulatory and mitigation mechanisms are put in place to minimize the risks, quantitative environmental impact assessments are also undertaken. When many gas wells are drilled in a wide area where many potential receptors are also spatially distributed, potential source-receptor combinations are too numerous to undertake detailed contamination risk assessment using contaminant transport modelling. However, valuable information can be gleaned from the analysis of groundwater flow directions and velocities to inform and prioritise contamination risk assessment and can precede computationally challenging stochastic contaminant transport modelling. A probabilistic particle tracking approach was developed as a computationally efficient screening analysis of contamination pathways for a planned CSG development near Narrabri in northern New South Wales, Australia. Particle tracking was run iteratively with a numerical groundwater flow model across a range of plausible parameter sets to generate an ensemble of estimated flow paths through the main Great Artesian Basin aquifer in the area. Spatial patterns of path lines and spatial relationships with potential receptors including neighbouring groundwater extraction wells and hydrologically connected ecological systems were analysed. Particle velocities ranged from 0.5 to 11 m/year and trajectories indicated dedicated contaminant transport modeling would be ideally focused at the local scale where wells are near potential receptors. The results of this type of analysis can inform the design of monitoring strategies and direct new data collection to reduce uncertainty and improve the effectiveness of adaptive management strategies and early detection of impacts.

Artesian springs in arid Australia house endemic species with very small geographic distributions (most <50 km 2 ). These species have limited dispersal capabilities, but little is known about environmental variance within and across these springs and how it, too, may limit their distribution and abundance. At the Pelican Creek springs complex, the full diversity of endemic gastropod fauna is found only in springs with deep pools, an area thought to provide greater environmental stability. This implies that the distributions of most snail species at this site may be restricted by their narrow environmental requirements and limits. This study monitored spatiotemporal environmental variance in a subset of the Pelican Creek springs (within Edgbaston Reserve) across one year to assess whether pool areas differ from tail areas, and how patterns of abundance of six snail species from three different families correspond to this variance. Springs fluctuated considerably in size, depth, water chemistry and temperature at daily and seasonal scales. Patterns of environmental variance differed across areas; pools were spatiotemporally stable, and tails were ephemeral and environmentally variable. The snail species occupied these areas in different ways. Species restricted to deep springs generally had significantly higher abundance in pool areas, and most had narrow environmental limits. In contrast, species found in a greater number of springs, including those with no pool, occupied pool and tail areas and generally had broader environmental limits. Environmental variance within and across springs affects the distribution of snails in a species-specific fashion. This has important implications for how we study springs and reveals that whilst the vast majority of species are restricted to areas of environmental stability, some can persist in the most environmentally variable areas.

Aim: Great Artesian Basin (GAB) springs in central Australia support several plant species otherwise not found in the arid zone. Evolutionary theory predicts that isolated populations will experience reductions in gene flow and genetic diversity, and higher levels of inbreeding. Our aim was to test this prediction by comparing the genetic structure of cutting grass, Gahnia trifida, (Cyperaceae) on disjunct GAB springs with coastal populations that have experienced recent fragmentation. Location: Naturally isolated GAB springs near Lake Eyre, central Australia, and coastal sites in southern Australia. Methods: We used 13 microsatellite markers to genotype 267 samples from six GAB spring and four coastal G. trifida populations. These data were used to estimate population genetic statistics and contemporary and historical measures of gene flow in the two regions. Results: GAB spring populations display lower levels of genetic diversity compared with coastal populations. Furthermore, GAB spring populations displayed much higher levels of genetic differentiation (F ST = 0.52) than populations at coastal sites (F ST = 0.22). Several coastal populations exhibited historical genetic connectivity, whereas analysis of molecular variation (AMOVA) and contemporary migration rate estimates indicate that populations from GAB spring groups are demographically independent. Main conclusions: Divergence estimates based on microsatellite data suggest restriction of central Australian G. trifida populations to refugial spring habitats since at least 15—28 ka, a period that spans the Last Glacial Maximum. Dispersal amongst spring groups is insufficient to counteract the effect of genetic drift, leading to a loss of genetic diversity. Species persisting in isolated or fragmented habitats are likely to suffer adverse effects on genetic traits, potentially increasing their risk of extinction.

The Great Artesian Basin (GAB) in Australia, the largest artesian basin in the world, is rich in groundwater resources. This study analyzed the spatio-temporal characteristics of terrestrial water storage (TWS) in the GAB for 2003–2014 using satellite (Gravity Recovery and Climate Experiment, GRACE) data, hydrological models’ outputs, and in situ data. A slight increase in TWS was observed for the study period. However, there was a rapid increase in TWS in 2010 and 2011 due to two strong La Nina events. Long-term mean monthly TWS changes showed remarkable agreements with net precipitation. Both GRACE derived and in situ groundwater disclosed similar trend patterns. Groundwater estimated from the PCR-GLOBWB model contributes 26.8% (26.4% from GRACE) to the total TWS variation in the entire basin and even more than 50% in the northern regions. Surface water contributes only 3% to the whole basin but more than 60% to Lake Eyre and the Cooper River. Groundwater, especially deeper than 50 meters, was insensitive to climate factors (i.e., rainfall). Similarly, the groundwater in the northern Cape York Peninsula was influenced by some other factors rather than precipitation. The time-lagged correlation analysis between sea surface height and groundwater storage indicated certain correlations between groundwater and sea level changes.