Detection, movement and persistence of invertebrate eDNA in groundwater.

Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.

Dynamics of microbiotic patterns reveal surface water groundwater interactions in intermittent and perennial streams.

Exchange between groundwater (GW), hyporheic zone waters (HZ) and surface waters (SW) is critical for water quality, quantity, and the ecological health and functioning of all three ecosystems. Hydrological exchange is particularly important in intermittent creeks, such as in the Murray Darling Basin, Australia, where stream reaches shift from losing to gaining depending on the volume of surface flows. In this study we used hydrochemistry to identify SW-GW exchange and combined this with eDNA data to analyse the response of eukaryote and prokaryote communities to differing flow conditions within intermittent and perennial stream reaches. Our study suggested that SW and GW microbial communities were only around 30% similar. Differences in microbiota between SW, HZ and GW habitats were driven by changes in relative abundances of surface water dominant organisms (such as those capable of photosynthesis) as well as anaerobic taxa typical of GW environments (e.g., methanogens), with GW and HZ microbial communities becoming increasingly different to those in SW as flow ceased in intermittent creeks. Fine-scale hydrologic changes were identified through microbial communities in the perennial Maules Creek, indicating the importance of GW-SW exchange to biotic communities. This study highlights the importance of flow in shaping microbial communities and biogeochemical cycling within intermittent creeks and their connected alluvial aquifers. Our results suggest that microbiota may prove a useful indicator of SW-GW exchange, and in some circumstances, may be more sensitive in demonstrating fine-scale changes in SW-GW interactions than water chemistry. This knowledge furthers our understanding of GW-SW exchange and its impacts on ecological health.

Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria.

Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.

River-aquifer interactions and their relationship to stygofauna assemblages: a case study of the Gwydir River alluvial aquifer (New South Wales, Australia).

In contrast to surface water ecosystems, groundwater ecosystems are usually considered to have relatively stable conditions and physically inert environments. However, many groundwater ecosystems undergo substantial changes through space and time, related to fluxes in groundwater flow, exchange and nutrient imports. In this study we used hydrochemical data to: 1) determine the different hydrogeological conditions in an alluvial system, the shallow Gwydir River alluvial aquifer (located in Northern New South Wales, Australia); and 2) analyze the relationship between hydrochemical conditions and the composition of stygofauna assemblages in the aquifer. Using hydrochemical modeling and multivariate analyses, four main hydrogeological situations were defined as occurring in the aquifer. Bores were classified as having either a high, low or no influence from or exchange with the river. The latter group was further subdivided into those of low and high salinity. Further analysis combining the biological and hydrochemical data identified two main groups of samples. The first group was composed mainly of samples related to the aquifer groundwater which had higher richness and abundance of fauna compared to samples in the second group which was comprised of samples affected by stream water leakage and samples related to the highest salinities. These results suggest that more stable conditions (mainly related to steadier groundwater head levels) and lower nitrate concentrations promoted a more diverse and abundant stygofauna community.

Groundwater Ecosystems Vary with Land Use across a Mixed Agricultural Landscape.

Changes in surface land use may threaten groundwater quality and ecosystem integrity, particularly in shallow aquifers where links between groundwater and surface activities are most intimate. In this study we examine the response of groundwater ecosystem to agricultural land uses in the shallow alluvial aquifer of the Gwydir River valley, New South Wales, Australia. We compared groundwater quality and microbial and stygofauna assemblages among sites under irrigated cropping, non-irrigated cropping and grazing land uses. Stygofauna abundance and richness was greatest at irrigated sites, with the composition of the assemblage suggestive of disturbance. Microbial assemblages and water quality also varied with land use. Our study demonstrates significant differences in the composition of groundwater ecosystems in areas with different surface land use, and highlights the utility of groundwater biota for biomonitoring, particularly in agricultural landscapes.