Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems

Saline mine water influences eukaryote life in shallow groundwater of a tropical sandy stream

Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to stable environmental conditions and often have narrow spatial distributions. Traditional methods for characterising these communities, focussing on groundwater-inhabiting macro- and meiofauna (stygofauna), are challenging because of limited taxonomic knowledge and expertise (particularly in less-explored regions), and the time and expense of morphological identification. The primary objective of this study was to evaluate the vulnerability of eukaryote communities in shallow groundwater to mine water discharge containing elevated concentrations of magnesium (Mg) and sulfate (SO4). The study was undertaken in a shallow sand bed aquifer within a wet-dry tropical setting. The aquifer, featuring a saline mine water gradient primarily composed of elevated Mg and SO4, was sampled from piezometers in the creek channel upstream and downstream of the mine water influence during the dry season when only subsurface water flow was present. Groundwater communities were characterised using both morphological assessments of stygofauna from net samples and environmental DNA (eDNA) targeting the 18S rDNA and COI mtDNA genes. eDNA data revealed significant shifts in community composition in response to mine waters, contrasting with findings from traditional morphological composition data. Changes in communities determined using eDNA data were notably associated with concentrations of SO42-, Mg2+ and Na+, and water levels in the piezometers. This underscores the importance of incorporating molecular approaches in impact assessments, as relying solely on traditional stygofauna sampling methods in similar environments may lead to inaccurate conclusions about the responses of the assemblage to studied impacts.

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.

Monitoring Groundwater Health Using Citizen Scientists in Semi-Arid Regional Australia

Citizen science (CS) around the world is undergoing a resurgence, potentially due to the utilization of new technologies and methods to capture information, such as data and photo entry via mobile phone apps. CS has been used in aquatic ecology for several decades, however the use of volunteers to collect data in groundwaters has rarely occurred. Groundwater research, particularly groundwater ecosystems, is unevenly distributed across the world, limiting our knowledge of these ecosystems and their functions. Here, we engaged six volunteer farmers in semi-arid region of north-western New South Wales, Australia to participate in an assessment of groundwater health using privately owned wells. Volunteers were supplied with sampling kits and instructions on sampling methods. Data retrieved indicated the health of the groundwater ecosystems, simultaneously providing information on water quality and groundwater biota present within the farm aquifers. Diverse stygofauna were collected from the trial, which reflected historical records of stygofauna within the same catchment indicating the viability of using citizen scientist for data collection. The citizen science project not only aided the collection of data and assessment of groundwater health, but also provided a tool for education, attracting media attention which furthered the education to a national audience. The amount of data still required to understand groundwater ecosystems, combined with the urgency to manage these environments, suggests that citizen scientists may complement the efforts of scientists around the globe to establish the impacts and consequences of human activities on this resource.

Groundwater microbial communities reflect geothermal activity on volcanic island

Studies of the effects of volcanic activity on the Hawaiian Islands are extremely relevant due to the past and current co-eruptions at both Mauna Loa and Kīlauea. The Big Island of Hawai'i is one of the most seismically monitored volcanic systems in the world, and recent investigations of the Big Island suggest a widespread subsurface connectivity between volcanoes. Volcanic activity has the potential to add mineral contaminants into groundwater ecosystems, thus affecting water quality, and making inhabitants of volcanic islands particularly vulnerable due to dependence on groundwater aquifers. As part of an interdisciplinary study on groundwater aquifers in Kona, Hawai'i, over 40 groundwater wells were sampled quarterly from August 2017 through March 2019, before and after the destructive eruption of the Kīlauea East Rift Zone in May 2018. Sample sites occurred at great distance (~80 km) from Kīlauea, allowing us to pose questions of how volcanic groundwater aquifers might be influenced by volcanic subsurface activity. Approximately 400 water samples were analyzed and temporally split by pre-eruption and post-eruption for biogeochemical analysis. While most geochemical constituents did not differ across quarterly sampling, microbial communities varied temporally (pre- and post-eruption). When a salinity threshold amongst samples was set, the greatest microbial community differences were observed in the freshest groundwater samples. Differential analysis indicated bacterial families with sulfur (S) metabolisms (sulfate reducers, sulfide oxidation, and disproportionation of S-intermediates) were enriched post-eruption. The diversity in S-cyclers without a corresponding change in sulfate geochemistry suggests cryptic cycling may occur in groundwater aquifers as a result of distant volcanic subsurface activity. Microbial communities, including taxa that cycle S, may be superior tracers to changes in groundwater quality, especially from direct inputs of subsurface volcanic activity.

Groundwater is a hidden global keystone ecosystem

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10⁷ mL^-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L^-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.

Geology and land use shape nitrogen and sulfur cycling groundwater microbial communities in Pacific Island aquifers

Resource-constrained island populations have thrived in Hawai'i for over a millennium, but now face aggressive new challenges to fundamental resources, including the security and sustainability of water resources. Characterizing the microbial community in groundwater ecosystems is a powerful approach to infer changes from human impacts due to land management in hydrogeological complex aquifers. In this study, we investigate how geology and land management influence geochemistry, microbial diversity and metabolic functions. We sampled a total of 19 wells over 2-years across the Hualālai watershed of Kona, Hawai'i analyzing geochemistry, and microbial communities by 16S rRNA amplicon sequencing. Geochemical analysis revealed significantly higher sulfate along the northwest volcanic rift zone, and high nitrogen (N) correlated with high on-site sewage disposal systems (OSDS) density. A total of 12,973 Amplicon Sequence Variants (ASV) were identified in 220 samples, including 865 ASVs classified as putative N and sulfur (S) cyclers. The N and S cyclers were dominated by a putative S-oxidizer coupled to complete denitrification (Acinetobacter), significantly enriched up to 4-times comparatively amongst samples grouped by geochemistry. The significant presence of Acinetobacter infers the bioremediation potential of volcanic groundwater for microbial-driven coupled S-oxidation and denitrification providing an ecosystem service for island populations dependent upon groundwater aquifers.

Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land-use and geology

Despite being the most important source of liquid freshwater on the planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It is thus extensively monitored for pollutants and declines in quantity. The organisms living in groundwater, however, are rarely the target of surveillance programmes and little is known about the fauna inhabiting underground habitats. The difficulties accessing groundwater, the lack of expertise, and the apparent scarcity of these organisms challenge sampling and prohibit adequate knowledge on groundwater fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome these limitations but is largely unexplored. Here, we sampled water in 20 communal spring catchment boxes used for drinking water provisioning in Switzerland, with a high level of replication at both filtration and amplification steps. We sequenced a portion of the COI mitochondrial gene, which resulted in 4917 ASVs, yet only 3% of the reads could be assigned to a species, genus, or family with more than 90% identity. Careful evaluation of the unassigned reads corroborated that these sequences were true COI sequences belonging mostly to diverse eukaryotic groups, not present in the reference databases. Principal component analyses showed a strong correlation of the community composition with the surface land-use (agriculture vs. forest) and geology (fissured rock vs. unconsolidated sediment). While incomplete reference databases limit the assignment of taxa in groundwater eDNA metabarcoding, we showed that taxonomy-free approaches can reveal large hidden diversity and couple it with major land-use drivers, revealing their imprint on chemical and biological properties of groundwater.

A deep continental aquifer downhole sampler for microbiological studies

To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.

Anthropogenic pollution gradient along a mountain river affects bacterial community composition and genera with potential pathogenic species

Mountain regions in Poland are among the most frequently visited tourist destinations, causing a significant anthropogenic pressure put on the local rivers. In this study, based on numbers of 9 microorganisms, content of 17 antibiotics and 17 physicochemical parameters, we determined a pollution gradient in six sites along Białka, a typical mountain river in southern Poland. The E.coli/Staphylococcus ratio varied evidently between polluted and non-polluted sites, indicating that the possible utility of this parameter in assessing the anthropogenic impact on river ecosystems is worth further investigation. Then, using next generation sequencing, we assessed the changes in bacterial community structure and diversity as a response to the pollution gradient. Proteobacteria and Bacteroidetes were the most abundant phyla in the majority of samples. Actinobacteria were the most abundant in the most pristine (groundwater) sample, while Firmicutes and Verrucomicrobia were more prevalent in polluted sites. Bacterial diversity at various levels increased with water pollution. Eleven bacterial genera potentially containing pathogenic species were detected in the examined samples, among which Acinetobacter, Rhodococcus, and Mycobacterium were the most frequent. At the species level, Acinetobacter johnsonii was most prevalent potential pathogen, detected in all surface water samples, including the pristine ones. Two bacterial taxa-genus Flectobacillus and order Clostridiales showed very distinct variation in the relative abundance between the polluted and non-polluted sites, indicating their possible potential as biomarkers of anthropogenic impact on mountain river waters.

Towards evidence-based conservation of subterranean ecosystems

Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.

Subterranean carbon flows from source to stygofauna: a case study on the atyid shrimp Stygiocaris stylifera (Holthuis, 1960) from Barrow Island (WA)

Groundwater biota are crucial for the ecological functioning of subterranean ecosystems. However, while knowledge of the taxonomic diversity of groundwater invertebrates (stygofauna) is increasing, functional ecological information is still limited. Here, we investigate seldom empirically tested assumptions around stygofaunal trophic plasticity in coping with oligotrophic habitats. We focus on Barrow Island (Western Australia), an ideal natural laboratory due to the occurrence of natural oil seeps in association with aquifers. The trophic position and food source use of the endemic atyid shrimp Stygiocaris stylifera (Holthuis, 1960) were assessed via δ¹³C and δ¹⁵N stable isotope analysis (SIA). Background information on the environmental conditions was gathered through hydrochemical data and δ¹³C SIA combined with ¹⁴C data from dissolved inorganic/organic carbon and particulate organic carbon from groundwater samples. Our results indicate carbon enrichment in proximity to the natural oil seepage coupled with changes in trophic positions of S. stylifera from higher consumers/predators to biofilm grazers/decomposers. These results are consistent with an increased involvement of hydrocarbon seeps and associated microbial communities in the carbon flows and confirm potential for the trophic flexibility in stygofauna. Further investigations involving other trophic groups will help elucidate the functioning of the ecosystems at a community level.

eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects

Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.

Current cave monitoring practices, their variation and recommendations for future improvement in Europe: A synopsis from the 6th EuroSpeleo Protection Symposium

This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted.

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.

Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential

Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.

Connectivity, not short-range endemism, characterises the groundwater biota of a northern Australian karst system

Groundwater ecosystems have a diverse and unique fauna, often dominated by Crustacea and generally characterised by short range endemics confined to single aquifers. Much of this knowledge has come from studies conducted either in fractured rock aquifers or alluvial aquifers. Karstic subterranean environments are present in the Cambrian Limestone Aquifer (CLA) in the Northern Territory, Australia, a freshwater aquifer which spans an area of ~28,000 km². The presence of underground caverns and channels potentially allows extensive connectivity within this groundwater system. The emerging shale gas industry in the Beetaloo region, which underlies the CLA, provided the impetus to undertake the first survey of the potential existence of a stygofaunal community. Twenty-six groundwater wells (bores) and two springs were sampled in August and October 2019, across a distance of ~500 km, from the sub-tropical Mataranka region in the north to the semi-arid Barkly Tablelands in the south. Plankton nets and motorised pumps were used to collect water samples and conventional microscope-based morphological examinations in conjunction with environmental DNA (eDNA) were used to determine the presence of stygofauna. COI barcoding and 16S rRNA regions were also used for phylogenetic analysis. All stygofaunal communities were dominated by crustaceans, namely shrimps, amphipods, ostracods, copepods and syncarids. This fauna showed little affinity with the stygofauna recorded from more extensively sampled aquifers in north-western Australia, with new genera and species present in the CLA. eDNA analysis showed the presence of diverse biota at sites where direct water sampling for intact animals was difficult. COI and 16S analysis confirmed that a species of blind shrimp, Parisia unguis, occurred extensively throughout the aquifer, over a distance of at least ~300 km. The presence of Pa. unguis at widely separated sites across the CLA is consistent with substantial connectivity within the aquifer. This connectivity indicates that the risk of groundwater contamination from fracking chemicals needs to be adequately mitigated to prevent widespread effects.

High diversity and local endemism in Aotearoa New Zealand's groundwater crustacean fauna

We used DNA barcoding to assess the diversity and distribution of New Zealand's groundwater amphipods and isopods (Crustacea) and to determine whether biodiversity and endemism within tectonically active New Zealand are similar to those of more tectonically stable continents. Sixty-five wells were sampled in seven aquifers across four regions within the North and South islands of New Zealand, and resident invertebrates were morphologically identified and then assessed using sequencing of the mitochondrial DNA cytochrome c oxidase subunit one (COI) gene. Invertebrates were found in 54 wells. Of the 228 individual amphipods and isopods found in 36 of the wells, 154 individuals were successfully sequenced for COI (68% success rate) from 25 wells, with at least one well in each aquifer containing sequenced individuals. Of the 45 putative species identified using Barcode Index Numbers (BINs), 30 BINs (78% of all taxa and 83% of amphipods) were previously unrecorded. Substantial morphologically cryptic, species-level diversity was revealed, particularly within the amphipod Family Paraleptamphopidae. Similarly, one isopod taxon morphologically identified as Cruregens fontanus was assigned to five well-separated BINs based on COI sequences. Endemism appeared high, with all taxa regionally endemic; 87% of species were restricted to one aquifer and more than 50% restricted to one well. Non-saturated species accumulation curves indicated that, while additional sampling may increase the range of some currently identified taxa, additional range-restricted taxa are also likely to be discovered. Patterns of diversity and short-range endemism were similar to those found elsewhere, including locations which are more tectonically stable. The predominance of local endemism within New Zealand's groundwater fauna suggests that land-use activities and groundwater extraction require careful evaluation to minimize threats to groundwater biodiversity.

Is thermal use of groundwater a pollution?

Thermal use of the shallow subsurface and its aquifers (< 400 m) is steadily increasing. Currently, more than 2800 aquifer thermal energy storage (ATES) systems are operating worldwide alongside more than 1.2 million ground source heat pump (GSHP) systems in Europe alone. These rising numbers of shallow geothermal energy (SGE) systems will put additional pressure on typically vulnerable groundwater systems. Hitherto, suitable criteria to control the thermal use of groundwater in national and international legislations are often still at a preliminary state or even non-existing. While the European Union (EU) Water Framework Directive (WFD) defined the release of heat into the groundwater as pollution in the year 2000, the cooling of groundwater for heating purposes is not explicitly mentioned yet. In contrast, some national legislations have stricter guidelines. For example, in Germany, detrimental changes in physical, chemical and biological characteristics have to be avoided. In the Swiss water ordinance, it is even recommended that the groundwater biocenosis should be kept in natural state. However, exact definitions of 'detrimental changes' and 'natural state' are still missing. Hence, the current study provides an overview on natural and affected thermal groundwater conditions and international and national legislations of the thermal use of groundwater. Also, it presents recent studies on groundwater ecosystems and proposes a sustainable policy framework for the thermal use of groundwater. In addition to geothermal heat sources, other anthropogenic heat sources such as climate change, underground car parks, heated basements, district heating systems, land fills, wastewater treatment plants and mining are considered, although no legislation on these anthropogenic heat sources and their impact on groundwater is currently in place. Finally, we intend to answer the above question and provide recommendations for the further discussions on the joint use of shallow groundwater systems for drinking water production and thermal use.

Anthropogenic drought dominates groundwater depletion in Iran

Using publicly-available average monthly groundwater level data in 478 sub-basins and 30 basins in Iran, we quantify country-wide groundwater depletion in Iran. Natural and anthropogenic elements affecting the dynamics of groundwater storage are taken into account and quantified during the period of 2002–2015. We estimate that the total groundwater depletion in Iran to be ~ 74 km³ during this period with highly localized and variable rates of change at basin and sub-basin scales. The impact of depletion in Iran’s groundwater reserves is already manifested by extreme overdrafts in ~ 77% of Iran’s land area, a growing soil salinity across the entire country, and increasing frequency and extent of land subsidence in Iran’s planes. While meteorological/hydrological droughts act as triggers and intensify the rate of depletion in country-wide groundwater storage, basin-scale groundwater depletions in Iran are mainly caused by extensive human water withdrawals. We warn that continuation of unsustainable groundwater management in Iran can lead to potentially irreversible impacts on land and environment, threatening country’s water, food, socio-economic security.

Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama

The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatened, and endangered taxa. However, there are few eDNA studies of groundwater fauna. Here we report the results of the development and implementation of an eDNA assay targeting a short fragment of the mitochondrial CO1 locus of a critically imperiled cave crayfish, the Sweet Home Alabama Cave Crayfish (Cambarus speleocoopi), known from just four cave systems in the Interior Plateau karst region of northern Alabama. We detected C. speleocoopi DNA from water samples collected at 5 of 16 sites sampled (caves and springs), including two historical sites as well as three additional and potentially new sites in Marshall County, Alabama. All three of these sites were within 2 km of historical sites. Our study is the first to detect a groundwater crustacean in the Interior Plateau karst region. Additionally, our study contributes to the growing literature that eDNA is a viable complementary tool for detection and monitoring of a fauna that is difficult to survey and study using traditional approaches.

Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia

Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.

Evaluation of groundwater bacterial community composition to inform waterborne pathogen vulnerability assessments

Microbial water quality evaluations are essential for determining the vulnerability of subsurface drinking water sources to fecal pathogen intrusion. Rather than directly monitor waterborne pathogens using culture- or enumeration-based techniques, the potential of assessing bacterial community using 16S rRNA gene amplicon sequencing to support these evaluations was investigated. A framework for analyzing 16S rRNA gene amplicon sequencing results featuring negative-binomial generalized linear models is demonstrated, and applied to bacterial taxa sequences in purge water samples collected from a shallow, highly aerobic, unconfined aquifer. Bacterial taxa relevant as indicators of fecal source and surface connectivity were examined using this approach. Observed sequences of Escherichia, a genus suggestive of fecal source, were consistently detected but not confirmed by culture-based methods. On the other hand, episodic appearance of anaerobic taxa sequences in this highly aerobic environment, namely Clostridia and Bacteroides, warrants further investigation as potential indicators of fecal contamination. Betaproteobacteria sequences varied significantly on a seasonal basis, and therefore may be linked to understanding surface-water groundwater interactions at this site. However, sequences that are often encountered in surface water bodies (Cyanobacteria and Flavobacteriia) were notably absent or present at very low levels, suggesting that microbial transport from surface-derived sources may be rather limited. This work demonstrates the utility of 16S rRNA gene amplicon sequencing for contextualizing and complementing conventional microbial techniques, allowing for hypotheses about source and transport processes to be tested and refined.

Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology

Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches

Water supply, in hydroponic greenhouses, can originate from groundwater, surface water or rainwater stored in open tanks. To limit contamination of water supply, several methods have been used including active and passive methods such as slow filtration techniques which consist in passing the nutrient solutions slowly through filters. The purpose of this study was to describe the microbiota associated with water sampled before entering greenhouses and in recirculating nutrient solutions, either before or after running through a biofiltration system. Metabarcoding analysis revealed that water ecosystems were unique niches for diverse bacterial and fungal communities. Microbial composition varied greatly across storage conditions (groundwater vs. rainwater) and among greenhouses, suggesting that water microbiota is site- and storage-condition-specific. Nonetheless, we found that microbiota structure in open-stored water (either coming from ground or rain) shared a higher degree of similarity than with water directly pumped out of the ground. Open-stored waters were characterized by predominant taxa, notably those involved in aerobic chemoheterotrophy, such as the Sphingomonadaceae and Hyphomicrobiaceae families. Water directly collected from the ground showed the lowest levels of fungal and bacterial richness while also characterized by a significantly higher level of bacterial equitability and an enrichment in taxa involved in N-cycling. Slow filtration allowed reducing cultivable bacterial loads as well Pythium spp. and Fusarium oxysporum propagules, based on culture-dependent results, without compromising microbiota richness and diversity. Although compositional structure was similar following biofiltration, significant differences in bacterial (but not fungal) taxa abundance were reported, with primarily an enrichment of Chelativorans, Mycobacterium, and Gemmata as well as a depletion of Rhodobacter, Aminobacter, and Ellin329. The exact mechanisms by which such taxa would be favored at the expense of other remained unknown. Besides the accurate description of microbiota found in water at both taxonomical and predicted functional levels, our study allowed comparing the water microbiota between various storage system and following biofiltration. Although preliminary, our results provide a first insight into the potential microbial diversity, which can increase ecosystem functionality.

Distinct bacterial communities in tropical island aquifers

The groundwater biome is a poorly characterized habitat hypothesized to harbor uniquely diverse bacterial communities; the degree to which these communities differ from associated soils is a central question in environmental microbiology. We characterized the Bacterial community composition in 37 aquifer and 32 surface soil samples across the island of O‘ahu, Hawaiʻi. Several bacterial phyla (Acetothermia, Omnitrophica, Parcubacteria, Peregrinibacteria) relatively abundant in the aquifer samples were rare to absent in the soils. Immense bacterial diversity detected in the deep aquifers indicates that these environments are not as homogenous as expected, but provide various niches and energy sources for wide variety of bacteria. A small proportion of OTUs were widespread in all the basal (0.63%) and all the dike aquifer (0.31%) samples. However, these core bacteria comprised an average of 31.8% (ranging 16.2%-62.0%) and 15.4% (0.1%-31.5%) of all sequences isolated from the basal and dike aquifers respectively. Bacterial community composition correlated significantly with the sodium, sulfate, potassium, total dissolved solids, nitrate, conductivity, and pH in the basal aquifers, while phosphate and bicarbonate levels were also highly important when dike water samples were included in the analyses. This was consistent with high relative abundance of putative chemolithoautoroph taxa in the aquifer communities relative to soils. Targeted molecular and culture-based fecal indicator microbial analyses indicated good water quality of aquifers. The dominance of unique, deeply branching lineages in tropical aquifers emphasizes a large adaptive potential in O‘ahu’s aquifers; variability among groundwater samples suggests that aquifer habitats are surprisingly variable potentially harboring a variety of chemolithotrophic energy sources. Although parallel analyses of conventional and alternative indicators indicated good groundwater quality, this study calls for groundwater monitoring programs which would consider public as well as ecosystem health.

Lessons from 10 Years of Experience with Australia’s Risk-Based Guidelines for Managed Aquifer Recharge

The Australian Managed Aquifer Recharge Guidelines, published in 2009, were the world’s first Managed Aquifer Recharge (MAR) Guidelines based on risk-management principles that also underpin the World Health Organisation’s Water Safety Plans. In 2015, a survey of Australian MAR project proponents, consultants and regulators revealed that in those states advancing MAR, the Guidelines were lauded for giving certainty on approval processes. They were also considered to be pragmatic to use, but there was feedback on onerous data requirements. The rate of uptake of MAR has varied widely among Australian state jurisdictions, for reasons that are not explained by the drivers for and feasibility of MAR. The states where MAR has progressed are those that have adopted the Guidelines into state regulations or policy. It was originally intended that these Guidelines would be revised after five to ten years, informed by experience of any hazards not considered in the guidelines, and by new scientific developments including advances in monitoring and control methods for risk management. As such revision has not yet occurred, this paper was prepared to give a precis of these Guidelines and review ten years of experience in their application and to identify issues and suggest improvements for consideration in their revision by Australian water regulators. This paper also discusses the factors affecting their potential international applicability, including the capabilities required for implementation, and we use India as an example for which an intermediate level water quality guideline for MAR was developed. This paper is intended to be useful information for regulators in other countries considering adopting or developing their own guidelines. Note that the purpose of these Guidelines is to protect human health and the environment. It is not a guide to how to site, design, build and operate a managed aquifer recharge project, for which there are many other sources of information.

Potential of A Trait-Based Approach in the Characterization of An N-Contaminated Alluvial Aquifer

Groundwater communities residing in contaminated aquifers have been investigated mainly through taxonomy-based approaches (i.e., analyzing taxonomic richness and abundances) while ecological traits have been rarely considered. The aim of this study was to assess whether a trait analysis adds value to the traditional taxonomy-based biomonitoring in N-contaminated aquifers. To this end, we monitored 40 bores in the Vomano alluvial aquifer (VO_GWB, Italy) for two years. The aquifer is a nitrate vulnerable zone according to the Water Framework Directive. The traditional taxonomy-based approach revealed an unexpectedly high biodiversity (38 taxa and 5725 individuals), dominated by crustaceans, comparable to that of other unpolluted alluvial aquifers worldwide. This result is in contrast with previous studies and calls into question the sensitivity of stygobiotic species to N-compounds. The trait analysis provided an added value to the study, unveiling signs of impairments of the groundwater community such as low juveniles-to-adults and males-to-females ratios and a crossover of biomasses and abundances curves suggestive of an intermediate alteration of the copepod assemblages.

Marble Slurry’s Impact on Groundwater: The Case Study of the Apuan Alps Karst Aquifers

Modern sawing techniques employed in ornamental stones’ exploitation produce large amounts of slurry that can be potentially diffused into the environment by runoff water. Slurry produced by limestone and marble quarrying can impact local karst aquifers, negatively affecting the groundwater quality and generating a remarkable environmental and economic damage. A very representative case-study is that of the Apuan Alps (north-western Tuscany, Italy) because of the intensive marble quarrying activity. The Apuan Alps region extends over about 650 km2; it hosts several quarries, known all over the world for the quality of the marble extracted, and a karst aquifer producing about 70,000 m3/day of high-quality water used directly for domestic purposes almost without treatments. In addition, Apuan Alps are an extraordinary area of natural and cultural heritage hosting many caves (about 1200), karst springs and geosites of international and national interest. During intense rain events, carbonate slurry systematically reaches the karst springs, making them temporarily unsuitable for domestic uses. In addition, the deterioration of the water quality threatens all the hypogean fauna living in the caves. This paper provides preliminary insights of the hydrological and biological indicators that can offer information about the impact of the marble quarrying activities on groundwater resources, karst habitats and their biodiversity.

Elucidating stygofaunal trophic web interactions via isotopic ecology

Subterranean ecosystems host highly adapted aquatic invertebrate biota which play a key role in sustaining groundwater ecological functioning and hydrological dynamics. However, functional biodiversity studies in groundwater environments, the main source of unfrozen freshwater on Earth, are scarce, probably due to the cryptic nature of the systems. To address this, we investigate groundwater trophic ecology via stable isotope analysis, employing δ¹³C and δ¹⁵N in bulk tissues, and amino acids. Specimens were collected from a shallow calcrete aquifer in the arid Yilgarn region of Western Australia: a well-known hot-spot for stygofaunal biodiversity. Sampling campaigns were carried out during dry (low rainfall: LR) and the wet (high rainfall: HR) periods. δ¹³C values indicate that most of the stygofauna shifted towards more ¹³C-depleted carbon sources under HR, suggesting a preference for fresher organic matter. Conversion of δ¹⁵N values in glutamic acid and phenylalanine to a trophic index showed broadly stable trophic levels with organisms clustering as low-level secondary consumers. However, mixing models indicate that HR conditions trigger changes in dietary preferences, with increasing predation of amphipods by beetle larvae. Overall, stygofauna showed a tendency towards opportunistic and omnivorous habits—typical of an ecologically tolerant community—shaped by bottom-up controls linked with changes in carbon flows. This study provides baseline biochemical and ecological data for stygofaunal trophic interactions in calcretes. Further studies on the carbon inputs and taxa-specific physiology will help refine the interpretation of the energy flows shaping biodiversity in groundwaters. This will aid understanding of groundwater ecosystem functioning and allow modelling of the impact of future climate change factors such as aridification.

Scratching the surface of subterranean biodiversity: Molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia

Like other crustacean families, the Parabathynellidae is a poorly studied subterranean and aquatic (stygobiontic) group in Australia, with many regions of available habitat having not yet been surveyed. Here we used a combined approach of molecular species delimitation methods, applied to mitochondrial and nuclear genetic data, to identify putative new species from material obtained from remote subterranean habitats in the Pilbara region of Western Australia. Based on collections from these new localities, we delineated a minimum of eight and up to 24 putative new species using a consensus from a range of molecular delineation methods and additional evidence. When we placed our new putative species into the broader phylogenetic framework of Australian Parabathynellidae, they grouped with two known genera and also within one new and distinct Pilbara-only clade. These new species significantly expand the known diversity of Parabathynellidae in that they represent a 22% increase to the 109 currently recognised species globally. Our investigations showed that sampling at new localities can yield extraordinary levels of new species diversity, with the majority of species showing likely restricted endemic geographical ranges. These findings represent only a small sample from a region comprising less than 2.5% of the Australian continent.

Clay beads as artificial trapping matrices for monitoring bacterial distribution among urban stormwater infiltration systems and their connected aquifers

Stormwater infiltration systems (SIS) have been developed to limit surface runoff and flooding in urban areas. The impacts of such practices on the ecological and biological quality of groundwater ecosystems remain poorly studied due to the lack of efficient methodologies to assess microbiological quality of aquifers. In the present study, a monitoring method based on the incubation of artificial matrices (clay beads) is presented to evaluate microbial biomass, microbial activities, and bacterial community structure. Four microbial variables (biomass, dehydrogenase and hydrolytic activities, bacterial community structures) were measured on clay beads incubated in three urban water types (stormwater surface runoffs, SIS-impacted and non-impacted groundwaters) for six SIS. Analyses based on next-generation sequencing (NGS) of partial rrs (16S rRNA) PCR products (V5-V6) were used to compare bacterial community structures of biofilms on clay beads after 10 days of incubation with those of waters collected from the same sampling points at three occasions. Biofilm biomass and activities on clay beads were indicative of nutrient transfers from surface to SIS-impacted groundwaters. Biofilms allowed impacts of SIS on groundwater bacterial community structures to be determined. Although bacterial communities on clay beads did not perfectly match those of waters, clay beads captured the most abundant bacterial taxa. They also captured bacterial taxa that were not detected in waters collected at three occasions during the incubation, demonstrating the integrative character of this approach. Monitoring biofilms on clay beads also allowed the tracking of bacterial genera containing species representing health concerns.

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56-9.25 × 10³ cells mL^-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

First insights into the living groundwater mycobiome of the terrestrial biogeosphere

Although fungi play important roles in biogeochemical cycling in aquatic ecosystems and have received a great deal of attention, much remains unknown about the living fractions of fungal communities in aquifers of the terrestrial subsurface in terms of diversity, community dynamics, functional roles, the impact of environmental factors and presence of fungal pathogens. Here we address this gap in knowledge by using RNA-based high throughput pair-end illumina sequencing analysis of fungal internal transcribed spacer (ITS) gene markers, to target the living fractions of groundwater fungal communities from fractured alternating carbonate-/siliciclastic-rock aquifers of the Hainich Critical Zone Exploratory. The probed levels of the hillslope multi-storey aquifer system differ primarily in their oxygen and nitrogen content due to their different connections to the surface. We discovered highly diverse living fungal communities (384 Operational Taxonomic Units, OTUs) with different taxonomic affiliations and ecological functions. The observed fungal communities primarily belonged to three phyla: Ascomycota, Basidiomycota and Chytridiomycota. Perceived dynamics in the composition of living fungal communities were significantly shaped by the concentration of ammonium in the moderately agriculturally impacted aquifer system. Apart from fungal saprotrophs, we also detected living plant and animal pathogens for the first time in this aquifer system. This work also demonstrates that the RNA-based high throughput pair-end illumina sequencing method can be used in future for water quality monitoring in terms of living fungal load and subsequent risk assessments. In general, this study contributes towards the growing knowledge of aquatic fungi in terrestrial subsurface biogeosphere.

Aquifer recharge with stormwater runoff in urban areas: Influence of vadose zone thickness on nutrient and bacterial transfers from the surface of infiltration basins to groundwater

Stormwater infiltration systems (SIS) have been built in urban areas to reduce the environmental impacts of stormwater runoff. Infiltration basins allow the transfer of stormwater runoff to aquifers but their abilities to retain contaminants depend on vadose zone properties. This study assessed the influence of vadose zone thickness (VZT) on the transfer of inorganic nutrients (PO₄^3-, NO₃^-, NH₄⁺), dissolved organic carbon (total -DOC- and biodegradable -BDOC-) and bacteria. A field experiment was conducted on three SIS with a thin vadose zone (<3 m) and three SIS with a thick vadose zone (>10 m). Water samples were collected at three times during a rainy period of 10 days in each infiltration basin (stormwater runoff), in the aquifer impacted by infiltration (impacted groundwater) and in the same aquifer but upstream of the infiltration area (non-impacted groundwater). Inorganic nutrients, organic matter, and dissolved oxygen (DO) were measured on all water samples. Bacterial community structures were investigated on water samples through a next-generation sequencing (NGS) scheme of 16S rRNA gene amplicons (V5-V6). The concentrations of DO and phosphate measured in SIS-impacted groundwaters were significantly influenced by VZT due to distinct biogeochemical processes occurring in the vadose zone. DOC and BDOC were efficiently retained in the vadose zone, regardless of its thickness. Bacterial transfers to the aquifer were overall low, but data obtained on day 10 indicated a significant bacterial transfer in SIS with a thin vadose zone. Water transit time and water saturation of the vadose zone were found important parameters for bacterial transfers. Most bacterial taxa (>60%) from impacted groundwaters were not detected in stormwater runoff and in non-impacted groundwaters, indicating that groundwater bacterial communities were significantly modified by processes associated with infiltration (remobilization of bacteria from vadose zone and/or species sorting).

Earthquake impacts on microcrustacean communities inhabiting groundwater-fed springs alter species-abundance distribution patterns

Earthquakes are important natural events, yet their impacts on animal communities are poorly known. Understanding earthquake impacts on groundwater communities is essential to assess their resilience and hence to perform conservation actions. We investigated how a 6.3 Mw earthquake that occurred in 2009 altered the community structure (diversity, evenness, dominance, species abundance distributions and beta-diversity) of microcrustaceans (Crustacea Copepoda) inhabiting springs fed by the Gran Sasso Aquifer (Central Italy). Sampling was done in low-discharge (1997), high-discharge (2005), and post-seismic (2012) hydrological years. Stygobites (obligate groundwater species) and non-stygobites (non-obligate groundwater species) showed different patterns. A high-water discharge in 2005 altered abundance patterns of non-stygobites. The earthquake re-established former abundance patterns. Stygobites were less affected by high-water discharge in 2005, and showed strong increases in diversity and evenness after the earthquake. This effect was due to the fact that the earthquake induced a strong population decline of previously dominant stygobites (especially of Nitocrella pescei) in the aquifer, and subsequently at the main spring outlets, thus allowing a more equitable species-abundance distribution. These results highlight the importance of considering species ecology to understand the effects of a significant earthquake event on animal communities.

Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions

Micro scale processes are expected to have a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-researched. In part, this is due to the fact that sampling is rarely carried out at the scale at which microorganisms, and their grazers and predators, function and thus we lack essential information. While set within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro scale adds variability, by providing heterogeneous zones at the micro scale which enable a wider range of redox reactions. Here we outline how understanding micro scale processes better may lead to improved appreciation of the range of ecosystems functions taking place at all scales. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modelling as well as engineering measures have to take into account, and use, understanding at the micro scale. We discuss the importance of integrating faunal processes and computational appraisals in research, in order to continue to secure sustainable water resources from groundwater.