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.

Insight into spatial variations of DOM fractions and its interactions with microbial communities of shallow groundwater in a mesoscale lowland river watershed

Dissolved organic matter (DOM) plays a crucial role in driving biogeochemical processes and determining water quality in shallow groundwater systems, where DOM could be susceptible to dynamic influences of surface water influx. This study employed fluorescence excitation-emission matrix (EEM) spectroscopy combined with principal component coefficients, parallel factor analysis (PARAFAC), co-occurrence network analysis and structural equation modeling (SEM) to examine changes of DOM fractions from surface water to shallow groundwater in a mesoscale lowland river basin. Combining stable isotope and hydrochemical parameters, except for surface water (SW), two groups of groundwater samples were defined, namely, deeply influenced by surface water (IGW) and groundwater nearly non-influenced by surface water (UGW), which were 50.34 % and 19.39 % recharged by surface water, respectively. According to principal component coefficients, reassembled EEM data of these categories highlighted variations of the tyrosine-like peak in DOM. EEMs coupled with PARAFAC extracted five components (C1-C5), i.e. C1, protein-like substances, C2 and C4, humic-like substances, and C3 and C5, microbial-related substances. The abundance of the protein-like was SW > IGW > UGW, while the order of the humic-like was opposite. The bacterial communities exhibited an obvious cluster across three regions, which hinted their sensitivity to variations in environmental conditions. Based on co-occurrence, SW represented the highest connectivity between bacterial OTUs and DOM fractions, followed by IGW and UGW. SEM revealed that microbial activities increased bioavailability of the humic-like in the SW and IGW, whereas microbial compositions promoted the evolution of humic-like substances in the UGW. Generally, these results could be conducive to discern dissimilarity in DOM fractions across surface water and shallow groundwater, and further trace their interactions in the river watershed.

Integrated management of groundwater quantity, physicochemical properties, and microbial quality in West Nile delta using a new MATLAB code and geographic information system mapping

Groundwater is an excellent alternative to freshwater for drinking, irrigation, and developing arid regions. Agricultural, commercial, industrial, residential, and municipal activities may affect groundwater quantity and quality. Therefore, we aimed to use advanced methods/techniques to monitor the piezometric levels and collect groundwater samples to test their physicochemical and biological characteristics. Our results using software programs showed two main types of groundwater: the most prevalent was the Na-Cl type, which accounts for 94% of the groundwater samples, whereas the Mg-Cl type was found in 6% of samples only. In general, the hydraulic gradient values, ranging from medium to low, could be attributed to the slow movement of groundwater. Salinity distribution in groundwater maps varied between 238 and 1350 mg L-1. Although lower salinity values were observed in northwestern wells, higher values were recorded in southern ones. The collected seventeen water samples exhibited brackish characteristics and were subjected to microbial growth monitoring. Sample WD12 had the lowest total bacterial count (TBC) of 4.8 ± 0.9 colony forming unit (CFU mg L-1), while WD14 had the highest TBC (7.5 ± 0.5 CFU mg L-1). None of the tested water samples, however, contained pathogenic microorganisms. In conclusion, the current simulation models for groundwater drawdown of the Quaternary aquifer system predict a considerable drawdown of water levels over the next 10, 20, and 30 years with the continuous development of the region.

Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater

Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.

Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites

In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.

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.

Groundwater fauna downtown - Drivers, impacts and implications for subsurface ecosystems in urban areas

Groundwater fauna (stygofauna) comprises organisms that have adapted to the dark subterranean environment over a course of thousands and millions of years, typically having slow metabolisms and long life cycles. They are crucial players in the groundwater of oxygenic aquifers, and contribute to various ecosystem services. Today's knowledge of their sensitivity to anthropogenic impacts is incomplete and a critical analysis of the general relevance of local findings is lacking. In this review, we focus on those areas with the highest interference between humans and stygofauna: cities. Here is where local pollution by various contaminants and heat strongly stresses the unique groundwater ecosystems. It is demonstrated that it is difficult to discern the influence of individual factors from the findings reported in field studies, and to extrapolate laboratory results to field conditions. The effects of temperature increase and chemical pollution vary strongly between tested species and test conditions. In general, previous findings indicate that heating, especially in the long-term, will increase mortality, and less adapted species are at risk of vanishing from their habitats. The same may be true for salinity caused by road de-icing in cold urban areas. Furthermore, high sensitivities were shown for ammonium, which will probably be even more pronounced with rising temperatures resulting in altered biodiversity patterns. Toxicity of heavy metals, for a variety of invertebrates, increases with time and chronic exposure. Our current knowledge reveals diverse potential impacts on groundwater fauna by urban pollution, but our insights gained so far can only be validated by standardized and long-term test concepts.

Sensitivity of a widespread groundwater copepod to different contaminants

Groundwater is an indispensable resource for humankind and sustainable biomes functioning. Anthropogenic disturbance threatens groundwater ecosystems globally, but to which extent groundwater organisms respond to stressors remains poorly understood. Groundwater animals are rare, with small populations, difficult to find and to breed in the lab, which poses a main challenge to the assessment of their responses to pollutants. Despite the difficulties, assessing the toxicity of a large spectrum of stressors to groundwater organisms is a priority to inform towards appropriate environmental protection of these ecosystems. We tested the sensitivity to CuSO₄, diclofenac, and NaCl of a groundwater population of the copepod Diacyclops crassicaudis crassicaudis and compared its sensitivity with the model organism Daphnia magna. We ranked its sensitivity using a species sensitivity distribution (SSD) approach using the feasible data available for groundwater and surface crustaceans. Our results show that the most toxic compound was CuSO₄ for which higher amount of data was recorded and wider variability in response was observed. It was followed by diclofenac, largely lacking data for groundwater-adapted organisms, and the least toxic compound was NaCl. The differential sensitivity between D. crassicaudis and D. magna was contaminant-dependent. As a general trend D. crassicaudis was always distributed in the upper part of the SSD curves together with other groundwater-adapted organisms. Our results highlight that the widespread groundwater populations of the D. crassicaudis species complex, which can be successfully breed in the lab, may provide a reasonable approach to assess the ecological effects of anthropogenic stressors in groundwater ecosystems.

Response of prokaryotic communities to extreme precipitation events in an urban coastal lagoon: A case study of Yundang lagoon, China

Increasing extreme precipitation events (EPEs) can induce biogeochemical disturbances in the coastal lagoon ecosystems. Very little is known about the response of prokaryotic communities to such influences, which are the key components mediating the biogeochemical cycling in lagoons. Here 16S rRNA gene amplicon sequencing and high-through quantitative PCR (HT-qPCR) were employed to investigate the distribution of prokaryotic communities and fecal indicator genes in the surface waters of Yundang lagoon, Xiamen, China during EPEs, respectively. Prokaryotic communities from rainwaters, influents (IFs) and effluents (EFs) from a nearby wastewater treatment plant were also characterised. The results indicated a significant variation in the composition of lagoon prokaryotic communities compared with rainwaters, IFs and EFs. Multivariate and phylogenetic signal analyses revealed that environmental filtering, mainly controlled by salinity, was the major ecological process responsible for the temporal succession of lagoon prokaryotic communities during EPEs. Moreover, the pollution indicator taxa (based on amplicon sequencing) and fecal indicator genes (based on HT-qPCR) demonstrated that EPEs may induce sewage overflows and fecal pollution (mainly from humans and dogs), resulting in an increase in the relative abundance of pollution indicator taxa and genes in Yundang lagoon. Network analysis illustrated that the number of network edges and keystone species decreased along the sampling times, implying that EPEs-induced disturbances may affect prokaryotic species associations. Taken together, this study provides an enhanced understanding of the responses of lagoon prokaryotic communities to EPEs-induced disturbances.

The D-A-(C) index: A practical approach towards the microbiological-ecological monitoring of groundwater ecosystems

Groundwater is not only a vital resource, but also one of the largest terrestrial aquatic ecosystems on Earth. However, to date, ecological criteria are often not considered in routine groundwater monitoring, mainly because of the lack of suitable ecological assessment tools. Prokaryotic microorganisms are ubiquitous in groundwater ecosystems even under the harshest conditions, making them ideal bioindicators for ecological monitoring. We have developed a simple, inexpensive approach that enables ecological groundwater monitoring based on three microbiological parameters that can be easily integrated into existing routine monitoring practices: prokaryotic cell density (D) measured by flow cytometry; activity (A) measured as prokaryotic intracellular ATP concentrations using a simple cell-lysis-luminescence assay; and, as an optional parameter, the bioavailable carbon (C) measured as the concentration of assimilable organic carbon in a simple batch growth assay. We analyzed data for three case studies of different disturbances representing some of the main threats to groundwater ecosystems, i.e. organic contamination with hydrocarbons, surface water intrusion, and agricultural land use. For all three disturbances, disturbed samples could be reliably distinguished from undisturbed samples based on a single index value obtained from multivariate outlier analyses of the microbial variables. We could show that this multivariate approach allowed for a significantly more sensitive and reliable detection of disturbed samples compared to separate univariate outlier analyses of the measured variables. Furthermore, a comparison of non-contaminated aquifers from nine different regions across Germany revealed distinct multivariate signatures along the three microbial variables, which should be considered when applying our approach in practice. In essence, our approach offers a practical tool for the detection of disturbances of groundwater ecosystems based on microbial parameters which can be seamlessly extended in the future by additional parameters for higher sensitivity as well as flexibility.

Recommendations for ecotoxicity testing with stygobiotic species in the framework of groundwater environmental risk assessment

As a consequence of the growing global dependence on groundwater resources, environmental risk assessments (ERA) for groundwater are increasingly required and, with that, ecotoxicological studies with groundwater fauna (stygofauna). However, the literature on the ecotoxicological studies with stygobiotic species (i.e. species that complete their life cycle exclusively in groundwater) has not expanded significantly since the first paper published in this field. The limitations regarding the use of stygobiotic species for ecotoxicological testing are clear and consistent across the globe; stygobiotic species are often 1) naturally present in low numbers, 2) difficult to collect, and 3) difficult to culture under laboratory conditions. This paper reviews the methods used in ecotoxicological studies performed with stygobiotic species, and provides ten recommendations for Good Laboratory Practice (GLP) for such tests. The recommendations focused on the following 10 points: 1) the taxonomic identification, the life stage/size and gender of the test organisms; 2) collection methodology of the organisms, including collection location, conditions and methods; 3) holding and acclimation conditions in the laboratory; 4) exposure conditions such as test set up and exposure time, number of replicates and densities of organisms in tests and in test vessels; 5) range-finding test set up and schedule; 6) final test design, including details of controls and treatments, and replication options; 7) incubation conditions, specifying temperature, pH and oxygenation levels throughout the test; 8) test duration; 9) observations and endpoints; 10) test validity criteria and compliance. The recommendations were developed for the purpose of supporting future short-term ecotoxicological testing with stygofauna through providing consistency in the protocols. A discussion of the potential implications for groundwater managers and decision-makers committed to ERA for groundwater is included.

Environmental risk or benefit? Comprehensive risk assessment of groundwater treated with nano Fe0-based Carbo-Iron®

Groundwater is essential for the provision of drinking water in many areas around the world. The performance of the groundwater-bearing aquifer relies on the ecosystem services provided by groundwater-related organisms. Therefore, if remediation of contaminated groundwater is necessary, the remediation method has to be carefully selected to avoid risk-risk trade-offs that might impact these ecosystems. In the present study, the environmental risk of the in situ remediation agent Carbo-Iron was performed. Carbo-Iron® is a composite of zero valent nano-iron and active carbon. Existing ecotoxicity data were complemented by studies with Daphnia magna (Crustacea), Scenedesmus vacuolatus (Algae), Chironomus riparius (Insecta) and nitrifying soil microorganisms. The predicted no effect concentration of 0.1 mg/L was derived from acute and chronic ecotoxicity studies. It was compared to measured and modelled environmental concentrations of Carbo-Iron applied in a groundwater contaminated with chlorohydrocarbons in a field study and risk ratios were derived. A comprehensive assessment approach was developed further based on existing strategies and used to identify changes of the environmental risk due to the remediation of the contaminated site with Carbo-Iron. With the data used in the present study, the total environmental risk decreased by approximately 50% in the heavily contaminated zones after the application of Carbo-Iron. Thus, based on the results of the present study, the benefit of remediation with Carbo-Iron seems to outweigh its negative effects on the environment.

Are dominant microbial sub-surface communities affected by water quality and soil characteristics?

Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO₃ and SO₄, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.

New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna

Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (¹⁴C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ¹³C) and nitrogen (δ¹⁵N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, ¹⁴C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and ¹⁴C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.

The Characterization of Microbial Communities Response to Shallow Groundwater Contamination in Typical Piedmont Region of Taihang Mountains in the North China Plain

Regional-scale nitrate and organic contaminants in the shallow groundwater were investigated in the Piedmont region of Taihang Mountains (PRTM), but the information of the microbial communities is limited. However, microorganisms provide a dominated contribution to indicate and degrade the contaminants in the aquifer. Therefore, this study investigates the microbial diversity and contamination microbial indicators of groundwater samples with different contaminated types to better understand the contamination in the PRTM. Seventy-six samples were collected between two rivers in the Tang-Dasha River Basin covering 4000 km2 in the PRTM. High-throughput sequencing was employed to determine the samples’ DNA sequences. The samples were divided into four groups: background (B), nitrate contamination (N), organic contamination (O) and organic-nitrate contamination (O_N) based on the cumulative probability distribution and the Chinese groundwater standard levels of NO3−, COD and DO concentrations. Then, the microbial diversity and contamination microbial indicators were studied in the four groups. The results showed that the O group exhibited lower diversity than other groups. Bacteria detected in these four groups covered 531 families, 987 genera, and 1881 species. Taxonomic assignment analysis indicated that Rhodobacter, Vogesella, Sphingobium dominated in the O_N group, N group, and O group, and accounted for 18.05%, 17.74%, 16.45% in each group at genus level, respectively. Furthermore, these three genera were identified as contamination microbial indicators to the three types of contamination, respectively. The results provide a potential molecular microbiological method to identity contamination in shallow groundwater, and established a strong foundation for further investigation and remediation in the PRTM.

Groundwater flow velocities in a fractured carbonate aquifer-type: Implications for contaminant transport

Contaminants that are highly soluble in groundwater are rapidly transported via fractures in mechanically resistant sedimentary rock aquifers. Hence, a rigorous methodology is needed to estimate groundwater flow velocities in such fractured aquifers. Here, we propose an approach using borehole hydraulic testing to compute flow velocities in an un-faulted area of a fractured carbonate aquifer by applying the cubic law to a parallel plate model. The Cadeby Formation (Yorkshire, NE England) - a Permian dolostone aquifer present beneath the University of Leeds Farm - is the fractured aquifer selected for this hydraulic experiment. The bedding plane fractures of this dolostone aquifer, which are sub-horizontal, sub-parallel and laterally persistent, largely dominate the flow at shallow (<~40 mBGL) depths. These flowing bedding plane discontinuities are separated by a rock matrix which is relatively impermeable (K_well-test/K_core-plug~10⁴) as is common in fractured carbonate aquifers. In the workflow reported here, the number of flowing fractures - mainly bedding plane fractures - intersecting three open monitoring wells are found from temperature/fluid conductivity and acoustic/optical televiewer logging. Following well installation, average fracture hydraulic apertures for screened intervals are found from analysis of slug tests. For the case study aquifer, this workflow predicts hydraulic apertures ranging from 0.10 up to 0.54 mm. However, groundwater flow velocities range within two order of magnitude from 13 up to 242 m/day. Notably, fracture apertures and flow velocities rapidly reduce with increasing depth below the water table; the upper ~10 m shows relatively high values of hydraulic conductivity (0.30-2.85 m/day) and corresponding flow velocity (33-242 m/day). Permeability development around the water table in carbonate aquifer-types is common, and arises where high pCO₂ recharge water from the soil zone causes calcite/dolomite dissolution. Hence, agricultural contaminants entering the aquifer with recharge water are laterally transported rapidly within this upper part. Computation of groundwater flow velocities allows determination of the Reynolds number. Values of up ~1, indicating the lower limit of the transition from laminar to turbulent flow, are found at the studied site, which is situated away from major fault traces. Hence, turbulent flow is likely to arise in proximity to tectonic structures, such as normal faults, which localize flow and enhance karstification. The occurrence of turbulent flow in correspondence of such tectonic structures should be represented in regional groundwater flow simulations.

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.

Groundwater contamination and land drainage induce divergent responses in boreal spring ecosystems

Degradation of freshwater ecosystems has engendered legislative mandates for the protection and management of surface waters while groundwater-dependent ecosystems (GDEs) have received much less attention. This is so despite biodiversity and functioning of GDEs are currently threatened by several anthropogenic stressors, particularly intensified land use and groundwater contamination. We assessed the impacts of land drainage (increased input of dissolved organic carbon, DOC, from peatland drainage) and impaired groundwater chemical quality (NO₃^--N enrichment from agricultural or urban land use) on biodiversity and ecosystem functioning in 20 southern Finnish cold-water springs using several taxonomic and functional measures. Groundwater contamination decreased macroinvertebrate and bacterial diversity and altered their community composition. Changes in macroinvertebrate and bacterial communities along the gradient of water-quality impairment were caused by the replacement of native with new taxa rather than by mere disappearance of some of the original taxa. Also species richness of habitat specialist (but not headwater generalist) bryophytes decreased due to impaired groundwater quality. Periphyton accrual rate showed a subsidy-stress response to elevated nitrate concentrations, with peak values at around 2500 μg L^-1, while drainage-induced spring water brownification (increased DOC) reduced both periphyton accrual and leaf decomposition rates already at very low concentrations. Our results highlight the underutilized potential of ecosystem-level functional measures in GDE bioassessment as they seem to respond to the first signs of spring ecosystem impairment, at least for the anthropogenic stressors studied by us.

Ecology-based evaluation of groundwater ecosystems under intensive agriculture: A combination of community analysis and sentinel exposure

Ecological criteria are needed for a comprehensive evaluation of groundwater ecosystem health by including biological components with the physical and chemical properties that are already required by European directives. Two methodological approaches to assess the ecological status of groundwater ecosystems were combined in two alluvial plains (the Ariège and Hers Rivers, southwestern France) varying in agriculture intensity (from grassland to crop rotation including maize and sunflower, and to maize monoculture). In the first approach, the composition of invertebrate assemblages (only obligate-groundwater crustaceans, i.e. stygobionts) sampled in 28 wells differing in their land use contexts was analysed. Abundance, species richness, and assemblage composition significantly changed with agricultural land use or urbanization around the wells. In the second approach, we tested an in situ exposure of sentinel organisms to quantify their response to the environmental pressures. The epigean and native amphipod species Gammarus cf. orinos was used as the sentinel species. Amphipods (30 individuals in each of 10 wells) were exposed for one week to the in situ conditions at two seasons with contrasted concentrations of pollutants. The Ecophysiological Index (EPI) synthetizing the survival rates and energetic storage decreased in wells with low oxygen and high nitrate concentrations, but only during the highest contamination period. Atrazine-related compounds negatively impacted sentinel health whatever the season. The combination of these two approaches may have major applications for orientating groundwater ecosystem management.

Response of invertebrates from the hyporheic zone of chalk rivers to eutrophication and land use

Whereas the response of lotic benthic macroinvertebrates to different environmental stressors is a widespread practice nowadays in assessing the water and habitat quality, the use of hyporheic zone invertebrates is still in its infancy. In this study, classification and regression trees analysis were employed in order to assess the ecological requirements and the potential as bioindicators for the hyporheic zone invertebrates inhabiting four lowland chalk rivers (south England) with contrasting eutrophication levels (based on surface nitrate concentrations) and magnitude of land use (based on percentage of fine sediments load and median interstitial space). Samples of fauna, water and sediment were sampled twice, during low (summer) and high (winter) groundwater level, at depths of 20 and 35 cm. Certain groups of invertebrates (Glossosomatidae and Psychomyiidae caddisflies, and riffle beetles) proved to be good indicators of rural catchments, moderately eutrophic and with high fine sediment load. A diverse community dominated by microcrustaceans (copepods and ostracods) were found as good indicators of highly eutrophic urban streams, with moderate-high fine sediment load. However, the use of other taxonomic groups (e.g. chironomids, oligochaetes, nematodes, water mites and the amphipod Gammarus pulex), very widespread in the hyporheic zone of all sampled rivers, is of limited use because of their high tolerance to the analysed stressors. We recommend the use of certain taxonomic groups (comprising both meiofauna and macroinvertebrates) dwelling in the chalk hyporheic zone as indicators of eutrophication and colmation and, along with routine benthic sampling protocols, for a more comprehensive water and habitat quality assessment of chalk rivers.

Nitrate pollution of groundwater; all right…, but nothing else?

Contamination from agricultural sources and, in particular, nitrate pollution, is one of the main concerns in groundwater management. However, this type of pollution entails the entrance of other substances into the aquifer, as well as it may promote other processes. In this study, we deal with hydrochemical and isotopic analysis of groundwater samples from four distinct zones in Catalonia (NE Spain), which include 5 different aquifer types, to investigate the influence of fertilization on the overall hydrochemical composition of groundwater. Results indicate that intense fertilizer application, causing high nitrate pollution in aquifers, also homogenize the contents of the major dissolved ions (i.e.; Cl(-), SO4(2-), Ca(2+), Na(+), K(+), and Mg(2+)). Thus, when groundwater in igneous and sedimentary aquifers is compared, significant differences are observed under natural conditions for Cl(-), Na(+) and Ca(2+) (with p-values ranging from <0.001 to 0.038), and when high nitrate concentrations occur, these differences are reduced (most p-values ranged between 0.054 and 0.978). Moreover, positive linear relationships between nitrate and some ions are found indicating the magnitude of the fertilization impact on groundwater hydrochemistry (with R(2) values of 0.490, 0.609 and 0.470, for SO4(2-), Ca(2+) and Cl(-), respectively). Nevertheless, the increasing concentration of specific ions is not only attributed to agricultural pollution, but to their enhancing effect upon the biogeochemical processes that control water-rock interactions. Such results raise awareness that these processes should be evaluated in advance in order to assess an adequate groundwater resources management.

Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds

Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.

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.

Coupling groundwater modeling and biological indicators for identifying river/aquifer exchanges

Future climate changes and the resulting modifications in anthropogenic activities will alter the interactions between rivers and groundwater. The quantification of these hydraulic interactions is absolutely necessary for achieving sustainable water use and requires accurate analytical methodologies. This report proposes an interdisciplinary approach to the quantitative and qualitative characterization of hydraulic interactions between rivers and shallow aquifers, wherein it outlines the advantages of coupling groundwater modeling with biological markers. As a first step, we built independent diagnostic maps of hydrological exchanges at the sector scale on the basis of hydrogeological modeling and biological indicators. In a second step, these maps were compared to provide a quantitative and qualitative understanding of exchanges between groundwater and surface water. This comparison significantly improved the calibration of groundwater models through a better assessment of boundary zones. Our approach enabled us to identify the conditions under which it could be possible to use biological indicators instead of a large set of piezometric measures. The integration of such combined tools in a future decision support system will assist governmental authorities in proposing appropriate long-term water policies for the preservation of groundwater resources, such as for supplying potable water and/or mitigating pollution risks.

The impact of water table drawdown and drying on subterranean aquatic fauna in in-vitro experiments

The abstraction of groundwater is a global phenomenon that directly threatens groundwater ecosystems. Despite the global significance of this issue, the impact of groundwater abstraction and the lowering of groundwater tables on biota is poorly known. The aim of this study is to determine the impacts of groundwater drawdown in unconfined aquifers on the distribution of fauna close to the water table, and the tolerance of groundwater fauna to sediment drying once water levels have declined. A series of column experiments were conducted to investigate the depth distribution of different stygofauna (Syncarida and Copepoda) under saturated conditions and after fast and slow water table declines. Further, the survival of stygofauna under conditions of reduced sediment water content was tested. The distribution and response of stygofauna to water drawdown was taxon specific, but with the common response of some fauna being stranded by water level decline. So too, the survival of stygofauna under different levels of sediment saturation was variable. Syncarida were better able to tolerate drying conditions than the Copepoda, but mortality of all groups increased with decreasing sediment water content. The results of this work provide new understanding of the response of fauna to water table drawdown. Such improved understanding is necessary for sustainable use of groundwater, and allows for targeted strategies to better manage groundwater abstraction and maintain groundwater biodiversity.

Developmental endpoints of chronic exposure to suspected endocrine-disrupting chemicals on benthic and hyporheic freshwater copepods

The aims of this study were: (i) to assess if carbamate pesticides and ammonium, widely detected in European freshwater bodies, can be considered ecologically relevant endocrine-disrupting chemicals (EDCs) for benthic and interstitial freshwater copepods; and (ii) to evaluate the potential of copepods as sentinels for monitoring ecosystem health. In order to achieve these objectives, four species belonging to the harpacticoid copepod genus Bryocamptus, namely B. (E.) echinatus, B. (R.) zschokkei, B. (R.) pygmaeus and B. (B.) minutus, were subjected to chronic exposures to Aldicarb and ammonium. A significant deviation from the developmental time of unexposed control cultures was observed for all the species in test cultures. Aldicarb caused an increase in generation time over 80% in both B. minutus and B. zschokkei, but less than 35% in B. pygmaeus and B. echinatus. Ammonium increased generation time over 33% in B. minutus, and 14, 12 and 3.5% for B. pygmaeus, B. zschokkei and B. echinatus, respectively. On the basis of these results it can be concluded that chronic exposure to carbamate pesticides and ammonium alters the post-naupliar development of the test-species and propose their potential role as EDCs, leaving open the basis to search what are the mechanism underlying. A prolonged developmental time would probably produce a detrimental effect on population attributes, such as age structure and population size. These deviations from a pristine population condition may be considered suitable biological indicators of ecosystem stress, particularly useful to compare polluted to unpolluted reference sites. Due to their dominance in both benthic and interstitial habitats, and their sensitivity as test organisms, freshwater benthic and hyporheic copepods can fully be used as sentinel species for assessing health condition of aquatic ecosystems as required by world-wide water legislation.

Response of microcrustacean communities from the surface-groundwater interface to water contamination in urban river system of the Jarama basin (central Spain)

In order to evaluate the water quality at the surface/groundwater interface (hyporheic zone), the pattern of microcrustacean assemblages in response to environmental stress caused by urban industrial contamination was studied in the Jarama River basin (central Spain) during high water discharges (March and April 2011). The clustering of biological variables and the concentration of urban contaminants in hyporheic waters showed that pristine hyporheic waters have moderate species diversity (two to seven species) and dominance of k strategist stygobites, whereas excessively contaminated sites are devoid by crustaceans. An intermediate level of disturbance in hyporheic waters is associated with a peak of species taxonomic diversity (four to nine species) and proliferation of r strategist more tolerant species. Typical species found in hyporheic zone, e.g., Paracyclops imminutus (Copepoda, Cyclopoida), Cryptocandona vavrai (Ostracoda) and Herpetocypris chevreuxi (Ostracoda), were good indicators of high concentrations of Cr, Mn, Ni, Cd, Pb and VOCs; whereas the stygobites do not show any significant correlation. The effectiveness of hyporheic crustaceans as efficient bioindicators for assessing the current ecological status of river ecosystems is emphasised.

Using boreholes as windows into groundwater ecosystems

Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m³ at 0.4–1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.

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.

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

Stygoregions--a promising approach to a bioregional classification of groundwater systems

Linked to diverse biological processes, groundwater ecosystems deliver essential services to mankind, the most important of which is the provision of drinking water. In contrast to surface waters, ecological aspects of groundwater systems are ignored by the current European Union and national legislation. Groundwater management and protection measures refer exclusively to its good physicochemical and quantitative status. Current initiatives in developing ecologically sound integrative assessment schemes by taking groundwater fauna into account depend on the initial classification of subsurface bioregions. In a large scale survey, the regional and biogeographical distribution patterns of groundwater dwelling invertebrates were examined for many parts of Germany. Following an exploratory approach, our results underline that the distribution patterns of invertebrates in groundwater are not in accordance with any existing bioregional classification system established for surface habitats. In consequence, we propose to develope a new classification scheme for groundwater ecosystems based on stygoregions.

Comparative analysis of microbial DNA extraction protocols for groundwater samples

A comparative analysis of four different DNA extraction protocols was performed to determine the best choice for groundwater microbial diversity studies using temperature gradient gel electrophoresis (TGGE) analysis. The methods used were a chelex-based method, a modified salting out procedure (MSOP), and the commercial kits Epicentre and FastDNA. Both commercial kits exhibited the greatest reproducibility in their methods; however, their band patterns were very different. The protocol that showed the highest diversity was the chelex-based method, and the one that showed the lowest diversity was the FastDNA kit.