Using boreholes as windows into groundwater ecosystems

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.

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem

Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.

The streamwater microbiome encodes hydrologic data across scales

Many fundamental questions in hydrology remain unanswered due to the limited information that can be extracted from existing data sources. Microbial communities constitute a novel type of environmental data, as they are comprised of many thousands of taxonomically and functionally diverse groups known to respond to both biotic and abiotic environmental factors. As such, these microscale communities reflect a range of macroscale conditions and characteristics, some of which also drive hydrologic regimes. Here, we assess the extent to which streamwater microbial communities (as characterized by 16S gene amplicon sequence abundance) encode information about catchment hydrology across scales. We analyzed 64 summer streamwater DNA samples collected from subcatchments within the Willamette, Deschutes, and John Day river basins in Oregon, USA, which range 0.03-29,000 km² in area and 343-2334 mm/year of precipitation. We applied information theory to quantify the breadth and depth of information about common hydrologic metrics encoded within microbial taxa. Of the 256 microbial taxa that spanned all three watersheds, we found 9.6 % (24.5/256) of taxa, on average, shared information with a given hydrologic metric, with a median 15.6 % (range = 12.4-49.2 %) reduction in uncertainty of that metric based on knowledge of the microbial biogeography. All of the hydrologic metrics we assessed, including daily discharge at different time lags, mean monthly discharge, and seasonal high and low flow durations were encoded within the microbial community. Summer microbial taxa shared the most information with winter mean flows. Our study demonstrates quantifiable relationships between streamwater microbial taxa and hydrologic metrics at different scales, likely resulting from the integration of multiple overlapping drivers of each. Streamwater microbial communities are rich sources of information that may contribute fresh insight to unresolved hydrologic questions.

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.

A Hotspot of Arid Zone Subterranean Biodiversity: The Robe Valley in Western Australia

Knowledge of subterranean fauna has mostly been derived from caves and streambeds, which are relatively easily accessed. In contrast, subterranean fauna inhabiting regional groundwater aquifers or the vadose zone (between surface soil layers and the watertable) is difficult to sample. Here we provide species lists for a globally significant subterranean fauna hotspot in the Robe Valley of the Pilbara region, Western Australia. This fauna was collected from up to 50 m below ground level using mining exploration drill holes and monitoring wells. Altogether, 123 subterranean species were collected over a distance of 17 km, comprising 65 troglofauna and 58 stygofauna species. Of these, 61 species were troglobionts and 48 stygobionts. The troglofauna occurs in small voids and fissures in mesas comprised mostly of an iron ore formation, while the stygofauna occurs in the alluvium of a river floodplain. The richness of the Robe Valley is not a localized aberration, but rather reflects the richness of the arid Pilbara region. While legislation in Western Australia has recognized the importance of subterranean fauna, mining is occurring in the Robe Valley hotspot with conditions of environmental approval that are designed to ensure species persistence.

Groundwater flow velocities in karst aquifers; importance of spatial observation scale and hydraulic testing for contaminant transport prediction

We review scale dependence of hydraulic conductivities and effective porosities for prediction of contaminant transport in four UK karst aquifers. Approaches for obtaining hydraulic parameters include core plug, slug, pumping and pulse tests, calibration of groundwater flow models and spring recession curves. Core plug and slug tests are unsuitable because they do not characterize a large enough volume to include a representative fracture network. Pumping test values match regional-scale hydraulic conductivities from flow modelling for the less intensively karstified aquifers: Magnesian Limestone, Jurassic Limestone and Cretaceous Chalks. Reliable bulk hydraulic conductivities were not available for the intensively karstified Carboniferous Limestone due to dominance of flow through pipe conduits in Mendips. Here, the only hydraulic conductivity value found from spring recession is one order of magnitude higher than that indicated by pumping tests. For all four carbonate aquifers, effective porosities assumed for transport modelling are two orders of magnitude higher than those found from tracer and hydrogeophysical tests. Thus, a combination of low hydraulic conductivities and assumed flowing porosities resulted in underestimated flow velocities. The UK karst aquifers are characterized by a range of hydraulic behaviours that fit those of karst aquifers worldwide. Indeed, underestimation of flow velocity due to inappropriate parameter selection is common to intensively karstified aquifers of southern France, north-western Germany and Italy. Similar issues arise for the Canadian Silurian carbonates where the use of high effective porosities (e.g. 5%) in transport models leads to underestimation of groundwater velocities. We recommend values in the range of 0.01-1% for such aquifers.

Shedding light on the hidden world of subterranean fauna: A transdisciplinary research approach

Subterranean environments contain a diverse and unique obligate fauna: either aquatic living in the groundwater or terrestrial living in voids above the water table. In the arid region of the western part of the Australian continent, a particularly rich subterranean fauna coincides with a concentration of natural resource extraction operations. Since the inclusion of subterranean fauna in assessments of environmental impact in the mid-1990s, taxonomic research in Australia on this group of mainly invertebrates has grown exponentially. However, remaining knowledge gaps continue to frustrate both environmental regulators and development proponents due to high uncertainty in the decision-making process. In early 2017, the Western Australian Biodiversity Science Institute was tasked with leading the development of a research program to improve on the current state of knowledge of subterranean fauna. To balance the diverse environmental, economic and social needs of a range of stakeholders, transdisciplinary principles were applied to program development. A clear consensus on five broad focus areas to progress include: (1) data consolidation; (2) resilience to disturbance; (3) survey and sampling protocols; (4) abiotic and biotic habitat requirements; and (5) species delineation. In the context of these focus areas; we describe the research program development, reviewing the status of knowledge within each focus area, and the research initiatives to close the gaps in knowledge. We argue that, by adopting a transdisciplinary approach, the likelihood of success of the research program, as measured by the effective translation and adoption of research findings, will be maximized. This review is timely given the ever-increasing demand on groundwater systems for water extraction worldwide. A holistic understanding of the influence of anthropogenic activities on these ecosystems, and the functional role of organisms within them, will help to ensure that their health is not compromised.

Online fluorescence spectroscopy for the real-time evaluation of the microbial quality of drinking water

We assessed the utility of online fluorescence spectroscopy for the real-time evaluation of the microbial quality of untreated drinking water. Online fluorimeters were installed on the raw water intake at four groundwater-derived UK public water supplies alongside existing turbidity sensors that are used to forewarn of the presence of microbial contamination in the water industry. The fluorimeters targeted fluorescent dissolved organic matter (DOM) peaks at excitation/emission wavelengths of 280/365 nm (tryptophan-like fluorescence, TLF) and 280/450 nm (humic-like fluorescence, HLF). Discrete samples were collected for Escherichia coli, total bacterial cell counts by flow cytometry, and laboratory-based fluorescence and absorbance. Both TLF and HLF were strongly correlated with E. coli (ρ = 0.71-0.77) and total bacterial cell concentrations (ρ = 0.73-0.76), whereas the correlations between turbidity and E. coli (ρ = 0.48) and total bacterial cell counts (ρ = 0.40) were much weaker. No clear TLF peak was observed at the sites and all apparent TLF was considered to be optical bleed-through from the neighbouring HLF peak. Therefore, a HLF fluorimeter alone would be sufficient to evaluate the microbial water quality at these sources. Fluorescent DOM was also influenced by site operations such as pump start-up and the precipitation of cations on the sensor windows. Online fluorescent DOM sensors are a better indicator of the microbial quality of untreated drinking water than turbidity and they have wide-ranging potential applications within the water industry.

High reactivity of deep biota under anthropogenic CO2 injection into basalt

Basalts are recognized as one of the major habitats on Earth, harboring diverse and active microbial populations. Inconsistently, this living component is rarely considered in engineering operations carried out in these environments. This includes carbon capture and storage (CCS) technologies that seek to offset anthropogenic CO₂ emissions into the atmosphere by burying this greenhouse gas in the subsurface. Here, we show that deep ecosystems respond quickly to field operations associated with CO₂ injections based on a microbiological survey of a basaltic CCS site. Acidic CO₂-charged groundwater results in a marked decrease (by ~ 2.5–4) in microbial richness despite observable blooms of lithoautotrophic iron-oxidizing Betaproteobacteria and degraders of aromatic compounds, which hence impact the aquifer redox state and the carbon fate. Host-basalt dissolution releases nutrients and energy sources, which sustain the growth of autotrophic and heterotrophic species whose activities may have consequences on mineral storage.

The impacts of carbon capture and storage (CCS) on subsurface microorganisms are poorly understood. Here, the authors show that deep ecosystems respond quickly to CO2 injections and that the environmental consequences of their metabolic activities need to be properly assessed for sustainable CCS in basalt.

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.

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

When compared to surface ecosystems, groundwater sampling has unique constraints, including limited access to ecosystems through wells. In order to monitor groundwater, a detailed understanding of groundwater biota and what biological sampling of wells truly reflects, is paramount. This study aims to address this uncertainty, comparing the composition of biota in groundwater wells prior to and after purging, with samples collected prior to purging reflecting a potentially artificial environment and samples collected after purging representing the surrounding aquifer. This study uses DNA community profiling (metabarcoding) of 16S rDNA and 18S rDNA, combined with traditional stygofauna sampling methods, to characterise groundwater biota from four catchments within eastern Australia. Aquifer waters were dominated by Archaea and bacteria (e.g. Nitrosopumilales) that are often associated with nitrification processes, and contained a greater proportion of bacteria (e.g. Anaerolineales) associated with fermenting processes compared to well waters. In contrast, unpurged wells contained greater proportions of pathogenic bacteria and bacteria often associated with denitrification processes. In terms of eukaryotes, the abundances of copepods, syncarids and oligochaetes and total abundances of stygofauna were greater in wells than aquifers. These findings highlight the need to consider sampling requirements when completing groundwater ecology surveys.

Nematodes in caves: a historical perspective on their occurrence, distribution and ecological relevance

Caves and cave-dwelling biota have fascinated scientists for centuries. Nevertheless, there is a considerable lack of information on subterranean realms and the ecosystems they host. Nematoda, for example, is a group of invertebrates that plays an important role in the functioning of epigean ecosystems, but whether or not the same is true for subterranean ecosystems remains unknown. For this reason it was decided to conduct an in-depth review of all reports related to cave-dwelling nematodes in order to provide a sound basis for future studies. A literature survey of 41 scientific works from over the last 138 years revealed 295 unique taxa reported from 78 different cave systems. The historical trends in cave nematology, peculiar findings from important studies and an ecological classification system are discussed. Lastly, the trophic distribution of the reported taxa is presented, whilst nematodes from other (non-cave) subterranean environments are also considered.

Macronutrient status of UK groundwater: Nitrogen, phosphorus and organic carbon

Groundwater is a large, slowly changing pool of the macronutrients nitrogen (N), phosphorus (P) and dissolved organic carbon (DOC), with impacts on receptors, surface waters, dependent wetlands and coastal marine ecosystems. Sources of N to groundwater include fertilisers, animal wastes and septic effluents. N species are well-quantified in groundwater and NO₃-N has a wide range of median values (0-12mg/L). The highest concentrations are in the Chalk of East Anglia and Humberside and the Permo-Triassic Sandstone (PTS) of Staffordshire. The highest concentrations of NH₄-N are found in confined aquifers. N concentrations have increased with time peaking during the 1980s. Changes in practice have led to the reduction observed in rapidly-responding aquifers. For the Chalk, where the unsaturated zone is thick, improvements may not be seen for decades. P is less well-characterised in UK groundwater reflecting the lack of historical interest in groundwater P, although it can be significant in some aquifer matrices. Groundwater P concentrations are elevated in sandstone formations compared to other lithology and highest in the PTS of the Midlands and northern England (median values>50μg/L). Overall half of the aquifers studied in the UK have median TDP>50μg/L, with values of up to 100μg/L under some urban areas, such as Manchester and Liverpool as well as the Lee Valley. P concentrations in arable areas are variable (20-100μg/L), whereas under semi-natural conditions they are lower (20-50μg/L). There is little information on P trends in groundwater. Most DOC is derived from soils, playing an important part in redox processes. The aquifer matrix can contain high OC and contribute significantly to groundwater DOC. Median values range between 0.4 and 9mg/L, but rarely exceed 5mg/L, except in the Chalk of Yorkshire and Humberside and PTS of Liverpool which have long legacies of anthropogenic pollution.

Emerging contaminants in urban groundwater sources in Africa

The occurrence of emerging organic contaminants within the aquatic environment in Africa is currently unknown. This study provides early insights by characterising a broad range of emerging organic contaminants (n > 1000) in groundwater sources in Kabwe, Zambia. Groundwater samples were obtained during both the dry and wet seasons from a selection of deep boreholes and shallow wells completed within the bedrock and overlying superficial aquifers, respectively. Groundwater sources were distributed across the city to encompass peri-urban, lower cost housing, higher cost housing, and industrial land uses. The insect repellent DEET was ubiquitous within groundwater at concentrations up to 1.8 μg/L. Other compounds (n = 26) were detected in less than 15% of the sources and included the bactericide triclosan (up to 0.03 μg/L), chlorination by-products - trihalomethanes (up to 50 μg/L), and the surfactant 2,4,7,9-tetramethyl-5-decyne-4,7-diol (up to 0.6 μg/L). Emerging contaminants were most prevalent in shallow wells sited in low cost housing areas. This is attributed to localised vulnerability associated with inadequate well protection, sanitation, and household waste disposal. The five-fold increase in median DEET concentration following the onset of the seasonal rains highlights that more mobile compounds can rapidly migrate from the surface to the aquifer suggesting the aquifer is more vulnerable than previously considered. Furthermore it suggests DEET is potentially useful as a wastewater tracer in Africa. There was a general absence of personal care products, life-style compounds, and pharmaceuticals which are commonly detected in the aquatic environment in the developed world. This perhaps reflects some degree of attenuation within the subsurface, but could also be a result of the current limited use of products containing emerging contaminants by locals due to unaffordability and unavailability. As development and population increases in Africa, it is likely a wider-range of emerging contaminants will be released into the environment.

Catchment-scale biogeography of riverine bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river.

Microbial stimulation and succession following a test well injection simulating CO2 leakage into a shallow Newark basin aquifer

In addition to efforts aimed at reducing anthropogenic production of greenhouse gases, geological storage of CO2 is being explored as a strategy to reduce atmospheric greenhouse gas emission and mitigate climate change. Previous studies of the deep subsurface in North America have not fully considered the potential negative effects of CO2 leakage into shallow drinking water aquifers, especially from a microbiological perspective. A test well in the Newark Rift Basin was utilized in two field experiments to investigate patterns of microbial succession following injection of CO2-saturated water into an isolated aquifer interval, simulating a CO2 leakage scenario. A decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), and increased bacterial cell concentrations in the recovered water. 16S ribosomal RNA gene sequence libraries from samples collected before and after the test well injection were compared to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injections, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia and microbial taxa often noted to be associated with iron and sulfate reduction. The concurrence of increased microbial cell concentrations and rapid microbial community succession indicate significant changes in aquifer microbial communities immediately following the experimental CO2 leakage event. Samples collected one year post-injection were similar in cell number to the original background condition and community composition, although not identical, began to revert toward the pre-injection condition, indicating microbial resilience following a leakage disturbance. This study provides a first glimpse into the in situ successional response of microbial communities to CO2 leakage after subsurface injection in the Newark Basin and the potential microbiological impact of CO2 leakage on drinking water resources.

Earthquakes trigger the loss of groundwater biodiversity

Earthquakes are among the most destructive natural events. The 6 April 2009, 6.3-M_w earthquake in L'Aquila (Italy) markedly altered the karstic Gran Sasso Aquifer (GSA) hydrogeology and geochemistry. The GSA groundwater invertebrate community is mainly comprised of small-bodied, colourless, blind microcrustaceans. We compared abiotic and biotic data from two pre-earthquake and one post-earthquake complete but non-contiguous hydrological years to investigate the effects of the 2009 earthquake on the dominant copepod component of the obligate groundwater fauna. Our results suggest that the massive earthquake-induced aquifer strain biotriggered a flushing of groundwater fauna, with a dramatic decrease in subterranean species abundance. Population turnover rates appeared to have crashed, no longer replenishing the long-standing communities from aquifer fractures, and the aquifer became almost totally deprived of animal life. Groundwater communities are notorious for their low resilience. Therefore, any major disturbance that negatively impacts survival or reproduction may lead to local extinction of species, most of them being the only survivors of phylogenetic lineages extinct at the Earth surface. Given the ecological key role played by the subterranean fauna as decomposers of organic matter and “ecosystem engineers”, we urge more detailed, long-term studies on the effect of major disturbances to groundwater ecosystems.