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Groundwater dependent ecosystems (GDEs) are defined as those ecosystems whose biological structure and ecological processes are directly or indirectly influenced by groundwater. Examples of GDEs are groundwater sensu strictu and springs (a transitional zone between ground and surface water), streams and their hyporheic zones (the latter defined as the water-saturated sediments below the stream bed), and seepage wetlands. Such surface-water ecosystems depend at least partially by groundwater seepage and the interchange of subterranean and surface fauna. Subterranean fauna sensu strictu is called stygofauna.

Groundwater hosts a high and valuable biodiversity, comprised of rare, often endemic, and particularly vulnerable species. GDE fauna includes a subterranean (the stygobites) and a surface-water component (surface-water species that actively or passively enter groundwater and/or GDEs). Ninety percent of stygobites are endemic and are a target group for the conservation of biodiversity: based on the Fauna Europaea (www.faunaeur.org) and BIOFRESH datasets, around 11–15% of the 17,000 freshwater animal species in Europe are stygobites. Some crustacean orders (Bathynellacea, Thermosbenacea) are entirely stygobiont.

A high number of aquatic species could be threatened by changes in groundwater quality. Among these are the crustaceans Proasellus, Microcharon (isopods), and Niphargus (amphipod) with their very limited distribution areas; many species of crustacean copepods, including some living fossils such as the genera Pseudectinosoma and Stygepactophanes (the latter currently monospecific); and the order Gelyelloida, restricted in groundwater in southern France. The latter remain a phylogenetic mystery, as their likely surface-water ancestors went extinct millions of years ago in the Tertiary era.

Many surface-water species depend on groundwater too. Among these are the salmonid fish Salmo macrostigma; and several benthic macroinvertebrates including especially limited-distribution plecopterans (such as Taeniopteryx mercuryi, found exclusively at the headwaters of the Vera creek in Abruzzo) and trichopterans (such as some spring-dwellers within the genus Beraea, which includes GDE-specific endemics like Beraea botosaneanui found only in Sardinia, Beraea crichtoni found only in a small area in southern Italy, and Beraea ilvae found only on Elba Island).

Only a few GDEs are Habitat Nature 2000 sites or Ramsar areas. Such ecosystems are cited in the Annex II, section 2. "Groundwater", pt. 2.2. of the Directive 2000/60/EC, and later in the so-called Groundwater Daughter Directive (Directive 2006/118/EC). A plethora of human activities have impacted or are impairing, sometimes severely, groundwater ecosystems and their ecology and biodiversity. Some of such damages are irreversible. Among the most damaging human activities are spring and headwater withdrawal, stream channelisation, in-stream excavation, spring and wetland filling, and wastewater discharge.

The impact of human activities on habitat and microhabitat structure and physico-chemistry in turn impacts the ecosystem biota, leading to severe declines in abundance or even the extinction of the most sensitive but otherwise common species. Species that depend on groundwater for only a part of their biological cycles (e.g., benthic invertebrates or fish that need the hyporheic zone for reproduction) also may be negatively affected, as may riparian plants that require a high water table to survive.

Many groundwater habitats and GDEs are excluded from any conservation plan unless located in protected areas. Unfortunately groundwater/GDE biodiversity is not well known to legislators and the public at large, and often to even to local conservation agencies. In fact, the groundwater portion of a GDE (which may comprise more than 90% of its extension) is often downplayed or even completely overlooked in management plans, whether nature-protection or development oriented.

The close relationship between the surface and the subterranean portion of GDEs, and how their conservation status affects surface biodiversity, are particularly poorly known. For example, physical modifications of the stream bed may decimate the hyporheic-obligate juveniles of fish and benthic macroinvertebrates, thus severely limiting recruitment and potentially leading to the local extinction of such organisms. Many current monitoring protocols for surface water bodies seem to ignore these aspects, despite what set forth in Directive 2000/60/EC. The result is a tendency to underestimate aquatic invertebrate biodiversity in absolute and relative terms with respect to terrestrial biodiversity.

As a result, nothing has been done so far to define for practical and methodological purposes an analysis and assessment protocol concerning GDE biodiversity, even though such protocols may easily focus only on invertebrate fauna. The scientific background and basic know-how about stygobiont occurrence and diversity as bioindicators of the conservation status of groundwater have been developed with the EU project PASCALIS (Protocols for the Assessment and Conservation of Aquatic Life in the Subsurface, PF7, EVK2-CT-2001-00121), with the University of L'Aquila as a partner and coordinator of two workpackages. The PASCALIS' main objective was the establishment of a rigorous protocol for the quantification of groundwater biodiversity and the development of tools for its conservation on a European scale. The University of L'Aquila then was an active external participant to the EU project BIOFRESH (Biodiversity of Freshwater Ecosystems: Status, Trends, Pressures, and Conservation Priorities. FP7, 226874), contributing to the development of a detailed pan-European database on subterranean biodiversity. The GENESIS project (Groundwater and Dependent Ecosystems: New Scientific and Technological Basis for Assessing Climate Change and Land-use Impacts on Groundwater. VII FP7 226536) integrated the up-to-date knowledge about methods, concepts and tools to support a revision of the Water Framework Directive (WFD) and the Groundwater Daughter Directive to include the comprehensive management of groundwater ecosystems. The GENESIS project identified the pressures and impacts on GDE physico-chemistry — described and utilized within Action A3 of the AQUALIFE project — but the quantitative effects on GDE biodiversity in particular remain unknown.

Therefore, a void must be filled to allow environmental monitoring agencies and other stakeholders to quantify groundwater and GDE biodiversity and correlate it to surface human activities. Only when such a step has been taken can effective, all-encompassing conservation and protection management plans be developed that also include the groundwater/GDE component.