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The idea that there are many subterranean habitats close to the surface that are little known and do not fit comfortably into any habitat classification scheme is introduced. Four of these shallow subterranean habitats (SSHs) are unique (strict sense shallow subterranean habitats)—hypotelminorheic and seepage springs, milieu souterrain superficiel (including talus and scree), epikarst, and calcrete aquifers—and have intermediate sized habitat spaces, no light, and close connections to the surface. Broad sense shallow subterranean habitats include habitats with large (lava tubes) or small (aquatic interstitial and soil) spaces. SSHs are generally broadly but patchily distributed across the landscape although some have restricted physical requirements, such as the presence of a shallow clay layer for hypotelminorheic habitats. Close surface connections have impacts on environmental conditions, nutrient fluxes, and movement of animals through SSHs. While SSHs can be ecotones, they are habitats in their own right, and not necessarily connected with deeper subterranean habitats. They are of general biological interest because of the presence of eyeless, depigmented species, their possible role as stepping stones to adaptation to deeper subterranean environments, their geographic pattern, and conservation issues raised by them. Brief examples of each type of SSH are discussed.

Epikarst is a nearly ubiquitous component of karst areas, which cover about 12.5 % of the earth’s surface. Epikarst is the site of most of the water storage above the water table, and an important shallow subterranean habitat. It is highly dissected, with many miniature (<100 m²) catchment areas, which in turn often differ in their water chemistry. Organic matter in the soil is broken down in epikarst, both making organic carbon available and releasing CO₂ that produces carbonic acid. Water exiting epikarst typically contains dissolved organic carbon at concentrations of approximately 1.0 mg L⁻¹. The epikarst fauna typically displays species richness, often with more than ten species known from drips in a single cave. In the Dinaric karst, the epikarst fauna is predominately of stygobionts, though troglobionts are also recorded. Copepoda generally dominate, but many other groups of crustaceans, such as amphipods, isopods, and syncarids are present. As is usually the case with subterranean fauna, local diversity is a small component of regional diversity, about 12 % in the case of six Slovenian caves which were extensively sampled. In some caves, there is evidence of a diverse terrestrial epikarst community which may be more diverse than the cave terrestrial fauna. Body size in epikarst species is smaller than that of species in other subterranean habitats, likely because the habitat dimensions in epikarst are smaller. Epikarst animals show morphological adaptations related to reducing washout and increasing metabolic efficiency.

The main subterranean habitats are: small cavities—interstitial spaces beneath surface waters; large cavities—caves; and shallow subterranean habitats—voids of various sizes close to the surface. The defining feature of all these habitats is the absence of light. Environmental variation is also reduced and most subterranean habitats rely on nutrients transported from the surface. The aquatic component of caves includes water percolating from the surface (including epikarst), streams, and resurgences. Terrestrial habitats include epikarst, and the vadose zone. The aquatic interstitial habitat is comprised of the water-filled spaces between grains of unconsolidated sediments. Shallow subterranean habitats are ones close to the surface. They include the hypotelminorheic, interstitial, epikarst, MSS, soil, lava tubes, calcrete aquifers, and iron-ore caves. They share an absence of light, close surface connections, relatively high nutrient levels relative to other subterranean habitats, and the presence of species highly modified for subterranean life.

Among shallow subterranean habitats, representative communities of hypotelminorheic (Lower Potomac seeps, Washington, DC), epikarst (Postojna–Planina Cave System, Slovenia), milieu souterrain superficiel (MSS) (central Pyrenees, France), soil (central Pyrenees, France), calcrete aquifers (Pilbara, Western Australia), lava tubes (Tenerife, Spain and Lava Beds National Monument, California), fluvial aquifers (Lobau wetlands, Austria), and iron-ore caves (Brazil) are described. Among non-cave deeper habitats, communities of phreatic aquifers (Edwards Aquifer, Texas), and deep phreatic aquifers (basalt aquifers, Washington) are described. Among cave habitats, representative tropical terrestrial (Gua Salukkan Kallang, Sulawesi, Indonesia), temperate terrestrial (Mammoth Cave, Kentucky), chemoautotrophic (Peştera Movile, Romania), hygropetric (Vjetrenica, Bosnia & Herzegovina), anchialine (Šipun, Croatia), cave streams (West Virginia and U.K.) and springs (Las Hountas, Baget basin, France) communities are discussed.