Stygofauna are any fauna that live within groundwater systems, such as caves and aquifers, or more specifically small, aquatic groundwater invertebrates, though terrestrial air-breathing subterranean animals are also sometimes included. Stygofauna and troglofauna are the two types of subterranean fauna (based on life-history). Both are associated with subterranean environments - stygofauna are associated with water and troglofauna with caves and spaces above the water table. Stygofauna can live within freshwater aquifers and within the pore spaces of limestone, calcrete or laterite, but are also found in marine caves and wells along coasts. Stygofaunal animals, like troglofauna, are divided into three groups based on their life history - stygophiles, stygoxenes and stygobites. As their names suggest, stygophiles are partial to aquatic, subterranean environments, but are not necessarily restricted to them. Stygoxenes are like stygophiles, except they are defined as accidental or occasional presence in subterranean waters. Stygophiles and stygoxenes may live for part of their lives in caves but do not complete their life cycle in them. Stygobites are obligate or strictly subterranean, aquatic animals and complete their entire life in this environment.
Extensive research has been done into the stygofauna of numerous other European countries (namely France and Slovenia), the USA and more recently in Australia, due to easy accessibility of caves and wells in these regions, as well as the high diversity and numbers of animals present here. Many species of stygofauna, especially obligate stygofauna, are endemic to particular regions or even particular caves. This makes them focal points for conservation of groundwater systems.
Several methods are currently used to sample stygofauna. The accepted method is to lower a haul net, which is a weighted plankton 'net' (with minimum 50µm mesh size), to the bottom of the bore, well or sinkhole and jiggled to agitate sediments at the base of the bore. The net is then slowly retrieved, filtering stygofauna out of the water column on the upward haul. A more destructive method is to pump bore water (using a Bou-Rouch pump) through a net on the surface (referred to as the Karaman-Chappuis method). These two methods provide animals for morphological and molecular analyses. A video camera can also be used down the hole, providing information on life-history of the organisms but, given the small size of the animals no species determinations can be made.
- Rubens M. Lopes, Janet Warner Reid, Carlos Eduardo Falavigna Da Rocha (1999). "Copepoda: developments in ecology, biology and systematics: proceedings of the Seventh international conference on Copepoda, held in Curitiba". Hydrobiologia. 453/454. Springer. p. 576.
- Environmental Protection Authority of Western Australia (2007). "Sampling methods and survey considerations for subterranean fauna in Western Australia (Technical Appendix to Guidance Statement No. 54)". p. 32.
- F. Malard, ed. (2002). "Sampling Manual for the Assessment of Regional Groundwater Diversity". p. 74.
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