Sampling stygofauna is both time consuming and labour intensive. The challenge is to get samples from as many bores as possible within a limited time. The essential assumption for this is that faunal communities inside bores are comparable and representative of the communities outside.To compare relative abundance, taxonomic richness and community composition of the fauna inside groundwater bores to the fauna of the surrounding aquifer, 20 monitoring bores in Palatinate, southwestern Germany, were sampled twice in 1 month. Initially, a sample of 4 l of water was collected from the bottom of each bore. A further sample of 51 l was collected from the groundwater surrounding the bore using a pneumatic piston pump with double packer sampler.Water chemistry inside and outside the bore was similar, but the relative amounts of sediments within the bores were higher compared to those from outside. Relative abundances of fauna inside the bores were higher than in the aquifer, but taxonomic composition was similar with the exception of the proportions of nematodes and amphipods, which were higher inside. As a result, the proportions of cyclopoids were lower inside. Higher nematode proportions are explained partially by the nearly complete extraction of bore sediment. A ''habitat heterogeneity effect'' states that in heterogeneous aquifers with few suitable habitats, faunal distribution is supposed to be extremely patchy. Thus, detritus accumulates in bores, attracting animals and providing ''habitat islands'' in the groundwater. This effect could explain the higher amphipode proportions inside the bores, which were generally more frequently populated than the surrounding groundwater. As a consequence, fauna is thought to be nearly absent from groundwater, where suitable habitats are lacking. In those sparsely populated aquifers, samples representative of the aquifer taxonomic richness and composition can only be collected by removing large volumes of water, or by sampling the bottom of bores. These findings also suggest that the use of unbaited colonisation chambers or traps in the groundwater, which are comparable with bores, would seem to be a promising approach.

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.

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