An important aspect of all aquatic subterranean ecosystems is the nature and connectivity of surface inputs. A theme common to both is heterogeneity of inputs that exist at even the smallest scale. At least in cave streams, carbon appears to be limiting. Studies at the scale of entire caves are of two very different kinds. For caves with surface inputs, inputs from percolation water are quantitatively less important than inputs from sinking streams, but are qualitatively more important because they occur throughout the cave and form the basis for the biofilm. Sulfur-oxidizing bacteria are the trophic base for most chemoautotrophic cave communities. Only two ecosystem studies of an entire karst basin have been carried out. For the Dorvan basin in France, most carbon entering the ecosystem is DOC, and there is considerable storage of organic carbon in sediments. In the Edwards Aquifer of Texas, chemolithoautotrophy contributes to all the components.
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