"The Ischia hydrothermal system was analysed through hydrogeological and microbial community investigations. Mesophilic communities were detected in two cold springs, suggesting a negligible influence of thermal circuits in freshwater sub-systems which are mainly or only fed by local precipitations. Thermophilic and extremely thermophilic bacteria were detected in two wells, according to higher water temperatures (61 and 85 degrees C), even if the two communities show significant differences. In one well, thermophilic and extremely thermophilic bacteria are associated with strains belonging to epsilon-Proteobacteria isolated in different sulphur-rich carbonate environments. This association suggests a greater influence on ascending hot fluids that interact with the carbonate basement of volcanic rocks. In the other well, thermophilic and extremely thermophilic bacteria are associated with strains isolated in cold hypersaline environments or in aquatic habitats where terrestrial and marine components are coupled. This association supports the fact that seawater intrusion can affect this part of Ischia, according to results of hydrogeological and geochemical surveys. Differences in groundwater temperature and bacterial communities are probably mainly due to differences in permeability between volcanic rocks and differences in hydrogeologic behaviour between faults in the upper carbonate basement, above the deep magma chamber, that influence relationships between ascending hot fluids and local recharge. This study contributes to discussion of the reliability of the actual behaviour models of the Ischia system, based on the results of geochemical and isotopic investigations, and, in a wider context, it shows that microbial community investigations may be a valuable supplementary tool for analysing hydrothermal system behaviour."