Public health concerns about pathogens present in animal manure are emerging constraints to water supplies in many areas of the world. The objective of this study was to examine the microbial community composition in aquifer material impacted by contaminants from different sources. Total microbial community profiles were compared by using eubacterial primers to amplify 16S rRNA genes from total bacterial DNA and RNA. PCR and reverse transcriptase (RT) PCR were used to amplify 16S ribosomal RNA,

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... and the products were subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis of RT-PCR products detected a subset of bands visible in the DNA-based analysis, indicating that some dominantly detected bacterial populations did not have high levels of metabolic activity. The sequences detected by the RT-PCR approach were, however, derived from a wide taxonomic range, suggesting that the activity in the aquifer sand material was not determined at broad taxonomic levels but rather was a strain-or species-specific phenomenon. Comparative analysis of DGGE profiles grouped all DNA-derived aquifer samples together in a cluster. At the end of the experimental period, the aquifer material entered a stable population state, which was characterized by a greater diversity of DNA-based fingerprints compared to viable bacteria. Our data showed that the active members of the community are a sub-population of that community that performs certain biological functions during water filtration through aquifer material. Therefore, recharging surface water through aquifer sand material may produce a microbial population quite different from the input source due to the availability of nutrients for bacterial growth.