Ammonia oxidation (amoA) and nitrogen fixation (nifH) genes along metasandstone and limestone caves of Brazil

Many cave-dwelling microorganisms have been studied, but little is known about whether genes related to the nitrogen cycle are present in this environment, particularly in sandstone caves. The profiles of nitrogen fixation (nifH) and archaeal and bacterial ammonia oxidation (amoA) genes were analyzed along a cave of metasandstone and limestone lithologies. Using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis and quantitative PCR to evaluate these genes, we analyzed the variations in the microorganisms and frequency of these genes along the caves. In both caves analyzed for nifH, different community profiles were observed, particularly in entrance samples. Quantitative PCR of the genes showed that samples from the entrance of the caves contained a larger number of copies of amoA. In addition, archaeal amoA was predominant compared to bacterial amoA. The present study demonstrated that the genes for nitrogen fixation and ammonia oxidation are present in both cave lithologies and that their frequency and the organisms present along the caves vary with factors such as the characteristics of the cave itself.