Investigation of Nitrogen Cycling in Carbonate Caves and Lava Tubes, Carlsbad Caverns National Park and El Malpais National Monument, New Mexico

Microbial communities require nitrogen, phosphorus, and other nutrients to sustain their growth and metabolism. These resources can be difficult to acquire in cave environments, where they occur naturally at low levels. There is limited research on microbial nutrient acquisition and cycling processes within caves. Recent studies of Spider Cave (New Mexico) that utilized 16S rDNA sequencing of microbial communities suggest the presence of ammonia oxidizers and nitrogen fixers. We investigated the potential for these activities in both carbonate and lava caves. Spider and Lechuguilla Caves, both located in Carlsbad Caverns National Park, New Mexico, are carbonate oligotrophic cave environments that receive modest nutrient input from the surface. Lava cave samples were obtained from four caves located within El Malpais National Park, New Mexico. The lava caves of our study are also oligotrophic environments. The presence of bacteria in samples was ascertained by polymerase chain reactions (PCR), using universal primers for the 16S rDNA gene. PCR amplification for the amoA gene (ammonia oxidation) and nifH gene (nitrogen fixation) was done by nested PCR utilizing two sets of primers. While only the lava caves were positive for amoA, both cave types were positive for nifH. Confirmation of the presence of the amoA gene in lava caves indicates bacteria present have the potential to oxidize ammonia, which is one key part of elucidating how nitrogen is cycled within arid-land caves. In addition, both cave environments contain bacterial organisms that have the potential to fix dinitogen.