Nitrification and denitrification: Probing the nitrogen cycle in aquatic environments

Methods designed to detect microorganisms involved in the biogeochemistry of nitrogen in the marine environment are rapidly being developed and deployed in ecological investigations. Probes based on phylogenetic sequences (usually rRNA) and those based on the sequences of functional genes or proteins have both been demonstrated in the nitrogen cycle. The most progress has been made for ammonia oxidizers; several sets of PCR primers have been described and their specificity may be optimized to allow detection of genetically and ecologically meaningful groups. For denitrifying bacteria, functional probes based on nitrite reductase show most promise. These approaches should complement the more familiar, but no less sophisticated, methods that focus on quantification of in situ transformation rates. Both approaches in combination will be useful in understanding regulation and environmental control of biogeochemical processes.