Nitrogen fixation is the conversion of gaseous dinitrogen to ammonium. Ammonium is readily used by most organisms, but atmospheric dinitrogen is only a source of nitrogen for organisms with the capability for nitrogen fixation.

Nitrogen availability limits the growth of organisms in many environments, including the open ocean. Therefore, nitrogen fixation is an important process that can potentially limit the productivity of the open ocean.

The biological productivity of the oceans is dependent upon the availability of nutrients, such as nitrogen, phosphorus, iron, etc. These nutrients are necessary to support the growth of microalgae and microorganisms that are the basis of marine food chains.

In the case of nitrogen, nitrogen sources are primarily the flux of nitrate from nutrient-rich deep water across the nutricline and thermocline, and the recycling of nitrogen from excretion of waste my microzooplankton, zooplankton and larger animals. A large reservoir of nitrogen is available in the Earth's atmosphere (approximately 80% of the atmosphere), but not all organisms have the capability to fix nitrogen.

Thus far, only prokaryotes (bacteria and archaea) have been demonstrated to fix nitrogen, or possess the genes that encode the enzyme that catalyzes nitrogen fixation (nitrogenase). Despite the fact that reduced nitrogen is found in low concentrations in the open ocean, measured rates of nitrogen fixation are low, and only a few nitrogen fixing organisms have been identified. Unfortunately, it is often difficult to culture organisms from the environment, so it is difficult to determine whether nitrogen fixation is limited by the presence of nitrogen fixing organisms, or other factors that may limit the expression of nitrogen fixation activity (e.g. availability of other nutrients). For this reason, it is important to assess the presence and distribution of nitrogen fixation genes, rather than simply assay the rate of nitrogen fixation.

The presence of nitrogen fixation genes can be determined by amplifying the nitrogenase gene using the polymerase chain reaction (PCR). The polymerase chain reaction makes it possible to determine if nitrogen fixing organisms are present, but more importantly, makes it possible to determine what kinds of nitrogen fixing organisms are present.

The sequence of the amplified fragment of nitrogenase contains taxonomic information, so phylogenetic analysis of cloned amplified nitrogenase genes provides information on taxonomic identity and diversity. Using this technique, we are assessing the presence and abundance of nitrogen fixing organisms in the central Atlantic and Pacific Oceans, by sampling during different seasons at the long-term monitoring sites near Bermuda (Bermuda Atlantic Time Series )and Hawaii (Hawaii Ocean Time Series).