In order to better understand the role of various bacteria in nitrogen transformations, the distribution (DNA) and activity (RNA) of different genes were analyzed and compared to geochemical data.

Planctomycetes diversity: A gradient in diversity was found through the suboxic zone based on 16S rDNA sequences. Distributions of anammox and other Planctomycetes bacteria were examined in relation to environmental conditions.

Surface productivity, N & C cycling: Utilizing a three-point time series, changes in the surface community as detected via nitrogenase reductase (nifH) and RuBisCO (rbcL) gene presence and expression were found. The presence of potential nitrogen fixing microbes was confirmed, though variable. On a seasonal basis, this variation appeared acyclical. Diazotrophs common in other basins worldwide were absent in the Black Sea; most sequences detected, including all those expressed, were heterotrophic. Low N-fixation rates were measured, while productivity rates fluctuated. C-fixation activity was detected by underrepresented picophytoplankton and previously documented organisms.

Dark N fixation: The activity of N fixing bacteria in deeper waters was also documented. Sampling in the suboxic zone and slightly deeper sulfidic waters yielded mRNA transcripts of nifH, even though fixed dissolved inorganic N was measured at non-zero levels. Two sequence clusters, I and III, were expressing nifH although the activity appeared variable and potentially related to shifts between S oxidation and reduction. Incubations with suboxic zone waters confirmed a low level of N fixation activity. The suboxic zone is still a net sink of fixed N, though the pathway was not found to be unidirectional.

Heterotrophic denitrification and anammox: While there has been much debate as to the relative contributions of these processes, both of these groups were found active in the Black Sea. However, their distributions appeared fundamentally different, with denitrification activity being much more variable. While some consistency was observed in the lower redoxcline, shallower depths where anammox bacteria were not active showed considerable variability in dissolved N₂ as well as the activity and community structure of denitrifying organisms. This suggests that the role for these organisms in the geochemical cycling of N could be temporally variable. Some correlation with surface productivity is discussed.