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Phylogeny
16s rRNA sequence analysis phylogenetically places Nitrobacter within the class of Alphaproteobacteria. Pairwise evolutionary distance measurements within the genus are low compared to other genera, at less than 1%. Nitrobacter are also closely related to other species within the alpha subdivision, including the photosynthetic Rhodopseudomonas palustris, the root-nodulating Bradyrhizobium japonicum, Blastobacter denitrificans, and the human pathogens Afipia felis, and Afipia clevelandensis.Nitrobacter bacteria are presumed to evolve from photosynthetic ancestors, and there are evidences that the nitrification phenotype evolved separately from photosynthetic bacteria on multiple occasions for individual nitrifying genera and species.

All known nitrite-oxidizing prokaryotes are restricted to a handful of phylogenetic groups. Beyond that, nitrite oxidation is known to occur only in the genus Nitrospira of the phylum Nitrospirae, and the genus Nitrolancetus from the phylum Chloroflexi. Before 2004, nitrite oxidation was believed to only occur within Proteobacteria, it is likely that further scientific inquiry will expand the list of known nitrite oxidizing species even more. The low diversity of species performing nitrite oxidation notably contrasts with other processes associated with the nitrogen cycle in the ocean, such as denitrification and N-fixation, where a diverse range of taxa perform analogous functions. This might change as future research identifies new prokaryotic species.

Nitrification
Nitrification is a crucial component of the nitrogen cycle, especially in the oceans. The oxidation of nitrite (NO2-) into nitrate (NO3-) in nitrification is a crucial step, as photosynthetic organisms such as phytoplankton are only able to take up nitrogen in the form of nitrate. For this reason, nitrification is a source of nitrate for much of the planktonic primary production that occurs in the world's oceans. Nitrification is the source of half of the nitrate consumed by phytoplankton globally. Phytoplankton are major contributors to oceanic production, and are therefore important for the oceanic biological pump. The process of nitrification is crucial for separating recycled production from production leading to export. Biologically metabolized nitrogen returns to the inorganic dissolved nitrogen pool in the form of ammonia. Microbe-mediated nitrification converts that ammonia into nitrate, which can subsequently be taken up by phytoplankton and recycled.

The nitrite oxidation reaction performed by the Nitrobacter is as follows;

2NO2− + H2O → NO3− + 2H+ + 2e−

2H+ + 2e− + ½O2 → H2O

The Gibbs' Free Energy yield for nitrite oxidation is:

ΔGο = -74 kJ mol-1 NO2-

In the oceans, nitrite-oxidizing bacteria such as Nitrobacter are usually found in close proximity to ammonia-oxidizing bacteria. These two reactions together make up the process of nitrification. The nitrite-oxidation reaction generally proceeds more quickly in ocean waters, and it is therefore not a rate-limiting step in nitrification. For this reason, it is rare for nitrite to accumulate in ocean waters.

The two-step conversion of ammonia to nitrate observed in bacteria species such as Nitrobacter is puzzling to researchers. Complete nitrification, the conversion of ammonia to nitrate in a single step, has an energy yield (∆G°′) of −349 kJ mol−1 NH3, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are −275 kJ mol−1 NH3, and −74 kJ mol−1 NO2−, respectively. These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate, rather than conduct only one of the two steps. The evolutionary motivation for a decoupled, two-step nitrification reaction is an area of ongoing research. In 2015, it was discovered that the genus Nitrospira possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does in fact occur. This discovery raises questions about evolutionary capability of Nitrobacter to conduct only nitrite-oxidation.

Metabolism and Growth
Nitrobacter oxidize nitrite as a source of energy and reductant, and use CO2 as a carbon source. Nitrite is not a particularly favourable substrate from which to gain energy. Thermodynamically, the nitrite oxidation reaction gives a yield (∆G°′) of only -74  kJ mol−1 NO2−. As a result, Nitrobacter has developed a highly specialized metabolism to derive energy from the oxidation of nitrite.

The enzyme responsible for the oxidation of nitrite to nitrate in Nitrobacter is Nitrite oxidoreductase (NXR), which is encoded by the gene nxrA. NXR is composed of two subunits, and likely forms an αβ-heterodimer. The enzyme exists within the cell on specialized membranes in the cytoplasm which can be folded into vesicles or tubes. The α-subunit is thought to be the location of nitrite oxidation, and the β-subunit is an electron channel from the membrane. The direction of the reaction catalyzed by NXR can be reversed depending on oxygen concentrations. The region of the nxrA gene which encodes for the β-subunit of the NXR enzyme is similar in sequence to the iron-sulfur centers of bacterial ferredoxins, and to the β-subunit of the enzyme nitrate reductase, found in Escherichia coli.