Nitrobacter

Nitrobacter are gram-negative bacteria and are either rod-shaped, pear-shaped or pleomorphic. Due to the presence of cytochromes c, they are often yellow in cell suspensions. The nitrate oxidizing system on membranes is cytoplasmic. Nitrobacter cells have been shown to recover following extreme carbon dioxide exposure and are non-motile. == Phylogeny ==

16s rRNA sequence analysis phylogenetically places Nitrobacter within the class of Alphaproteobacteria. Pairwise evolutionary distance measurements within the genus are low compared to those found in other genera, and are less than 1%. All known nitrite-oxidizing prokaryotes are restricted to a handful of phylogenetic groups. This includes the genus Nitrospira within the phylum Nitrospirota, and the genus Nitrolancetus from the phylum Chloroflexota (formerly Chloroflexi). Before 2004, nitrite oxidation was believed to only occur within Pseudomonadota; it is likely that further scientific inquiry will expand the list of known nitrite-oxidizing species. The low diversity of species oxidizing nitrite oxidation 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. == Nitrification ==

Nitrification is a crucial component of the nitrogen cycle, especially in the oceans. The production of nitrate () by oxidation of nitrite () is accomplished by nitrification – the process that produces the inorganic nitrogen that meets much of the demand of marine oxygenic, photosynthetic organisms such as phytoplankton, particularly in areas of upwelling. For this reason, nitrification supplies much of the nitrogen that fuels planktonic primary production in the world's oceans. Nitrification is estimated to be the source of half of the nitrate consumed by phytoplankton globally. Phytoplankton are major contributors to oceanic production, and are therefore important for the biological pump which exports carbon and other particulate organic matter from the surface waters of the world's oceans. 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. These two reactions together make up the process of nitrification. The nitrite-oxidation reaction generally proceeds more quickly in ocean waters, and therefore is 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 ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria (such as Nitrobacter) is puzzling to researchers. Complete nitrification, the conversion of ammonia to nitrate in a single step known as comammox, has an energy yield (∆G°′) of NH3, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are NH3, and , respectively. These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate (comammox), 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 species Nitrospira inopinata possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does occur. This discovery raises questions about evolutionary capability of Nitrobacter to conduct only nitrite-oxidation. == Metabolism and growth ==

Members of the genus Nitrobacter use nitrite as a source of electrons (reductant), nitrite as a source of energy, and CO2 as a carbon source. NXR is composed of two subunits, and likely forms an αβ-heterodimer. The enzyme exists within the cell on specialized membranes in the cytoplasm that can be folded into vesicles or tubes. == Ecology and distribution ==

The genus Nitrobacter is widely distributed in both aquatic and terrestrial environments. Since all members in the genus Nitrobacter are obligate aerobes, oxygen along with phosphorus tend to be factors that limit their capability to perform nitrite oxidation. The distribution and differences in nitrification rates across different species of Nitrobacter may be attributed to differences in the plasmids among species, as data presented in Schutt (1990) imply, habitat-specific plasmid DNA was induced by adaptation for some of the lakes that were investigated. A follow-up study performed by Navarro et al. (1995) showed that various Nitrobacter populations carry two large plasmids. In conjunction with Schutts’ (1990) study, Navarro et al. (1995) illustrated genomic features that may play crucial roles in determining the distribution and ecological impact of members of the genus Nitrobacter. Nitrifying bacteria in general tend to be less abundant than their heterotrophic counterparts, as the oxidizing reactions they perform have a low energy yield and most of their energy production goes toward carbon-fixation rather than growth and reproduction. == History ==

In 1890, Ukrainian-Russian microbiologist Sergei Winogradsky isolated the first pure cultures of nitrifying bacteria which are capable of growth in the absence of organic matter and sunlight. The exclusion of organic material by Winogradsky in the preparation of his cultures is recognized as a contributing factor to his success in isolating the microbes (attempts to isolate pure cultures are difficult due to a tendency for heterotrophic organisms to overtake plates with any presence of organic material). In 1891, English chemist Robert Warington proposed a two-stage mechanism for nitrification, mediated by two distinct genera of bacteria. The first stage proposed was the conversion of ammonia to nitrite, and the second the oxidation of nitrite to nitrate. Winogradsky named the bacteria responsible for the oxidation of nitrite to nitrate Nitrobacter in his subsequent study on microbial nitrification in 1892. Winslow et al. proposed the type species Nitrobacter winogradsky in 1917. The species was officially recognized in 1980. == Main Species ==

• Nitrobacter winogradskyi • Nitrobacter hamburgensis • Nitrobacter vulgaris • Nitrobacter alkalicus == See also ==