User:Spflueger/sandbox

Original -- "Nitrospira" Nitrospira is a genus of bacteria in the phylum Nitrospirae. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. The second member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow heating system. The bacterium was named Nitrospira moscoviensis and is a gram-negative nitrite-oxidising organism with a helical to vibroid morphology 0.9–2.2 × 0.2–0.4 micrometres in size. Members of Nitrospira with the capabilities to perform complete nitrification (Comammox bacteria) has also been discovered.

Genome
Researchers discovered Nitropsira members with genes encoding ammonia monooxygenase (Amo) and hydroxlyamine dehydrogenase (hao), enzymes that ammonia-oxidizing bacteria (AOB), use to convert ammonia into nitrite. The bacteria possess all necessary sub-units for both enzymes and the necessary cell membrane associated proteins and transporters to carry out the first step of nitrification. Current findings indicate that the Amo gene is phylogenetically distinct from the Amo gene present in other AOB, meaning that they acquired them long ago, likely by horizontal gene transfer. Origins of the hao gene are more debatable as one study found that it is similar to other AOB, while another found the hao gene to be genetically distinct from other lineages.

Nitrospira also carry the gene encoding for all the sub-units of nitrite oxidoreductase (nxr), the enzyme that catalyzes the second step of nitrification.

N. moscoviensis, Nitrospira lenta, and newly described Nitropsira species 1 and N. species 2 encode for urease too.

Implications of Complete Nitrification
Since nitrifying bacteria were discovered it was accepted that nitrification occurred in two steps, although it would be energetically favourable for one organism to do both steps. The discovery of Commamox organisms within Nitrospira redefine the way bacteria contribute to the Nitrogen cycle and thus there will be a lot of future studies dedicated to it.

In addition, a new feeding type involving microbial cooperation, coined reciprocal feeding, has emerged. A Nitrospira species capable of using urea or cyanate for energy produces ammonia which an ammonia-oxidizing bacteria such as Nitrosomonas uses, producing nitrite which Nitrospira then converts into nitrate.

Assignment 5--Final Edit
Nitrospira is a genus of bacteria in the phylum Nitrospirae. The first member of this genus was described in 1986 by Watson el al., isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. The second member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow heating system. The bacteria was named Nitrospira moscoviensis and is a gram-negative organism with a helical to vibroid morphology 0.9-2.2 x 0.2-0.4 micrometers in size. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. In addition, Nitrospira bacteria's 16s rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed.

Nitrification
All members of this genus have the nitrite oxidoreductase genes, and thus are all thought to be nitrite-oxidizers. Ever since nitrifying bacteria were discovered it was accepted that nitrification occurred in two steps, although it would be energetically favourable for one organism to do both steps. Recently some Nitrospira members with the abilities to perform complete nitrification (Commamox bacteria) have also been discovered. The discovery of Commamox organisms within Nitrospira redefine the way bacteria contribute to the Nitrogen cycle and thus a lot of future studies will be dedicated to it.

With these new findings there's now a possibility to mainly use complete nitrification instead of partial nitrification in engineered systems like wastewater treatment plants because complete nitrification results in lower emissions of the greenhouse gases: nitrous oxide and nitric oxide, into the atmosphere.

Genome
After sequencing and analyzing the DNA of Nitrospira members researchers discovered both species had genes encoding ammonia monooxygenase (Amo) and hydroxlyamine dehydrogenase (hao), enzymes that ammonia-oxidizing bacteria (AOB), use to convert ammonia into nitrite. The bacteria possess all necessary sub-units for both enzymes as well as the necessary cell membrane associated proteins and transporters to carry out the first step of nitrification. Origins of the Amo gene are debatable as one study found that it is similar to other AOB, while another study found the Amo gene to be genetically distinct from other lineages. Current findings indicate that the hao gene is phylogenetically distinct from the hao gene present in other AOB, meaning that they acquired them long ago, likely by horizontal gene transfer. Nitrospira also carry the genes encoding for all the sub-units of nitrite oxidoreductase (nxr), the enzyme that catalyzes the second step of nitrification.