Nitrospira inopinata

Classification

Domain Bacteria; Phylum Nitrospirota; Class Nitrospira; Order Nitrospirales; Family Nitrospiraceae; Genus Nitrospira

Species

Candidatus Nitrospira inopinata

Figure 1: Major microbial processes involved in nitrogen transformations.

Description and Significance

Nitrospira inopinata was first obtained in 2011 from a microbial biofilm formed on the metal surface of a pipe which was raised from 1,200m deep oil exploration well in Russia. A pure culture of N. inopinata was later obtained in 2017.

Nitrospira inopinata is a bacterium within the phylum Nitrospirota. Nitrospirota is a phylum containing nitrite-oxidizing bacteria that play an important role in nitrification. Nitrification is the oxidation of ammonia via nitrite to nitrate. Ammonia oxidizing bacteria (AOB) convert ammonium (NH4+) to nitrite (NO2-) and nitrite-oxidizing bacteria (NOB) convert nitrite (NO2-) to nitrate (NO3-). N. inopinata is the first complete ammonium oxidating (comammox) bacterium to be discovered, and it has the ability to perform the nitrification process in one step. This involves the complete ammonia (NH4+) oxidation to nitrate (NO3-).

In biological wastewater treatment, nitrification by microbial organisms plays an important role in the removal of excess nitrogen compounds.

Genome Structure

The complete genome sequencing of N. inopinata was first completed in December of 2015, and later published in "Nature." The genome size is 3.3 Mbp, and includes 3,105 genes with a 59.2% GC content.

16S rRNA-based methods cannot be used to distinguish comammox bacteria from nitrite-oxidizing bacteria. Thus, other molecular techniques such as metagenomics and functional gene-based PCR assays are used to detect complete nitrifiers. Comammox bacteria can also be found using direct-geneFISH, and the detection of the amoA gene or AMO protein, which tends to be higher in abundance.

The genus Nitrospira is classified into six sublineages. Due to the presence of ammonia monooxygenase (amo) genes, comammox Nitrospira fit into sublineage two, which is further comprised of clades A and B (Vijayan et al., 2020).

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Ecology

The population stricture and ecological diversity of Nitrospira is closely related to the nitrite oxidation pathway. The utilization of organic compounds such as nitrite and carbon dioxide creates metabolic versatility among species. Other environmental factors such as temperature and water quality can also affect the diversity of species found in ecosystems. For commamox Nitrospira, systems with low or limited substrate input was found to have a higher comammox response (Vijayan et al., 2020). Due to the high ammonia affinity ofN. inopinata, it is suggested that this species prefers oligotrophic, or low nutrient, environments (Li et al., 2022).

N. inopinata and other comammox Nitrospira play a key role in the oxidation of nitrogen compounds in natural and engineered ecosystems. In engineered systems such as waster water treatment plants, comammox Nitrospira are often more abundant than ammonia oxidizers. This may be due to their ability to thrive in low ammonium environments.

Cell Structure & Metabolism

N. inopinata is spiral shaped with the presence of a flagellum. Size of the species ranges from 0.18-0.3 x 0.7-1.6μm (Vijayan et al., 2020).

Comammox bacteria are characterized by slow growth rates but higher growth yields. Biofilm formation is commonly associated within Nitrospira lineages, and these formations tend to increase with stress. Species such as N. inopinata commonly develop microcolonies, or aggregates, in which their growth is visible in the form of densely packed cells. These colonies vary in size but tend to have a diameter between 5-20μm. During starvation or with the presence of other environmental stressors, the cells could return to a plankton state. This interchanging behavior serves as an adaptation which is a beneficial survival mechanism.

N. inopinata displays a mixotrophic lifestyle in which they have the ability to utilize both autotrophic and heterotrophic pathways. This allows them to use both organic and inorganic energy sources. New research shows that N. inopinata and other comammox species could exhibit chemolithoautotrophic growth during complete nitrification (Vijayan et al., 2020).

Literature Cited

Daims, H., Lebedeva, E. V., Pjevac, P., Han, P., Herbold, C., Albertsen, M., ... & Wagner, M. (2015). Complete nitrification by Nitrospira bacteria. Nature, 528(7583), 504-509.

Han, P., Yu, Y., Zhou, L., Tian, Z., Li, Z., Hou, L., ... & Men, Y. (2019). Specific micropollutant biotransformation pattern by the comammox bacterium Nitrospira inopinata. Environmental science & technology, 53(15), 8695-8705.

Koch, H., van Kessel, M. A., & Lücker, S. (2019). Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Applied microbiology and biotechnology, 103, 177-189.

Li, C., He, Z. Y., Hu, H. W., & He, J. Z. (2023). Niche specialization of comammox Nitrospira in terrestrial ecosystems: Oligotrophic or copiotrophic?. Critical Reviews in Environmental Science and Technology, 53(2), 161-176.

Lu, S., Sun, Y., Lu, B., Zheng, D., & Xu, S. (2020). Change of abundance and correlation of Nitrospira inopinata-like comammox and populations in nitrogen cycle during different seasons. Chemosphere, 241, 125098.

U.S. National Library of Medicine. (n.d.). Candidatus nitrospira inopinata - NCBI - NLM. National Center for Biotechnology Information. Retrieved March 20, 2023, from https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/1715989/

Vijayan, A., Vattiringal Jayadradhan, R. K., Pillai, D., Prasannan Geetha, P., Joseph, V., & Isaac Sarojini, B. S. (2021). Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. Journal of Basic Microbiology, 61(2), 88-109.

Wikimedia Foundation. (2022, May 13). Nitrospira inopinata. Wikipedia. Retrieved March 20, 2023, from https://en.wikipedia.org/wiki/Nitrospira_inopinata

Author

Alexis Ludwig; Dr. Hideotoshi Urakawa - Microbial Ecology Spring 2023