Nitrosarchaeum limnium

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Transmission electron photomicrograph of a typical flagellated (archaellum) Candidatus Nitrosarchaeum limnium cell. Image credit: J. Herrmann, Stanford Univ.

Classification

Archaea; Thaumarchaeota; Nitrososphaeria; Nitrosopumilales; Nitrosopumilaceae

Species

NCBI: [1]

Candidatus Nitrosarchaeum limnium

Description and Significance

Nitrosarchaeum limnium (formerly Nitrosoarchaeum limnia) is a member of the low-salinity ammonia-oxidizing archaea (AOA), first enriched from sediments in north San Francisco Bay estuary, CA, USA (Blainey et al., 2011; Mosier et al., 2012).

As a member of the ammonia-oxidizing archaea (AOA), N. limnium grows using energy obtained from the oxidation of ammonia (NH4+) to nitrite (NO2-), the first step in nitrification. This process is a critical step in the global nitrogen cycle (Francis et al., 2007), as buildup of ammonia in environments can lead to eutrophication and other consequences.

Genome Structure

Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?

Cell Structure, Metabolism and Life Cycle

As with other members of the Nitrospumilales family, N. limnium cells are small rods and have a crystalline S-layer as their exterior (see image here; alsoTolar et al., 2019). N. limnium is also motile via a single archaeal flagellum, or "archaellum"

Similar to most Thaumarchaeota, N. limnium is a chemolithoautotroph. This organism gains carbon by fixing CO₂ via the 3-hydroxypropionate/4-hydroxybutyrate pathway that is modified in thaumarchaea (see Könneke et al., 2014) relative to the pathway described in the crenarchaeote Metallosphaera sedula (Berg et al., 2007). N. limnium uses energy derived from the oxidation of ammonium to fuel this carbon fixation and other metabolic pathways. Ammonia oxidation in the Nitrosopumilales has been shown to be highly sensitive to small concentrations of ammonium in the environment due to an incredibly high substrate affinity (see Martens-Habbena et al., 2009), which is thought to influence their ability to survive in oligotrophic (low-nutrient) environments.

Less is known about specific metabolites produced by N. limnium, though other Thaumarchaeota have been shown to produce ectoine and cobalamin (vitamin B12) that are thought to be important contributions to the overall microbial community (Doxey et al., 2015; Widderich et al., 2016; Heal et al., 2017).

Ecology and Environment

N. limnium was first enriched from the San Francisco Bay estuary, and has been found in numerous low-salinity environments worldwide including rivers, lakes, aquifers, and soils. It is free-living and motile, allowing for response to environmental signals and interactions with other microorganisms within aquatic communities.

In such communities, the ammonia oxidized by N. limnium to nitrite is then available for other microorganisms to take up as a nitrogen source (e.g., phytoplankton) or use in other portions of the nitrogen cycle. This includes nitrite oxidation, which is performed by different guilds of bacteria such as Nitrospira, Nitrospina, Nitrococcus, and Nitrobacter. In systems where anoxic regions border oxic regions (water/sediment interfaces in estuaries, for example), nitrite produced by this organism could also be used as a substrate for anaerobic nitrogen cycle processes including denitrification and anammox.

As ammonia oxidation is the first and rate limiting step of nitrification, it plays an important role in the nitrogen cycle the environment and thus N. limnium is an important contributor to nitrogen biogeochemistry in low-salinity environments.

References

Berg IA, Kockelkorn D, Buckel W, Fuchs G. (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318: 1782-6. https://doi.org/10.1126/science.1149976

Blainey PC, Mosier AC, Potanina A, Francis CA, & Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS One 6: e16626. https://doi.org/10.1371/journal.pone.0016626

Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD (2014) Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J 9: 461-71. https://doi.org/10.1038/ismej.2014.142

Francis C, Beman J, Kuypers M (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1:19–27 https://doi.org/10.1038/ismej.2007.8

Heal KR, Qin W, Ribalet F, Bertagnolli AD, Coyote-Maestas W, Hmelo LR, Moffett JW, Devol AH, Armbrust EV, Stahl DA, Ingalls AE (2017) Two distinct pools of B₁₂ analogs reveal community interdependencies in the ocean. Proc Natl Acad Sci U S A 114: 364-369. https://doi.org10.1073/pnas.1608462114

Mosier AC, Lund MB, & Francis CA (2012) Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Environ Microbiol 64: 955–963. https://doi.org/10.1007/s00248-012-0075-1

Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H. (2019) Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J 13: 2150-2161. https://doi.org/10.1038/s41396-019-0418-8

Tolar BB, Mosier AC, Lund MB, & Francis CA (2019) Nitrosarchaeum (gbm01289). In: Bergey’s Manual of Systematics of Archaea and Bacteria, Ed: WB Whitman, John Wiley & Sons: Hoboken, NJ. https://doi.org/10.1002/9781118960608.gbm01289

Widderich N, Czech L, Elling FJ, Konneke M, Stoveken N, Pittelkow M, et al. (2016) Strangers in the archaeal world: osmostressresponsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol. 18: 1227–48. https://doi.org/10.1111/1462-2920.13156

Author

Page authored by Prof. Bradley Tolar at UNC Wilmington.