Complete nitrification by Nitrospira bacteria

By H. Daims, E. Lebedeva, Petra Pjevac, P. Han, C. Herbold, Mads Albertsen, N. Jehmlich, M. Palatinszky, J. Vierheilig, Alexandr Bulaev and 6 more. Nature, 2015

2,323 citations recorded by the source corpus.

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

Subfields: Ecology, Environmental Engineering, Pollution

View Paper: https://www.semanticscholar.org/paper/5b17c86a0a5cbd643ed0f5d18259ad8d853000ae

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In Ecology

1. J. Damashek
2. C. A. Francis
3. B. Kartal
4. H. Marchant
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Citations in the corpus

• Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle (2017, neutral): “As previously reported, four years of enrichment yielded a culture containing the comammox organism Nitrospira inopinata (~60% of the community) and a betaproteobacterium (~40%)1.”
• Microbial Nitrogen Cycling in Estuaries: From Genes to Ecosystem Processes (2018, background): “Recently, some Nitrospira bacteria were shown to completely oxidize ammonia to nitrate in one step, a completely novel “comammox” (complete ammonia oxidation) metabolism (Daims et al. 2015; van Kessel et al. 2015).”
• The microbial nitrogen-cycling network (2018, background): “1; reaction 7), nitric oxide dismutation 61 to dinitrogen gas and oxygen(9) (9), hydrazine synthesis(10) (12), and hydrazine oxidation to 62 dinitrogen gas(10) (13).”
• Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea (2016, neutral): “Although recent evidence reveals the capacity for some Nitrospira to perform complete nitrification (Daims et al., 2015), aerobic chemoautotrophic nitrification has historically been considered a two-step process whereby ammonia-oxidizing bacteria (‘AOB’ from b- and Y- classes of Proteobacteria)…”
• Nitrification gene ratio and free ammonia explain nitrite and nitrous oxide production in urea-amended soils (2017, background): “…populations resulted in a tighter coupling of the two steps of nitrification, due in large part to both processes being carried out by the same organism (Daims et al., 2015; van Kessel et al., 2015), although direct evidence of comammox occurring in agricultural soil has not been reported.”
• Mainstream partial nitritation–anammox in municipal wastewater treatment: status, bottlenecks, and further studies (2017, background): “Recently, Holger et al. (2015) and Van Kessel et al. (2015) reported the existence of Bcomplete ammonia oxidizer (comammox),^ a specific species of Nitrospira, which can perform both nitritation and nitratation.”