Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

By K. D. Kits, C. Sedlacek, E. V. Lebedeva, P. Han, Alexandr Bulaev, Petra Pjevac, Anne Daebeler, S. Romano, Mads Albertsen, L. Stein and 2 more. Nature, 2017

742 citations recorded by the source corpus.

Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2−) to nitrate (NO3−), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.

Subfields: Ecology, Health, Toxicology and Mutagenesis, Pollution

View Paper: https://www.semanticscholar.org/paper/c94cd5cdfef1811b10178fc0e083f7b183db9a28

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In Ecology

1. B. Kartal
2. H. Marchant
3. Q. Shen
4. M. Kuypers
5. Wu Xiong

In Health, Toxicology and Mutagenesis

1. M. Kuypers
2. H. Marchant
3. B. Kartal

In Pollution

1. M. Kuypers
2. H. Marchant
3. B. Kartal

Citations in the corpus

• The microbial nitrogen-cycling network (2018, background): “Recently, however, it was shown that the terrestrial bacterium Nitrospira inopinata , which performs the comammox process, has a higher ammonia affinity than all cultured terrestrial ammonia-oxidizing archaea 39 .”
• Specialized metabolic functions of keystone taxa sustain soil microbiome stability (2021, background): “Nitrospira are ammonia- and nitriteoxidizing bacteria [81, 82], whereas Rhizobacter, Mesorhizobium, and Burkholderia comprise nitrogenfixers [83, 84].”