Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

  title={Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria},
  author={Willm Martens-Habbena and Paul M. Berube and Hidetoshi Urakawa and Jos{\'e} R. de la Torr{\'e} and David A. Stahl},
The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon ‘Candidatus Nitrosopumilus maritimus’ strain SCM1… 
Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.
Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle
A pure culture of a comammox bacterium is isolated and it is shown 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.
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often
Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments
The results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments, and data suggest that despite the alkaline conditions within the cave, the low NH3 concentrations measured continue to favor growth of AOA over AOB populations.
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 is reported, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria.
Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea
This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment.
Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria
The experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments, and that archaeal cells became the dominant prokaryotes after biweekly transfers for 20 months.
Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea
This minireview provides a synopsis of the current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide.
Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds
Physiological diversity within AOA species and between different AOA genera is demonstrated and different preferences for organic compounds potentially influence the favoured localisation of ammonia oxidisers within the soil and the structure of ammonia-oxidising communities in terrestrial ecosystems.


Isolation of an autotrophic ammonia-oxidizing marine archaeon
The isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite—the first observation of nitrification in the Archaea is reported, suggesting that nitrifying marine Cren archaeota may be important to global carbon and nitrogen cycles.
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.
Using PCR primers designed to specifically target archaeal amoA, AOA is found to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments.
A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring
The enriched AOA, which is provisionally classified as “Candidatus Nitrososphaera gargensis,” is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level.
Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment.
Current evidence for the relative importance of bacteria and archaea in the global nitrogen cycle is reviewed, based on metagenomic analysis and molecular techniques for estimation of gene and gene transcript abundance, changes in ammonia oxidizer community structure during active nitrification and phylogeny of natural communities.
Kinetic studies on ammonia and methane oxidation by Nitrosococcus oceanus
  • B. B. Ward
  • Chemistry, Biology
    Archives of Microbiology
  • 2004
The kinetics of ammonia oxidation and the ability of a marine ammonia-oxidizing bacterium, Nitrosococcus oceanus, to metabolize methane were investigated in semicontinuous batch culture and inhibitors and coreactants were determined in order to elucidate the behavior of the ammonia oxygenase enzyme in N. oceanus.
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.
The cultivation of a thermophilic nitrifier ('Candidatus Nitrosocaldus yellowstonii'), an autotrophic crenarchaeote growing up to 74 degrees C by aerobic ammonia oxidation, providing the first direct evidence for its synthesis by a thermophile.
Archaea predominate among ammonia-oxidizing prokaryotes in soils
It is shown that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts, and crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.
Archaeal nitrification in the ocean
Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoB, suggesting a major role for Archaea in oceanic nitrification.
Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre.
The data suggest that amoA-containing Crenarchaea are more phylogenetically diverse than previously reported and distributional patterns of planktonic Cren archaeal and Nitrospina species suggest potential metabolic interactions between these groups in the ocean's water column.
Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures
The oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter winogradskyi serotype agilis were determined with cells grown in mixed culture in chemostats at different growth rates and oxygen tensions to observe differences in specific affinities for oxygen.