Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Kits, K. Dimitri; Jung, Man‐Young; Vierheilig, Julia; Pjevac, Petra; Sedlacek, Christopher J.; Liu, Shurong; Herbold, Craig W.; Stein, Lisa Y.; Richter, Andreas; Wissel, Holger; Brüggemann, Nicolas; Wagner, Michael; Daims, Holger

doi:10.1038/s41467-019-09790-x

Cited by 141 publications

(118 citation statements)

References 68 publications

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“…PTIO inhibition is similar to that in AOA, suggesting similar tight regulation of NO production, although a NO reductase has yet to be identified (Kits et al, 2019). PTIO inhibition is similar to that in AOA, suggesting similar tight regulation of NO production, although a NO reductase has yet to be identified (Kits et al, 2019).…”

Section: Hydroxylamine Oxidationmentioning

confidence: 77%

“…This reaction generates only three electrons and NO may then be converted abiotically to NO − 2 . Although this may fulfill this role in some AOB, nycA homologues are not present in all AOB genomes or in comammox bacteria (Kits et al, 2019). Caranto, Vilbert, and Lancaster (2016) suggested that under aerobic conditions, NO could be rapidly oxidized to NO − 2 by NO − 2 reductase, encoded by nirK, as this enzyme can act reversibly.…”

Section: Hydroxylamine Oxidationmentioning

confidence: 99%

“…An alternative explanation is redox balancing, in which electrons generated by hydroxylamine dehydrogenase are shuttled to denitrification enzymes when they exceed the capacity of terminal oxidases (Hink, Lycus, et al, 2017). Comammox bacteria and AOA lack homologues of AOB NO reductase, suggesting low yields of N 2 O, and abiotic production with a yield of 0.07% has been reported in N. inopinata (Kits et al, 2019). This is consistent with the assumption that N 2 O is produced only from abiotic reactions of intermediate compounds (Kozlowski, Stieglmeier, et al, 2016), although enzymatic production has been reported in N. oleophilus .…”

Section: Dis Tin C Tion Of Archae Al and Bac Terial N 2 O Produc Tionmentioning

confidence: 99%

“…PTIO inhibits N. inopinata and N. maritimus Kits et al, 2019) and is therefore not specific for AOA activity, and both PTIO and 1-octyne can inhibit both AOA and AOB at sufficiently high concentrations (Shen et al, 2013;Taylor et al, 2013). Care must be taken in interpreting results, inhibitor specificity may require more rigorous testing and additional inhibitors may be required to differentiate comammox bacteria.…”

Section: Terre S Trial Ecosys Temsmentioning

confidence: 99%

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Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Prosser

Hink

Gubry‐Rangin

et al. 2019

Global Change Biology

254

157

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Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N 2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle.Direct N 2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N 2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N 2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N 2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N 2 O emissions.

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Section: Hydroxylamine Oxidationmentioning

confidence: 77%

Section: Hydroxylamine Oxidationmentioning

confidence: 99%

Section: Dis Tin C Tion Of Archae Al and Bac Terial N 2 O Produc Tionmentioning

confidence: 99%

Section: Terre S Trial Ecosys Temsmentioning

confidence: 99%

See 2 more Smart Citations

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Prosser

Hink

Gubry‐Rangin

et al. 2019

Global Change Biology

254

157

View full text Add to dashboard Cite

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“…To our knowledge, PTIO has not previously been used in sponge microbiome research (but is commonly applied to eukaryotic tissues including sponges; Müller et al, 2006;Ueda et al, 2016) and further optimization of the concentration is recommended for future applications in these animals. Study design of such experiments should also take into consideration that PTIO has been shown to be cytotoxic for some microbes (Kits et al, 2019). In 29 of the 33 sponge incubations (incubations with added PTIO or inhibited by addition of 100 μM NH 4 + were excluded) ( Fig.…”

Section: Mixotrophy Of Thaumarchaeotamentioning

confidence: 99%

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

Moeller

Webster

Herbold

et al. 2019

Environmental Microbiology

Self Cite

135

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Summary Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia‐oxidizers in many environments. However, in most studies, direct demonstration of ammonia‐oxidation by these archaea within sponges is lacking, and little is known about sponge‐specific adaptations of ammonia‐oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope‐based functional assays. ‘Candidatus Nitrosospongia ianthellae’ is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite‐oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin‐like proteases, a metalloprotease unique among archaea, as well as a putative branched‐chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge‐associated, but not in free‐living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic‐like proteins, and a DNA‐phosporothioation system, represent important adaptations of AOA to life within these ancient filter‐feeding animals.

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Expanding perspectives of soil nitrification to include ammonia‐oxidizing archaea and comammox bacteria

Lü

Taylor

Myrold

et al. 2020

Soil Science Soc of Amer J

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Catalyzed by multiple groups of phylogenetically distinct microorganisms, soil nitrification impacts ground water quality, greenhouse gas emissions, and agricultural practices. This review explores known microbial players involved in nitrification, encompassing aspects of biogeography, phylogenetic diversity, physiology, and activity. We discuss distributions and activities of ammonia-oxidizing archaea and bacteria as they relate to environmental and edaphic factors and highlight a newly discovered role for terrestrial comammox bacteria. Ecological interactions of ammonia oxidizers and nitrite oxidizers are discussed, as are their respective contributions to N 2 O emissions.Given these expanding perspectives of soil nitrification, we underline the importance of combining culture-based methods with metagenomic approaches to help address remaining knowledge gaps.Abbreviations: AOA, NH 3 -oxidizing archaea; AOB, NH 3 -oxidizing bacteria; NOB, NO 2 − -oxidizing bacteria.This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Cited by 141 publications

References 68 publications

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

Expanding perspectives of soil nitrification to include ammonia‐oxidizing archaea and comammox bacteria

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