Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

ABSTRACTAmmonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in thein situquantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ15NNO2−and δ18ONO2−, respectively) are geochemical tracers for evaluating the sources and thein siturate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilicThaumarchaeotapopulations composed almost entirely of “CandidatusNitrosocaldus.” The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ18O value of nitrite produced from ammonia oxidation varied with the δ18O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilicThaumarchaeotacould be estimated using δ18ONO2−in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments.IMPORTANCEBecause ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilicThaumarchaeotaand elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation.

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Determining high precision, in situ, oxygen isotope ratios with a SHRIMP II: Analyses of MPI-DING silicate-glass reference materials and zircon from contrasting granites

Chemical Geology ◽

10.1016/j.chemgeo.2008.08.024 ◽

2008 ◽

Vol 257 (1-2) ◽

pp. 114-128 ◽

Cited By ~ 178

Author(s):

R.B. Ickert ◽

J. Hiess ◽

I.S. Williams ◽

P. Holden ◽

T.R. Ireland ◽

...

Keyword(s):

Oxygen Isotope ◽

Silicate Glass ◽

High Precision ◽

Reference Materials ◽

Isotope Ratios ◽

Oxygen Isotope Ratios

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Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

Applied and Environmental Microbiology ◽

10.1128/aem.02028-13 ◽

2013 ◽

Vol 79 (22) ◽

pp. 6911-6916 ◽

Cited By ~ 28

Author(s):

Tatsunori Nakagawa ◽

David A. Stahl

Keyword(s):

Ammonia Oxidation ◽

Physiological State ◽

Transcriptional Response ◽

Ammonia Oxidizer ◽

Mrna Levels ◽

Marine Microorganisms ◽

Transcript Levels ◽

Content Type ◽

Ammonia Oxidizing Archaea ◽

Ammonia Transport

ABSTRACTThe ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeonNitrosopumilus maritimusSCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above theKmfor ammonia oxidation (∼500 μM) and the other well below theKm(<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.

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Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea

Science ◽

10.1126/science.1208239 ◽

2011 ◽

Vol 333 (6047) ◽

pp. 1282-1285 ◽

Cited By ~ 276

Author(s):

Alyson E. Santoro ◽

Carolyn Buchwald ◽

Matthew R. McIlvin ◽

Karen L. Casciotti

Keyword(s):

Ammonia Oxidation ◽

Stratospheric Ozone ◽

Isotopic Signature ◽

Primary Sources ◽

Ammonia Oxidizing Bacteria ◽

Isotopic Signatures ◽

Ozone Destruction ◽

Ammonia Oxidizing Archaea ◽

Isotope Measurements ◽

Archaeal Ammonia Oxidation

The ocean is an important global source of nitrous oxide (N2O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N2O, but the isotopic signatures of N2O produced by these processes are not consistent with the marine contribution to the global N2O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N2O. Natural-abundance stable isotope measurements indicate that the produced N2O had bulk δ15N and δ18O values higher than observed for ammonia-oxidizing bacteria but similar to the δ15N and δ18O values attributed to the oceanic N2O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N2O source.

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In situ Measurement of Oxygen Isotope Ratios by Laser Ablation Mass Spectrometry — an Example from the Torre Alfina Volcano, Central Italy

Mineralogical Magazine ◽

10.1180/minmag.1998.62a.1.63 ◽

1998 ◽

Vol 62A (1) ◽

pp. 120-121

Author(s):

P. Barnekow

Keyword(s):

Mass Spectrometry ◽

Laser Ablation ◽

Oxygen Isotope ◽

Central Italy ◽

Isotope Ratios ◽

In Situ Measurement ◽

Oxygen Isotope Ratios

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Nitrogen and oxygen isotopic constraints on the origin of atmospheric nitrate in coastal Antarctica

Atmospheric Chemistry and Physics ◽

10.5194/acp-7-1925-2007 ◽

2007 ◽

Vol 7 (8) ◽

pp. 1925-1945 ◽

Cited By ~ 144

Author(s):

J. Savarino ◽

J. Kaiser ◽

S. Morin ◽

D. M. Sigman ◽

M. H. Thiemens

Keyword(s):

Isotopic Composition ◽

Oxygen Isotope ◽

Transition Period ◽

Isotope Effects ◽

Isotope Ratios ◽

Background Concentration ◽

Night Time ◽

Oxygen Isotope Ratios ◽

Period 2 ◽

Oxygen Isotopic

Abstract. Throughout the year 2001, aerosol samples were collected continuously for 10 to 15 days at the French Antarctic Station Dumont d'Urville (DDU) (66°40' S, l40°0' E, 40 m above mean sea level). The nitrogen and oxygen isotopic ratios of particulate nitrate at DDU exhibit seasonal variations that are among the most extreme observed for nitrate on Earth. In association with concentration measurements, the isotope ratios delineate four distinct periods, broadly consistent with previous studies on Antarctic coastal areas. During austral autumn and early winter (March to mid-July), nitrate concentrations attain a minimum between 10 and 30 ng m−3 (referred to as Period 2). Two local maxima in August (55 ng m−3) and November/December (165 ng m−3) are used to assign Period 3 (mid-July to September) and Period 4 (October to December). Period 1 (January to March) is a transition period between the maximum concentration of Period 4 and the background concentration of Period 2. These seasonal changes are reflected in changes of the nitrogen and oxygen isotope ratios. During Period 2, which is characterized by background concentrations, the isotope ratios are in the range of previous measurements at mid-latitudes: δ18Ovsmow=(77.2±8.6)‰; Δ17O=(29.8±4.4)‰; δ15Nair=(−4.4±5.4)‰ (mean ± one standard deviation). Period 3 is accompanied by a significant increase of the oxygen isotope ratios and a small increase of the nitrogen isotope ratio to δ18Ovsmow=(98.8±13.9)‰; Δ17O=(38.8±4.7)‰ and δ15Nair=(4.3±8.20‰). Period 4 is characterized by a minimum 15N/14N ratio, only matched by one prior study of Antarctic aerosols, and oxygen isotope ratios similar to Period 2: δ18Ovsmow=(77.2±7.7)‰; Δ17O=(31.1±3.2)‰; δ15Nair=(−32.7±8.4)‰. Finally, during Period 1, isotope ratios reach minimum values for oxygen and intermediate values for nitrogen: δ18Ovsmow=63.2±2.5‰; Δ17O=24.0±1.1‰; δ15Nair=−17.9±4.0‰). Based on the measured isotopic composition, known atmospheric transport patterns and the current understanding of kinetics and isotope effects of relevant atmospheric chemical processes, we suggest that elevated tropospheric nitrate levels during Period 3 are most likely the result of nitrate sedimentation from polar stratospheric clouds (PSCs), whereas elevated nitrate levels during Period 4 are likely to result from snow re-emission of nitrogen oxide species. We are unable to attribute the source of the nitrate during periods 1 and 2 to local production or long-range transport, but note that the oxygen isotopic composition is in agreement with day and night time nitrate chemistry driven by the diurnal solar cycle. A precise quantification is difficult, due to our insufficient knowledge of isotope fractionation during the reactions leading to nitrate formation, among other reasons.

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Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

Applied and Environmental Microbiology ◽

10.1128/aem.00432-12 ◽

2012 ◽

Vol 78 (16) ◽

pp. 5773-5780 ◽

Cited By ~ 113

Author(s):

Elizabeth French ◽

Jessica A. Kozlowski ◽

Maitreyee Mukherjee ◽

George Bullerjahn ◽

Annette Bollmann

Keyword(s):

Growth Rates ◽

Ammonia Oxidation ◽

Light Exposure ◽

Enrichment Culture ◽

Ammonia Oxidizing Bacteria ◽

Content Type ◽

Ammonia Oxidizing Archaea ◽

Group I ◽

Nitrosomonas Oligotropha

ABSTRACTAerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “CandidatusNitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from theNitrosomonas oligotrophagroup (Nitrosomonascluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

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

10.1101/527234 ◽

2019 ◽

Cited By ~ 1

Author(s):

Florian U. Moeller ◽

Nicole S. Webster ◽

Craig W. Herbold ◽

Faris Behnam ◽

Daryl Domman ◽

...

Keyword(s):

Ammonia Oxidation ◽

Indirect Evidence ◽

Marine Sponges ◽

Ammonia Oxidizer ◽

Filter Feeding ◽

Ammonia Oxidizing Archaea ◽

Branched Chain Amino Acid ◽

Direct Demonstration ◽

Branched Chain

SummaryMarine sponges represent one of the few eukaryotic groups that frequently harbor symbiotic members of theThaumarchaeota, 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 spongeIanthella bastausing metaproteogenomics, fluorescencein situhybridization, qPCR and isotope-based functional assays. “CandidatusNitrosospongia bastadiensis” is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia inI. bastathat surprisingly does not harbor 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.Originality-Significance StatementMany marine sponges harbor symbiotic members of theThaumarchaeota, but there is generally only indirect evidence available about their functional role within these filter-feeding animals. Furthermore, the specific adaptations of thaumarchaeal symbionts to their sponge hosts are incompletely understood. In this study, we thoroughly characterized a thaumarchaeal symbiont residing in the reef spongeIanthella bastaand demonstrate by using a combination of molecular tools and isotope techniques, that it is the only ammonia-oxidizer in its host. In contrast to other sponges,I. bastadoes not contain nitrite-oxidizing microbes and thus excretes considerable amounts of nitrite. Furthermore, using metagenomics and metaproteomics we reveal important adaptations of this symbiont, that represents a new genus within theThaumarchaeota, and conclude that it most likely lives as a mixotroph in its sponge host.

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Initial Results with a UV Laser Based Microanalytical Preparation Technique for in-situ Determination of Oxygen Isotope Ratios of Silicates and Oxides

Mineralogical Magazine ◽

10.1180/minmag.1994.58a.2.241 ◽

1994 ◽

Vol 58A (2) ◽

pp. 973-974 ◽

Cited By ~ 1

Author(s):

U. Wiechert

Keyword(s):

Oxygen Isotope ◽

Isotope Ratios ◽

Preparation Technique ◽

Uv Laser ◽

Oxygen Isotope Ratios ◽

Initial Results

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Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

Applied and Environmental Microbiology ◽

10.1128/aem.02577-13 ◽

2013 ◽

Vol 80 (2) ◽

pp. 653-661 ◽

Cited By ~ 22

Author(s):

Trinity L. Hamilton ◽

Evangeline Koonce ◽

Alta Howells ◽

Jeff R. Havig ◽

Talia Jewell ◽

...

Keyword(s):

Nitrogen Fixation ◽

Acetylene Reduction ◽

Ammonia Oxidation ◽

Hot Spring ◽

Transcript Levels ◽

Content Type ◽

Geothermal Springs ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

N Pool

ABSTRACTSource waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “CandidatusNitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacteriumThermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increasedamoAtranscript levels while it suppressed rates of acetylene reduction and decreasednifHtranscript levels. Sequencing of amplifiednifHandamoAtranscripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2fixation are closely affiliated withCa. Nitrosocaldus yellowstonii andT. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such asCa. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of nitrogen fixation in geothermal communities. These observations help to explain the strong pattern in the codistribution of ammonia-oxidizing archaea and diazotrophs in circumneutral-to-alkaline geothermal springs.

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