Ammonium in thermal waters of Yellowstone National Park: Processes affecting speciation and isotope fractionation

Ammonia 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 the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (␦ 15 N NO2؊ and ␦ 18 O NO2؊ , respectively) are geochemical tracers for evaluating the sources and the in situ rate 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 thermophilic Thaumarchaeota populations composed almost entirely of "Candidatus Nitrosocaldus." The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The ␦ 18 O value of nitrite produced from ammonia oxidation varied with the ␦ 18 O 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 thermophilic Thaumarchaeota could be estimated using ␦ 18 O NO2؊ 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 thermophilic Thaumarchaeota and 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.

Section: Discussionmentioning

confidence: 99%

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

Nishizawa

Sakai

Konno

et al. 2016

“…Dissolved nitrate (NO 3 Ϫ ), nitrite (NO 2 Ϫ ), and total ammonia [NH 4 (T)] were determined with AccuVac ampoules for nitrate or nitrite and an AmVer ammonia reagent set for total ammonia (Hach Company). NH 4 (T) refers to the sum of the dissolved species of aqueous NH 3 and NH 4 ϩ , as measured by colorimetry (26). For organic acid analyses, 10 ml of spring water was filtered through 0.2-m-pore-size polyethersulfone syringe filters into precombusted glass vials with polytetrafluoroethylene-lined silicone septa.…”

Section: Methodsmentioning

confidence: 99%

Carbon Source Preference in Chemosynthetic Hot Spring Communities

Urschel

Kubo

Hoehler

et al. 2015

Rates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73°C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (K m ) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in hightemperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available.

“…Water for analysis was filtered through a 0.2-m Supor filter prior to analysis. NH 4 (T) refers to the sum of the dissolved species of aqueous NH 3 and NH 4 ϩ as measured by colorimetry (18).…”

Section: Methodsmentioning

confidence: 99%

“…Nitrosocaldus yellowstonii (11,17), tend to be low (Ͻ100 M) relative to those in acidic geothermal springs (18) (Fig. 1A).…”

mentioning

confidence: 96%

“…1A). The low concentrations of NH 4 (T) in alkaline geothermal springs is due, in part, to geological, chemical, and hydrological factors, most notably, the equilibration of aqueous NH 4 ϩ (aq) with NH 3(g) (pK ϭ 7.6 at 90°C) and the subsequent volatilization of NH 3(g) out of the system (18). The success of NH 4 (T)-oxidizing archaea in other NH 4 (T)-limited ecosystems, such as the marine water column, has been attributed to their high affinity for reduced nitrogen (19), which enables these populations to obtain NH 4 (T) at ambient concentrations much lower (Ͼ10 nM) than those of bacterial NH 4 (T) oxidizers and other members of the community.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

Hamilton

Koonce

Howells

et al. 2014

Source 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 "Candidatus Nitrosocaldus yellowstonii" and the putatively nitrogen-fixing (diazotrophic) bacterium Thermocrinis 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 N 2 fixation) 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 increased amoA transcript levels while it suppressed rates of acetylene reduction and decreased nifH transcript levels. Sequencing of amplified nifH and amoA transcripts 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 N 2 fixation are closely affiliated with Ca. Nitrosocaldus yellowstonii and T. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such as Ca. 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.