University of Viennagrid.10420.37, Centre for Microbiology and Environmental Systems Science, Vienna, Austria.
University of Viennagrid.10420.37, The Comammox Research Platform, Vienna, Austria.
mSphere. 2021 Dec 22;6(6):e0063421. doi: 10.1128/mSphere.00634-21. Epub 2021 Dec 8.
Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH) via nitrite (NO) to nitrate (NO) (ε and ε). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH to NO. At high ammonium (NH) availability (1 mM) and pH between 6.5 and 8.5, its ε ranged from -33.1 to -27.1‰ based on substrate consumption (residual substrate isotopic composition) and -35.5 to -31.2‰ based on product formation (cumulative product isotopic composition), while the ε ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus , suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH concentrations influenced the isotope effects in . The ε based on product formation was smaller at pH 6.5 (-31.2‰) compared to pH 7.5 (-35.5‰) and pH 8.5 (-34.9‰), while ε was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via ε and ε was smaller at 0.1 mM NH compared to 0.5 to 1.0 mM NH. Environmental factors, such as pH and NH availability, therefore need to be considered when using isotope effects in N isotope fractionation models of nitrification. Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of ε and ε in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.
氮同位素分馏效应的分析有助于追踪生物地球化学氮循环过程。通过亚硝酸盐（NO）到硝酸盐（NO）（ε 和 ε）的酶促氧化作用，硝化作用可导致较大的氮同位素效应。氨氧化细菌（AOB）和古菌（AOA）以及亚硝酸盐氧化细菌（NOB）的氮同位素效应已被分析过。在这里，我们研究了将氨氧化为硝酸盐的完整氨氧化菌（comammox）Nitrospira inopinata 的氮同位素效应。在高铵（NH）可用性（1 mM）和 pH 值在 6.5 到 8.5 之间时，其 ε 值基于基质消耗（残留基质同位素组成）范围为-33.1 到-27.1‰，基于产物形成（累积产物同位素组成）范围为-35.5 到-31.2‰，而基于基质消耗的 ε 值范围为 6.5 到 11.1‰。这些值类似于 AOB、AOA 和属中的 NOB 的同位素效应，表明 comammox 和经典硝化作用中用于氨和亚硝酸盐氧化的关键酶之间不存在基本的机制差异。然而，环境 pH 值和初始 NH 浓度会影响 comammox 中的同位素效应。与 pH 值为 7.5（-35.5‰）和 pH 值为 8.5（-34.9‰）相比，基于产物形成的 ε 值在 pH 值为 6.5 时较小（-31.2‰），而与 pH 值为 7.5（8.8‰）和 pH 值为 6.5（11.1‰）相比，ε 值在 pH 值为 8.5 时较小。与 0.5 到 1.0 mM NH 相比，在 0.1 mM NH 时通过 ε 和 ε 进行的同位素分馏较小。因此，在硝化作用的 N 同位素分馏模型中使用同位素效应时，需要考虑 pH 值和 NH 可用性等环境因素。硝化作用是陆地和水生环境中重要的氮循环过程。comammox 的发现改变了传统观点，即认为只有典型的 AOA、AOB 和 NOB 是催化硝化作用的唯一化能自养生物。然而，comammox 对环境和技术系统中硝化作用的贡献远未完全被理解。本研究表明，尽管氨氧化的系统发育上有明显不同的酶谱，但 comammox 的氮同位素效应 ε 和 ε 与典型硝化作用者没有显著差异。因此，氮同位素效应不适合作为解析环境样品中 comammox 对硝化作用贡献的指标。此外，这是第一项系统研究表明环境 pH 值和 NH 浓度会影响硝化作用者的同位素效应。因此，在不同生长条件和环境样品中进行硝化作用者同位素效应的比较分析时，应考虑这些关键参数。
