Mellbye Brett L, Giguere Andrew, Chaplen Frank, Bottomley Peter J, Sayavedra-Soto Luis A
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, USA.
Appl Environ Microbiol. 2016 May 16;82(11):3310-3318. doi: 10.1128/AEM.00294-16. Print 2016 Jun 1.
Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2 IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on the dilution rate and Na2CO3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3 oxidation from growth and increased N2O production.
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO2) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of Nitrosomonas europaea, a model ammonia-oxidizing bacterium, and report on increased production of N2O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N2O emissions from nitrification in soils and wastewater treatment.
欧洲亚硝化单胞菌是一种化能自养细菌，它氧化氨（NH₃）以获取在二氧化碳（CO₂）上生长所需的能量，并且还能产生一氧化二氮（N₂O），一种温室气体。我们研究了欧洲亚硝化单胞菌在充足（>5.2 mM）和有限无机碳（IC）条件下的生长、生理和转录组反应，充足条件下通过添加大气中的CO₂，有限条件下分别添加1.0 mM或0.2 mM碳酸钠（Na₂CO₃）。IC受限培养物将25%至58%的可用NH₃氧化为亚硝酸盐，这取决于稀释率和Na₂CO₃浓度。与NH₃受限培养物相比，IC限制导致细胞维持能量需求增加2.3倍。在两种IC受限条件下，N₂O产生速率分别增加了2.5倍和6.3倍，将氧化的NH₃-N转化为N₂O-N的百分比从0.5%（充足）提高到4.4%（0.2 mM Na₂CO₃）。转录组分析表明，在充足和IC受限条件之间有488个基因（占基因库的20%）差异表达（P≤0.05），但在两种IC限制处理之间检测到的差异很少。IC受限条件导致铵/氨转运蛋白和氨单加氧酶亚基的表达降低，并增加了参与C1代谢的基因的表达，包括RuBisCO（cbb基因簇）、碳酸酐酶、C1部分的叶酸连接代谢以及由于RuBisCO加氧酶活性导致的假定C挽救相关基因。亚硝酸还原酶（基因簇NE0924至NE0927）表达增加与N₂O产生增加相关。总之，这些数据表明欧洲亚硝化单胞菌在IC受限的稳态生长过程中进行生理适应，这导致NH₃氧化与生长解偶联并增加N₂O产生。
硝化作用，即氨通过亚硝酸盐有氧氧化为硝酸盐，是全球氮循环中的一个重要过程。这个过程通常依赖于氨氧化微生物和亚硝酸氧化细菌。大多数硝化菌是化能自养菌，它们固定无机碳（CO₂）用于生长。在这里，我们研究无机碳限制如何改变模式氨氧化细菌欧洲亚硝化单胞菌的生理和转录组，并报告一种强效温室气体N₂O产生增加。这项研究以及之前的工作表明，无机碳限制可能是控制土壤和废水处理中硝化作用产生N₂O排放的一个重要因素。
