Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Abstract

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

Keywords: dinitrogen oxide; isotopic signature; microsensors; molecular tools; nitrogen monoxide; pathway identification; quantum cascade laser absorption spectroscopy (QCLAS); site preference.

Figure 1

Biological pathways for NO and N₂O turnover in the catabolic branch of the N-cycle plus NO synthesis and detoxification. Different colors are allocated to different microbial guilds or turnover pathways: AOB (red), ammonia oxidizing bacteria; NOB (green), nitrite oxidizing bacteria; anammox (orange), anaerobic oxidation of ammonia; DNRA (blue), dissimilatory nitrate/nitrite reduction to ammonia; N-AOM (purple), oxygenic nitrite-dependent anaerobic oxidation of methane. Key enzymes of each microbial guild are depicted that are known to mediate the conversion from one chemical N-species into another: AMO, ammonia monooxygenase; HAO, hydroxylamine oxidoreductase; NXR, nitrite oxidoreductase; Nar, membrane-bound nitrate reductase; Nap, periplasmic nitrate reductase; NirK, copper-containing nitrite reductase; NirS, cytochrome cd₁ nitrite reductase; Nrf, cytochrome c nitrite reductase; NirB, cytoplasmic nitrite reductase; cNor, nitric oxide reductase that accepts electrons from c-type cytochromes; qNor, nitric oxide reductase that accepts electrons from quinols; c554, cytochrome c₅₅₄; NorVW, flavorubredoxin, Hmp, flavohemoglobins; HZS, hydrazine synthase; HDH, hydrazine dehydrogenase; Nos, nitrous oxide reductase; NOS, nitric oxide synthase; unknown enzymes, nitric oxide dismutation to N₂ and O₂ during N-AOM and nitrous oxide producing enzyme in NOB. Roman numbers in brackets denote the oxidation state of the chemical N-species. The red and the black box denote the isotopic composition (δ¹⁵N) and the site preference (SP) in isotopomers of N₂O produced by AOB and denitrifiers, respectively.

Figure 2

NO microelectrodes. (A) Depicts a typical single-anode type NO sensor with a long sensing anode, which is coated with Nafion to confer selectivity against charged interferences. The anode and reference cathode are directly emerged into the sample medium. Some sensor designs integrate the cathode into the electrode shaft. (B) Depicts the NO microelectrode for measurements in biofilms and sediments as reported by Schreiber et al. (2008). This sensor is also an example for a combined NO sensor (Clark-type) where sensing anode and reference cathode are separated from the sample medium by a gas permeable membrane. Drawing is not to scale.