Anaerobic methane oxidation by nitrate: kinetic isotope effect

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The ratio of stable carbon isotopes (13C/12C) in different environments serves as a significant limitation in estimating the global balance of methane [Hornibrook et al., 2000]. In this case, the value of 13C/12C largely depends on the kinetic isotope effect associated with the metabolism of microorganisms that produce and consume CH4. The article suggests a dynamic model of the processes of methane formation and its anaerobic oxidation with nitrate by methanotrophic denitrifying microorganisms (DAOM), which allowed estimating the fractionation factor of stable carbon isotopes. In the experiment with peat from the minerotrophic bog [Smemo, Yavitt, 2007], the dynamics of the amount of methane and was measured. The dynamic model showed that the introduction of nitrate leads to a slow decrease in the partial pressure of methane. Since methane in the DAOM process is a substrate, methane is enriched with heavier carbon 13C in the system under study. This leads to an increase in the value . The carbon isotope fractionation factor during methane oxidation with nitrate was equal to 1.018 and comparable with the fraction of carbon isotope fractionation in the process of acetoclastic methanogenesis (1.01). Model calculations have shown that during incubation the apparent fractionation factor of carbon isotopes with the simultaneous formation of methane and DAOM slowly decreases. The ratio of 13C/12C isotopes in dissolved and gaseous methane practically does not differ. The model showed that an increase in the initial concentration of nitrate increases the rate of DAOM, which leads to a decrease in the concentration of dissolved methane. In this case, the value of 13C/12C increases. In field studies, Shi et al. (2017) showed that the presence of DAOM in peat bogs in which fertilizers penetrate can be controlled by the amount of nitrate used and the depth of penetration into the anoxic layer. Two MATLAB files describing DAOM are attached to the article.

About the authors

Vasiliy A. Vavilin

Water problems institute of the Russian Academy of Sciences

Author for correspondence.
Russian Federation


  1. Галимов ЭМ, 1973. Изотопы углерода в нефтегазовой геологии. Наука, Москва; 384 с. [Galimov EM, 1973. Izotopy Ugleroda v Neftegazovoy Geologii. Nauka, Moscow: 384 pp (In Russian)].
  2. Batstone DJ, Keller J, Angelidaki I, 2002. Anaerobic Digestion Model No.1 (ADM1). Water Science & Technology. 45:65–73.
  3. Bridgham R, Cadillo-Quiroz H, Keller J, Zhuang Q, 2013. Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales. Glob. Change Biol. 19:1325–1346. doi: 10.1111/gcb.12131
  4. Conrad R, 2005. Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal. Organ. Geochem. 36:739–752. doi: 10.1016/j.orggeochem.2004.09.006
  5. Craig H, 1957. Isotopic standards for carbon and oxygen and correction factors for mass-spectrometric analysis of carbon dioxide. Geochim. Cosmochim. Acta. 12:133–149. doi: 10.1016/0016-7037(57)90024-8
  6. Ettwig K, Butler M, Le Paslier D, 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature. 464:543–550.
  7. Hornibrook E, Longstaffe F, Fyfe W, 2000. Evolution of stable carbon isotope compositions for methane and carbon dioxide in freshwater wetlands and other anaerobic environments. Geochim. Cosmochim. Acta. 64:1013–1027. doi: 10.1016/s0016-7037(99)00321-x
  8. Kallistova AY, Merkel AY, Pimenov NV, Tarnovetskii IY, 2017. Methane formation and oxidation by prokaryotes. Microbiology (Mikrobiologiya). 86:671–691. doi: 10.7868/S002636561706009X
  9. Knox M, Quay P, Wilbur D, 1992. Kinetic isotopic fractionation during air-water gas transfer of O2, N2, CH4, and H2. Journal of Geophys. Res. 97:20335–20343. doi: 10.1029/92jc00949
  10. Lynd LR, Weimer P, Zyl W van, Pretorius I, 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Molecul. Biol. Rev. 66:506–577. doi: 10.1128/mmbr.66.4.739.2002
  11. MathWorks Inc., 1984. The MathWorks, Inc., Natick, Massachusetts, USA.
  12. Penning H, Claus P, Casper P, Conrad R, 2006. Carbon isotope fractionation during acetoclastic methanogenesis by Methanosaeta concilii in culture and lake sediment. Appl. Environ. Microbiol. 72:5648–5652. doi: 10.1128/aem.00727-06
  13. Rasigraf O, Vogt C, Richnow H, Jetten M, Ettwig K, 2012. Carbon and hydrogen isotope fractionation during nitrite-dependent anaerobic methane oxidation by Methylomirabilis oxyfera. Cosmochim. Acta. 89:256–264. doi: 10.1016/j.gca.2012.04.054
  14. Rayleigh J, 1896. Theoretical consideration respecting the separation of gases by diffusion and similar processes. Philos. Mag. 42:493–498. doi: 10.1080/14786449608620944
  15. Rittmann B, McCarty P, 2001. Environmental Biotechnology: Principles and Applications. McGraw-Hill, New York: 768 pp.
  16. Shi Y, Wang Z, He C, Zhang X, Sheng L, Ren X, 2017. Using 13C isotopes to explore denitrification-dependent anaerobic methane oxidation in paddy-peatland. Nature Publ. Group. Sci. Rep. 7:40848. doi: 10.1038/srep40848. 10.1038/srep40848
  17. Smemo K, Yavitt J, 2007. Evidence for anaerobic CH4 oxidation in freshwater peatlands. Geomicrobiol. J. 24:583–597. doi: 10.1080/01490450701672083
  18. Smemo K, Yavitt J, 2011. Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems? Biogeosciences. 8:779–793. doi: 10.5194/bg-8-779-2011
  19. Vavilin V, Rytov S, 2015. Nitrate denitrification with nitrite or nitrous oxide as intermediate products: Stoichiometry, kinetics and dynamics of stable isotope signatures. Chemosphere. 134:417–426. doi: 10.1016/j.chemosphere.2015.04.091
  20. Vavilin V, Rytov S, Lokshina L, 2018. Dynamic isotope equations for 13CH4 and 13CO2 describing methane formation with a focus on the effect of anaerobic respiration in sediments of some tropical lakes. Ecol. Modell. 386:59–70. doi: 10.1016/j.ecolmodel.2018.08.005
  21. Vavilin V, Rytov S, Lokshina L, 2018. Modelling the specific pathway of CH4 and CO2 formation using carbon isotope fractionation: an example for a boreal mesotrophic fen. Isotope Env. Health Studies. 54:475–493. doi: 10.1080/10256016.2018.1478820
  22. Vavilin VA, Rytov SV, 2016. Inhibition by nitrite ion in the process of methane anaerobic oxidation by microorganisms and fractionation dynamics of stable carbon and hydrogen isotopes. Water Resources 43:663–667. doi: 10.7868/S0321059616040167
  23. Vavilin VA, Rytov SV, Conrad R. Modelling methane formation in sediments of tropical lakes focusing on syntrophic acetate oxidation: Dynamic and static isotope equations. Ecol. Modell. 2017;363:81-95. doi: 10.1016/j.ecolmodel.2017.08.024
  24. Whiticar M, 1999. Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem. Geology. 161:291–314. doi: 10.1016/s0009-2541(99)00092-3
  25. Zinder S, 1993. Physiological Ecology of Methanogens., p. 128–206 In: Ferry J (ed.), Methanogenesis, Ecology, Physiology, Biochemistry and Genetics., New York: Chapman & Hall. doi: 10.1007/978-1-4615-2391-8_4

Supplementary files

Supplementary Files
1. Supplement 1. DAOM: main program (MatLab)
Download (36KB)
2. Supplement 2. DAOM: function for right-hand side of ODEs (MatLab)
Download (29KB)

Copyright (c) 2019 Vavilin V.A.

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