Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China


Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. Alam MS, Jia Z (2012) Inhibition of methane oxidation by nitrogenous fertilizers in a paddy soil. Front Microbiol 3:246

  2. Angel R, Matthies D, Conrad R (2011) Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One. doi:10.1371/journal.pone.0020453

  3. Angel R, Claus P, Conrad R (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6:847–862

  4. Bao Q, Huang Y, Wang F, Nie S, Nicol GW, Yao H, Ding L (2016) Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Appl Microbiol Biot 13:5989–5998

  5. Bodelier PL, Roslev P, Henckel T, Frenzel P (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403:421–424

  6. Brioukhanov A, Netrusov A, Sordel M, Thauer RK, Shima S (2000) Protection of Methanosarcina barkeri against oxidative stress: identification and characterization of an iron superoxide dismutase. Arch Microbiol 174:213–216

  7. Dan JG, Krüger M, Frenzel P, Conrad R (2001) Effect of a late season urea fertilization on methane emission from a rice field in Italy. Agric Ecosyst Environ 83:191–199

  8. Erkel C, Kube M, Reinhardt R, Liesack W (2006) Genome of rice cluster I archaea—the key methane producers in the rice rhizosphere. Science 313:370–372

  9. Eusufzai MK, Tokida T, Okada M, Si S, Liu GC, Nakajima M, Sameshima R (2010) Methane emission from rice fields as affected by land use change. Agric Ecosyst Environ 139:742–748

  10. Fan X, Yu H, Wu Q, Ma J, Xu H, Yang J, Zhuang Y (2016) Effects of fertilization on microbial abundance and emissions of greenhouse gases (CH4 and N2O) in rice paddy fields. Ecol Evol 6:1054–1063

  11. Freitag TE, Prosser JI (2009) Correlation of methane production and functional gene transcriptional activity in a peat soil. Appl Environ Microbiol 75:6679–6687

  12. Hales BA, Edwards C, Ritchie DA, Hall G, Pickup RW, Saunders JR (1996) Isolation and identification of methanogen-specific DNA from blanket bog feat by PCR amplification and sequence analysis. Appl Environ Microbiol 62:668–675

  13. Hanson R, Hanson T (1996) Methanotrophic bacteria. Microbiol Mol Biol R 60:439–471

  14. Henckel T, Friedrich M, Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65:1980–1990

  15. Ho A, Lüke C, Reim A (2016) Resilience of (seed bank) aerobic methanotrophs and methanotrophic activity to desiccation and heat stress. Soil Biol Biochem 101:130–138

  16. Hu HW, Zhang LM, Yuan CL, He JZ (2013) Contrasting Euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns. Soil Biol Biochem 64:18–27

  17. Intergovernmental Panel on Climate Change (IPCC) (2013) In: Denman KL (ed) Couplings between changes in the climate system and biochemistry. Climate change 2013: the physical science basis. Cambridge University Press, Cambridge

  18. Inubushi K, Furukawa Y, Hadi A, Purnomo E, Tsuruta H (2003) Seasonal changes of CO2, CH4 and N2O fluxes in relation to land-use change in tropical peatlands located in coastal area of South Kalimantan. Chemosphere 52:603–608

  19. Jaatinen K, Knief C, Dunfield PF, Yrjala K, Fritze H (2004) Methanotrophic bacteria in boreal forest soil after fire. FEMS Microbiol Ecol 50:195–202

  20. Jäckel U, Schnell S, Conrad R (2001) Effect of moisture, texture and aggregate size of paddy soil on production and consumption of CH4. Soil Biol Biochem 33:965–971

  21. Jetten MSM, Stams AJM, Zehnder AJB (1990) Purification and some properties of the methyl-com reductase of Methanothrix-Soehngenii. FEMS Microbiol Lett 66:183–186

  22. Knief C, Kolb S, Bodelier PL, Lipski A, Dunfield PF (2006) The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environmen Microbol 8:321–333

  23. Krüger M, Frenzel P, Kemnitz D, Conrad R (2005) Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol Ecol 51:323–331

  24. Lammel DR, Feigl BJ, Cerri CC, Nüsslein K (2015) Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in southern Amazonian soils. Front Microbiol 6. doi:10.3389/fmicb.2015.01057

  25. Lee HJ, Kim SY, Kim PJ, Madsen EL, Jeon CO (2014) Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem. FEMS Microbiol Ecol 88:195–212

  26. Liu D, Ishikawa H, Nishida M, Tsuchiya K, Takahashi T, Kimura M, Asakawa S (2015a) Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil. Microb Ecol 69:160–168

  27. Liu S, Hu Z, Wu S, Li S, Li Z, Zou J (2015b) Methane and nitrous oxide emissions reduced following conversion of Rice paddies to inland crab–fish aquaculture in Southeast China. Environ Sci Technol 50:633–642

  28. Liu H, Liu G, Li Y, Wu X, Liu D, Xu M, Dai X, Yang F (2016) Effects of land use conversion and fertilization on CH4 and N2O fluxes from typical hilly red soil. Environ Sci Pollut Res 23:20269–20280

  29. Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309:1088–1090

  30. Ma K, Lu Y (2011) Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiol Ecol 75:446–456

  31. McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74:1305–1315

  32. Metje M, Frenzel P (2007) Methanogenesis and methanogenic pathways in a peat from subarctic permafrost. Environ Microbiol 9:954–964

  33. Mohanty SR, Bodelier PL, Floris V, Conrad R (2006) Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 72:1346–1354

  34. Mohanty SR, Tiwari S, Dubey G, Ahirwar U, Kollah B (2016) How methane feedback response influence redox processes in a tropical vertisol. Biol Fert Soils 53:479–490

  35. Nishimura S, Yonemura S, Sawamoto T, Shirato Y, Akiyama H, Sudo S, Yagi K (2008) Effect of land use change from paddy rice cultivation to upland crop cultivation on soil carbon budget of a cropland in Japan. Agricul Ecosys Environ 125:9–20

  36. Noll M, Frenzel P, Conrad R (2008) Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiol Ecol 65:125–132

  37. Reay DS, Nedwell DB (2004) Methane oxidation in temperate soils: effects of inorganic N. Soil Biol Biochem 36:2059–2065

  38. Sass RL, Fisher FM, Lewis ST, Jund MF, Turner FT (1994) Methane emissions from rice fields—effect of soil properties. Global Biogeochem CY 8:135–140

  39. Scavino AF, Ji Y, Pump J, Klose M, Claus P, Conrad R (2013) Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields. Environ Microbiol 15:2588–2602

  40. Scheer C, Wassmann R, Kienzler K, Ibragimov N, Lamers J, Martius C (2008) Methane and nitrous oxide fluxes in annual and perennial land-use systems of the irrigated areas in the Aral Sea basin. Glob Chang Biol 14:2454–2468

  41. Schimel J (2000) Global change: rice, microbes and methane. Nature 403:375–377

  42. Singh BK, Tate KR (2007) Biochemical and molecular characterization of methanotrophs in soil from a pristine New Zealand beech forest. FEMS Microbiol Lett 275:89–97

  43. Singh BK, Tate KR, Ross DJ, Singh J, Dando J, Thomas N, Murrell JC (2009) Soil methane oxidation and methanotroph responses to afforestation of pastures with Pinus radiata stands. Soil Biol Biochem 41:2196–2205

  44. Szubert J, Reiff C, Thorburn A, Singh BK (2007) REMA: a computer-based mapping tool for analysis of restriction sites in multiple DNA sequences. J Microbiol Meth 69:411–413

  45. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Bio Evol 30:2725–2729

  46. Wang L, Pan Z, Xu H, Wang C, Gao L (2015) The influence of nitrogen fertiliser rate and crop rotation on soil methane flux in rain-fed potato fields in Wuchuan County, China. Sci Total Environ 537:93–99

  47. Watanabe T, Kimura M, Asakawa S (2007) Dynamics of methanogenic archaeal communities based on rRNA analysis and their relation to methanogenic activity in Japanese paddy field soils. Soil Biol Biochem 39:2877–2887

  48. Yan XY, Akiyama H, Yagi K, Akimoto H (2009) Global estimations of the inventory and mitigation potential of methane emissions from rice cultivation conducted using the 2006 intergovernmental panel on climate change guidelines. Global Biogeochem CY. doi:10.1029/2008GB003299

  49. Zheng Y, Liu X, Zhang L, Zhou Z, He J (2010) Do land utilization patterns affect methanotrophic communities in a Chinese upland red soil? J Environ Sci-China 22:1936–1943

  50. Zhou B, Wang Y, Feng Y, Lin X (2016) The application of rapidly composted manure decreases paddy CH4 emission by adversely influencing methanogenic archaeal community: a greenhouse study. J Soils Sediments 16:1889–1990

  51. Zou JW, Huang Y, Jiang JY, Zheng XH, Sass RL (2005) A 3-year field measurement of methane and nitrous oxide emissions from rice paddies in China: effects of water regime, crop residue, and fertilizer application. Global Biogeochem CY. doi:10.1029/2004gb002401

Download references


This work was supported by the National Natural Science Foundation of China (41471095) and the Ministry of Science and Technology of China (2012CB417103). We would like to thank the staffs of the Qianyanzhou Experimental Station for their fruitful assistance in field sampling. Special thanks go to the anonymous reviewers for constructive comments on the previous version of the manuscript.

Author information

Correspondence to Xing Wu or Guohua Liu.

Additional information

Responsible editor: Robert Duran

Electronic supplementary material


(DOC 123 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Liu, H., Wu, X., Li, Z. et al. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. Environ Sci Pollut Res 24, 8731–8743 (2017). https://doi.org/10.1007/s11356-017-8628-y

Download citation


  • Land-use conversion
  • CH4 fluxes
  • Methanogens
  • Methanotrophs
  • Fertilization