Monitoring Greenhouse Gas Fluxes in Agro-ecosystems

  • Sunayan SahaEmail author
  • Paramjit Singh Minhas
  • Ramlal Choudhary


Monitoring net exchange fluxes of greenhouse gases (GHGs) over agricultural fields is done either by chamber-based measurement approaches or using micrometeorological techniques. Chamber-based methods provide point-based measurements, but those can be customized and implemented at low costs in the field. Micrometeorological techniques, on the other hand, provide area-integrated measurement of gas exchanges without altering the natural canopy microclimate condition. With recent advances in instrumentation, fluxes can be measured at a very high temporal frequency of the order of hours to minutes. However, instrumentation is costly, often requires power supply and a homogeneous crop cover of a certain minimum area and knowledge of micrometeorology on the part of the user for a comprehensive GHG budgeting. Eddy covariance (EC) is regarded as the most robust micrometeorological technique which provides the most direct measurement of energy and GHG fluxes. This chapter mainly deals with CO2 flux measurement using eddy covariance technique. Guidance on various measurement protocols such as site selection, sensor configuration, and its orientation is provided. Sources of error in the eddy covariance data, data screening steps and various gap-filling measures such as mean diurnal variations, linear and non-linear regressions and look-up tables and flux validation have been addressed. It further includes a brief review of GHG exchange dynamics over agricultural landscapes, emerging challenges and case study of flux monitoring in three different crop ecosystems of semiarid Deccan plateau of peninsular India.


Greenhouse gas Agro-ecosystem Flux Instrumentation 


  1. Alavi N, Warland JS, Berg AA (2006) Filling gaps in evapotranspiration measurements for water budget studies: evaluation of a Kalman filtering approach. Agric Forest Meteorol 141:57–66CrossRefGoogle Scholar
  2. Allen RG, Pereira LS, Raes D, Smith M (1998) Crop evapotranspiration - guidelines for computing crop water requirements. FAO irrigation and drainage paper 56. Food and agriculture organization, RomeGoogle Scholar
  3. Anthoni PM, Freibauer A, Kolle O, Schulze ED (2004) Winter wheat carbon exchange in Thuringia. Germany Agric Forest Meteorol 121:55–67CrossRefGoogle Scholar
  4. Aubinet M, Grelle A, Ibrom A, Rannik U, Moncrieff J, Foken T, Kowalski AS, Martin PH, Berbigier P, Bernhofer CH, Clement R, Elbers J, Granier A, Grunwald T, Morgenstern K, Pilegaard K, Rebmann C, Snijders W, Valentini R, Vesala T (2000) Estimates of the annual net carbon and water exchange of forests: the EUROFLUX methodology. Adv Ecol Res 102:113–175Google Scholar
  5. Aulakh MS, Khera TS, Doran JW, Bronson K (2001) Denitrification, N2O, and CO2 fluxes in rice-wheat cropping systems as affected by crop residues, fertilizer N and legume green manure. Biol Fert Soils 34:375–389CrossRefGoogle Scholar
  6. Baldocchi DD (2003) Assessing the eddy covariance technique for evaluating carbon dioxide exchange rates of ecosystem: past, present and future. Glob Chang Biol 9:479–492CrossRefGoogle Scholar
  7. Baldocchi DD, Falge E, Wilson K (2000) A spectral analysis of biosphere-atmosphere trace gas flux densities and meteorological variables across hour to year time scales. Agric For Meteorol 107(1):1–27CrossRefGoogle Scholar
  8. Baldocchi D, Falge E, Gu L, Olson R, Hollinger D, Running S, Anthoni P, Bernhofer C, Davis K, Evans R, Fuentes J, Goldstein A, Katul G, Law B, Lee X, Malhi Y, Meyers T, Munger W, Oechel W, Paw UKT, Pilegaard K, Schmid HP, Valentini R, Verma S, Vesala T, Wilson K, Wofsy S (2001) FLUXNET: a new tool to study the temporal and spatial variability of ecosystem-scale carbon dioxide, water vapor, and energy flux densities. Bull Am Meteorol Soc 82:2415–2434CrossRefGoogle Scholar
  9. Béziat P, Ceschia E, Dedieu G (2009) Carbon balance of a three crop succession over two cropland sites in south West France. Agric For Meteorol 149:1628–1645CrossRefGoogle Scholar
  10. Bhatia A, Pathak H, Aggarwal PK (2004) Inventory of methane and nitrous oxide emissions from agriculture soils of India and their global warming potential. Curr Sci 87:317–324Google Scholar
  11. Bhattacharya P, Neogi S, Roy KS, Dash PK, Tripathi R, Rao KS (2013) Net ecosystem CO2 exchange and carbon cycling in tropical lowland flooded rice ecosystem. Nutr Cycl Agroecosyst 95:133–144CrossRefGoogle Scholar
  12. Boni G, Entekhabi D, Gastelli F (2001) Land data assimilation with satellite measurements for the estimation of surface energy balance components and surface control on evaporation. Water Resour Res 37(6):1713–1722CrossRefGoogle Scholar
  13. Bouwman AF (1990) Exchange of greenhouse gases between terrestrial ecosystems and the atmosphere. In: Bouwman AF (ed) Soil and greenhouse effect. Wiley, New York, pp 61–127Google Scholar
  14. Bowen IS (1926) The ratio of heat losses by conduction and by evaporation from any water surface. Phys Rev 27:779–787CrossRefGoogle Scholar
  15. Braswell BH, Sacks B, Linder E, Schimel DS (2005) Estimating ecosystem process parameters by assimilation of eddy flux observations of NEE. Glob Chang Biol 11:335–355CrossRefGoogle Scholar
  16. Burba G (2013) Eddy covariance method for scientific, industrial, agricultural and regulatory applications. LI-COR Biosciences. Lincoln, Nebraska. ISBN 978-0-615-76827-4Google Scholar
  17. Businger JA, Oncley SP (1990) Flux measurement with conditional sampling. J Atmos Ocean Technol 7:349–352CrossRefGoogle Scholar
  18. Chao CC (1999) Nitrous oxide emission and mitigation of composting and application of Livestock manure. In: Yang (ed.) Flux and mitigation of greenhouse gases. pp. 128-146. S. S., Department of Agricultural Chemistry and Global Change Research Center, National Taiwan University, Taipei, TaiwanGoogle Scholar
  19. Chen GX, Huang GH, Huang B, Yu KW, Wu J, Xu H (1997) Nitrous oxide and methane emissions from soil-plant systems. Nutr Cycl Agroecosyst 49:41–45CrossRefGoogle Scholar
  20. Desai AR, Bolstad P, Cook BD, Davis KJ, Carey EV (2005) Comparing net ecosystem exchange of carbon dioxide between an old-growth and mature forest in the upper Midwest. USA Agric For Meteorol 128(1-2):33–55CrossRefGoogle Scholar
  21. Desjardins RL (1977) Description and evaluation of a sensible heat flux detector. Boundary-Layer Meteorol 11:147–154CrossRefGoogle Scholar
  22. Dutaur L, Verchot LV (2007) A global inventory of the soil CH4 sink. Glob Chang Biol 21. doi:10.1029/2006GB002734. ISSN:0886-6236CrossRefGoogle Scholar
  23. Falge E, Baldocchi D, Olson R, Anthoni P, Aubinet M, Bernhofer C, Burba G, Ceulemans R, Clement R, Dolman H, Granier A, Gross P, Grunwald T, Hollinger D, Jensen NO, Katul G, Keronen P, Kowalski A, Lai CT, Law BE, Meyers T, Moncrieff J, Moors E, Munger JW, Pilegaard K, Rannik U, Rebmann C, Suyker A, Tenhunen J, Tu K, Verma S, Vesala T, Wilson K, Wofsy S (2001) Gap filling strategies for defensible annual sums of net ecosystem exchange. Agric For Meteorol 107:43–69CrossRefGoogle Scholar
  24. Fowler D, Pilegaard K, Sutton MA, Ambus P et al (2009) Atmospheric composition change: ecosystems-atmosphere interactions. Atmos Environ 43(33):5193–5267CrossRefGoogle Scholar
  25. Garg A, Bhattacharya S, Shukla PR, Dadwal VK (2001) Regional and sectoral assessment of greenhouse gas emission in India. Atmos Environ 35:2679–2695CrossRefGoogle Scholar
  26. Guo Q, Li WW, Liu DD, Wu W, Liu Y, Wen XX, Liao YC (2013) Seasonal characteristics of CO2 fluxes in a rain-fed wheat field ecosystem at the loess plateau. Spanish J Agric Res 11(4):980–988CrossRefGoogle Scholar
  27. Hamotani K, Uchida Y, Monji N et al (1996) A system of the relaxed eddy accumulation method to evaluate CO2 flux over plant cano-pies. J Agric Meteorol 52:135–139CrossRefGoogle Scholar
  28. Hartmann DL, Klein Tank AMG, Rusticucci M, Alexander LV, Brönnimann S, Charabi Y, Dentener FJ, Dlugokencky EJ, Easterling DR, Kaplan A, Soden BJ, Thorne PW, Wild M, Zhai PM (2013) Observations: atmosphere and surface. In: Stocker TF, Qin D, Plattner GK, Tignor M, Allen SK, Boschung J, Nauels A, Xia Y, Bex V, Midgley PM (eds) Climate change 2013: the physical science basis. Contribution of working group I to the fifth assessment report of the intergovernmental panel on climate change. Cambridge University Press, Cambridge, UK/New YorkGoogle Scholar
  29. Hernandez-Ramirez G, Hatfield JL, Parkin TB, Sauer TJ, Prueger JH (2011) Carbon dioxide fluxes in corn-soybean rotation in the midwestern U.S.: inter- and intra-annual variations, and biophysical controls. Agric For Meteorol 151:1831–1842CrossRefGoogle Scholar
  30. Hollinger DY, Aber J, Dail B, Davidson EA, Goltz SM, Hughes H, Leclerc MY, Lee JT, Richardson AD, Rodrigues C, Scott NA, Achuatavarier D, Walsh J (2004) Spatial and temporal variability in forest-atmosphere CO2 exchange. Glob Chang Biol 10:1689–1706CrossRefGoogle Scholar
  31. Hollinger SE, Bernacchi CJ, Meyers TP (2005) Carbon budget of mature no-till ecosystem in north central region of the United States. Agric For Meteorol 130:59–69CrossRefGoogle Scholar
  32. Hsieh C, Katul G, Chi T (2000) An approximate analytical model for footprint estimation of scalar fluxes in thermally stratified atmospheric flows. Adv Water Resour 23:765–772CrossRefGoogle Scholar
  33. Hui D, Wan S, Su B, Katul G, Monson R, Luo Y (2004) Gap filling missing data in eddy covariance measurements using multiple imputation (MI) for annual estimations. Agric For Meteorol 121:93–111CrossRefGoogle Scholar
  34. Intergovernmental Panel on Climate Change (IPCC) (2007) Climate change: the scientific basis. Cambridge University Press, CambridgeGoogle Scholar
  35. Jarvis AJ, Stauch VJ, Schulz K, Young PC (2004) The seasonal temperature dependency of photosynthesis and respiration in two deciduous forests. Glob Chang Biol 10:939–950CrossRefGoogle Scholar
  36. Kljun N, Calanca P, Rotach M, Schmid H (2004) A simple parameterization for flux footprint predictions. Boundary-Layer Meteorol 112:503–523CrossRefGoogle Scholar
  37. Knorr W, Kattge J (2005) Inversion of terrestrial ecosystem model parameter values against eddy covariance measurements by Monte Carlo sampling. Glob Chang Biol 11:1333–1351CrossRefGoogle Scholar
  38. Kormann R, Meixner F (2001) An analytical footprint model for non-neutral stratification. Boundary-Layer Meteorol 99:207–224CrossRefGoogle Scholar
  39. Lenschow DH, Mann J, Kristensen L (1994) How long is long enough when measuring fluxes and other turbulence statistics? J Atmos Oceanic Technol 11:661–673CrossRefGoogle Scholar
  40. Li Z, Yu G, Wen X, Zhang L, Ren C, Fu Y (2005) Energy balance closure at China flux sites. Science in China series D. Earth Sci 48(Supp I):51–62Google Scholar
  41. MacPherson JI, Desjardins RL (1991) Airborne tests of flux measurement by the relaxed eddy accumulation technique. In: Proceedings of the seventh symposium on meteorological observations and instrumentation. Am Meteorol Soc Boston, MA, pp 6–11Google Scholar
  42. Moffat AM, Papale D, Reichstein M, Hollinger DY, Richardson AD, Barr AG, Beckstein C, Braswell BH, Churkina G, Desai AR, Falge E, Gove JH, Heimann M, Hui D, Jarvis AJ, Kattge J, Noormets A, Stauch VJ (2007) Comprehensive comparison of gap-filling techniques for eddy covariance net carbon fluxes. Agric For Meteorol 147:209–232CrossRefGoogle Scholar
  43. Monji N (2003) Plants and micrometeorology-turbulence and fluxes in plant atmosphere. Osaka Municipal Universities Press, OsakaGoogle Scholar
  44. Moureaux C, Debacq A, Hoyaux J, Suleau M, Tourneur D, Vancutsem F, Bodson B, Aubinet M (2008) Carbon balance assessment of a Belgian winter wheat crop (Triticum aestivum L). Global Change Biol 14:1353–1366CrossRefGoogle Scholar
  45. Munro DS, Oke TR (1975) Aerodynamic boundary-layer adjustment over a crop in neutral stability. Boundary-Layer Meteorol 9:53–61CrossRefGoogle Scholar
  46. Noormets A, Chen J, Crow TR (2007) Age-dependent changes in ecosystem carbon fluxes in managed forests in northern Wisconsin, USA. Ecosystems 10:187–203CrossRefGoogle Scholar
  47. Oenema O, Wrage N, Velthof GL, Van Groenigen JW, Dolfing J, Kuikman PJ (2005) Trends in global nitrous oxide emissions from animal production systems. Nutr Cycl Agroecosyst 72:51–65CrossRefGoogle Scholar
  48. Oke TR (2007) Chapter 6: Siting and exposure of meteorological instruments at urban sites. In Air pollution modeling and its application XVII (online ISBN. 978-0-387-68854-1). Springer, pp 615–631. DOI:
  49. Papale D, Valentini A (2003) A new assessment of European forests carbon exchange by eddy fluxes and artificial neural network spatialization. Glob Chang Biol 9:525–535CrossRefGoogle Scholar
  50. Parashar DC, Kulashrestha UC, Sharma C (1998) Anthropogenic emissions of NOx, NH3 and N2O in India. Nutr Cycl Agroecosyst 52:255–259CrossRefGoogle Scholar
  51. Pattey E, Desjardins RL, Rochette P (1993) Accuracy of the relaxed eddy-accumulation technique evaluated using CO2 flux measurements. Boundary-Layer Meteorol 66:341–355CrossRefGoogle Scholar
  52. Pattey E, Edwards G, Strachan IB, Desjardins RL, Kaharabata S, Wagner Riddle C (2006) Towards standards for measuring greenhouse gas fluxes from agricultural fields using instrumented towers. Can J Soil Sci 86:373–400CrossRefGoogle Scholar
  53. Posse G, Richter K, Corin JM, Lewczuk NA, Achkar A, Rebella C (2010) Carbon dioxide fluxes on a soybean field in Argentina: influence of crop growth stages. Open Agric J 4:8–63CrossRefGoogle Scholar
  54. Raupach MR, Legg BJ (1984) The uses and limitations of flux-gradient relationships in micrometeorology. Agric Water Manag 8:119–131CrossRefGoogle Scholar
  55. Reichstein M, Falge E, Baldocchi D, Papale D, Aubinet M, Berbigier P, Bernhofer C, Buchmann N, Gilmanov T, Granier A, Grunwald T, Havrankova K, Ilvesniemi H, Janous D, Knohl A, Laurila T, Lohila A, Loustau D, Matteucci G, Meyers T, Miglietta F, Ourcival JM, Pumpanen J, Rambal S, Rotenberg E, Sanz M, Tenhunen J, Seufert G, Vaccari F, Vesala T, Yakir D, Valentini R (2005) On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Glob Chang Biol 11:1424–1439CrossRefGoogle Scholar
  56. Richardson AD, Braswell BH, Hollinger DY, Burman P, Davidson EA, Evans RS, Flanagan LB, Munger JW, Savage K, Urbanski SP, Wofsy SC (2006) Comparing simple respiration models for eddy flux and dynamic chamber data. Agric For Meteorol 141:219–234CrossRefGoogle Scholar
  57. Rubin DB (1987) Multiple imputation for non response surveys. Wiley, New YorkCrossRefGoogle Scholar
  58. Saha S, Bal SK, Minhas PS, Singh Y (2014) Net carbon-dioxide exchange in green manuring ecosystem, Sesbania aculeata: assessment through eddy covariance approach. J Agrometeorol 16(2):149–156Google Scholar
  59. Saha S, Bal SK, Bhagat K (2016) Fluxes and production efficiency of irrigated wheat ecosystem under edaphic constraints of western Maharashtra plateau: a micrometeorological investigation. J Agrometeorol 18(2):175–183Google Scholar
  60. Schafer JL (1997) Analysis of incomplete multivariate data. Chapman and Hall, LondonCrossRefGoogle Scholar
  61. Schafer JL, Olsen MK (1998) Multiple imputation for multivariate missing-data problems: a data analyst’s perspective. Multivar Behav Res 33:545–571CrossRefGoogle Scholar
  62. Sharma C, Gupta PK, Parashar DC (1995) Nitrous oxide estimates from paddy fields and forests in India. Indian J Radio Space Phys 24:311–313Google Scholar
  63. Soegaard H, Jensen NO, Boegh E, Hasager CB, Schelde K, Thomsen A (2003) Carbon dioxide exchange over agricultural landscape using eddy correlation and footprint modelling. Agric For Meteorol 114:153–173CrossRefGoogle Scholar
  64. Stull R (1988) An introduction to boundary layer meteorology. Kluwer Academic Publishers, Dordrecht/Boston/London, p 666CrossRefGoogle Scholar
  65. Suyker AE, Verma SB, Burba GG, Arkebauer TJ, Walters DT, Hubbard KG (2004) Growing season carbon dioxide exchange in irrigated and rainfed maize. Agric For Meteorol 124:1–13CrossRefGoogle Scholar
  66. US-EPA (2007) Global mitigation of non-CO2 greenhouse gases. United States Environmental Protection Agency, EPA 430-R-06-005, Washington DC, USA. econ-inv/downloads/GlobalMitigationFullReport.pdf. Accessed on 26 March 2007
  67. Watanabe T, Yamanoi K, Yasuda Y (2000) Testing of the bandpass eddy covariance method for a long-term measurement of water vapor flux over a forest. Bound-Layer Meteorol 96:473–491CrossRefGoogle Scholar
  68. Webb EK, Pearman GI, Leuning R (1980) Correction of flux measurements for density effects due to heat and water vapour transfer. Q J R Meteorol Soc 106:85–100CrossRefGoogle Scholar
  69. Williams M, Schwarz PA, Law BE, Irvine J, Kurpius MR (2005) An improved analysis of forest carbon dynamics using data assimilation. Glob Chang Biol 11:89–105CrossRefGoogle Scholar
  70. Wilson K, Goldstein A, Falge E, Aubinet M, Baldocchi D, Berbigier P, Bernhofer C, Ceulemans R, Dolman H, Field C, Grelle A, Ibrom A, Law BE, Kowalski A, Meyers T, Moncrieff J, Monson R, Oechel W, Tenhunen J, Verma S, Valentini R (2002) Energy balance closure at FLUXNET sites. Natural resources paper 153.
  71. Zhilin Z, Xiaomin S, Yanlian Z, Jinping X, Guofu Y, Renhua Z (2005) Correcting method of eddy covariance fluxes over non-flat surfaces and its application in China FLUX. Sci China Ser D Earth Sci 48(Supp 1):42–50Google Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Sunayan Saha
    • 1
    Email author
  • Paramjit Singh Minhas
    • 2
  • Ramlal Choudhary
    • 3
  1. 1.ICAR-Central Potato Research StationJalandharIndia
  2. 2.ICAR-National Institute of Abiotic Stress ManagementBaramatiIndia
  3. 3.ICAR-National Institute of Abiotic Stress ManagementBaramatiIndia

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