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Analysing uncertainties in the calculation of fluxes using whole-plant chambers: random and systematic errors

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Abstract

Aims

Gas exchange measurements on individual plants depend largely on chamber systems, and uncertainties and corrections in current flux calculation procedures require further assessment.

Methods

We present a practical study with novel methods for analyses of flux uncertainties in an original chamber design excluding soil fluxes and allowing simultaneous measurements of whole-plant photosynthesis and transpiration.

Results

Results indicate that random errors caused by IRGA noise and the lack of criteria to optimize the time window (TW) of chamber enclosure lead to significant flux uncertainties (12 %). Although enclosure should be rapid to minimize plant disturbances, longer TWs (3 min) increase confidence in flux estimates. Indeterminate stabilization periods in existing calculation protocols cause significant systematic errors. Stabilization times were identified via the change-point detection method, and flux uncertainties were reduced. Photosynthesis was overestimated by up to 28 % when not correcting the evolving CO2 molar fraction for water vapour dilution. Leakage can compromise flux estimates, but was negligible (ca. 2 %) here due to the large chamber-headspace and relatively small values of both collar contact length and closure time.

Conclusions

A bootstrapping, resampling-based flux calculation method is presented and recommended to better assess random errors and improve flux precision. We present practical recommendations for the use of whole-plant chambers.

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References

  • Anthony WH, Hutchinson GL, Livingston GP (1995) Chamber measurement of soil-atmosphere gas exchange: linear vs. diffusion-based flux models. Soil Sci Soc Am J 59(5):1308–1310

    Article  CAS  Google Scholar 

  • Breuninger C, Oswald R, Kesselmeier J, Meixner FX (2012) The dynamic chamber method: trace gas exchange fluxes (NO, NO2, O3) between plants and the atmosphere in the laboratory and in the field. Atmos Meas Tech 5(5):955–989

    Article  CAS  Google Scholar 

  • Christiansen J, Korhonen JJ, Juszczak R, Giebels M, Pihlatie M (2011) Assessing the effects of chamber placement, manual sampling and headspace mixing on CH4 fluxes in a laboratory experiment. Plant Soil 343(1–2):171–185

    Article  CAS  Google Scholar 

  • Corelli-Grappadelli L, Magnanini E (1993) A whole-tree system for gas-exchange studies. HortSci 28(1):41–45

    Google Scholar 

  • Dariah A, Marwanto S, Agus F (2014) Root- and peat-based CO2 emissions from oil palm plantations. Mitig Adapt Strateg Glob Chang 19(6):831–843

    Article  Google Scholar 

  • Denmead OT (1984) Plant physiological methods for studying evapotranspiration: problems of telling the forest from the trees. Agric Water Manag 8:167–189

    Article  Google Scholar 

  • Denmead OT (2008) Approaches to measuring fluxes of methane and nitrous oxide between landscapes and the atmosphere. Plant Soil 309(1-2):5–24

    Article  CAS  Google Scholar 

  • Denmead OT, Dunin FX, Wong SC, Greenwood EAN (1993) Measuring water use efficiency of Eucalypt trees with chambers and micrometeorological techniques. J Hydrol 150(2–4):649–664

    Article  Google Scholar 

  • Flexas J et al (2007) Analysis of leakage in IRGA’s leaf chambers of open gas exchange systems: quantification and its effects in photosynthesis parameterization. J Exp Bot 58(6):1533–1543

    Article  CAS  PubMed  Google Scholar 

  • Grau A (1995) A closed chamber technique for field measurement of gas exchange of forage canopies. N Z J Agric Res 38(1):71–77

    Article  Google Scholar 

  • Hall P, Martin MA (1988) On bootstrap resampling and iteration. Biometrika 75(4):661–671

    Article  Google Scholar 

  • Heinemeyer A, McNamara N (2011) Comparing the closed static versus the closed dynamic chamber flux methodology: Implications for soil respiration studies. Plant Soil 346(1-2):145–151

    Article  CAS  Google Scholar 

  • Held AA, Steduto P, Orgaz F, Matista A, Hsiao TC (1990) Bowen ratio/energy balance technique for estimating crop net CO2 assimilation, and comparison with a canopy chamber. Theor Appl Climatol 42(4):203–213

    Article  Google Scholar 

  • Hinkley DV (1970) Inference about the change-point in a sequence of random variables. Biometrika 57:1–17

    Article  Google Scholar 

  • Hooper DU, Cardon ZG, Chapin FS, Durant M (2002) Corrected calculations for soil and ecosystem measurements of CO2 flux using the LI-COR 6200 portable photosynthesis system. Oecologia 132:1–11

    Article  Google Scholar 

  • Hupp J (2011) The importance of water vapor measurements and corrections. LI-COR Biosciences Inc. Application Note, 129, p 8

  • Jassal RS, Black TA, Nesic Z, Gaumont-Guay D (2012) Using automated non-steady-state chamber systems for making continuous long-term measurements of soil CO2 efflux in forest ecosystems. Agric For Meteorol 161:57–65

    Article  Google Scholar 

  • Jones HG (1998) Stomatal control of photosynthesis and transpiration. J Exp Bot 49(Special Issue):387–398

    Article  Google Scholar 

  • Juszczak R, Humphreys E, Acosta M, Michalak-Galczewska M, Kayzer D, Olejnik J (2013) Ecosystem respiration in a heterogeneous temperate peatland and its sensitivity to peat temperature and water table depth. Plant Soil 366(1-2):505–520

    Article  CAS  Google Scholar 

  • Killick R, Eckley IA (2010) Changepoint: analysis of changepoint models. Lancaster University, Lancaster

    Google Scholar 

  • Killick R, Fearnhead P, Eckley IA (2012) Optimal detection of change points with a linear computational cost. JASA 107(500):1590–1598

    Article  CAS  Google Scholar 

  • Kutzbach L et al (2007) CO2 flux determination by closed-chamber methods can be seriously biased by inappropriate application of linear regression. Biogeosciences 4(6):1005–1025

    Article  CAS  Google Scholar 

  • Langensiepen M, Kupisch M, van Wijk MT, Ewert F (2012) Analyzing transient closed chamber effects on canopy gas exchange for optimizing flux calculation timing. Agric For Meteorol 164:61–70

    Article  Google Scholar 

  • Le Dantec V, Epron D, Dufrêne E (1999) Soil CO2 efflux in a beech forest: comparison of two closed dynamic systems. Plant Soil 214(1-2):125–132

    Article  Google Scholar 

  • Leiber-Sauheitl K, Fuß R, Voigt C, Freibauer A (2014) High CO2 fluxes from grassland on histic Gleysol along soil carbon and drainage gradients. Biogeosciences 11(3):749–761

    Article  Google Scholar 

  • Leuning R, Foster IJ (1990) Estimation of transpiration by single trees: comparison of a ventilated chamber, leaf energy budgets and a combination equation. Agric For Meteorol 51(1):63–86

    Article  Google Scholar 

  • Levy PE, Gray A, Leeson SR, Gaiawyn J, Kelly MPC, Cooper MDA, Dinsmore KJ, Jones SK, Sheppard LJ (2011) Quantification of uncertainty in trace gas fluxes measured by the static chamber method. Eur J Soil Sci 62(6):811–821

    Article  CAS  Google Scholar 

  • Livingston GP, Hutchinson GL (1995) Enclosure-based measurement of trace gas exchange: applications and sources of error. In: Matson PA, Harriss RC (eds) Biogenic trace gases: measuring emissions from soil and water. Blackwell Science Ltd, Oxford, pp 15–51

    Google Scholar 

  • McLeod MK, Daniel H, Faulkner R, Murison R (2004) Evaluation of an enclosed portable chamber to measure crop and pasture actual evapotranspiration at small scale. Agric Water Manag 67(1):15–34

    Article  Google Scholar 

  • Pedersen AR, Petersen SO, Schelde K (2010) A comprehensive approach to soil-atmosphere trace-gas flux estimation with static chambers. Eur J Soil Sci 61:888–902. doi:10.1111/j.1365-2389.2010.01291.x

    Article  Google Scholar 

  • Pérez-Peña Tarara J (2004) A portable whole canopy gas exchange system for several mature field-grown grapevines. Vitis 43(1):7–14

    Google Scholar 

  • Pérez-Priego O, Testi L, Orgaz F, Villalobos FJ (2010) A large closed canopy chamber for measuring CO2 and water vapour exchange of whole trees. Environ Exp Bot 68(2):131–138

    Article  Google Scholar 

  • Pickering NB, Jones JW, Boote KJ (1993) Evaluation of the portable chamber technique for measuring canopy gas exchange by crops. Agric For Meteorol 63(3–4):239–254

    Article  Google Scholar 

  • Pihlatie MK et al (2013) Comparison of static chambers to measure CH4 emissions from soils. Agric For Meteorol 171–172:124–136

    Article  Google Scholar 

  • Pumpanen J et al (2004) Comparison of different chamber techniques for measuring soil CO2 efflux. Agric For Meteorol 123:159–176

    Article  Google Scholar 

  • Reicosky DC (1990) Canopy gas exchange in the field: closed chambers. Remote Sens Rev 5(1):163–177

    Article  Google Scholar 

  • Reicosky DC, Wagner SW, Devine OJ (1990) Methods of calculating carbon dioxide exchange rates for maize and soybean using a Portable Field Chamber. Photosynthetica 24(1):22–38

    Google Scholar 

  • Rodeghiero M, Niinemets Ü, Cescatti A (2007) Major diffusion leaks of clamp-on leaf cuvettes still unaccounted: how erroneous are the estimates of Farquhar et al. model parameters? Plant Cell Environ 30(8):1006–1022

    Article  CAS  PubMed  Google Scholar 

  • Savage K, Davidson EA, Richardson AD (2008) A conceptual and practical approach to data quality and analysis procedures for high-frequency soil respiration measurements. Funct Ecol 22(6):1000–1007

    Article  Google Scholar 

  • Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6(2):461–464

    Article  Google Scholar 

  • Serrano-Ortiz P et al (2007) Variations in daytime net carbon and water exchange in a montane shrubland ecosystem in southeast Spain. Photosynthetica 45(1):30–35

    Article  Google Scholar 

  • Steduto P, Çetinkökü Ö, Albrizio R, Kanber R (2002) Automated closed-system canopy-chamber for continuous field-crop monitoring of CO2 and H2O fluxes. Agric For Meteorol 111(3):171–186

    Article  Google Scholar 

  • Venterea RT, Spokas KA, Baker JM (2009) Accuracy and precision analysis of chamber-based nitrous oxide gas flux estimates. Soil Sci Soc Am J 73(4):1087–1093

    Article  CAS  Google Scholar 

  • Wagner SW, Reicosky DC (1992) Closed-chamber effects on leaf temperature, canopy photosynthesis, and evapotranspiration. Agron J 84(4):731–738

    Article  Google Scholar 

  • Wagner SW, Reicosky DC, Saamuel Alessi R (1997) Regression models for calculating gas fluxes measured with a closed chamber. Agron J 89:279–284

    Article  CAS  PubMed  Google Scholar 

  • 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 106:85–100

    Article  Google Scholar 

  • Welles JM, Demetriades-Shah TH, McDermitt DK (2001) Considerations for measuring ground CO2 effluxes with chambers. Chem Geol 177(1–2):3–13

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded in part by Spanish Science Ministry projects Carborad (CGS2011-27493), ICOS-SPAIN (AIC10-A-000474), Carbored-II (CGL2010-22193-C04-02), and SOILPROF (CGL2011-15276-E) and also by the regional government (Junta de Andalucía) projects GEOCARBO (P08-RNM-3721) and CARBOLIVAR (RNM-7186). Oscar Perez-Priego was funded by a postdoctoral fellowship from the European Commission (FP7) through GHG-Europe project (Call FP7-ENV-2009-1.1.3.1; Project Code 244122). Authors thank Mirco Migliavacca and Thomas Wutzler for providing valuable comments on the manuscript. Critical comments from reviewers improved this manuscript from a previous version.

Compliance with ethical standards

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Conflict of interest

All authors state that there are no conflicts of interest.

Human and animal rights and informed consent

In this work no research involving human participants or animals were conducted.

Author information

Author notes

  1. Oscar Pérez-Priego

    Present address: Biogeochemical Integration Department, Max Planck Institute for Biogeochemistry, Jena, Germany

Authors and Affiliations

  1. Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Granada, Avenida Fuentenueva, S/N, 18071, Granada, Spain

    Oscar Pérez-Priego, Ana López-Ballesteros, Enrique P. Sánchez-Cañete, Penélope Serrano-Ortiz & Andrew S. Kowalski

  2. Departamento de Desertificación y Geoecología, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Carretera de Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain

    Ana López-Ballesteros, Enrique P. Sánchez-Cañete & Francisco Domingo

  3. Institut für Bodenkunde, University of Hamburg, Allende-Platz 2, 20146, Hamburg, Germany

    Lars Kutzbach

  4. Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092, Zürich, Switzerland

    Werner Eugster

  5. Instituto Interuniversitario del Sistema Tierra en Andalucía, Centro Andaluz de Medio Ambiente (IISTA-CEAMA), Avenida Mediterraneo, S/N, 18006, Granada, Spain

    Andrew S. Kowalski

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  1. Oscar Pérez-Priego
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Corresponding author

Correspondence to Oscar Pérez-Priego.

Additional information

Responsible Editor: Per Ambus.

Appendix

Appendix

Fig. 10

Fig. 10
figure 10

Spectral transmission of the translucent film “NRS90 clear” measured with a Li-Cor 1800-12 integrating sphere (Li-Cor, Lincoln, NE, USA) coupled to a fiber optic spectrometer (Ocean Optics model USB2000 spectrometer, Ocean Optics, Dunedin, FL, USA)

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Pérez-Priego, O., López-Ballesteros, A., Sánchez-Cañete, E.P. et al. Analysing uncertainties in the calculation of fluxes using whole-plant chambers: random and systematic errors. Plant Soil 393, 229–244 (2015). https://doi.org/10.1007/s11104-015-2481-x

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