Plant and Soil

, Volume 393, Issue 1–2, pp 229–244 | Cite as

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

  • Oscar Pérez-PriegoEmail author
  • Ana López-Ballesteros
  • Enrique P. Sánchez-Cañete
  • Penélope Serrano-Ortiz
  • Lars Kutzbach
  • Francisco Domingo
  • Werner Eugster
  • Andrew S. Kowalski
Regular Article



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


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 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.


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.


Canopy chamber Closed chamber Flux calculation methods Flux uncertainties Shrublands 



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-; 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

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.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Oscar Pérez-Priego
    • 1
    • 2
    Email author
  • Ana López-Ballesteros
    • 1
    • 3
  • Enrique P. Sánchez-Cañete
    • 1
    • 3
  • Penélope Serrano-Ortiz
    • 1
  • Lars Kutzbach
    • 4
  • Francisco Domingo
    • 3
  • Werner Eugster
    • 5
  • Andrew S. Kowalski
    • 1
    • 6
  1. 1.Departamento de Física Aplicada, Facultad de CienciasUniversidad de GranadaGranadaSpain
  2. 2.Biogeochemical Integration DepartmentMax Planck Institute for BiogeochemistryJenaGermany
  3. 3.Departamento de Desertificación y Geoecología, Estación Experimental de Zonas ÁridasConsejo Superior de Investigaciones CientíficasAlmeríaSpain
  4. 4.Institut für BodenkundeUniversity of HamburgHamburgGermany
  5. 5.Institute of Agricultural SciencesETH ZurichZürichSwitzerland
  6. 6.Instituto Interuniversitario del Sistema Tierra en Andalucía, Centro Andaluz de Medio Ambiente (IISTA-CEAMA)GranadaSpain

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