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Measuring the δ13C of the soil surface efflux

John Hunt , Andy Midwood
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Author details:

Andy Midwood, Macaulay Land Use Research Institute, Aberdeen, AB15 8QH, UK
John Hunt, Landcare Research, Lincoln, 7640, New Zealand


The δ13C of the soil surface efflux (δ13CRS) has emerged as a powerful tool enabling investigation of a wide range of soil processes, from detailed compound specific isotope studies to characterising entire ecosystem respiration. δ13CRS can be used to trace assimilated carbon (C) transfer below ground and be used to partition the overall surface efflux into heterotrophic and autotrophic components.


Methodologies for measuring the rate at which CO2 leaves the soil surface are well established and are largely based on chamber systems. In contrast, currently no consensus exists on the best approach for measuring the isotopic composition of the soil surface efflux (δ13CRS) although chamber systems of one form or another are generally used1.

A key challenge for both rate and isotopic measurements is avoiding any disturbance of the CO2 diffusion process from the soil surface by the measurement procedure itself. With isotopic measurements there is the additional complication that δ13C value of atmospheric air is very different from that of the efflux being measured and in C3 systems the difference can be >10‰ while in C4 systems the difference is generally 4-5‰.


  • A specialised chamber
  • Dependent on the approach taken (see below) the equipment list can be quite long and include mass flow controllers, pumps, dataloggers, infrared gas analysers, and lots of tubing.
  • Instrument to measure isotopic composition of air samples (either bagged or on-line), options include gas isotope ratio mass spectrometer, tunable diode laser spectrometer or cavity ring-down spectrometer.


Units, terms, definitions

Efflux rate is usually measured in μmol CO2.m-2.s-1 or g CO2.m-2.h-1, isotope measurements are typically given in parts per thousand (‰) relative to the international standard Vienna Peedee Belemnite (V-PDB): δ13C = (RSAMPLE/RVPDB-1) x 1000 (‰), and RSAMPLE and RVPDB are the 13C/12C of the sample and reference material V-PDB, respectively.


Closed Chambers

Chamber systems deployed to measure the δ13CRS can be broken down into 3 types, closed, open and dynamic. The closed chamber system is technically by far the simplest; a chamber is placed on the soil surface enclosing a volume of air. Over time the isotopic composition changes and concentration of CO2 increases as the soil derived CO2 accumulates. By taking a series of samples at different time intervals, a simple mixing model which uses the intercept of a so called ‘Keeling plot’ can then be used to provide an estimate δ13CRS 2-4. The disadvantage of this approach is that small changes in this data can have a significant impact in the intercept value and the estimate δ13CRS. Also, it has been argued that as CO2 accumulates within the chamber, the change in partial pressure has the potential to disrupt the CO2 diffusion process from the soil and importantly it’s isotopic composition. Other issues with this approach include the use of a ‘linear’ mixing model within the confines of a chamber. Recently, it has been suggested that Keeling plots are non-linear in a non-steady state diffusive environment, such as within a closed respiration chamber 5.

Open Chambers

Open chambers are more complex than closed chambers, air is continually drawn through the chamber and the difference between the chamber exit flow and the inflow are measured to determine both the efflux rate and δ13CRS (Fig. 1). Because there is no build up of CO2 in the headspace of an open chamber, isotope diffusion from the soil profile is less likely to be disrupted by the measurement process than with a closed system; this makes open systems attractive for measuring δ13CRS. Recently, a number of on-line measurement techniques involving the use of continuous-flow isotope ratio mass spectrometry (IRMS) and tunable diode laser spectrometry (TDLS) have been used with open chamber systems to measure δ13CRS 6-8.

Figure 1: Example of an open chamber, air is continuously drawn through the chamber and the soil derived CO2 leads to an increase in the outflow CO2 concentration and change in isotope composition

A limitation of the open chamber system is that with low efflux rates the flows in and out of the chamber have to be carefully controlled to minimise pressure effects. Since this approach relies on a differential measurement of both CO2 concentration and δ13C, all the errors are additive 9 and may result in unacceptably high uncertainty on the δ13CRS.

Dynamic Chamber

Dynamic chambers use a controlled supply of CO2-free air balanced with an outflow to maintain ambient CO2 concentrations within the sample chamber (Fig. 2,3). Because CO2 free air is used, the CO2 which accumulates in the chamber is entirely derived from the soil surface. Such systems have the disadvantage, liked open chambers of being complex, but are capable of measuring the δ13CRS with high accuracy and have been used in conjunction with both IRMS 10 and TDLS 11,12 systems.

Figure 2: Dynamic chamber under test, CO2 free air supply is balanced with pumped withdrawal, CO2 concentration is monitored by an infra red gas analyser and rates adjusted as necessary to keep CO2 levels in the chamber at ambient levels.

Figure 3: Dynamic multiplex chamber system being used in the field.

Other resources

Notes and troubleshooting tips

When making isotope measurements using either open or closed chambers, it is essential that the measurement system has stabilised before collecting any gas samples for analysis. This not only ensures the collected gas in the chamber is truly representative of the respired CO2 but is also necessary for the measurement of accurate flux rates. Depending on the soil temperature and respiration rate, it can take an hour or more to reach steady state conditions.


Literature references

  1. Midwood, AJ and Millard P. Rapid Commun. Mass Spectrom. 2011; 25: 232.
  2. Högberg P, Ekblad A. Soil Biol. Biochem. 1996; 28: 1131.
  3. Paterson E, Thornton B, Midwood AJ, Osborne SM, Sim A, Millard P. Soil Biol. Biochem. 2008; 40: 2434.
  4. Soe ARB, Giesemann A, Anderson TH, Weigel HJ, Buchmann N. Plant Soil. 2004; 262: 85.
  5. Nickerson N, Risk D. Geophys. Res. Lett. 2009; 36: L08401.
  6. Bahn M, Schmitt M, Siegwolf R, Richter A, Brüggemann N. New Phytol. 2009; 182 (2): 451-460.
  7. Plain C, Gerant D, Maillard P, Dannoura M, Dong YW, Zeller B, Priault P, Parent F, Epron D. Tree Physiol. 2009; 29: 1433.
  8. Subke JA, Vallack HW, Magnusson T, Keel SG, Metcalfe DB, Högberg P, Ineson P. New Phytol. 2009; 183: 349.
  9. Midwood AJ, Thornton B, Millard P. Rapid Commun. Mass Spectrom. 2008; 22: 2073.
  10. Midwood AJ, Gebbing T, Wendler R, Sommerkorn M, Hunt JE, Millard P. Rapid Commun. Mass Spectrom. 2006; 20: 3379.
  11. Millard P, Midwood AJ, Hunt JE, Barbour MM, Whitehead D. Soil Biol. Biochem. 2010; 42: 935.
  12. Powers HH, Hunt JE, Hanson DT, McDowell NG. A dynamic soil chamber system coupled with a tunable diode laser for online measurements of δ13C, δ18O, and efflux rate of soil-respired CO2. Rapid Commun. Mass Spectrom. 2010; 24: 243.


Health, safety & hazardous waste disposal considerations


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