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Chamber. Mean del. del_std. Mean flux. flux_std. autotrophic fraction. partition_ stddv. 1. -29.56 b. 4.36. 2.63 d. 0.4. 0.5. 0.2. 2. -30.44 bc. 3.15. 3.4 c. 0.7. 0.39. 0.18. 3. -28.25 a. 2.79. 5.46 a. 1.1. 0.66. 0.16. 4. -31.66 c. 4.87. 2.6 d. 0.6. 0.22. 0.17. 5.

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Mean del


Mean flux


autotrophic fraction

partition_ stddv











































Partitioning soil respiration between auto- and heterotrophs using stable carbon-13 isotope discrimination

David Y. Hollinger1, D. Bryan Dail2, Eric A. Davidson3, Holly Hughes3, Andrew D. Richardson4

1.USDA Forest Service, Durham, NH ([email protected]), 2. University of Maine, 3. The Woods Hole Research Center, 4. Harvard University


Virtually all major terrestrial carbon cycle models postulate a decreasing future C sink and, in fact, a positive feedback to increasing atmospheric CO2 concentration as the climate warms (Friedlingstein et al. 2006). A particularly striking example of this behavior is the coupled carbon-climate HadCM3 model results (Cox et al. 2000) that showed a runaway increase of 250 ppm CO2 between 2050 and 2100. The mechanism for such future releases of CO2 from terrestrial systems in these models is the loss of soil carbon via enhanced respiration.

In order to have confidence in these future predictions, models must be able to duplicate present patterns of soil respiration in natural stands and experimental manipulations. Estimating the contributions of autotrophic respiration from roots and the rhizosphere (RA) and heterotrophic respiration (RH) to total soil respiration (RS) can provide powerful constraints to ecosystem carbon models (Smith and Fang 2010, Trumbore 2006).

Using an inverse modeling analysis at the Howland forest, we have demonstrated that both annual woody biomass increment and soil respiration measurements provide valuable constraints to eddy covariance NEE measurements and contribute to marked reductions in uncertainties in parameter estimates and model predictions (Richardson et al. 2010). However, although model skill for predicting total ecosystem respiration improved when soil respiration constraints were added, root and soil C pool dynamics and fluxes remained poorly constrained in the DALEC ecosystem carbon model, suggesting that these should be targets for future measurement efforts.


Chambers differed significantly in their mean flux and d13C (Fig. 3). They also differed in the amplitude of diurnal variation. We hypothesized that these variations were associated with differences in the relative contribution of autotrophic and heterotrophic respiration in each chamber.

Solving for the best combination of RA and RH for each chamber yields a range of solutions that result from the uncertainty in flux and isotope measurements (Fig. 4). A relatively limited range in the dA and dH, source signatures for RA and RH, provide the best overall fit:

dA = -25.2 ± 1.5

dH = -34.0 ± 1.7

For the site (all chambers, total flux weighted) the mean partitioning observed was 53 ± 1% autotrophic and 47± 1% heterotrophic respiration.

These results suggest this approach may be useful for partitioning soil respiration and further constraining ecosystem carbon model fluxes.

Fig. 4. MCMC parameter estimates for autotropic and heterotrophic d13C end-members and fraction of total respiration from autotrophs for 3 chambers.


  • Autotrophic and heterotrophic respiration can be partitioned by a variety of techniques including root exclusion or trenching, separating roots from soil and integrating the respiratory contribution of each, and various techniques utilizing carbon isotopes (Hanson et al. 2000). The isotopic methods are potentially attractive as they minimize disturbance of the soil and roots. We assess here a separation method based on measuring the flux and 13C isotopic signal of soil respiration via cavity ringdown spectroscopy (CRDS) from a series of automatic chambers at the Howland Forest in Maine, USA. In this system chambers are closed sequentially for 10 minutes and the airstream circulated through the analyzer and back to the chamber. The analyzer monitors the increasing CO2 concentration and changing isotopic d13C of the airstream (Fig. 1) to estimate the isotopic discrimination of soil respiration via the Keeling plot approach (Fig. 2).

  • There are a number of technological and theoretical issues that may impede the interpretation of these data:

  • 1)     Instrumentation issues – (air leakage in the instrument pump, transient response errors, dilution and band broadening effects of water vapor, cross sensitivity of d13C to CO2).

  • 2)     Disturbance of the depth profile of δ13CO2 caused by soil chambers could produce artifacts in δ13CRS measurements (Bowling et al., 2003).

  • 3)     δ13C enrichment of SOM often increases with soil depth, and this depth distribution must be measured and/or the depth from which most CO2 production occurs must be known.

  • 4)     Variation in canopy conditions throughout the day, with passing synoptic weather patterns, and as seasons change, affects the isotopic discrimination of photosynthesis (Farquhar et al. 1989, Ekblad and Hogberg 2001; Ekblad et al. 2005), which can cause variation in the isotopic signature of RA (Gessler et al. 2007).

  • 5)     Isotopic fractionation in non-equilibrium diffusive environments can obscure (or mimic) a true time-varying signal (Nickerson and Risk 2009, Moyes et al. 2010).

  • If we assume each chamber measures a combination of RA and RH, for each chamber i, we have the total CO2 flux (RSi) and a flux-weighted d13Ci (di );

  • RSi = RAi + RHi

  • di = (dA RAi + dH RHi) / RSi

  • Although this system is underdetermined (fewer equations than unknowns), because we have a variety of constraints (all RAi and RHi >=0) and differences between chambers, if the d13C of RA and RH are distinct then the system can be ‘solved’ (or more correctly, a range of solutions obtained, here using the Metropolis algorithm) for dA, dH, the isotopic discrimination of auto- and heterotrophs and the partitioning of each chamber.

Fig. 1 (above). Raw [CO2] and del value of recirculating airstream. Fig. 2 (right). Example inverse (Keeling) plot from one 10-min series of chamber measurements.

Fig. 2


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  • Richardson, A.D., M. Williams, D.Y. Hollinger, D.J. P. Moore, D.B. Dail, E.A. Davidson, N.A. Scott, R.S. Evans, H. Hughes, J.T. Lee, C. Rodrigues, and K. Savage. 2010. Estimating parameters of a forest ecosystem C model with measurements of stocks and fluxes as joint constraints. Oecologia 164:25-40.

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  •  This work was supported by the USDA Forest Service and Office of Science (BER), U.S. Department of Energy, through the Terrestrial Carbon Program under Interagency Agreement No. DE-AI02-07ER64355.

Fig 3. Diurnal pattern of soil respiration and source del13C.