U.S. Department of Energy, Office of Science

Program for Ecosystem Research

Research Project   Heterotrophic soil respiration in warming experiments: using microbial indicators to partition contributions from labile and recalcitrant soil organic carbon

Principal investigator:   Mark A. Bradford

Project goal

Develop a nucleic acid--based approach that elucidates the mechanisms underlying observed effects of soil warming on forest floor CO2 efflux.

Ecosystem being studied

Northern hardwood forest. The field study site is generally representative of northern components of the deciduous forest biome, which covers a large geographic area in the United States. The biome provides numerous, high-value goods and services. It also exchanges significant amounts of CO2 with the atmosphere.


The overarching hypothesis to be tested is that the initial, short-lived augmentation of soil CO2 efflux caused by a step-change soil warming is a result of the depletion of temperature-sensitive, relatively labile soil organic carbon pools. Repeated sampling at the site last year and in the current year supports this hypothesis. The data data indicate, however, that this mechanism alone cannot explain the equalization of soil CO2 efflux rates, during the early growing season, between soils warmed for 16 years and control, unwarmed soils. In addition, the data show that warming not only depletes more labile soil organic carbon pools but also more recalcitrant pools about which there is substantial debate with regard their temperature sensitivity.

The field data do not support hypotheses relating to temperature-acclimation of soil microorganisms, nor do the mechanistic modeling approaches that are being used in the project to test questions related to acclimation. Associated with the 16-year warming, however, there are substantial changes in soil microbial function, biomass, and community structure. The project design facilitates the linking of these microbial community level data with ecosystem carbon dynamics and this linking will constitute a substantial effort in the second half of the project. Already, the combined carbon substrate-genomic approaches that are being used are permitt tests of dogma in microbial ecology. Evidence of specialization in resource utilization by different fungal species on common plant-carbon inputs to soils was found.

Why this is important

Potential effects of warming on the rate of soil organic matter oxidation and/or the chemical fractions of organic matter that are decomposed could be important to soil biology, biogeochemistry, and plant mineral nutrition, and a positive feedback to warming caused by an increasing concentration of carbon dioxide in the atmosphere. Project data support the expectation that loss of soil organic carbon with warming will feedback positively to climatic change. By doing so, the data advance the current debate on the sensitivity of mineralization rates of the bulk of soil organic carbon to increasing temperature. The debate has so far been limited by a lack of long-term experimental data. This study provides these data and in a form that is suitable to test the latest set of mechanistic, multi-pool, soil organic carbon meatblism models. The data indicate that the concepts underlying these models are, at least in part, correct. Those microbial data being collecting will permit an incorporation of the underlying biology into these models, which should facilitate improved forecasting of soil organic carbon responses to changing temperatures (and hence improved prediction of future climatic change).


The project uses two ongoing soil warming experiments at Harvard Forest that represent two temporally distinct phases in the response of soil CO2 efflux to a step-change soil warming. The first experiment was initiated in 1991, and showed an immediate stimulatory effect of a step-change soil warming (+5 degrees Celsius, relative to ambient, in 5 x 5 m plots) on soil CO2 efflux rate that then declined progressively during 10 years, after which the CO2 release rate in warmed plots was (and still is) equivalent to the rate in unwarmed (control) plots. The second experiment began in 2003, again using a step-change +5 degrees Celsius warming treatment, but in a larger 30 x 30 m plot (unreplicated) matched with a 30 x 30 m control plot. To date, the second experiment has mirrored the first experiment, with an immediate large stimulation of soil CO2 efflux caused by the step-change warming.

The project is integrating techniques in molecular biology, field ecology and biogeochemistry, and ecological modeling to study potential links between the abundance of specific microbial nucleic acids and soil CO2 efflux rate in warmed and unwarmed soil plots. The approach involves four general activities:

(1) identify microbial indicator species associated with the degradation of labile and recalcitrant soil organic carbon compounds,

(2) estimate the abundances (i.e., quantity of DNA) and activities (i.e., quantity of RNA) of these microbial indicator species in warmed and unwarmed soils,

(3) evaluate relationships between the nucleic acid abundances of the microbial indicator species and the turnover of added 13-C-labeled labile (sucrose, L-asparagine) and recalcitrant (lignin, chitin, cellulose) carbon substrates, and

(4) develop a mathematical model to link quantitatively the activities of the microbial indicator species to rates of soil CO2 efflux.

Techniques being used include stable isotope probing, DNA-DNA hybridization, clone library, quantitative real-time polymerase chain reaction (PCR), and stable isotope pulse-chase experiments. Measurements in the field and the laboratory are being conducted.


Mark A. Bradford, University of Georgia

Jerry M. Melillo, Marine Biological Laboratory (subaward)

James F. Reynolds, Duke University (subaward)

Kathleen K. Treseder, University of California, Irvine (subaward)

Matthew D. Wallenstein, University of California, Santa Barbara (unfunded collaborator)

Funding period:   August 2004 to present