Stable carbon isotope fractionation as tracer of carbon cycling in anoxic soil ecosystems

While the structure of microbial communities can nowadays be determined by applying molecular analytical tools to soil samples, microbial function can usually only be determined by physiological experiments requiring incubation of samples. However, analysis of stable isotope fractionation might be able to analyse microbial function without incubation in soil samples. We describe the limitations of diagnosing and quantifying carbon flux pathways in soil by using the determination of stable carbon isotope composition in soil compounds and emphasize the importance of determining stable isotope fractionation factors for defined biochemical pathways. Fractionation factors are sufficiently different for some central biochemical pathways in anaerobic degradation of organic carbon. Thus, it is possible to quantify the relative contribution of CH4 production by hydrogenotrophic or aceticlastic methanogenic pathways, and of acetate formation by chemolithotrophic (acetyl-CoA synthase) or heterotrophic (fermentation) pathways. In addition, stable isotope analysis may allow the differentiation between different organic substrates used for degradation, for example, the relative contribution of root exudation versus soil organic matter degradation, provided the different substrates are sufficiently distinct in their isotopic compositions (e.g., mixture of C-3 and C-4 plants) and the carbon conversion pathways display only small fractionation factors or are identical for the different substrates.