Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes

Despite the fundamental importance of rhizosphere C-flow in managed and natural systems, reliable measurement/resolution of C-flow and assessment of its consequences have largely remained elusive to soil biologists. Techniques involving both radioactive (¹⁴C) and stable (¹³C) isotopes of carbon have made some progress in terms of studying rhizosphere C-flow. Pulse-chase techniques have been used effectively to study dynamics of C-transfer to the rhizosphere and rhizosphere microbial biomass. The information obtained through pulse-chase is strongly dependent on the chase period following the labelling event. Continuous labelling is primarily used to determine plant inputs to soil over an extended time period and includes all kinds of C input – from root turnover, root respiration, root exudation, production of mucilage, etc. One of the main constraints to both approaches is that distinguishing root from microbial respiration is difficult, if not impossible. ¹³C techniques have gone some way towards resolving this difficulty, although ¹³C signatures in the plant–soil system are not easy to interpret and detailed resolution of carbon flow through different components of the rhizosphere biomass is unlikely to be achieved in such an inherently `noisy' system. Recent developments in molecular biology now provide a new opportunity to resolve rhizosphere C-flow and its implications. Reporter gene systems where, for example, rhizobacteria are marked with lux and unstable gfp reporters, overcome the difficulty of distinguishing root and microbial C fluxes and complement the isotopic and more traditional approaches. Reporter systems have now begun to resolve the competitive C sink strengths of different components of the rhizosphere microbial community and assess how a rhizobacterial inoculum may change C-flow in applications such as disease control and rhizoremediation of contaminated land. Fusion of reporter genes to nutrient (N and P) starvation genes in rhizobacteria has also enabled in situ characterisation of nutrient depletion around the root and assessment of the impact of changes in C-flow (such as those induced by climate change) on nutrient depletion dynamics. The availability of an integrated approach involving isotopic, molecular biological and other techniques now offers an exciting new era where reliable measurement and resolution of rhizosphere C-flow (and its consequences) can contribute to our understanding of ecosystem function and to management of crop-microbe interactions.