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J Sci Food Agric. 2014 Sep;94(12):2362-71. doi: 10.1002/jsfa.6577. Epub 2014 Mar 6.

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems.

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Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of Reading, RG6 6DW, United Kingdom.


It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant-soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.


agro-ecosystem management; carbon cycling; carbon tracking; climate change; decomposition; methods; rhizosphere carbon flow; soil microbial respiration

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