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

Abstract

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.

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

Figure 1

The terrestrial carbon cycle with the major processes mediated by soil microorganisms (adapted from Prosser125).

Figure 2

Fate of primary production inputs to soil. Plant-derived organic carbon (after appropriate extracellular depolymerisation) is processed by soil microorganisms to CO₂, microbial biomass and extracellular substances. Microbial necromass and metabolites are the precursors for stable soil organic matter, while extracellular microbial carbon may also influence the stability of soil organic carbon (SOC). Enzymes may catalyse the depolymerisation of soil macromolecular constituents, while other extracellular substances may promote aggregation and the physical protection of SOC. SOC (red boxes) is depicted as a continuum of structures derived from the progressive decomposition of litter and exudates and includes the microbial biomass carbon. Dissolved and exposed organic carbon (A) is available for microbial cellular uptake and metabolism (catabolism + anabolism) to produce CO₂ and new biomass respectively. Macromolecular or sorbed or occluded SOC is metabolically non-available (B) but may become available via enzymatic depolymerisation, desorption or exposure (I–III respectively), assuming adequate water, electron acceptors, heat, pH and nutrients for microbial activity.

Figure 3

Cereal crop production, Warwickshire, UK (image courtesy of JM Clark). Soils are often seen as simply ‘growing media’ for food crops; however, functioning of microbiological communities within soils not only influences the supply of essential plant nutrients but also has great implications for the global carbon cycle and climate system that determines whether environmental conditions are favourable for crop growth.