A range of molecular methods (including PCR with universal and selective primers; metagenomic cloning to target functional genes; direct high-throughput sequencing; microarray analyses) is being developed to identify and monitor the population dynamics of the predominant soil microorganisms involved in nutrient cycling, remediation of pollutants or root colonisation. Microbial community DNA and RNA will be analysed at micro-scale and larger scales (from root sections to field-collected whole root systems) to determine which microbial groups are associated with beneficial properties and which genes are active in the rhizosphere. Uplift funding is used in close collaboration with WP1 to examine genes responsible for different parts of the nitrogen cycle in soil and the impact of metal pollution on the population size and diversity of three groups of microbes with different growth and survival strategies.

In agriculture, soil nutrients are supplied in excess to ensure that all the requirements for maximal yields are achieved. As inputs are decreased, we aim through collaboration with work in WP3 and WP4, to manipulate the rhizosphere to trap more nutrients, decrease leaching and to improve root health. Roots change their pattern of growth and localised gene expression to modify the rhizosphere and improve access to nutrients, either directly by changing the local physico-chemical environment or indirectly, by influencing rhizosphere microbial populations. The relevance of this information (collected in vitro) to the root/soil interface will be investigated using microelectrode measurements on the surface of roots (rhizoplane). Observed changes of several pH units over just a few microns are likely to have large effects on the local populations of bacteria and may also influence root development. To examine these potential effects, the root surface will be inoculated with specific types of bacteria and specific promoters will be used to target gene expression in specific root cell types. These very local pH microsites may be very important for increasing nutrient availability for nutrients such as phosphate which are known to be less mobile in the soil. Long term experiments at Rothamsted will provide phosphate depleted soils that will be used to test this hypothesis.