Award details

Manipulating the rhizosphere for function

Reference	BB/C512853/1
Principal Investigator / Supervisor	Professor Ken Killham
Co-Investigators / Co-Supervisors	Professor Marcel Jaspars, Professor James I Prosser, Dr Dominic Standing
Institution	University of Aberdeen
Department	School of Medical Sciences
Funding type	Research
Value (£)	313,424
Status	Completed
Type	Research Grant
Start date	11/04/2005
End date	10/04/2008
Duration	36 months

Abstract

Functional manipulation of the rhizosphere (for biocontrol, biofertilisation and bioremediation) remains one of the most important yet elusive goals in plant soil biotechnology. The main barrier to realising this immense potential is lack of understanding of how plants, through the many forms of carbon released from their roots, select for key rhizosphere microorganisms and switch on their associated functional genes. The recent development of combined molecular and isotopic techniques now makes it possible to resolve this critical issue. The aim of this research is to use stable isotope probing (SIP), to link components of plant-derived rhizosphere carbon flow directly to a group of rhizosphere microbes (fluorescent pseudomonads) known to be involved in an important rhizosphere function (antagonism of the wheat Take-all fungus Gaeumannomyces graminis ¿ Ggt) and to link the carbon flow to the genes involved in that function. This is an entirely new approach to rhizosphere research. It offers a platform technology that will provide information on linkage between many different microbes, and their associated processes to carbon triggers. This offers the scope for manipulating rhizosphere carbon flow via genomics or other approaches. In this way, rhizosphere function itself can be managed in a sustainable manner. We will use a high throughout physiological screen to allow a focussed assessment (using Response Surface Analysis) of an increased capacity for a model rhizosphere bacterial community to produce antibiotics known to control Ggt. The model will contain a high degree of realism through use of natural soil microcosms of known matric potential and a novel artificial root which simulates rhizosphere carbon flow. Using this system, we will apply combinations of C compounds (substrates and signals) found in root exudates, informed by both the literature and from screening healthy and Ggt infected wheat plants. To characterise and quantify chemical species in root exudates we will use evaporative light scattering detection (ELSD) linked to MS and HPLC. This approach will allow us to separate and quantify metabolites that are usually missed by standard UV detection. Metabolites of interest will be collected and purified by repeated semi-preparative HPLC and fractions will be collected for structural determination using 1D nuclear isotope probing (SIP) of targeted mRNA genes and analytical verification of the presence of the antibiotics phenazine and DAPG. Selection of fluorescent pseudomonads, which are known to be involved in antagonism of Ggt, by low molecular weight exudates and signals mimics blockers will be tested by SIP of pseudomonad communities following amendment of soil with a pulse-chase of 13C-labelled substrates, targeting both extracted DNA and RNA. Extractions and purifications will be carried out using existing methods. Extraction of mRNA requires additional procedures and we will use recently published successful methods. Following extraction, 12C- and 13C-labelled nucleic acids will be separated by centrifugation and PCR or RT-PCR amplification will be carried out to target DNA for presence of communities growing on 13C- substrates or RNA for activity of metabolising community components. The combined isotopic molecular techniques developed in this project will be used to investigate the conditions required for selection of antibiotic-producing fluorescent pseudomonads by wheat rhizosphere carbon flow and to relate this information to plant and microbial genomics for potential rhizosphere antibiotic manipulation to exert biocontrol. The development of this platform technology opens the way for broader, functional manipulation of the rhizosphere.

Summary

unavailable

Committee	Closed Committee - Agri-food (AF)
Research Topics	Crop Science, Microbiology, Plant Science, Soil Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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