SCIENCE PROJECT

ROOTS OF DECLINE? ASSEMBLY AND FUNCTION OF THE RHIZOSPHERE MICROBIOME IN RELATION TO CROP YIELD

Investigating and understanding the contribution of root-associated microorganisms to the health of oilseed rape and to maintaining crop yields.

PROJECT SUMMARY

START DATE:

Monday, March 9, 2015 - 14:45

DURATION:

4 years

PROJECT LEADER:

FUNDERS:

  • BBSRC

GRANTS:

The microorganisms that colonise the root and soil closely associated with the root zone, collectively known as the rhizosphere microbiota, have major influences on crop growth and yield. In oilseed rape (OSR) and other crops, the development of a detrimental microbiome is associated with substantial declines in yield. Here we will use OSR cropping systems to determine for the first time how the rhizosphere microbiome is organised at scales from the individual plant to the whole landscape, the factors which drive community assemblage, its functional significance for the crop, and the extent to which the microbiome can be manipulated using crop genotype and soil management to benefit crop productivity. The work will open avenues to predict and manage the rhizosphere microbiome to improve yields in cropping systems.

DETAIL

Plant roots live in close association with diverse microbial communities selectively recruited from soil via root-exuded carbon: detrimental biota recruited by crop plant rhizospheres cause significant annual global losses. Strategies to robustly predict and manipulate the communities which assemble in the rhizosphere can potentially deliver great benefits but there is a fundamental lack of understanding of the processes involved. Currently knowledge of how microbial communities interact with each other and plant roots is limited to specific microbes that are amenable to laboratory study but next generation sequencing (NGS) offers potential for a paradigm shift in our ability to resolve the structure and function of rhizosphere microbial communities. We will use the latest NGS methods with oilseed rape (OSR) as a model system. OSR yields suffer 6-25 % annual yield decline due to development of detrimental rhizosphere biota for which there is no treatment. We will elucidate the relative roles of local climate, soil biodiversity and properties, rotation and geographical distance in shaping rhizosphere microbial communities to understand factors which control the enrichment of detrimental rhizosphere biota, by resolving specific microbe-microbe interactions which lead to exclusion or recruitment of microbes including pathogens. Metatranscriptomics will determine the specific genes expressed by plants and microbes in the rhizosphere. Importantly, our work will be conducted in the field so we can understand the specific changes associated with a change from a healthy rhizosphere to one in which yield is impacted by development of detrimental biota and identify the potential to manipulate rhizosphere recruitment using crop genotype and soil management. Using commercial OSR crops means results will have immediate agronomic relevance and deliver tangible short/ medium term opportunities for industrial stakeholders to increase crop productivity.

Sampling - copyright Rothamsted Research

The project will provide fundamental new understanding about the factors which control the assembly of rhizosphere communities facilitated by cutting edge NGS methods. As well as providing soil management options for farmers to mitigate development of yield decline within the project timeframe, research will benefit the academic community, particularly those with interests in agricultural systems biology, plant-soil interactions, plant pathology and environmental microbiology. Researchers will particularly benefit from our use of NGS approaches to unravel plant-microbe-soil interactions, and demonstration of engineering the rhizosphere biota for beneficial functions. We will engage with researchers through journal papers and at key scientific conferences. The sequencing experiments are a valuable experimental resource for workers in related fields. We will open this data to other researchers for complimentary work, providing added value to the experiments. Other potential benefits include new scientific knowledge providing novel approaches to manage the rhizosphere: we will identify microbial contributors to yield at the landscape scale including new pathogens and soil and environmental characteristics which relate to pathogen distribution. This will underpin development of new crop protection strategies (e.g. via pesticides). We will identify co-exclusion and co-occurrence relationships within the microbiome which could facilitate development of novel biocontrol approaches and changes in microbial function and associated plant responses as it changes from a healthy to unhealthy state. This could lead to targeted gene and physiology based crop improvement strategies. The potential for rhizosphere microbiome engineering through crop genotype could lead to rotational strategies, and breeding approaches, to manipulate the rhizosphere.

COLLABORATORS

  • University of Warwick - Professor Gary Bending; Dr Sally Hilton; Dr Emma Picot; Dr Graham Teakle 
  • Earlham Institute - Dr Jonathan Moore
  • Manchester Metropolitan University - Professor Chris van der Gast
  • Harper Adams University - Professor Peter Mills
  • Natural History Museum/ CEFAS - Dr David Bass 
  • Velcourt - Keith Norman

EXTERNAL RESOURCES

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