Roots of Decline? Assembly and Function of the Rhizosphere Microbiome in Relation to Yield Decline
Lead Research Organisation:
Natural History Museum
Department Name: Life Sciences
Abstract
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Technical Summary
Using established field sites across the UK, rhizosphere samples will be collected from 32 OSR cropping locations. Prokaryotic and eukaryotic microbe community composition will be determined using amplicon sequencing. Communities will be differentiated into core species which are widely distributed and locally abundant, and satellite species which are infrequent and rare. We will elucidate the role of management, environmental variables and distance as drivers of community assembly. Co-occurrence and co-exclusion relationships of rhizosphere taxa will also be determined. We will also focus on understanding those factors which determine distribution and assembly of specific taxa which our earlier work has suggested contribute to OSR yield decline. We will also determine relationships between microbiome composition and yield. Field experiments will be used to investigate changes in microbial community organisation and functioning during the transition from a healthy to a diseased state associated with yield decline. We will use 3 separate locations in order to investigate the extent to which changes in function are conserved across the landscape. Rhizosphere soil metatranscriptomes and root transcriptomes will be sequenced, and in particular, networks associated with microbial pathogenesis, and host defence and nutrition will be characterised. We will investigate the potential to manipulate the assembly of the rhizosphere microbiome through crop genotype and soil management. Four OSR genotypes which we have shown have contrasting root metabolomes will be grown in rotational field experiments and targeted amplicon sequencing used to study community assembly, including pathogens associated with yield decline. We will use a unique field resource at Rothamsted to determine scope for using soil management to influence recruitment of taxa into the root microbiome, including pathogens associated with yield decline.
Planned Impact
Plant -microbe interactions in the rhizosphere can have major impacts on crop yields, with pathogens generating global losses of billions of pound annually. In this project we provide fundamental new understanding about the factors which control the assembly of rhizosphere communities, and will use cutting edge next generation sequencing (NGS) methods to unravel the mechanisms by which plants affect, and are affected by, microbial communities. Importantly, we will use oilseed rape (OSR) as the model system for our research since it suffers from 'yield decline' arising from the development of a detrimental microbiome, which causes UK losses of £43-86 million/year. Our research will impact the following groups:
(1) 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 from 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.
(2) The agricultural industry, particularly stakeholders with an interest in promoting productivity and sustainability, including crop breeders, land managers and farmers. Industry will benefit from new scientific knowledge which will provide novel approaches to manage the rhizosphere: (a) we will identify microbial contributors to yield at the landscape scale, including, potentially, new pathogens, and soil and environmental characteristics which relate to pathogen distribution. This will underpin development of new crop protection strategies (eg via pesticides) (b) we will identify co-exclusion and co-occurrence relationships within the microbiome which could facilitate development of novel biocontrol approaches (c) we will identify 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 (d) we will provide soil management options to mitigate development of yield decline; this will provide tangible outputs to farmers within the project timeframe (e) we will elucidate the potential for rhizosphere microbiome engineering through crop genotype which could lead to rotational strategies, and breeding approaches, to manipulate the rhizosphere.
While providing outputs to the OSR industry (see letters of support from United Oilseeds and Elsoms) the principles of the work, and the tools we will develop, will be relevant to stakeholders across the industry (see letters of support from Agrii and Origin Fertilisers).
(3) Government (eg Defra) and industry organisations (eg NFU, HGCA) with a role in supporting and promoting the competitiveness of UK agriculture; in particular the research addresses the priorities of HGCA (see letter of support).
We will form a project steering group with industrial and government stakeholders which will advise on technology transfer. We will engage with these stakeholders through workshops at Warwick in months 24 and 42, project newsletters and the project website, which will provide a summary of project progress.
We also intend to engage strongly with the public. In addition to press releases, production of a video iCast and a project website, we plan a series of events at the Natural History Museum, London, where science derived from the project will be communicated directly to the public, including schoolchildren.
Society will benefit from trained researchers adept at multidisciplinary working, with skills in ecology, agricultural science and microbiology, and cutting edge NGS methods.
(1) 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 from 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.
(2) The agricultural industry, particularly stakeholders with an interest in promoting productivity and sustainability, including crop breeders, land managers and farmers. Industry will benefit from new scientific knowledge which will provide novel approaches to manage the rhizosphere: (a) we will identify microbial contributors to yield at the landscape scale, including, potentially, new pathogens, and soil and environmental characteristics which relate to pathogen distribution. This will underpin development of new crop protection strategies (eg via pesticides) (b) we will identify co-exclusion and co-occurrence relationships within the microbiome which could facilitate development of novel biocontrol approaches (c) we will identify 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 (d) we will provide soil management options to mitigate development of yield decline; this will provide tangible outputs to farmers within the project timeframe (e) we will elucidate the potential for rhizosphere microbiome engineering through crop genotype which could lead to rotational strategies, and breeding approaches, to manipulate the rhizosphere.
While providing outputs to the OSR industry (see letters of support from United Oilseeds and Elsoms) the principles of the work, and the tools we will develop, will be relevant to stakeholders across the industry (see letters of support from Agrii and Origin Fertilisers).
(3) Government (eg Defra) and industry organisations (eg NFU, HGCA) with a role in supporting and promoting the competitiveness of UK agriculture; in particular the research addresses the priorities of HGCA (see letter of support).
We will form a project steering group with industrial and government stakeholders which will advise on technology transfer. We will engage with these stakeholders through workshops at Warwick in months 24 and 42, project newsletters and the project website, which will provide a summary of project progress.
We also intend to engage strongly with the public. In addition to press releases, production of a video iCast and a project website, we plan a series of events at the Natural History Museum, London, where science derived from the project will be communicated directly to the public, including schoolchildren.
Society will benefit from trained researchers adept at multidisciplinary working, with skills in ecology, agricultural science and microbiology, and cutting edge NGS methods.
People |
ORCID iD |
David Bass (Principal Investigator) |
Publications
Adl SM
(2019)
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.
in The Journal of eukaryotic microbiology
Bass D
(2019)
The Pathobiome in Animal and Plant Diseases.
in Trends in ecology & evolution
Bass D
(2018)
Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity.
in Frontiers in microbiology
Bateman KS
(2022)
Amoebic crab disease (ACD) in edible crab Cancer pagurus from the English Channel, UK.
in Diseases of aquatic organisms
Bøgwald M
(2022)
Infection cycle of Marteilia pararefringens in blue mussels Mytilus edulis in a heliothermic marine oyster lagoon in Norway.
in Diseases of aquatic organisms
Collins E
(2022)
High prevalence of Paramarteilia canceri infecting velvet swimming crabs Necora puber in Ireland
in Diseases of Aquatic Organisms
Del Campo J
(2019)
The eukaryome: Diversity and role of microeukaryotic organisms associated with animal hosts
in Functional Ecology
Geisen S
(2019)
A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses
in bioRxiv
Hilton S
(2021)
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale
in Microbiome
Description | Increased awareness of diversity of microbes associated with larger organisms - the holobiont - and the roles such symbionts play, is becoming increasingly recognised by the general public. This awareness is also now influencing government policy with respect to animal, plant, and environmental health, and methods of monitoring and surveillance. |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink,Education,Leisure Activities, including Sports, Recreation and Tourism,Government, Democracy and Justice |
Impact Types | Policy & public services |
Description | August 2019: Past President's Plenary address at ISoP, Rome |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Plenary presentation at the annual meeting of the International Society of Protistologists, in role of Past President |
Year(s) Of Engagement Activity | 2019 |
Description | February 2019: Invited seminar, Oslo University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Research presentation with collaborators and wider audience in Oslo University Biosciences department |
Year(s) Of Engagement Activity | 2019 |
Description | Science Uncovered 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Science Uncovered event at The Natural History Museum (NHM), attended by c. 10,000 people - part of European Researchers' Night (EU funded). Showcasing the science and research at NHM. I contributed to two stalls - one of microeukaryotic diversity, the other on the SARISA (BBSRC) Roots of Decline project. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.nhm.ac.uk/visit/exhibitions/science-uncovered-2016.html |
Description | Symposium chair: eDNA, ecology and environment, World Aquaculture Society meeting New Orleans |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 40 people in symposium (eDNA, ecology and environment, World Aquaculture Society meeting, New Orleans). 5 talks followed by discussion and information sharing. |
Year(s) Of Engagement Activity | 2019 |