Roots of Decline? Assembly and Function of the Rhizosphere Microbiome in Relation to Crop Yield
Lead Research Organisation:
Rothamsted Research
Department Name: Sustainable Agriculture Sciences-H
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.
Publications
Stroud J
(2016)
Population collapse of Lumbricus terrestris in conventional arable cultivations and response to straw applications
in Applied Soil Ecology
Stroud J
(2017)
Cover cropping with oilseed radish ( Raphanus sativus ) alone does not enhance deep burrowing earthworm ( Lumbricus terrestris ) midden counts
in Soil and Tillage Research
Hilton S
(2021)
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale.
in Microbiome
Description | The Roots of Decline project has confirmed that crop yields are improved by increasing rotation length. This increase was associated with a decrease in plant pathogens. Microbial community structure was shown to be influenced by niche (roots, rhizosphere, bulk soil), treatment (rotation length), location (both locally and on the landscape scale) and abiotic factors such as pH. In addition, next generation sequencing identified specific bacteria, fungi and protists, previously unidentified microbes, potential new and known pathogens that correlated to rotation length and yield. It is hoped that correlations between high yielding cropping systems and associated microbial communities will lead to better farm management and the potential identification of plant growth promoting microbes. Comparison between metagenomic (DNA based) and metatranscriptomic (RNA) microbial methodologies showed that DNA based analysis of soil microbial populations within the crop showed evidence of the previous years crop and hence could potentially be used to determine potential plant pathogen levels in the following year. RNA based analysis showed the active microbes at the time sampling, future analysis should identify the level of plant growth promoting populations as well as the active plant pathogens. |
Exploitation Route | It is hoped that correlations between high yielding cropping systems and associated microbial communities will lead to better farm management and the potential identification of plant growth promoting microbes and whether it is a cohort of plant pathogens that contribute to yield decline and not just a single organism. |
Sectors | Agriculture Food and Drink |
Description | Public talk for the International Year of Soil "Microbial biodiversity in agricultural soils - does it matter?", Rothamsted Research, Harpenden (July 16th 2015) Interactive public display "Journey to the centre of the earth - the first 23 cm" at the "Soil is Life" open day, Rothamsted Research, Harpenden (17 May 2015) Talk to farmers and agronomists "Can we manage the soil and root microbiome?", Laws Fertilisers Soils Seminar, Great Massingham, Norfolk (28 January 2016) Talk to farmers and agronomists at the RRA Spring meeting Managing Soil: Inputs vs Outputs - "The potential for controlling the N cycle in soil: reducing nitrous oxide emission", Rothamsted, Harpenden (3 March 2016) Interviewed by Brooke Borel for her online publication "Mental Floss" to discuss launch of the Global Soil Biodiversity Atlas (29 April 2016) Interviewed by Amanda Yorwerth from Radio Verulam for her programme "Environment Matters" (17 May 2016) Poster presentation: Life beneath your feet: the soil food web - Cereals 2016, Cambridgeshire (16 June 2016) Poster and presentation at "Science Uncovered" at the Natural History Museum, London (30 September 2016) Presentation: Yield Gap workshop, Rothamsted Research, Harpenden (19 December 2016) Presentation and interactive display: 'Roots of Decline: Oil Seed Rape Yield Decline' - Cereals 14th -15th June 2017) |
First Year Of Impact | 2015 |
Sector | Agriculture, Food and Drink,Environment |
Impact Types | Cultural Societal |
Description | Environment, Food and Rural Affairs (EFRA) parliamentary committee visit to Rothamsted. |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Title | Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale |
Description | The datasets generated and/or analysed during the current study are available in the NCBI Sequence Read Archive under BioProject ID PRJNA548438. The sequences of OTUs highlighted in this study are deposited in the NCBI GenBank database under accession numbers MN045353-MN045395 (16S rRNA), MN047171-MN047210 (ITS) and MN046118-MN046154 (18S rRNA). |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Data indicates that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Importantly, this study demonstrates agronomic management, such as crop rotation, plays an important role in promoting beneficial microbes, and reducing pathogens. Targeted isolation of these newly identified beneficial biota, such as strains related to Tetracladium spp. and Flavobacterium is critical to develop our understanding of plant-microbe and microbe-microbe interaction mechanisms. This will provide a platform to devise novel strategies to promote plant health |
Description | 18th International Symposium of Microbial Ecology, Lausanne, Switzerland. 14-19 August 2023 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Adriana Torres-Ballesteros presented 'Microbiome Connectivity Drives Productivity in Oilseed Rape Crops' |
Year(s) Of Engagement Activity | 2022 |
Description | 2nd Plant Microbiome Symposium Amsterdam 19th - 21st Feb 2018 - Roots of Decline? - Assembly and Function of the Rhizosphere Microbiome in Relation to Crop Yield |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presented by S Schreiter, IM Clark, & PR Hirsch |
Year(s) Of Engagement Activity | 2018 |
Description | AICC (Association of Independent Crop Consultants) Workshop |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The importance of maintaining healthy soils in agricultural systems by improving crop rotations to increase beneficial rhizosphere microbiomes and reducing the abundance and impact of crop pathogenic microbes and hence improve crop yields. Also presented work on the potential use of plant growth promoting bacteria to improve crop yields by improving nutrient use efficiency for crops and potential protection against crop fungal pathogens. Work was also presented on the improved technologies for monitoring soil health, including wireless moisture probes and optic fibres to measure CO2 emissions and structural changes to agricultural soils during the growing season. |
Year(s) Of Engagement Activity | 2022 |
Description | Cereals 14th -15th June 2017 'Roots of Decline: Function of the rhizosphere microbiome' |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Cereals is the leading technical event for the UK arable industry, attracting over 20,000 visitors. The presentation showed the importance of crop rotations in reducing yield decline, reducing the build up of below ground microbial pests and in maintaining a healthy soil. |
Year(s) Of Engagement Activity | 2016,2017 |
Description | Cereals 2022 (Duxford) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The importance of maintaining healthy soils in agricultural systems by improving crop rotations to increase beneficial rhizosphere microbiomes and reducing the abundance and impact of crop pathogenic microbes and hence improve crop yields. |
Year(s) Of Engagement Activity | 2022 |
Description | Festival of Ideas |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Celebration of 175th year with a Festival of Ideas. The festival brought together activities, exhibitions and demonstrations to immerse the general public in the science of feeding the world. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.rothamsted.ac.uk/events/rothamsted-festival-ideas |
Description | Interactive public display at the "Soil is Life" open days |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | We updated our "Journey to the centre of the earth - the first 23 cm" interactive display for school and public open days to mark the International Year of Soils, exhibited at Rothamsted Research, Harpenden at part of the "Soil is Life" open days. New exhibits added to display included oilseed rape plants and a poster to explain the "Roots of Decline" Project |
Year(s) Of Engagement Activity | 2015 |
Description | Invited Lecture: Rothamsted, The Long Game: classical and long-term experiments. 5th July 2017. Centre for AgriBioscience and Latrobe University, Victoria, Australia |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | As part of the BBSRC OCP Award 'Kenyak-yeye: UK-Australian Global Soil Meta-omic Programme' visited Centre for AgriBioscience and Latrobe University, Victoria, Australia. Station Seminar. Covered long-term experiments, yield decline and molecular approaches to N and P cycling in agricultural systems. Questions and discussions followed as similar experiments set up in Australia and interest in soil/plant and DNA archiving. |
Year(s) Of Engagement Activity | 2017 |
Description | Invited Speakers '2nd International Workshop on Food Security' UFLA, Lavras/MG - Brazil |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Tim Mauchline, Ian Clark, Tessa Reid and Rodrigo Taketani all gave presentations about the current and future research at Rothamsted to 50 students and staff members of Federal University of Lavras, Brazil. Potential future collaborations and funding opportunities were discussed. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited participant in AgMicrobiomes, NSF-funded workshop held in the Asilomar conference centre in California, USA |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Invited to take part in AgMicrobiomes workshop in the USA, organised to discuss the best approaches for obtaining funding for microbiome research in the field of crop science |
Year(s) Of Engagement Activity | 2016 |
Description | John Innes Center, Women of the future, talk to students about careers for women in science |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | About 160 pupils attended the Women in Science event at the John Innes Centre. Scientists from a wide background presented their work and talked to students about the opportunities and variety of careers available. |
Year(s) Of Engagement Activity | 2020 |
Description | MMEG 2017: 14-15th December 2017: Warwick University 'Effect of land use intensity on soil microbial functions' Aimeric Blaud |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Molecular microbial ecology group, annual conference. Intended for PhDs and new post-docs to show case their current and developing research areas. Ideal conference for new collaborations and exchange of ideas and methodologies. |
Year(s) Of Engagement Activity | 2016,2017 |
Description | MPs Visit: Environment, Food & Rural Affairs Committee roundtable discussion and tours. |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | MPs Visit: Environment, Food & Rural Affairs Committee roundtable discussion and tours. Threats & opportunities for soil health; ELMs & government support, research on healthy soils, including metrics & data. Lab tours, potential of microbiomes within farming practice, pathogen monitoring, healthy soils and ELMS. |
Year(s) Of Engagement Activity | 2023 |
Description | New Scientist Live (ExCel Centre, London) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Over 18,000 people attended New Scientist Live and at least 300 attended our display (Journey to the Centre of the Earth, the first 23 cm). Display included the importance of crop rotations to reduce crop yield decline, the introduction of the potential of beneficial microbes for reducing the reliance on inorganic fertilisers and control plant crop pathogens. |
Year(s) Of Engagement Activity | 2022 |
Description | Poster and presentation at "Science Uncovered" at the Natural History Museum, London |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Presentation - display and posters - at the "Science Uncovered" event held at the Natural History Museum, London aimed at the general public and schoolchildren |
Year(s) Of Engagement Activity | 2016 |
Description | Poster presentation: Cereals 2016, Cambridgeshire |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Presented a poster "Life beneath your feet: the soil food web" at Cereals 2016, the main event for those involved in arable agriculture. |
Year(s) Of Engagement Activity | 2016 |
Description | Public talk for the International Year of Soil "Microbial biodiversity in agricultural soils - does it matter?" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Public lecture held in the evening at Rothamsted Research to mark the International Year of Soils, aimed at a general audience drawn from the locality, well attended, many questions from audience, based on my long research experience at Rothamsted but also highlighting new work |
Year(s) Of Engagement Activity | 2015 |
Description | School Visit (Harpenden). Diversity of life in Soil |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Demonstrations of soil erosion, diversity and benefits of the living things in soils (microbes to mesofauna) and how germs can be spread on hands. Given to a local junior school class of 32 pupils. |
Year(s) Of Engagement Activity | 2020 |
Description | Talk to farmers and agronomists at the RRA Spring meeting Managing Soil: Inputs vs Outputs, Rothamsted Research, Harpenden |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Talk to farmers and agronomists "The potential for controlling the N cycle in soil: reducing nitrous oxide emission" at a RRA meeting in Harpenden |
Year(s) Of Engagement Activity | 2016 |
Description | UK Department for Business and Trade, New Zealand |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Broad range of topics, from agricultural practices (rotations, legacy effects for pathogen and break crops), plant growth bacteria as inoculum, syncoms or mechanisms. Agricultural tipping points and Soil Health Indicators |
Year(s) Of Engagement Activity | 2023 |
Description | Workshop: Omya Environmental Solutions (Switzerland) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Presented research on LTEs, Plant Growth Promoting Bacteria, UK Crop Microbiome Cryobank project and their potential future uses. |
Year(s) Of Engagement Activity | 2023 |
Description | Yara (Lancrop Laboratories) workshop |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Feasibility for using amplicon sequencing as part of their analytical portfolio. Discussed pros and cons. Potential for future collaborations and proposals |
Year(s) Of Engagement Activity | 2023 |
Description | member of the Microbiology Society Microbiome Expert Working Group |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | An expert working group set up by the Microbiology Society which has organised a stakeholder workshop and is drawing up a document to advise government and funding agencies on the important of microbiome research |
Year(s) Of Engagement Activity | 2016,2017 |
Description | talk to farmers and agronomists at the Laws Fertilisers Soils Seminar, Great Massingham, Norfolk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Industry/Business |
Results and Impact | Gave a talk to farmers in Norfolk "Can we manage the soil and root microbiome?" and answered questions |
Year(s) Of Engagement Activity | 2016 |