PUSHING THROUGH HARD TIMES: uncovering how roots sense soil compaction
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Biosciences
Abstract
Food security represents a major global issue. Topsoil, the most precious "natural capital assets", provides nearly 95% of food. The sense of urgency over topsoil is growing as the population is projected to reach 9 billion by 2050. Compaction hampers soil's ability to filter water, absorb carbon and retain water and nutrient to support the crop plants. The ability of a crop to efficiently absorb water and nutrients relies on its root system to fully explore soil available.
Use of heavy farming equipment, intensity of farm traffic and overgrazing lead to soil compaction. For example, the average weight of vehicles used on farms has approximately tripled since 1966 and maximum wheel loads have risen by a factor of six. Soil compaction can reduce crop yields by as much as 60%. Therefore, developing compaction resistant crops is of paramount importance. Despite its increasing global agronomic importance, little is known about how crop roots may respond to soil compaction.
My BBSRC Discovery Fellowship investigates how crop roots respond to soil compaction and then use this knowledge to develop crops with improved penetration ability. My project initially attempts to 'fill in the gaps' between roots sensing soil compaction and then altering their growth and shape of their root tips. To help my studies, I have already identified plant signals and genes such as ethylene and EIN2 that are important for this process. Several promising approaches will also be conducted including modifying roots to be less sensitive to ethylene.
The knowledge gained from my fellowship will provide new information about the key genes and processes controlling root responses to soil compaction, helping breeders design novel approaches to manipulate root growth to enhance resource capture and yield in crops. Developing future crops resistant to soil compaction can help their roots forage deeper for water to help mitigate drought stress (hard soil which is tough to penetrate), reduce flooding (compacted soil poses increased risk of flooding by restricting the water absorption from the surface), nitrogen stress (as this nutrient leach deeper in soil) and also capture more carbon in the soil.
My fellowship project will be undertaken in Plant Sciences at the University of Nottingham. The University hosts a world leading multidisciplinary team of researchers composed of experts from Maths, Plant, Crop, Soil and Computer Sciences, all dedicated to 'uncover' the hidden half of plants. To achieve this, these researchers have created the Hounsfield Facility which hosts state-of-the-art microCT scanners and other advanced imaging platforms.
I will also benefit from the unparalleled support of my host Prof. Malcolm Bennett and colleagues Soil Scientist Prof. Sacha Mooney and Crop Scientists Dr. Sean Mayes, Dr. Rahul Bhosale and Dr. Darren Wells. My project also involves international and UK collaborators which include experts in Sweden (Prof. Karin Ljung for hormone analysis), China (Prof. Dabing Zhang providing rice resources and expertise) and Rothamsted Research (Dr. Steve Thomas and Dr. Richard Whalley, wheat genetics and soil compaction expertise).
Use of heavy farming equipment, intensity of farm traffic and overgrazing lead to soil compaction. For example, the average weight of vehicles used on farms has approximately tripled since 1966 and maximum wheel loads have risen by a factor of six. Soil compaction can reduce crop yields by as much as 60%. Therefore, developing compaction resistant crops is of paramount importance. Despite its increasing global agronomic importance, little is known about how crop roots may respond to soil compaction.
My BBSRC Discovery Fellowship investigates how crop roots respond to soil compaction and then use this knowledge to develop crops with improved penetration ability. My project initially attempts to 'fill in the gaps' between roots sensing soil compaction and then altering their growth and shape of their root tips. To help my studies, I have already identified plant signals and genes such as ethylene and EIN2 that are important for this process. Several promising approaches will also be conducted including modifying roots to be less sensitive to ethylene.
The knowledge gained from my fellowship will provide new information about the key genes and processes controlling root responses to soil compaction, helping breeders design novel approaches to manipulate root growth to enhance resource capture and yield in crops. Developing future crops resistant to soil compaction can help their roots forage deeper for water to help mitigate drought stress (hard soil which is tough to penetrate), reduce flooding (compacted soil poses increased risk of flooding by restricting the water absorption from the surface), nitrogen stress (as this nutrient leach deeper in soil) and also capture more carbon in the soil.
My fellowship project will be undertaken in Plant Sciences at the University of Nottingham. The University hosts a world leading multidisciplinary team of researchers composed of experts from Maths, Plant, Crop, Soil and Computer Sciences, all dedicated to 'uncover' the hidden half of plants. To achieve this, these researchers have created the Hounsfield Facility which hosts state-of-the-art microCT scanners and other advanced imaging platforms.
I will also benefit from the unparalleled support of my host Prof. Malcolm Bennett and colleagues Soil Scientist Prof. Sacha Mooney and Crop Scientists Dr. Sean Mayes, Dr. Rahul Bhosale and Dr. Darren Wells. My project also involves international and UK collaborators which include experts in Sweden (Prof. Karin Ljung for hormone analysis), China (Prof. Dabing Zhang providing rice resources and expertise) and Rothamsted Research (Dr. Steve Thomas and Dr. Richard Whalley, wheat genetics and soil compaction expertise).
Technical Summary
Soil compaction represents a major challenge facing modern agriculture due to changing tillage practices and increased weight of modern farming equipment. When soil strength becomes excessive crop roots are unable to penetrate soil due to mechanical impedance. Despite its importance, there is a significant knowledge gap concerning how crop roots overcome soil compaction. I recently discovered that the gaseous hormone signal ethylene regulates root responses to mechanical impedance in crops after I demonstrated rice roots of ethylene response mutants can penetrate highly compacted soil, in stark contrast to wild type plants.
My BBSRC Discovery fellowship aims to discover how ethylene controls compaction responses in crop roots and then exploit this knowledge to engineer novel compaction resistant cereal crops. To achieve these ambitious goals, I will address 3 key objectives. Objective 1 will determine if reduced diffusion of the gaseous signal ethylene acts as a regulatory mechanism to trigger root adaptive growth changes in compacted soil environments.
Objective 2 will pinpoint the key downstream signals and genes underpinning root-soil compaction responses and later functionally validate promising candidate genes to manipulate root penetration traits in cereal crops.
Objective 3 will validate ethylene regulates wheat root soil compaction responses and then deliver high throughput phenotypic screens, germplasm and markers to accelerate breeding efforts to select compaction resistant wheat lines.
My BBSRC Discovery fellowship project is very timely, novel and employs cutting-edge interdisciplinary tools and technologies available and/or developed at the host Institute that includes state-of-art tomographic imaging, deep learning and genomic resources that I will exploit to address this major global agronomic problem.
My BBSRC Discovery fellowship aims to discover how ethylene controls compaction responses in crop roots and then exploit this knowledge to engineer novel compaction resistant cereal crops. To achieve these ambitious goals, I will address 3 key objectives. Objective 1 will determine if reduced diffusion of the gaseous signal ethylene acts as a regulatory mechanism to trigger root adaptive growth changes in compacted soil environments.
Objective 2 will pinpoint the key downstream signals and genes underpinning root-soil compaction responses and later functionally validate promising candidate genes to manipulate root penetration traits in cereal crops.
Objective 3 will validate ethylene regulates wheat root soil compaction responses and then deliver high throughput phenotypic screens, germplasm and markers to accelerate breeding efforts to select compaction resistant wheat lines.
My BBSRC Discovery fellowship project is very timely, novel and employs cutting-edge interdisciplinary tools and technologies available and/or developed at the host Institute that includes state-of-art tomographic imaging, deep learning and genomic resources that I will exploit to address this major global agronomic problem.
Publications
De La Fuente C
(2024)
Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet.
in eLife
Fusi R
(2022)
Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.
in Proceedings of the National Academy of Sciences of the United States of America
Huang G
(2022)
Ethylene inhibits rice root elongation in compacted soil via ABA- and auxin-mediated mechanisms.
in Proceedings of the National Academy of Sciences of the United States of America
Leftley N
(2021)
Uncovering How Auxin Optimizes Root Systems Architecture in Response to Environmental Stresses.
in Cold Spring Harbor perspectives in biology
Li Y
(2024)
The OsEIL1-OsWOX11 transcription factor module controls rice crown root development in response to soil compaction
in The Plant Cell
Mehra P
(2022)
OsJAZ11 regulates spikelet and seed development in rice.
in Plant direct
Mehra P
(2022)
Hydraulic flux-responsive hormone redistribution determines root branching.
in Science (New York, N.Y.)
Pandey B
(2021)
How roots help us fight against hard soils
in TheScienceBreaker
Pandey BK
(2024)
Uncovering root compaction response mechanisms: new insights and opportunities.
in Journal of experimental botany
Title | Hydro-signalling : How air gaps in soils alter the distribution of root water and hormones fluxes, thereby blocking root lateral branching |
Description | EGU23 presentation |
Type Of Art | Film/Video/Animation |
Year Produced | 2023 |
URL | https://figshare.com/articles/presentation/Hydro-signalling_How_air_gaps_in_soils_alter_the_distribu... |
Description | 1-Ethylene acts as a signal to sense soil compaction. 2-Root growth inhibition in compacted is associated with higher accumulation of ABA in rice root tips. 3-Root growth inhibition in compacted is also regulated by Auxin. |
Exploitation Route | Engineering ethylene signalling in just key root tip tissues can enable the plants to grow in compacted soil conditions without negatively affecting the other crucial plant performances associated with ethylene signalling. |
Sectors | Agriculture Food and Drink Environment |
Description | BREAKTHRU: developing soil compaction resistant wheat |
Amount | £1,063,748 (GBP) |
Funding ID | BB/W008874/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2022 |
End | 01/2025 |
Description | EMBO ALTF 619-2022 |
Amount | € 146,400 (EUR) |
Funding ID | 619-2022 |
Organisation | European Molecular Biology Organisation |
Sector | Charity/Non Profit |
Country | Germany |
Start | 03/2023 |
End | 03/2025 |
Description | Nanoscale Characterisation of Biological and Bioinspired Materials using Integrated Fluidic Force - High-Resolution Confocal Microscopy |
Amount | £777,905 (GBP) |
Funding ID | BB/W019639/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2022 |
End | 07/2023 |
Description | Nottingham Research Fellowships |
Amount | £500,000 (GBP) |
Funding ID | SCI2105 |
Organisation | University of Nottingham |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2023 |
End | 09/2026 |
Description | Royal Society Research Grant |
Amount | £70,000 (GBP) |
Funding ID | RGS\R1\231374 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2023 |
End | 03/2024 |
Title | High-throughput plant phenotype for ethylene sensitivity |
Description | Compaction represents one of the most important issues associated with soil degradation, representing 39% of losses in the UK for example, Europe has the highest agricultural area prone to soil compaction in the world (36 mha out of a total global area affected of 68 mha).We recently discovered that plant roots employ the gaseous hormone ethylene to sense soil compaction. Remarkably, roots of rice mutants insensitive to ethylene were able to penetrate highly compacted soil (1.6 BD [1.6 g/cm3 Bulk Density]), while significantly reducing wildtype root growth. Close anatomical inspection revealed that in contrast to wildtype, ethylene insensitive mutants remain narrow and able to penetrate highly compacted soil. Based on this seminal discovery, I have developed a high-throughput ethylene bio-assay platform where I can screen 2000 plants/week for their ethylene sensitivity including root growth, coleoptile length and root hair elongation. This phenotyping platform can be used to screen large germplasm for various biotic and abiotic challenges. |
Type Of Material | Physiological assessment or outcome measure |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This method has been used to screen 1000 Watkins genotypes (Wheat landraces) and 3 NAM populations (-250 genotypes). This method has also been used to screen 76 tomato intogression lines for their ethylene sensitivity. Currently, 156 IRRI rice populations has also been phenotyped using this new phenotyping platform. |
Title | Non-invasive Imaging of Rice Roots in Non-compacted and Compacted Soil |
Description | Roots are the prime organ for nutrient and water uptake and are therefore fundamental to the growth and development of plants. However, physical challenges of a heterogeneous environment and diverse edaphic stresses affect root growth in soil. Compacted soil is a serious global problem, causing inhibition of root elongation, which reduces surface area and impacts resource foraging. Visualisation and quantification of roots in soil is difficult due to this growth substrate's opaque nature; however, non-destructive imaging technologies are now becoming more widely available to plant and soil scientists working to address this challenge. We have recently developed an integrated approach, combining X-ray Computed Tomography (X-ray CT) and confocal microscopy to image roots grown in compacted soil conditions from a plant to a cellular scale. |
Type Of Material | Technology assay or reagent |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | This method has been used in rice, wheat and tomato plants to visualize root architecture in compacted soil. One PNAS research article is invited for re-submission and three manuscripts are under preparation. |
URL | https://bio-protocol.org/e4252 |
Title | Spatial transcriptomics and single cell transcriptomic in soil conditions |
Description | I optimised spatial and single cell transcriptomics of rice roots grown in compacted and non compacted soil conditions. |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | No |
Impact | The manuscript is under review in Nature. |
Description | MiNute Transport: How Mineral Nutrient Transport happens in the root? |
Organisation | Chinese Academy of Agricultural Sciences |
Country | China |
Sector | Academic/University |
PI Contribution | - The China Partnering award would promote the exchange of staff, expertise and facilities between China and UK labs working in the area of mineral nutrition, microbiome, and root phenotyping. - China researchers gain access to the state-of-art microCT and Laser Ablation Tomography (LAT) facilities at Nottingham to image root architecture in soil in 3/4D, and root anatomy. - China researchers will have access to the state of the art ICP-MS for high-throughput and single cell ionomic analyses. - UK researchers gain access to the newly established protocol for efficient cellular Pi visualisation. - UK researchers would gain access to a novel system for genome editing in rice. - UK researchers would gain access to platforms with different long-term field experiments on soils with different nutritional characteristics |
Collaborator Contribution | UK and China Partners would hold workshops and networking events to share expertise in phenotyping, mineral nutrients quantification, genome editing techniques in rice with other members of the scientific communities. |
Impact | We are sharing new knowledge, techniques and resources to discover the mechanism of nutrient transport through roots. |
Start Year | 2022 |
Description | Multi-Knock |
Organisation | Tel Aviv University |
Country | Israel |
Sector | Academic/University |
PI Contribution | We have screened 150 rice genotypes for ethylene sensitivity, and we plan to profile the contrasting genotypes for their rhizospheric signals. Our Israeli partner will be creating multiple CRISPR lines to identify the causative genes. |
Collaborator Contribution | This Israel Partnering award would promote the exchange of staff, expertise, and facilities between Israel and UK labs working in the area of plant genomics, mineral nutrition, microbiome, and root development and phenotyping to support future pump-priming research funding. This multi-disciplinary collaborative effort is the first demonstration of a genome-scale, multi-targeted CRISPR tool in plants to overcome functional gene redundancy and reveal the hidden nutrient uptake transporters in Arabidopsis and rice. UK researchers will gain access to · the newly established Multi-knock CRISPR collections in Arabidopsis and rice that allow overcoming genetic redundancy in a genome-scale manner. · the Nutrient-Multi-knock CRISPR tool for the design and construction of novel nutrient transporters specific libraries. |
Impact | Published a high quality research workin Science: Hydraulic flux-responsive hormone redistribution determines root branching. PMID: 36395221 DOI: 10.1126/science.add3771 |
Start Year | 2022 |
Description | BBC interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | BBC eastmidland channel aired news of my research and interview related to the discovery of how to make plant roots to grow in hard soil in drier environment. We discovred that plants employ a stress signal which causes swelling and prevents the root growth in hard soil. |
Year(s) Of Engagement Activity | 2022 |