Completed Projects

Microcosm Farm: developing low carbon protected growing in Oman

2017-2019

£397K – British Council (institutional links)

The 9th five year plan of the Sultanate of Oman has identified the need to accelerate economic diversification. This diversification is to be achieved through the expansion of a number of critical sectors including agriculture. Food and particularly water security are identified as pressing concerns with some 60% of consumer food imported and 93% of fresh water use in Oman dedicated to farming purposes. We addressed these challenges by collaborating with Sohar University in the development and demonstration of an innovative capability for the expansion of agriculture in Oman that significantly reduces fresh water consumption. The collaboration built the in-country research capacity and in the medium term demonstrate the technological and business potential for a sustainable, resource-efficient ‘soil-less agriculture sector’ optimised for the environmental and market conditions in Oman. The collaboration supported joint research, development, and demonstration of installed novel growing technologies using state of the art facilities at University of Sheffield, and mirroring this work in the practical environment of a demonstrator greenhouse in Oman . The project included include two main research challenges. The first challenge is related to the experimentation on the use of novel, biologically active soil substitutes, novel plant varieties, methods for water conservation, support with demonstrating plant maintenance, pest control and pollination. Whereas the second challenge was the investigation of developing efficient water desalination and irrigation/pumping systems for this greenhouse using renewable (solar) energy. For both challenges work was undertaken to develop low cost instrumentation to measure and control key system parameters. The project also facilitated teaching of agricultural techniques and renewable energy. More details available here.

Co-Investigator with Tony Ryan

MycoRhizaSoil: Combining wheat genotypes with cultivation methods to facilitate mycorrhizosphere organisms improving soil quality and crop resilience

2017-2019

£702K – BBSRC

Loss of soil organic matter content and soil macroaggregates (crumbs) as a result of arable cultivation reduces soil water and nutrient holding capacity and are major global constraints on crop yields and efficient use of fertilizer. In the UK wheat yield have not increased over nearly 20 years due to interactions between genetic, environment and management constraints.
Modern wheat breeding has focussed on selection for disease resistance and increasing yield and quality of the grain, without consideration of other traits that can influence soil quality and ultimately, the long-term sustainabilty of soil. Soil erosion is a major global problem exacerbated by ploughing, loss of soil organic matter and the macroaggregates that hold soil together against water and wind erosion. One of the most important functional groups of organisms that are involved in stabilizing soil macroaggregates and contributing to soil organic matter storage are symbiotic fungi called mycorrhizas that receive sugars from plant roots in return for providing nutrients and water to the plants. We have recently shown that some modern wheat varieties have limited or no ability to form mycorrhizal symbiosis, and members of our consortium were amongst the first to show that conventional arable farming reduces the diversity and functioning of these symbionts. Loss of these symbionts and their functioning is thought to be contributory to loss of soil quality, both directly through effects on soil organic matter and soil structure, and indirectly though reductions in defences against pathogens which are induced by the symbiosis and plant growth promoting rhizobacteria that are thought to act synergistically with mycorrhizas.
MycoRhizaSoil will determine the crucial roles mycorrhiza and co-associated soil microorganisms play in maintaining soil structure and organic matter content, which are required for high yields, and directly addresses for the first time the benefits of selecting wheat genotypes and less intensive management to enhance the functional benefits of these crop-microbe interactions to deliver lower input, more sustainable and resilient wheat production.
Our approach combines laboratory and field based research using wheat lines that differ in mycorrhiza-forming capacity but are otherwise genetically very similar, selected over 500 lines of wheat bred from two parents that differed in mycorrhiza-forming ability. The laboratory-based research will resolve the mechanistic basis of mycorrhiza-induced systemic defenses to important root and shoot pathogens that cause major yield losses of wheat in the UK and globally. In a series of sequential field trials using the selected wheat lines we will determine the extent to which artificial inoculation with mycorrhizal fungi, the temporary conversion of crop land to grassland (to restore mycorrhiza) and adoption of no-tillage leads to improvements in soil quality and crop resilence to drought, excess water and native diseases compared to wheat grown conventionally with annual tillage.
Our agenda-setting research programme identifies a new set of targets for optimising plant breeding and arable management for sustainable wheat production. Our ambitious ultimate goal is to provide the scientific evidence to evaluate the benefits of simultaneously reducing the need for ploughing (one of the most fossil-fuel demanding farm operations and one of the most damaging to soil conservation and sustainability) and increasing the activities of beneficial soil microorganisms through wheat genotype selection. In combination we predict these approaches will increase the storage of soil organic carbon in the surface soil, help restore water-stable macroaggregates and increase crop resilience to climate stress (too much and too little water) and diseases.

Co-Investigator with Jonathan Leake (PI), Jurriaan Ton, Julie Scholes, Steve Banwart and industrial lead partner Richard Summers (RAGT Seeds).

A mobile gas chromatograph-mass spectrometer for measurement of metabolites and volatile substances in biological systems

2017-2018

£121K – BBSRC

To improve our ability to develop a sustainable agriculture that uses lower inputs and can respond to climate change requires experimentation in the field with agricultural crops. Such experiment require measurements of compounds such as metabolites, or compounds which are characteristic of organisms that live in close proximity to crops, and which provide important components for sustainable agriculture. Unfortunately many of these compounds are not very stable. Currently much expense and effort is required to transport samples to the laboratory for analysis, and it is not clear that the analyses that result accurately reflect the dynamics of plants in their field environment. Field experiments need large amounts of replication because the field is not a very uniform environment. Mass spectrometry is a very powerful analytical tool to identify and measure these compounds but the machines tend to be very large. Thus until recently such field experiments have required expensive procedures to transport material back to the laboratory. However during the last 18 months a new mass spectrometer has become available. It is the size of a large brief case and can be taken to the field for the measurements required. The aim of this proposal was to purchase this machine so that the machine can be taken to the sample in the field, rather than the sample taken to the machine in the laboratory. This improves both the accuracy and the efficiency of field experiments, while at the same time reducing costs associated with current sampling practice.
This new equipment is maintained by the biOMICS Mass Spectrometry Facility in the Faculty of Science at the University of Sheffield.

Principle Investigator with co-investigators Heather Walker, Mike Burrell and Carl Smythe

Ecological drivers of evolutionary transitions in mutualistic symbioses

2013-2017

£159K (Sheffield fraction) – NERC split-lead award

Intimate and prolonged associations between different organisms – symbioses – are widespread and important in the natural environment. A key form of symbiosis are associations involving photosynthetic organisms which provide their hosts with energy from sunlight: so called photosymbioses. Examples of photosymbioses include lichens, where a fungus hosts an green alga, and corals, where a cnidaria hosts a zooxanthellae alga. Through photosymbiosis pairs of organisms can survive in environments where neither would alone, therefore photosymbioses increase biodiversity and underpin the functioning of ecosystems. An important feature of photosymbiosis is that the benefits to hosts of carrying symbionts depend upon the environmental conditions: for instance in well-lit habitats symbionts are highly beneficial to hosts whereas in dark environments symbionts may be costly for hosts to maintain. Here, we want to understand how environmental variation in light intensity shapes the long-term evolution of photosymbioses Despite their widespread importance, little is known about the evolutionary origins of photosymbioses. Possible reasons for this are that lichens and corals are ancient associations and are very slow growing and hard to cultivate in the lab. Our approach is to observe the real-time evolution of a photosymbiosis created by us in the lab between a single-celled eukaryote host (Paramecium) and a photosynthetic cyanobacteria symbiont (Synechocystis). Although many Paramecium-alga symbioses exist in nature, by using a ‘synthetic’ symbiosis we will capture the entire evolutionary history of the symbiosis from the moment of its inception. We will exploit the short generation times, and large population sizes of Paramecium to observe evolution in real time for 100s of generations. We will discover and contrast the adaptations of both hosts and symbionts that occur as they co-evolve across a gradient of light intensity from near dark to bright light. To fully understand the physiological, biochemical and genetic bases of adaptations we will employ cutting edge cell-imaging, mass spectrometry and genome sequencing technologies.

Co-PI with Mike Brockhurst (PI) and co-investigators Jamie Wood and Chris Lowe

Did artificial selection deprive crops of beneficial symbioses?

2015-2018

£293K – Royal Society University Research Fellowship Extension

In 1937, Franklin D. Roosevelt said: “A nation that destroys its soils destroys itself”. Indeed, all too often, we neglect the important role that soil and symbioses between different organisms that inhabit the soil, play in underpinning the success and stability of the food supply. Modern farming practices, such as ploughing and the application of chemicals and fertilisers have impaired the diversity and functioning of beneficial soil microbes agricultural soils, depriving plants of these essential symbioses. It is these organisms and the soil that they inhabit that is the focus of this research project; aiming to understand the benefits that they provide to the crop plants that associate with them and how we can harness beneficial microbes to help us produce more food, more sustainably.
One such group of beneficial microbes form the mycorrhizal symbiosis, a symbiosis between plant roots and soil fungi is characterised by the exchange of plant carbon (sugars made by photosynthesis) for nutrients obtained from the soil by the fungus (for example phosphate and nitrates). Some plants however do not form the mycorrhizal symbiosis (e.g. the cabbage family) because, under ample soil nutrient conditions, the carbon drain of mycorrhizal fungi is a cost that is not outweighed by the extra nutrients obtained from the fungus. If high soil nutrients persist in the long-term, then the mycorrhizal trait will be selected against by evolution. Crucially, it is under high nutrient conditions that we have bred our crop plants; supplied with ample mineral nutrients from fertilisers, selected for increasing yields and grown in soils where the numbers of mycorrhizal fungal spores have been reduced by modern agricultural practices such as ploughing. We have recently shown that breeding crops under these high nutrient/low mycorrhiza conditions has resulted in the loss of the ability of many wheat varieties to form mycorrhizal associations. The consequences of this loss of the mycorrhizal symbiosis by wheat are profound in a world where sustainable increases in food production are essential to meet future food requirements; depriving crop plants of their natural mechanisms of nutrient capture leaves them ever reliant on the application of fertilisers by farmers. While mycorrhizal fungi can substantially aid crop nutrition, this is dependent on our crops interacting with the mycorrhizal fungal spores that remain, albeit depleted in number and diversity, in agricultural soils. The mechanisms leading to mycorrhizal incompatibility in wheat are unknown and need to be understood before they can be deployed in agricultural systems.

Principal Investigator

13 ERA-CAPS: Biosynthesis, transport and exudation of 1,4-benzoxazin-3-ones as determinants of plant biotic interactions

2014-2017

£300K – BBSRC

The establishment of a suitable biotic niche is essential for plant survival and agricultural productivity. One important mechanism by which plants shape their environment is the release of phytochemicals. Low molecular weight compounds in particular can initiate the interaction with beneficial microbes in the soil and ward off herbivores. However, the same signalling molecules may also be exploited by specialized pests and pathogens. A detailed understanding of their biosynthesis, transport and release will be essential to disentangle these seemingly contradicting effects and to harness the full potential of secondary metabolite exudation in sustainable cropping systems. Yet to date, no secondary metabolite exporters have been identified in crop model systems. Here we united the expertise of different research groups across Europe to study the molecular basis of 1,4-benzoxazin-3-one (BX) exudation in maize. Previous work by the consortium members has identified BXs as important resistance factors in maize and other grasses and has elucidated their biosynthesis in detail. We have also shown that BXs are the dominant secondary metabolites in maize root exudates and the leaf-apoplast and that they are important recruitment signals for beneficial microbes as well as for one of the most damaging pests of maize, the western corn rootworm Diabrotica virgifera. Given their obvious importance for crop productivity and their strong involvement in extracellular signalling, BXs are an ideal and relevant model to study the molecular ecology of secondary metabolite exudation. The overall aim of BENZEX was to create the most advanced molecular toolkit in extracellular plant-environment interactions to date.

Co-Investigator with Jurriaan Ton (PI) and Steve Rolfe

MYCOCROP: Using mycorrhizal-induced resistance as a sustainable alternative to chemical pesticides in cereal agriculture

2014-2017

€309K – EU FP7

In this proposal we applied a novel high throughput methodology to study interactions between fungal mycorrhiza, host plants and soil bacteria, in order to develop wheat lines with induced resistance to fungal diseases. Implementation of the revision of 9/414/EEC means most of the effective fungicides against diseases in cereals will be withdrawn, increasing the risk of major crop failure. Arbuscular mycorrhizal fungi increase host plant nutrient uptake and often induce systemic resistance against other pathogens. Selecting crops more suitable to act as host of mycorrhizal fungi will provide varieties with broad and durable spectrum resistance or tolerance to diseases, and increase competitiveness of the crop for uptaking soil nutrients (useful against weeds). These will reduce dependence on chemical treatments (both, fertilizers and pesticides), and as a consequence, the input cost for the farmers will be reduced, the environmental impact minimised, and the food security increased.

Principle investigator with Alex Perez-de-Luque (Marie Curie Fellow)

Inducing novel broad spectrum disease resistance in wheat

2010-2014

£239K (To Sheffield) – InnovateUK (via EPSRC & BBSRC). With RAGT seeds (Industrial lead partner)

The UK farming industry spends about 30m on wheat fungicides, spraying an area of over 2 million hectares. This helps to maintain higher yields than for organically-grown wheat, but with significant financial and environmental costs. Now, implementation of the revision of 91/414/EEC means most of the effective fungicides (Cyproconazole, Fenbuconazole, Bitertanol, Carbendazim, Dinocap, Epoxiconazole, Fenbuconazole, Flusilazole, Iprodione, Mancozeb, Maneb, Metconazole, Quinoxyfen, Tebuconazole) against diseases of wheat are likely to be withdrawn, so that the risks of major crop failure are increased. This has serious implications for food security and farmer’s incomes. The aim of this project was to combine recent advances in (1) fundamental plant biology, (2) high-throughput mass-spectrometry and (3) modern plant breeding techniques, in an innovative way to produce new varieties of wheat less dependant on pesticides and chemical inputs for optimal yields. The varieties will be selected with enhanced, and durable, broad spectrum resistance or tolerance to disease making them equally suited for use in conventional and organic farming systems. Field trials of candidate new varieties will be used to select the best variety for commercial development. Wheat will be used in this programme but, once implemented, the technology can be applied to many other crops.

Principle Investigator with Richard Summers (Industrial lead partner) and co-investigators, Mike Burrell and Jonathan Leake

How do plants parasitise fungi? The physiology and evolution of mycoheterotrophy

2010-2015

£498K Royal Society University Research Fellowship

In excess of 80% of plants, form pole to pole, engage in a mutualistic symbiosis with soil fungi called mycorrhiza (literally meaning “fungus-root”). In the classical view of the mycorrhizal symbiosis, the plant gives sugars (synthesised through photosynthesis) to the fungus partner and in return, the plants receives mineral nutrients, most significantly nitrogen and phosphorus. However, about 10% of plants produce seeds or spores that are so small that they do not have enough carbon and mineral nutrients to germinate unaided. In these plants, all of these resources required for germination and establishment are provided by the fungus partner (mycoheterotrophy) and so the plant is effectively parasitic on the fungus. We usually view fungi as parasites and pathogens of plants and animals rather than victims of parasites themselves and so the observation that some plants have become parasitic on fungi is striking. Moreover, mycoheterotrophy is a widespread and common strategy for seedling recruitment, and is employed by many of the worlds’ most rare and threatened plant species, including almost all orchids, but despite the ecological importance of the mycoheterotrophic habit, virtually nothing is known about the mechanisms through which 10% of all plants have evolved to parasitise fungi. In order to conserve these often rare keystone species, we urgently need to understand their basic biology.

During the tenure of my NERC fellowship, I have used stable isotopes of carbon and nitrogen (13-C and 15-N) as tracers fed to plant and fungus partners to measure the amount of carbon transported from the plant to the fungus and the amount of carbon and nitrogen transported from the fungus to the plant. My work has shown that green-leaved orchid Creeping Lady’s Tresses (Goodyera repens) while parasitizing a fungus in order to germinate can repay the carbon initially invested by the fungus with interest establishing a “take now, pay later” carbon economy although this novel ecological strategy has never been investigated in other plants that rely on mycoheterotrophic recruitment. Furthermore, the mechanisms through which compounds (metabolites) are exchanged between symbiotic partners are unknown. I have recently developed new imaging mass spectrometry methods allowing the identification and spatial mapping of the metabolites exchanged between plants and fungi to be resolved for the first time and make the resolution of the mechanisms through which plants parasitise fungi tractable for the first time.

Cellular-scale mapping of isotopically labelled metabolites has the potential to resolve many currently intractable pathways of nutrient exchanges between organisms. The development of these methods has the potential to revolutionise our understanding of the functioning of other symbiotic systems (including other kinds of mycorrhizas, lichens, and pathogenic fungi). Furthermore, applying these emergent technologies to understanding the currently unresolved functioning of the mycoheterotrophic symbiosis, and the extent to which a taxonomically diverse group of plants employ this strategy has profound impacts for understanding the evolution of mycoheterotrophy, understanding how complex communities function in nature and downstream, for informing targeted conservation efforts.

Principle Investigator and Fellow