Role of the SYM pathway in selecting the root microbiota

Plant roots are critical for the uptake of mineral nutrients by plants. In addition, they interact with the soil environment and a complex assemblage of bacteria, fungi, single celled animal cells, nematodes and other organisms. The area directly around roots that is occupied by these organisms is known as the rhizosphere and the collective name for the organisms is the rhizosphere microbiota. Microorganisms also reside inside plant roots, usually between plant cells and are knows as endophytes. Together the rhizosphere and endosphere microbiotas makes up the root microbiota of a plant. It has been shown over the last few years that the root microbiota is critical for the health and growth of plants, with many microorganisms shown to be plant growth promoting. Bacteria are simple single celled microorganisms that lack the membrane bound structures found in higher cells of plants and animals. However, while bacteria may have a less complex cellular organisation they carry out a huge range of chemical reactions not found in plants and animals. Bacteria are responsible for the cycling of many nutrients such as N2 (N2 is also known as nitrogen gas and consists of two nitrogen atoms bound by a strong triple bond), which is a very inert atmospheric gas. N2 makes up 78% of the atmosphere but is very unreactive and cannot be used directly as a source of nitrogen, which is needed for amino acid, protein and DNA synthesis. However, a small number of bacteria can reduce (add hydrogen) to N2 and convert it into ammonia (NH3), which is readily incorporated into amino acids and then all the other building blocks of life, by a wide range of organisms including bacteria and plants. In many parts of the world the limitation to growth of plants, which in turn support animal life, is the supply of nitrogen as ammonia or nitrate. In the past, much of the nitrogen was provided by biological nitrogen fixation, particularly by a group of plants known as legumes. The legumes form nodules on their roots which house bacteria, called rhizobia, which reduce N2 to ammonia and supply it to plants in return for a carbon and energy source. However, more recently legume use has declined and nitrogen is mainly provided to crops by chemically synthesised fertiliser. One of the other limiting nutrients in the biosphere is phosphate, which is often naturally provided to the plant by a group of fungi known as the arbuscular mycorrhizae (AM fungi). Nitrogen and phosphate are so crucial to plant growth and crop yield that they are often both added in very large amounts to agricultural soils. This has led to widespread pollution of ground water with these nutrients, leading to run off into water ways and oceans that causes eutrophication where the growth in particular of algae is promoted. Remarkably it turns out that both AM fungi and rhizobia interact with plants using a common signalling network known as the common symbiosis pathway (SYM). In this work, we are investigating how the SYM pathway controls the microbiota of legumes and cereals. Our aim is to understand how the pathways control different members of the microbiota. In addition, we will move beyond simple characterisation of the components of the microbiota to examine the mechanism of control. This research will lead to a step change in characterisation of the plant microbiota of agriculturally critical crops, including pea and rice. Not only will we characterise which microorganisms are present but we will also culture and characterize the function of key members of the microbiota. This work moves beyond simple characterisation of which microorganisms are present to identification of functional community members.

The best-characterised and probably most important plant microbe interactions are between legumes and Rhizobium, leading to nodulation, and between most land plants and arbuscular mycorrhizae (AM). These symbioses are critical drivers of plant productivity and agricultural yield. N2-fixation by rhizobia in association with crop legumes provides up to 22 Tg of nitrogen a year (15), while around 80% of land plants are infected by mycorrhizal fungi, which make a substantial contribution to plant nutrition particularly of phosphate but also nitrogen and water among others . A common SYM pathway controls both nodulation of legumes and mycorrhization of most land plants. This suggests that legume nodulation, which evolved approximately 60 Million Years Ago, adapted to use the more ancient AM symbiosis (~400 MYA) pathway. In this study, we will use Medicago truncatula as our main test plant to examine the impact of the SYM pathway on the root microbiota. Results in M. truncatula will then be compared to pea SYM mutants defective in either nodulation or nodulation and mycorrhization and rice mutants defective in mycorrhization. This work will then be followed by the isolation of bacteria for combination into Synthetic Communities (SynComs), to bridge the hitherto insuperable barrier between community analysis and molecular understanding. The role of the SYM pathway in controlling bacterial chemotaxis, adhesion, colonisation and tissue localisation will be determined. Metabolite secretion from roots of wildtype and SYM mutant lines will be compared to determine if altered secretion profiles directly control the microbiota. This will pave the way for future work on transcriptomics and genetic analysis to pinpoint the bacterial factors controlling interaction with roots and survival in complex root communities.

Within this proposal, we will extend established work within our groups to develop a selection platform for the isolation and manipulation of members of the root microbiota. In particular, we will gain deep insight into how the common SYM pathway controls the root microbiota. This is particularly important to nitrogen and phosphate utilisation, but also has relevance to disease resistance and herbicide and pesticide use. In the bigger context nitrogen is at double its preindustrial level and now beyond the safe operating boundary of the earth, with widespread pollution of groundwater and ocean coastal zones by nitrates and phosphates leading to eutrophication and costal dead zones. These nutrients are leading players in the perfect storm, demanding increased agricultural production but requiring changes in agricultural practice to avoid environmental carnage. In addition, we will develop a synthetic community of bacteria (SynCom) that is a powerful resource to help tackle these issues and therefore has over-arching relevance to society and government policy. Furthermore, in a regulatory environment where less fertilizer and pesticide use are becoming mandatory, this work will offer tangible results to help meet these targets and assist the competitiveness of UK industry. We will maximize the potential impact of our research by directly engaging with a range of stakeholders, including crop breeders, policymakers and farmers via our existing knowledge transfer networks, including the UK Wheat Genetic Improvement Network (WGIN), landowner/farmers groups (e.g. NFU, SNFU, NFUW, HCC, Growers association, Soil Association), academic societies (BES, BSSS), conservation bodies and local/national government departments (Defra; EA), agencies (SEPA; Natural England; Natural Resources Wales, SNH), who will directly benefit from our findings and the formation of robust SynComs. Reducing inputs into agriculture while maintaining yields has direct benefits to British farming but also to maintenance of the countryside and its use and recreation by the British public. It will help the UK meet local and European environmental targets and help the long-term sustainability and stability of our environment. We will also be training the next generation of scientists to develop practical solutions to environmental problems and develop a whole raft of new microbial inoculants.