Role of the SYM pathway in selecting the root microbiota

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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.