Genetic Determinants of Microbiome Assembly on Plant Roots

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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. Other bacteria are crucial to make phosphate available to plants which with nitrogen are the two main nutrients limiting plant growth. However, we now realise that bacteria do not work alone but rather they work as complex communities, also known as a microbiome, with hundreds or even thousands of members interacting with each other and host plants. Just as for the human gut and body the health and growth of plants is profoundly altered by the bacterial microbiome. A recent breakthrough is the demonstration that we can study how microbiomes develop using just 6 or 7 key members which simplifies the analysis. In this proposal we have developed ways to track how 7 bacteria interact and to study the underlying genetic causes. This enables us to move beyond simple characterisation of the components of the microbiota to examine the genetic mechanisms of control and how a microbiome stably colonises plant roots. This research will lead to a step change in characterisation of plant microbiota of agriculturally critical crops, including cereals such as barley and wheat.