Diversity and function of plant microbiomes

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There is growing recognition that plants, like animals, including humans, are not self-sufficient organisms, but are inhabited by a multitude of assorted microorganisms, including fungi, bacteria and archaea. Many of these microorganisms provide valuable benefits for the host, such as cycling of nutrients like nitrogen and phosphorus and providing protection against pathogens and other stresses, such as drought, in return for living in a carbon-rich habitat. This mutual dependency of plants and their associated microorganisms in known as the plant microbiome. Understanding the plant microbiome, is now recognized as being key to achieving sustainable forest and agro-ecosystems in the face of climate change, increasing pests, pathogens and invasive species coupled with increased demand for food and fibre with decreasing fertilizer and pesticide application. However, our understanding of the variety of microorganisms associated with different plant species, and their functions, is still in its infancy because until recently many of these microorganisms could not be identified because we lacked techniques to study them. With recent advances in molecular biology that mean microorganisms do not have to be grown in the lab in order to be studied, along with new “omics” technologies which enable us to link microorganisms to functions we are set to unravel the complexity of plant microbiomes. This research will use a variety of novel molecular and “omics” techniques, coupled with stable isotope labelling and probing approaches to understand the relationships between plants and their microbiome and in turn how this affects ecosystem function, with a view to optimizing these partnerships for sustainability. One of the most universal unions between plants and microbes, and one that plants are largely obliged to form for survival, is the mycorrhizal (fungus-root) alliance. There are two main mycorrhizal associations in nature, ectomycorrhizae (ECM) found on most temperate tree species and arbuscular mycorrhizae (AM), found in crops and herbaceous plants. However, one of the key tree species in BC, western redcedar is unusual in that it forms a relationship with fungi forming AM, not ECM. We know very little about the diversity of fungi forming AM on cedar, though without these fungi cedar cannot survive. There is increasing evidence that carbon released by plants through their roots, root exudates, shape microbiomes. In order to augment these partnerships we need to characterize the complete microbial diversity in plant microbiomes and we also need better understanding of the flows of carbon, biochemical signals and molecular interactions between plants, their mycorrhizal associates and other closely-associated microorganisms. In future, understanding of the functions of a healthy plant microbiome could lead to novel approaches e.g. manipulation of the microbiome, to improve food and fibre production and protect plants from biotic and abiotic stress.