Unravelling the diversity and function of fine root endophytes

Plants interact with diverse communities of microbes, which constitute their microbiome, and which have major impacts on their growth and development. In most ecosystems the microbiome is dominated by mycorrhizal symbioses, in which the plant provides the fungus with sugars and lipids in exchange for nutrients assimilated by the fungus from the soil.

The most widespread mycorrhizal symbiosis is the arbuscular (AM) type, which is recognized as a key determinant of ecosystem processes, through its role in biogeochemical cycling and in supporting the diversity and productivity of plant communities. Until recently, it was assumed that the fungi which form AM comprise the phylum Glomeromycota, and our understanding of the ecosystem roles of AM is based almost exclusively on this group of fungi. However we have recently shown that fungi which form the distinctive 'fine root endophyte (FRE)' AM morphotype are members of the Order Endogonales within the phylum Mucoromycota so that the AM symbiosis is actually formed by two distinct groups of fungi which diverged over 700 million years ago.

Although we know that FREs are globally distributed and can be abundant within ecosystems we know almost nothing about the diversity, ecology or ecosystem function of the fungi involved. However, evidence suggests that FRE and Glomeromycota have contrasting interactions with the environment and may perform different functional roles in ecosystems.

In this project we will use existing DNA archives collected as part of the NERC Countryside Survey to determine the diversity and abundance of FREs across major British habitat types, and compare the environmental, vegetation and climatic factors which determine distribution of FREs and Glomeromycota. Currently FRE are 'dark fungi' known only as environmental sequences. Our research suggests that FREs represent multiple species, and we will collaborate with Australian and Swedish researchers to define these based on both their genetics and morphology, and determine the extent to which these have global distribution patterns. We have evidence to suggest that FREs and glomeromycota have different interactions with soil phosphorus, with FREs more abundant under conditions of very low phosphorus availability. We will collaborate with Irish researchers to investigate how soil phosphorus status affects diversity and abundance of FREs using a unique 50 year pasture experiment in Wexford.

We will establish whether FREs function as mutualistic symbionts which promote plant growth and nutrient supply, similar to the interactions that Glomeromycota have with their host plants. A key part of the programme will be to assemble genomes of FREs and use these to understand the functional roles of FREs in ecosystems, and the interactions which determine their distribution across ecosystems. Since FREs can't be grown in the absence of plants, or under pure culture conditions, we will take advantage of emerging long read DNA sequencing technology which now opens the exciting possibility of assembling FRE genomes directly from DNA extracted from environmental metagenomes.

In addition to providing fundamental understanding of the diversity and function of the AM formed by FREs, we will provide technological advances which will facilitate a major advance in our ability to characterise the function and ecological significance of microbial eukaryotes such as fungi and protists, which are largely unculturable and have been neglected in environmental genome sequencing efforts to date.

As new discoveries and applications are developed in this project, beneficiaries will include the microbiology, ecology, agriculture, and wider scientific research community interested in unravelling the complexities of the plant microbiome and its link to plant growth and ecosystem functions. Our programme will inform on the importance of fine root endophyte symbioses across UK ecosystems and a range of stakeholders will benefit from our research including landowners, farmers' groups, conservation bodies and local and national government departments, agencies, and charities. Additionally our work will be of interest to biotechnology companies which produce and market microbial products for use in horticulture and agriculture. Our project will also benefit members of the general public with interests in science and the environment. Our proposal will be of immediate benefit for the staff employed on the project at Warwick and Reading. An important outcome will be highly trained staff with training in cutting edge approaches to the study of microbiomes and communication of science.

Benefits will be realised in the following way:

1. Engagement with stakeholders and promotion of knowledge transfer: We will engage directly with stakeholders via two workshops. The first workshop will seek input from stakeholders on key areas in which the project could generate societal impact including conservation strategies, environmental quality indicators, and biotechnology. The second workshop will focus on examining the potential for commercial exploitation of our research.

2. To raise public awareness of our research: The PI/Co-I's have a strong track record of being actively involved in outreach activities, promoting public awareness of our science through local and national public science communication events and to school children via science events and demonstrations within local schools, and this programme will be maintained within this project.

3. Dissemination of research findings to an international audience: This will be achieved through the publication of research findings in leading international journals, and via presentations by PDRAs and PIs at international conferences and workshops

4. Transferable skills training: We will deliver highly trained staff with training in multi-disciplinary approaches to the study of plant-soil-microbe interactions including cutting edge genomic approaches and tools.