Understanding the impact of tree diversification on ecosystem functionality of microbial diversity

Principal Supervisor: Dr Mojgan Rabiey

Co-supervisor: Prof Murray Grant and Prof Rob Jackson

PhD Project title: Understanding the impact of tree diversification on ecosystem functionality of microbial diversity

University of Registration: University of Warwick, School of Life Sciences

Project Outline:

Understanding why plants resist pathogens is complex (e.g. host genotype and environment), but one novel area of discovery is the recognition that leaf microbiomes play a critical role in protecting plants from pathogens. This raises the question, can increased tree species diversity enhance ecosystem functionality through increased microbial diversity and thus conferring greater pathogen resistance?

Increased plant diversity can drive increased ecosystem functionality at macro-scales. For example, increased crop diversity results in a greater range of biological control species being present, driving a reduction in pests and pathogens, and hence increased resilience. However, it is unknown if increased plant diversity also drives increased ecosystem functionality at the microbial scale. Evidence is emerging that microbial diversity is key to plant health and that the resident microbiomes of plant leaves (the microbes on the leaves) are important contributors to the plant’s defences against foliar pathogens. For example, in ash the microbiome influences susceptibility to ash dieback. Understanding the influence of increased tree diversity on the leaf microbiome, and whether this leads to the establishment of a genetically and functionally more diverse population of microbes that can enhance resistance to pathogen infection, facilitates work towards a nature-based solution to tree pathogens.

Many UK woodlands, both semi-natural and plantations, are dominated by a few tree species. Tree species differ in the biodiversity they support and their ecosystem functioning. However, we lack collated lists of the biodiversity supported by different tree species and information on how tree species differ in their ecosystem functioning. We require this information to identify which tree species can substitute for each other, supporting similar biodiversity (Figure 1) and providing similar functioning, and thus, increasing functional redundancy. We therefore hypothesise that mixed species woodlands support highly diverse leaf microbial populations that can outcompete pathogens compared to a monoculture woodland microbiome. This will determine whether mixed species planting results in a more diverse and functionally useful microbiome to protect against foliar pathogens which is essential to inform management strategies for diversification of woodlands.

Project Highlights:

• Tree diversity impacts microbial community
• Link between pathogen establishment, microbial community and tree diversity
• Tree species diversity for a resilient woodland

Methodology:

1. Does leaf microbial diversity increase with tree diversity? Leaves will be collected from different woodland settings. Microbial communities will be collected, DNA extractions and PCR carried out. Amplicon sequencing of bacteria/fungi using 16S/ITS rRNA gene will be done to assess the diversity of leaf microbiomes.
2. Does the microbial biodiversity play a role in preventing pathogens establishment? To understand the presence, distribution, and abundance of the pathogen for each tree species, PCR and Droplet Digital PCR for DNA samples collected in Obj. 1 will be undertaken. The effect of individual or combinations of culturable bacteria and fungi on pathogen suppression will be tested.
3. Which tree species will provide resilience for the biodiversity associated with woodlands? To understand which tree species can be planted to increase the woodland resilience to pathogens, mathematical modelling will be used to correlate the diversity of microbial community, abundance of pathogens and tree species.

Further reading:

Aguilera, G., Roslin, T., Miller, K., Tamburini, G., Birkhofer, K., Caballero-Lopez, B., Lindström, S.A.M., Öckinger, E., Rundlöf, M., Rusch, A., Smith, H.G., and Bommarco, R. (2020) ‘Crop diversity benefits carabid and pollinator communities in landscapes with semi-natural habitats’. Journal of Applied Ecology, 57: 2170. Doi: 10.1111/1365-2664.13712

Berg, G., Köberl, M., Rybakova, D., Müller, H., Grosch, R., Smalla, K. (2017) ‘Plant microbial diversity is suggested as the key to future biocontrol and health trends’. FEMS Microbiology Ecology, 93(5): fix050. doi:10.1093/femsec/fix050.

Munir S, Li Y, He P, He P, He P, Cui W, Wu Y, Li X, Li Q, Zhang S, Xiong Y, Lu Z, Wang W, Zong K, Yang Y, Yang S, Mu C, Wen H, Wang Y, Guo J, Karunarathna SC, He Y. (2022) ‘Defeating Huanglongbing pathogen Candidatus Liberibacter asiaticus with indigenous citrus endophyte Bacillus subtilis L1-21. Frontier in Plant Science. 12:789065. doi: 10.3389/fpls.2021.789065.

Roy, S.R. (2019) ‘Evaluating the impact of tree provenance, tree phenotype and emergent disease on microbial and insect populations in tree ecosystems’, PhD Thesis, University of Reading.

Vogel, C.M., Potthoff, D.B., Schäfer, M. (2021) ‘Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen’. Nature Microbiology, 6, 1537–1548. Doi: 10.1038/s41564-021-00997-7.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food - Plant and Crop Science, and Understanding the Rules of Life - Microbiology, and Plant Science

Techniques that will be undertaken during the project:

The student will have access to Birmingham Institute of Forest research (BIFoR)-Free Air Carbon Dioxide Enrichment facility (FACE) which is only such facility in the Northern Hemisphere. It is the state of art facility researching the impact of climate change and elevated CO2 on forests and woodlands. The student will also have access to Norbury Park, a multi species woodland plantation. This will allow the student to conduct their field sampling. Molecular work will include DNA isolation of collected samples, PCR and Droplet Digital PCR, amplicon sequencing of bacteria and fungi using 16S/ITS rRNA gene and data analysis will be conducted. Microbiology skills will include culturing culturable bacteria and fungi and testing their impact on pathogen suppression. The student will learn mathematical modelling and statistical analysis in collaboration with the Alan Turing Institute in Warwick to correlate the diversity of microbial community, abundance of pathogens and tree species.

Contact: Dr Mojgan Rabiey