QUADRAT DTP: Genomics approaches to explore the secrets of remarkable plants: Soil/root microbiome interaction and edaphic stress adaptation

Background:

The wild grasses Holcus lanatus, Agrostis capillaris and Deschampsia cespitosa are characterised by their extensive environmental range and resilience to environmental stress. They can grow in a wide range of soils; from acid peats to high pH calcareous, including acid mine spoils characterised by elevated arsenic, copper, cadmium and zinc. Interestingly there is considerable phenotypic/genotypic variation, and not all individuals within any one population are equally resilient. If growing in normal grassland soil for example, about 50% of these grasses have been shown to exhibit a high level of tolerance to arsenic, this increasing to near 100% in populations growing on arsenic contaminated mine spoils. Hence, we know that edaphic stress provides a strong selection pressure for tolerant phenotypes. Edaphic factors also drive the diversity of soil microbial communities. Furthermore, there is evidence that via root exudates and cell wall deposits etc., plants can enhance or limit colonisation by certain groups of microbes in the rhizosphere and within roots. Understanding the role of plant associated microbes in response to environmental change, such as soil degradation (acidification, metal(loid) contamination), is crucial for development of strategies that promote environmental resilience. Wild grasses are an ideal model system to explore this concept. They have considerable phenotypic/genotypic variation to abiotic stresses, as well as being excellent at restoring degraded sites due to their fibrous root systems.

Aims:

1. To characterise and contrast the soil and shoot chemical composition and the diversity of the rhizosphere and root microbiome in wild grass ecotypes collected across a gradient of pH and metal(loid) pollution.
2. To investigate the effects of global warming on the rhizosphere and root microbiome in wild grass ecotypes collected across a gradient of pH and metal(loid) pollution.
3. To investigate the interaction effects of grass ecotype, edaphic stress and global warming on the rhizosphere and root microbiome of wild grasses.

Methodology and training:

Ecology: Wild grass ecotypes of H. lanatus, A. capillaris and D. cespitosa collected across a gradient of pH and metal(loid) pollution will be investigated. A reciprocal transplant experiment will be conducted where wild grass ecotypes will be grown under different temperature regimes on multiple soils.
Environmental chemistry: Root and shoot yield, chemical analysis (pH, eH, ICP-MS, XRF) of soil and plant material.
Molecular Microbiology: Root staining, DNA extraction, PCR, Amplicon sequencing.
Bioinformatics/Statistics: Amplicon sequencing data analysis (fastqc, Qiime2), statistical analysis in R (Phyloseq, Deseq2, Vegan) and SPSS (dimensional reduction, co-variant, regression, clustering, modelling). Integration of chemical and molecular data.

Outputs:

This project will improve our understanding of the complex interaction between plants and their environment, with a focus on the rhizosphere and root microbiome of wild grasses. Publications will be centred on natural variation, edaphic stress adaptation, global warming, resilience to environmental change, plant driven selection of rhizosphere and root microbiomes.

Start date:

1 October 2020

Duration:

42 months

Eligibility:

Candidates should have (or expect to achieve) a minimum of a 2.1 Honours degree in a relevant subject. Applicants with a minimum of a 2.2 Honours degree may be considered providing they have a Distinction at Master’s level.

Application procedure:

• Apply for Degree of Doctor of Philosophy in Biological Sciences at Queen’s University Belfast
• State name of the lead supervisor as ‘Name of Proposed Supervisor’ on application
• State ‘QUADRAT DTP’ as Intended Source of Funding
• Select ‘Visit Website’ to apply now