Microbial communities are vital components of plant health. Finding ways to effectively manipulate their composition for human benefit is of urgent importance. Microbes do not live insolation and their interaction with each other is a key factor in community composition and function. However, research on microbe-microbe interactions is limited.

Our research group has identified an abundant and ecologically important group of plant bacteria, within the family Flavobacteraceae, specialise in the break down (hydrolysis) other bacteria cell wall polymers, such as complex polysaccharides and phospholipids.

We hypothesise that hydrolysis of neighbouring cell wall polymers provides Flavobacteraceae with a competitive advantage in the plant microbiome, by killing competitors.

In this project the student will:

1.     Screen a diverse set of plant Flavobacteraceae for their ability to degrade cell wall polymers from other common plant bacteria

2. Identify and characterise the newly identified peptidoglycan, teichoic acid and associated polysaccharide hydrolases

3.     Investigate whether cell wall hydrolysis confers a competitive advantage to Flavobacteraceae when invading the plant microbiome 

To achieve these objectives, the student will perform high throughput hydrolytic assays and combine comparative proteomics, zymography, bacterial genetics and recombinant protein biochemistry. Scope for structural resolution of newly identified protein through X-ray crystallography is possible. 

Climate change and land management are altering soil biogeochemical cycles with consequences for soil-climate feedbacks, including changing the balance of sequestered carbon (C) versus respired C (as CO2). Soil microbial communities regulate this important feedback to climate. Our grassland Free Air Carbon Enrichment (FACE) experiment, running at our Peak District field station, has identified that both soil phosphorus and soil type (acid v calcareous) play a major regulating role in how grassland productivity responds to elevated CO2, with control exerted though alterations in microbial C and P enzyme activity.  

We therefore hypothesise that: Below-ground responses to elevated CO2 are dependent on soil pH and nutrient limitation through altering soil microbial community composition (relative activity of different groups) and functionality (C, N, and P cycling pathways). 

Objectives

1. Investigate the in-situ contribution of soil microbes to soil nutrient cycling under contrasting land management regimes (long-term field station)

2. Identify the interaction of soil type, elevated CO2, and nutrient availability on microbial nutrient cycling (Bradfield field trial)

The student will join the Lidbury lab, who have recently published one of the first soil rhizosphere metaproteomes and identified key soil P and C cycling enzymes in bacteria, using genetics and molecular biology. These approaches and knowledge will be combined with expertise in soil fungi and nitrogen cycling (Hodge, York), and in soil-ecosystem processes (Phoenix, Sheffield). Metaproteomics (enzyme production) is the next frontier of microbiome research and can transform our understanding of soil function compared to less informative approaches, such as metagenomics (genetic potential) and metatranscriptomics (gene expression). Thus, applying metaproteomics to understand climate-soil feedback represents cutting-edge research tackling a global issue.