Our Research

We have a wide ranging interest in soil and environmental microbiology. Some of our key research areas are outlined below.

The soil microbiome

Our soils are teeming with microbial life! These microbes carry out many essential functions that are critical for sustaining life on the planet. Despite their importance we know relatively little about them. It’s been estimated that we have only identified about 1% of soil microbes to date. However, new research techniques including ‘omic’ technologies are offering a window into the life beneath our feet, and hitherto unattainable insights into microbial community composition and function. We’re interested in investigating what constitutes a healthy soil microbiome and how this knowledge can be used to inform agricultural management strategies.  We’re using new technologies to identify the microbes and pathways that underpin functions related to productivity, nutrient cycling and carbon sequestration. In addition, we’re investigating the effect of management, environmental and edaphic factors on the soil microbiome.

Nutrient cycling

Microbes are the main drivers of nutrient cycling in soils, and essential for providing plants with key nutrients they need to grow. They transform nutrients from unavailable forms into plant available forms and can very effectively scavenge nutrients for plant partners in nutrient limiting soils. They are the main recyclers of organic material and several important nutrient cycling processes are carried out exclusively by microbes. Their activity is also a critical determinant of nutrient losses from soil to air and water. The focus of our research is on harnessing the natural capacity of soil microbes to provide nutrients for plants, while at the same time limiting environmentally deleterious losses. We aim to understand the organisms and pathways involved in important nutrient cycles (incl. N,C and P) to predict when nutrients will become available and to manage soils in such a way as to link nutrient transformations to plant growth requirements.

Mediating greenhouse gas emissions

The imperative to substantially reduce greenhouse gases (GHGs) that contribute to climate change is a major global challenge. From an agricultural perspective, the necessity to reduce nitrous oxide (N20), methane (CH4) and carbon dioxide (C02) emissions is likely to constrain food production into the future unless more efficient practices can be devised with reduced gaseous losses. As GHGs result from microbial processes, insights into functioning of microbial communities offer a unique opportunity to mitigate emissions while increasing farming efficiency. We investigate the microbial communities responsible for the production of N20 (denitrifiers, nitrifiers) in soils and manures, with the aim of identifying regulators of each pathway and potential mitigation options. We are also interested in identifying land management options favouring C sequestration in soils.

Plant-soil-microbial Interactions

A key research focus of our group is on Plant-Soil-Microbial interactions and how they impact on soil fertility. We’re interested in understanding how the plant influences the function and composition of the microbial community in the rhizosphere and how the plant is impacted (either positively or negatively) by the interaction. We’re also interested in determining the impact of land management, environmental and edaphic factors on the dynamics of the interaction. We are currently investigating the mineralisation of soil organic matter in response to the release of plant exudates (the priming effect) and the impact this has on nutrient availability. In addition, we investigate the colonisation of ready-to-eat crops with pathogenic bacteria.

Enteropathogens in the environment

The natural environment plays an important role in the transmission of many human and animal pathogens, and insights into their fate within the environment can offer opportunities for the development of mitigation options to break the cycle of infection. We study the prevalence, fate and transport of microbial enteropathogens and their indicators in the environment within soil, water, plants and organic amendments. We’re interested in the factors (biotic and abiotic) affecting the persistence of enteric bacteria within the vadose zone. We assess the risk to water and ready-to-eat crops from activities such as landspreading, and are investigating novel methods of pathogen detection in environmental matrices. We are also interested in the spread of antimicrobial resistance in the environment. 

Soil persistent E. coli

Although the primary habitat of E. coli has long been considered to be in the animal host, there is now considerable evidence to suggest that E. coli can survive for long periods of time in the natural environment, and that populations can even become naturalised in soil. This has implications for its use as an indicator of water quality, the validity of which is based on the assumption that the bacterium is faecally specific. With collaborators we have isolated a large collection of naturalised E. coli (>9-13 years residence) from maritime temperate soil. We are currently investigating their capacity to survive in soil and aim to elucidate the phenotypic and genotypic characteristics that favour their persistence in that niche.       

Microbial adaptation to the environment

Microbes have a remarkable capacity to adapt to the environment around them through gene regulation, evolution, mobile genetic elements and cooperation with their neighbours. Conditions in the natural environment are highly dynamic and often response strategies are required to enable microbes to rapidly react to environmental stimuli, or adapt to available nutrient sources, in order to survive and to maintain populations. We’re interested in how organisms regulate their metabolic function in response to environmental conditions, how their populations evolve towards fitness in specific habitats and how they develop symbiotic or antagonistic relationships within complex mixed communities.