Ecogenomics at the James Hutton Institute

What is Ecogenomics?

Within the James Hutton Institute, ecogenomics encompasses state-of-the-art experimental and computational approaches to mine genomic data in order to gain understanding of microbial and fungal contributions to ecosystems services. We have taken up the challenges and opportunities offered by next generation sequencing approaches to investigate a range of important issues regarding the structure and function of organisms within ecological contexts. Culture independent approaches including community structure analysis using amplicon deep sequencing, shotgun metagenomic and transcriptomic approaches on environmental samples are coupled with de novo genome sequencing and comparative genomic analyses of environmental isolates are enhancing our understanding of an array of ecological issues including:

• The relationships between microbial community structure and functional diversity
• The influence of climate and soil parameters on microbial distribution at different spatial scales;
• The consequences of induced shifts in microbial and fungal community diversity
• Phenotypic and genotypic adaptation of enteropathogens, including pathogenic Escherichia coli, Salmonella enterica and Campylobacter jejuni to diverse environments

One of our primary aims at the James Hutton Institute is to utilise the knowledge we generate to devise novel strategies enhancing the sustainability of ecosystem services.

Approach

We are linking the new approaches in next generation sequencing and computational biology with our strengths in ecological theory, biological taxonomy, experimentation, surveying and modelling. Supporting our approach, we have a wealth of primary ecological and environmental data which have been obtained from sampling diverse global ecosystems and long term experiments (such as Centre for Sustainable Cropping (CSC) [1], Long-term Sludge Experiment (LTSE) [2], Environmental Change Network (ECN) [3]) and from national / regional surveys (for example  the National Soils Data [4]). We also utilise our own scientific collections (National Soil Archive (NSA) [5], National Waters Inventory [6], and Germplasm collections such as Soft fruits [7],  Commonwealth Potato Collection (CPC) [8], Barley [9] (external link to the Barley Genome Project [10]), Pest and Pathogens [11]).

People Involved

Click on the names and visit their staff pages to find more about us and what we do

• Rebekka Artz [12], Peatland ecologist
• Davide Bulgarelli [13], Plant-microbiota interactions
• Peter Cock [14], Bioinformatician
• David Cooke [15], Plant pathologist
• Tim Daniell [16], Soil ecologist
• Thomas Freitag [17], Molecular microbiologist
• Nicola Holden [18], Molecular bacteriologist
• Sue Jones [19], Computational biologist
• Leighton Pritchard [20], Computational biologist
• Andy Taylor [21], Fungal molecular ecologist
• Ian Toth [22], Bacterial pathogens

Recent and ongoing PhD projects:

• Patrizia Vannucchi [23]: Developing Molecular Approaches to Elucidate the Ecology and Function of Oribatid Mite Communities [24]
• Peggy Ehrlich [25]: Host Identity and Climate as Determinants of Ectomycorrhizal Fungal Distribution in Scotland [26]
• Alessandro Bergna: "Meta-omic approaches to understanding and predicting soil biodiversity ecosystem function relationships”
• Rodrigo Alegria-Terrazas [27]: Exploiting Root-Microbiota Interactions for Sustainable Barley Production. Scottish Food Security Alliance-Crops PhD student.