Environmental Genomics and Microbiology

Environmental Genomics and Microbiology

Why this Theme?

Links between climate change and abundance, range and phenology of populations are commonly reported, but detailed understanding of the biota’s potential to adapt, and our capacity to predict and manage such changes, remain limited. Combining expertise in the genetics and ecology of key animal, plant and microbial taxa with climate and paleoclimate science and modelling will enable informed predictions of how climate change will impact on biodiversity and ecosystem functioning, translating this knowledge into policy and planning.

eDNA approaches are rapidly being adopted in fields as diverse as forensics, invasive species mitigation, energy flow and biodiversity assessment, generating wide interest from governmental and non-governmental organisations. However, this topic requires careful integration and communication between scientific capabilities and end-user expectations. Adoption of eDNA technology as a ‘silver bullet’ approach in environmental issues is problematic, requiring more rigorous research into how sampling and environmental conditions affect the reliability of eDNA as a surrogate for species presence or abundance.


ARIES has considerable capability across the whole partnership for integrating strengths in evolution, ecology, work with key model organisms and ‘omics technologies (UEA, UoE, UoP, UoK, IoZ, CEH, BTO, PML, MBA, JIC, EI) with climate-change and paleoclimate science, social science, and modelling (RHL, UEA, BGS, BAS). This integration of phylogenetic, experimental and modelling-based methods allows us to understand the capacity of populations (including interacting populations) to adapt to different climate-change scenarios, including the study of additional drivers (such as pathogens), and the actions required to facilitate such adaptation. The involvement of key policy makers in ARIES projects will facilitate the application of new understanding and knowledge.

Projects in this area will also exploit ARIES expertise in eDNA-based and conventional population and community ecology over a range of ecosystems. ARIES has a wealth of expertise in conservation across several partners, with a particular focus at UoK’s Durrell Institute of Conservation and Ecology (DICE), IoZ and UEA, as well as in eDNA analysis, (e.g. at UoE, PML, MBA, CEH, UEA and EI).

Student training and employability

This topic will equip students with advanced molecular biological, bioinformatic, taxonomic, modelling and ecological skills. These skills, combined with those developed via cohort training, advanced training courses and opportunities to work with end users, will result in rounded, versatile environmental scientists, whose skills will be in demand in a wide range of sectors within and beyond conservation.

Wider engagement

The Natural History Museum will provide excellent research and outreach opportunities. Nature Metrics is a partnering company whose business is the application of eDNA technologies, providing important contributions to research and training in this topic. In addition, ARIES has a large number of partners who can contribute to, and benefit from, this topic, as well as providing expert training and placement opportunities, e.g. major policy makers (the Defra group: EA, Cefas, JNCC, FR, MMO, NE), water, infrastructure and engineering organisations (e.g. Anglian Water, Balfour Beatty, Mott MacDonald, Royal Haskonings DHV), consultancies (e.g. MarineSpace Ltd., PML Applications, RPA), conservation bodies (e.g. Amphibian & Reptile Conservation Trust, Broads Authority, Bumblebee Conservation Trust, Chester Zoo, RSPB, WWF-UK), in addition to links to international governmental and non-governmental organisations. The understanding of pathogen adaptations to changing climate will benefit greatly from input from the Pirbright Institute and Public Health England (PHE).

Hot Topics in this Theme

❖ Vertebrate and plant adaptation to a changing environment

❖ Evidence on whether, or to what extent, acclimatisation occurs (in the marine environment), whether acclimation is species dependant and the conditions under which acclimation occurs such as in interaction with other pressures.

❖ Mechanisms of plant immunity

❖ Pathogen adaptation and specialisation

❖ Marine microbes, phytoplankton, fungi and viruses: Controlling factors, interactions, variability and adaptation to change.

Theme Leaders

Prof Anthony Hall, Head of Plant Genomics, Anthony Hall Group, Earlham Institute
Anthony Hall received his PhD from the University of Leicester from the Botany Department and has worked as an Arabidopsis molecular geneticist for 18 years, focusing on the field of plant circadian biology. He is now the head of Plant Genomics at Earlham Institute, after moving from the University of Liverpool where he held the Holbrook Gaskell Chair of Botany at the University of Liverpool. Previously, he has been research lead for the Institute of Integrative Biology, Director at the Centre for Genomic Research (CGR) and academic lead of the Liverpool GeneMill (£3.8M investment).
Anthony’s plant genomics group started in 2009, and has focused on using and developing next generation genetic approaches to address key questions in plant science. In 2010 he was awarded a senior BBSRC research fellowship entitled “Developing Next Generation Genetic Tools for Wheat”. To date he has played a leading role in generating both the first draft wheat genome and epigenome. His group have developed novel strategies for the identification of EMS induced point mutations in Arabidopsis using high throughput sequencing and extended these to wheat. Anthony currently leads three international wheat genomics and epigenetic program grants in collaboration with India, Mexico, Australia, USA and Germany. His groups overarching aim is to understand how domestication, breeding programmes and adaptation has driven the evolution of the crop genomes.
Dr Karen Tait, Microbiologist, Plymouth Marine Laboratory
Karen Tait is a Senior Scientist at Plymouth Marine Laboratory. Her research has focused on the involvement of bacterial quorum sensing (QS) signalling molecules in the development of marine communities. Bacteria use these QS signal molecules to regulate expression of many genes, including those involved in biofilm formation, motility, secondary metabolism and virulence. Within marine biofouling communities, Karen has demonstrated these consortia are hot-spots of both signal-producing and signal-degrading bacteria, and that key members of this community utilise QS to aid their attachment to surfaces. In addition, QS also influences the settlement of higher fouling organisms. Karen has demonstrated the problematic fouling alga, Ulva sp., and, more recently, the barnacle Balanus improvisus, tap in on this signalling system when locating surfaces for settlement. Also of interest are signalling interactions amongst coral- and sponge-associated microbes, and the production of signal-mimic compounds by micro-algae.
More recently, Karen has expanded her interests of complex microbial communities to sediments. This work aims to determine the environmental drivers influencing microbial community structure and diversity in benthic habitats, particularly those microbes associated with nitrogen cycling, and the impact of environmental change on microbial community structure and function. Much of this work has involved studies of the impact of elevated CO2 and temperature on benthic microbes.
Dr Jonathan Todd, Senior Lecturer, School of Biological Sciences, University of East Anglia
Jonathan Todd is a molecular microbiologist who is interested in how a broad range of microbes, both Prokaryotic and Eukaryotic, participate in biogeochemical cycling. His research group focuses on the specific mechanisms that allow such organisms to synthesise and breakdown key biological molecules and importantly regulate these processes as to allow them to sense and respond to environmental cues.
Jonathan’s current research interests include studies into microbial DMSP catbolism and its place in the global sulfur cycle.
Dr Corinne Whitby, Senior Lecturer in Environmental Microbiology, School of Biological Sciences, University of Essex
Dr Corinne Whitby obtained her PhD in Environmental Microbiology from the University of Liverpool, and has since held posts as a Postdoctoral Research Fellow at the Universities of Liverpool, and Exeter. She began lecturing at the University of Essex in 2006 and is now a senior lecturer in Environmental Microbiology. Her research interest areas include studes of microbial commutinties and impact the environment may have on them, and microbial nitrogen and carbon cycling.
Corinne is a Fellow of Higher Education Academy (FHEA), the Vice Chair of ISMOS Technical and Scientific Committee, and the Founder & Co-Organiser of ISMOS.