Genes, Populations, and Ecosystems: The NERC Environmental Genomics Programme

The Human Genome Project may have grabbed all the headlines, but whole or partial genome sequence data exist for an ever increasing range of organisms. Funding and training the UK environmental biology community to exploit those data is the aim of the £16.5 million, 5-year Environmental Genomics thematic programme launched by the Natural Environment Research Council (NERC) in December 2000 as part of a wider UK government funded genomics initiative.

The term genomics is used to encompass everything from genome sequencing, annotation of function to genes, and genome architecture to studying patterns of gene expression (transcriptomics), protein expression (proteomics), and metabolite flux (metabolomics; Figure 1). The environmental genomics programme aims to integrate these approaches into traditional ecology and physiology to test ecological and evolutionary theory. It must be emphasised that genomics is a tool, not a science, that must be used as part of an integrated approach at the whole organism, population, or ecosystem level ( Figure 2). The principles of genomics are no different to how molecular biology has been used in environmental science and biology over recent years. It is just that technological advances have increased the scale at which biological events can be observed and, more importantly, analysed and interpreted. It could be said that the days of the single-gene, single-postdoctorate are numbered.

The molecular basis of life.

Central to the aim of the Environmental Genomics programme is the establishment of a community of researchers, both empiricists and theoreticians, who are proficient in the development and application of postgenome technologies to the study of organism and ecosystem function. It is envisaged that the integration of molecular genome science with ecology and evolution will generate exciting and novel interdisciplinary research opportunities. Effort will focus on those questions and organisms of highest environmental relevance, and on sequences likely to give reasonably rapid answers of maximum applicability across systems and habitats.

A core objective of the Environmental Genomics programme is to gain ecological value at the whole organism and ecosystem level through mechanistic research.

The first of two calls for funding under the programme has closed. In total, 176 outline bids for funds were received, and 40 applicants were invited to submit full proposals. These full proposals are currently being peer-reviewed and awards will be announced in September 2001. Award holders will be recruiting to fill vacant research positions (postdoctorate and postgraduate) in late 2001. A focused second call for proposals will be announced early in 2002.

Until the first awards are made, the precise direction that the programme will take remains undefined. However, the full proposals provide some pointers. Most wish to apply transcriptomics to study the impact of environmental and chemical stresses on gene expression. Only three proposals address proteomics, whilst none of the proposals consider the metabolome. In total, 30 test organisms have been described with representatives from the microbial, invertebrate, vertebrate, and plant kingdom. Generic issues being addressed in the full proposals include:

  • What genes determine ecological fitness?

  • Which genes are turned on under specific circumstances? and what do they do?

  • Environmental impact(s) on gene and protein expression?

  • Chemical impact(s) on gene and protein expression?

  • Are changes in gene and protein expression adaptive? and do they serve an evolutionary purpose?

  • What genetic variability exists (inter- and intraspecies) and are there sensitive subpopulations?

  • Can changes in gene and protein expression lead to wider community and ecosystem impacts?

Natural Environment Research Council

The mission of NERC is:

  • to promote and support, by any means, high-quality basic, strategic, and applied research; survey; long-term environmental monitoring; and related postgraduate training in terrestrial, marine and freshwater biology, and Earth, atmospheric, hydrological, oceanographic and polar sciences and Earth observation;

  • to advance knowledge and technology, and to provide services and trained scientists and engineers, which meet the needs of users and beneficiaries (including the agricultural, construction, fishing, forestry, hydrocarbons, minerals, process, remote sensing, water and other industries), thereby contributing to the economic competitiveness of the United Kingdom, the effectiveness of public services and policy and the quality of life;

  • to provide advice on, disseminate knowledge, and promote public understanding of the fields aforesaid.

The provision of high-quality training to develop a core UK expertise in the application of transcriptomics and proteomics to answer ecological questions is an essential part of the Environmental Genomics programme. NERC are currently providing opportunities for postgraduate students and recent postdoctorates to identify and attend training courses in transcriptomics, proteomics, and bioinformatics. Up to £600 is available per applicant for up to 50 applicants. The programme will also offer specially devised short courses for the education and training of the NERC biological science community in environmental genomics techniques, and focused training, specifically in bioinformatics, will form a major component of the programme to maximise the knowledge gained from the postgenomic data generated.

The biggest challenge faced in genomics is interpreting the vast quantities of data available to gain knowledge that can be applied to whole-organism physiology. In order to meet this challenge, highly competent bioinformaticians are required to recognise distinct patterns of gene expression from data that can be inherently noisy. NERC have committed £2 million of the programme budget to address issues of data management and analysis, and links are being made to with other research councils (particularly the EPSRC/BBSRC Bioinformatics Initiative), both to avoid reinventing the wheel and to benefit from their expertise and facilities.

With the increasing availability of ecologically relevant genome sequence data, coupled to advances in postgenomic techniques and information technology, NERC is in a unique position to provide the UK environmental science community with opportunities to exploit these technological advances to study earth system science.

For more information please visit the NERC Environmental Genomics Web page or contact the Science Coordinator: Dr. Jason Snape, Brixham Environmental Laboratory, AstraZeneca, Freshwater Quarry, Brixham, South Devon, TQ5 8BA; e-mail:; tel: 01803 884273; fax: 01803 882974.

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