Environmental Genomics

Report from the mini-workshop on Environmental Genomics
held as part of the European Conference "Functional Genomics and Disease"
(draft)

conference report | photos

The Scientific Context

Environmental genomics is an entirely new area of research which attempts to expose and comprehend the complex interactions between living entitities and their physico-chemical scenarios with the tools of modern genomics. The field includes distinct aspects such as
[i] The molecular interplay of host-parasite or commensal interactions,
[ii] the production and cataloguing of metagenomic libraries of enviromental DNA,
[iii] the modelization of the global metabolism of the biosphere (which is predominantly mediated by microorganisms) and their genetic regulation with a Systems Biology approach and
[iv] the direct or indirect effect of physico-chemical environmental inputs in the expression and fucntionality of genes relevant for human health.

This context provided the scenario for a small session (formally a Mini-Workshop) on Environmental Genomics as a satellite event to the larger European Conference. The broad areas mentioned above related to Environmental Genomics were just sketched during the Workshop, with the expectation to create a good basis for future activities. This topic clearly belongs to the strategic mission of the ESF Programme on Integrated Approaches to Functional Genomics. Further, European Laboratories and research groups have a degree of leadership on these topics, which was clearly boosted through the stimulus that the mini-Workshop brought about. In addition, the celebration of the mini-workshop within the wider context of the European Conference was extremely fortunate. In this respect, the celebration of the Workshop in this privileged scenario contributed to overcome the notion of prokaryotes as simple models for tackling more complex problems, and expose instead the microbial world as a genuine source of pivotal biological questions, which spread through many environmental and health problems and which deserve an specific focus by themselves.

Apart of the summaries of the talks, included in the Abstract book, it is pertinent to make some extra remarks here on some emerging issues that this Workshop addressed.

First, there is a growing evidence that Bioinformatics applied to Environmental Microbiology allows integration of data coming from many different experimental systems connected to envirronmental problems. Such integration reveals new angles of a problem which are not evident of experimentalists in single systems. In this context, Alfonso Valencia and Ildefonso Cases explained how massive analysis of microbial reactions and gene clusters for biodegradation of toxic chemicals reveal novel global capacities of the biosphere to take xenobiotic compounds. This implies not only networking of biochemical reactions, but also intricate connections between transcriptional regulation and environmental lifestyles.

A second feature which was central to this meeting is the emergence of the whole of materials, techniques and concepts known as Metagenomics. Both Christa Schleper and Rolf Daniel disclosed an amazing repertoire of procedures to gain acess to the genomes and the activities of microbes which cannot be cultivated in the Laboratory. These techniques will allow not only a better understanding of the global ecology of non-culturable bacteria (which make up >95% of all the bacterial world) but will doubtless reveal also novel enzymatic recations with applications in bioremediation and the chemical industry.

Finally, one fascinating feature of examining interacting genomes in action is the analysis of the molecular interplay between given hosts (for instance, insects) and endosymbiontic bacteria. In this respect, Siv Andersson explained how analysis of the genome of various strains of endosymbiotic bacteria helso to understand key evolutionary processed of adaptation to new environmenst mediated by acquisition or deletion of pre-existing genes.

The Final Round Table discussion, triggered by the shorter intervention of Emilio Rodriguez, attempted to make connections between the world of enviromental microbial genomics and human Enviromics. This last term is much liked by EU and JRC scientific policy-makers to highlight the need to investigate the long-term effects of changing environmental conditions in human health. The interface between the two worlds will surely be one of the future priorities for research at an european scale.

Outlook: making the connection environment-human health?

What is the relevance of Environmental Genomics for Human Health? There is growing evidence that much of such Health is directly dependent on the external physico-chemical conditions. Although the facts are clear that the ultimate root of most avoidable health problems is the pollution created by a human (industrial, urban) activities, the last few years bear witness of entirely new angles of the problem, which are bound to become more pronounced in the imminent future:

• The consequences of the pollution caused by the discharge of large amounts of pharmaceuticals of all types into the environment (antibiotics, hormones, other medicaments) following their use in human and animals (as well as industrial wastes of their production), has not yet been addressed to any significant extent. Their action on living ecosystems will have an impact that we cannot predict thus far.

• The hormonal effects of xenobiotic compounds and their biodegradation intermediates caused by microbial metabolism remain largely unknown. These have been demonstrated in some cases, but the larger picture is still unknown. So far, the main warning of these effects has been the devastating consequences of long-term exposure of humans and animals to such a hormone-like products or intermediates. We are now in the situation of making predictive biodegradation simulations and foresee the environmental fate of many compounds.

• The sites polluted with industrial wastes and xenobiotic compounds create niches where these toxics act as agents for selection of new microbial variants, press gene transfer between bacteria and stimulate the evolution of new virulence factors and infectious diseases. Novel contaminants can create unexpected environmental reservoirs of pathogens. In this respect, we ignore much of the environmental effects of the new chemicals that are increasingly used at an industrial scale (flame retardants, fragrances, new explosives).

The main take-home message of this mini-Workshop was that contamination by novel chemical species and their metabolism by microorganisms is an issue of Public Health, which cannot be separated from the emergence of new diseases. It is a problem that deserves a focus and a home in any strategic research effort or in any policy oriented towards Human Health. These connections can now be explored with the tools of Genomics and Bioinformatics, which will take us into a better understanding of our surrounding world.