Message from the Director
Environmental Genomics
Huntington F. Willard, PhD
If you read just the headlines or even the Congressional Record, you would be forgiven for concluding that the only purpose of the Human Genome Project was to enhance the future of medicine. To be sure, that is no small part of its promise, both here at Duke and beyond. However, even a cursory tour through the many genome web sites should be enough to convince you that the major deliverable thus far has been the sequence of genomes, not just of the human, but of nearly 200 species and organisms with whom we share this planet.
"The most sobering and exciting aspect of ecosystem genomic research is that so much remains to be explored. "Indeed, the major scientific (and philosophical) breakthrough of the genome sciences to date has not been new medicines or diagnostics (although there have been those), but an awareness of our oneness with other organisms and a deepening appreciation for both the wonder and the importance of global genomic diversity.
The availability of complete genome sequences has opened up new ways to study biology as well as pathology, to explore animal and plant development and to gain novel, even striking, insights into the evolution of animal, plant and microbial diversity. While those in medicine are still largely warming up their voices in the wings, preparing thoughtfully (but increasingly impatiently!) for breakthroughs yet to come, genome sequencing has already fundamentally changed our approach to other biological systems, from the tiniest microbe to the tallest tree.
Duke already has made its contribution to understanding fungal genomes, both in the IGSP and in the Center for Microbial Pathogenesis. Now, as the lead story in this issue of GenomeLIFE explains, Claire Williams of the Nicholas School wants to be sure that Duke doesn't miss out on the largest genomes that dominate the landscape, both in the Duke Forest and in forests around the world.
Why forests? Principally for two reasons. First, trees are of unquestioned importance economically. In forest-rich countries like Canada, Sweden and New Zealand, for example, there are major genomics programs designed to tap the genetic potential of important species and to focus on areas critical to forest health, tree growth, wood quality and the future of the forestry industry. Second and of likely broader impact, the forests represent one of earth's major ecosystems, one constantly challenged by population growth and environmental change. How diverse is the range of genomes to be found in forests around the globe? Why are tree genomes so giant? Is this just so much flotsam and jetsam from evolution's failed experiments? Or part of an adaptive response to changing biotic pressures, a distinctive mechanism to defend against insects and disease and ensure genomic survival? To get to the root of these questions will require a concerted effort to explore forest genomes at many levels, from applied tree improvement to the evolutionary ecology of natural tree populations. As Williams avers, genomics can serve as a platform technology to provide approaches, tools and datasets, ranging from whole genome sequences to surveys of ESTs (expressed sequence tags), to catalogues of allele frequencies to document and track forest diversity.
As we've seen before, this isn't just about the science. The promise of forestry genomics is clear: healthier, faster-growing trees. But, as those in the Nicholas School well recognize, biotechnology and genetic engineering hold as much peril as promise for our forests and ecosystems. Hundreds of permits for trials of genetically engineered trees have been issued, without much open consideration of the potential dangers of such new genomes being, literally, cast to the winds. The Nicholas Environmental Leadership Forum in November will go far to address many of these policy concerns.
And what of other ecosystems—the oceans, shorelines, wetlands, atmosphere? What array of organisms populate these natural ecosystems, and how do they adapt to living in often unusual, even hostile environments? Craig Venter has begun to sample microbial diversity in the seas of the world, first in the Sargasso Sea off the shores of Bermuda, then the Galapagos, then Polynesia. With every sampling comes a rich collection of new genes—millions of them— that we didn’t know existed. A team from Berkeley has taken a different approach, sampling microbial communities created by acidic mine drainage. What new genes have emerged to allow microbes to tolerate life at pH <1? Might some of these genomic tricks be borrowed to allow productive use of "extremophilic" microbes in other unsavory environments, as in cleaning up toxic waste or detecting or defending against exposures from bioterrorism?
The most sobering and exciting aspect of ecosystem genomic research is that so much remains to be explored. One suspects that we're only seeing the tip of an iceberg of hidden biodiversity, from the ocean floor to the rainforest. There are literally billions of genes yet to be discovered out there. After the sequencing is done, what then? Reflection on what it all means—for our planet, for our own species and for our role as a bit player on the larger stage of biodiversity.
Huntington F. Willard
Director