Cover of Microbial Ecology and Genomics: A Crossroads of Opportunity
Microbes have dominated life on Earth for most of its 4.5 billion year history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans.

Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. A past colloquium organized by the American Academy of Microbiology ("The Microbial World: Foundation of the Biosphere," 1997) made 2 key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

At the time the 1997 Academy report was written, the recommendation to sequence 1 genome from each major division was an ambitious objective. Now, with the remarkable advances in sequencing technology and bioinformatics, genome sequencing is nearly routine. Comparative genomics is a robust and rapidly growing research arena. In addition, other technologies are coming to the fore. For example, DNA arrays now provide unprecedented insights into the physiology of an organism. The scientific and technological developments of the last several years have been so rapid as to bring us to a new crossroads of opportunity—analysis of the tremendous complexity of natural microbial systems in more complete terms. Thus, there is a pressing need to reexamine and clearly articulate new opportunities in microbial biology.

In Feb. 2001, a selected group of scientists attended a 3-day colloquium sponsored by the American Academy of Microbiology entitled, "Microbial Ecology and Genomics: A Crossroads of Opportunity." The colloquium participants discussed where the field should be going next in light of the rapid and heretofore unanticipated development of genomics sequencing and proteomics technologies. Just as knowledge of the human genome promises to revolutionize medical science, the application of genomic technologies to microbial evolution and environmental biology promises to revolutionize microbial biology. The rewards of carrying out such work are not just increased knowledge, but also economic ones.

A more complete understanding of microbial diversity and the environmental processes they control will require much more than a biotic inventory. It will require a deeper understanding of the basic units of organization and their interactions. Communities, not total biomass, control net process rates driving the biogeochemical cycles sustaining the biosphere. Thus, descriptions of the temporal and spatial dimensions of microbial community structure and the complex gene expression patterns that underlie trophic interactions are fundamental to a more complete understanding of our biosphere. In turn, this understanding will be incomplete without knowledge of the fundamental mechanisms contributing to genetic variation and speciation. Genome sequencing has revealed totally unexpected genetic plasticity within and among named microbial species, and horizontal DNA exchange is now recognized to be a major force in the shaping of their genomes and fostering biochemical innovation.

Rapid advances in genome science must be complemented by investment in systematics, developing a taxonomy better adapted to genomic information. Traditional taxonomic concepts (i.e., species, genus, family) do not serve microbial systematics, in which problems of horizontal gene transfer and mechanisms of speciation and evolution are varied and complex. Currently, the strain is the unit of taxonomy and research, but this needs to be refined, not only for more effective ecological and evolutionary research, but also for better storage and retrieval of cultures, genomic data, identification of organisms in samples, patenting and bioprospecting.

Although the general patterns of macroorganismal diversity are relatively well known, spatial patterns of microorganismal diversity are completely unknown. Intensive microbial genetic/biodiversity surveys, covering the full range of environmental conditions and geological/evolutionary histories, will be required to determine the patterns that exist. This is a prerequisite to developing hypotheses to explain these patterns and linking patterns to processes at local and global levels.

These studies will generate very large amounts of data, as is now most clearly shown by the explosive growth of genome sequence information. However, reducing sequence data to a more useful form through annotation lags far behind the accumulation of sequences. As yet there is no provision for systematic inclusion of environmental information in sequence repositories. Thus, an important need is the ability to get data out in usable form. Although a universally accessible database would be a step toward sharing data and communicating information to the scientific community, more specific steps need to be taken.

10 years from now, we hope that we will have integrated genome sequence information with the environment. The environment is the context in which genomes evolved, function and continue to evolve. It is the only context in which they can be fully understood. The future includes a 10-year plan, in which techniques, outreach and training, and targeted areas for specific research programs, will provide a road map for a structured, rapid integration of genomics with microbial systematics, evolution and ecology.

Genomics, including analysis, is tool driven. Thus, mechanisms need to be established to encourage and reward development of new technology needed to efficiently and broadly deploy these new techniques.


David A. Stahl, James Tiedje. 2002. Microbial ecology and genomics: a crossroads of opportunity.

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