Priorities for
Microbial Biodiversity Research

Summary and Recommendations

Wetlands Dictoglomus Pharmaceuticals
Pollutant Destruction Cryptosporidium Ants

Report of a Workshop held at Michigan State University

Organized by The Center for Microbial Ecology

Sponsored by:
U.S. National Science Foundation
U.S. Department of Energy
U.S. Environmental Protection Agency
Bergey's Manual Trust


CME is interested in any comments you may have about the contents of this report. Please
contact tiedjej@msu.edu with any questions or comments you may have.


Microbial diversity is an unseen national as well as international resource that deserves greater attention. Too small to be seen no longer means too small to be studied or valued. Microbial diversity encompasses the spectrum of microscopic organisms including bacteria, fungi, algae, protozoa. These organisms populate the soil, water and air that surround us as well as live in more unusual environments such as the boiling water of hydrothermal vents, deep ocean trenches and alkali lakes.

Microbes: The earth's engine
Microorganisms have been evolving for nearly 4 billion years and are capable of exploiting a vast range of energy sources and thriving in almost every habitat. For 2 billion years microbes were the only form of life on Earth. During this long history, all of the basic biochemistries of life evolved, and all life forms have developed from these microbial ancestors. It is estimated that 50% of the living protoplasm on this planet is microbial. Microorganisms represent by far the richest repertoire of molecular and chemical diversity in nature. They underlie basic ecosystem processes such as the biogeochemical cycles and food chains, as well as maintain vital and often elegant relationships between themselves and higher organisms. Microbes provide the fundamental underpinning of all ecosystems. Without microorganisms, all life on Earth would cease.

Microbes: The biological frontier
Because microorganisms are small, they are least known, and this gap in knowledge is particularly apparent for bacteria and other small organisms. Current evidence suggests that perhaps 1.5 million species of fungi exist yet only 5% are described. For bacteria there may be 300,000 to 1 million species on earth yet only 3,100 bacteria are described in Bergey's Manual, the treatise of described bacteria. A gram of typical soil contains about 1 billion bacteria, but only 1% of those can be cultured. Similarly low fractions of microorganisms have been cultured from fresh water and ocean environments. Hence, most microbes remain to be discovered.

The value of microbial diversity
Focusing on microbial diversity is timely. Diverse microorganisms are essential to a sustainable biosphere. They are able to recycle nutrients, produce and consume gases that affect global climate, destroy pollutants, treat our wastes, and they can be used for biological control of plant and animal pests. The study of microbial diversity is also important to solve new and emerging disease problems and to advance biotechnology. New technologies, particularly in nucleic acid analysis, computer science, analytical chemistry, and habitat sampling and characterization place the study of microbial diversity on the cutting edge of science.

Humans over the ages have been highly successful in applying processes carried out by microorganisms to solve problems in agriculture, food production, human health, environmental quality, and industry. Recently developed technologies in molecular biology and genetics offer great promise for new opportunities to develop the potential of microbial diversity.

The Value of Microbial Biodiversity Research

Microorganisms are the major sources of antimicrobial agents and produce a wide range of other important medicinal compounds including enzymes, enzyme inhibitors, antihelminthics, antitumor agents, insecticides, vitamins, immunosuppressants, and immunomodulators. These agents have all been discovered during the past 50 years and represent only a small portion of what is likely present in nature. Pharmaceuticals of microbial origin have a market value (at the wholesale level in the developed world) of approximately $35-50 billion annually.

Identifying research priorities
Forty-three scientists representing expertise in different habitats, different groups of organisms, different methodological expertise and from different regions of the world met to discuss and identify research and infrastructure needs in microbial diversity. The workshop participants identified four general areas of importance to better understand, manage and utilize our vast microbial resource. The first area addresses gaps in our basic understanding of how microbial diversity originates and where it resides. The second area focuses on the discovery of the unknown microbes, including the new methods that are needed to culture and rapidly characterize the previously unculturable organisms. The third area addresses the need of preserving newly discovered, often fastidious organisms, including in situ and consortia preservation as well as more rapid and efficient methods for preservation. The fourth area focuses on organizational and infrastructure needs, including improvements in databases, centralized facilities for specialized and routine efforts, and training of a new generation of microbial diversity and taxonomy experts. The group recommends that microbial diversity efforts be coordinated at an international level in so far as possible to bring the full talents of the scientific community to this large and exciting problem.


Recommendations

The following topics were recommended as high priority needs if we are to better understand, manage, and utilize the vast microbial resource.

1. Understand the origins and patterns of microbial biodiversity

a.) Select key habitats for coordinated, focal, and long-term study. A few habitats should be intensively studied; others should be studied extensively.

b.) Achieve a better understanding of spatial and temporal patterns of microbial diversity, and how environment determines those patterns.

c.) Enhance our understanding about the rate and range of global dispersal, evolution, and extinction of microbial species.

2. Discover and characterize microbial diversity a.) Refine appropriate taxonomic units that define microbial diversity, and develop the appropriate methodology to measure those units.

b.) Discover new microbial forms, biochemistries, evolutionary branches, and habitats.

c.) Improve methodologies to characterize, isolate, and identify non-culturable and rare members of communities.

d.) Develop advanced instrumentation and software that provides new and more rapid methods to characterize isolates and communities.

e.) Foster research on polyphasic taxonomy, particularly the integration of phenotypic, genetic, and ecologic information.

3. Preserve microbial diversity a.) Conduct research leading to the preservation of mixed communities, e.g., consortia, natural communities.

b.) Improve culture preservation strategies, such as robotic preservation, miniaturization, and optimized regimes for difficult to preserve microbial groups.

c.) Maintain B and coordinated network of culture collections that are accessible worldwide.

d.) Conserve habitats with rare or threatened species.

4. Organizational and infrastructure needs a.) Because of the large effort needed, develop means to coordinate microbial diversity research at an international level.

b.) Develop integrated electronic databases that include habitat, geographic, phenotypic, genotypic, morphological, and accession information.

c.) Involve researchers from other fields, especially computer science, optics, electronics, device engineering, chemistry, remote sensing, and macrobial ecologists and systematists.

d.) Centralized efforts are recommended where specialized facilities are needed, routine measurements are made, and for database and archival activities.

e.) Expand the training of new scientists knowledgeable in modern microbial diversity, physiology, and taxonomy.

f.) Enhance the public's awareness of the vital role microbial diversity plays in their lives and the frontier this field offers.

Microbial diversity is a key frontier. It is the largest untapped resource for both understanding how biological systems function as well as for new biotechnologies. Advances in the molecular, chemical, optical, computer and information sciences has now made the exploration of this frontier practical. A coordinated effort by an international community of interested scientists over 10 years should make a new level of understanding possible.

Workshop Participants
David Boone, Oregon Graduate Institute;
Richard Castenholz, University of Oregon;
Rita Colwell, Maryland Biotechnology Institute;
Frank Dazzo, Michigan State University;
Richard Devereaux, Environmental Protection Agency;
Larry Forney, Michigan State University;
Robert Frederick, Environmental Protection Agency;
Robert Gherna, American Type Culture Collection;
William Ghiorse, Cornell University;
James Gosz, Ecological Society of America;
Jay Grimes, U.S. Department of Energy;
Kay Gross, Kellogg Biological Station;
Chris Haber, The Upjohn Company;
William Holben, Michigan State University;
John Holt, Bergey's Manual Trust;
L.H. Huang, Pfizer, Inc.;
Jeannie C. Hunter-Cevera, Society of Industry Microbiology;
Barbara Kirsop, University of Cambridge;
Carole Klopatek, U.S. Forest Service;
Michael Klug, Kellogg Biological Station;
Micah Krichevsky, National Institute of Dental Research;
Richard Lenski, Michigan State University;
Larry Moore, Oregon State University;
R.G.E. Murray, University of Western Ontario;
Norman Pace, Indiana University;
Jeanne Poindexter, Barnard College;
Daniel Prieur, Universite de Paris & CNRS;
Margaret Riley, Yale University;
Joann Roskoski, National Science Foundation;
Tom Schmidt, Michigan State University;
Peter Sneath, University of Leicester;
James Staley, University of Washington;
Hideaki Sugawara, RIKEN Institute, Tokyo;
Jean Swings, University of Gent;
James Tiedje, Michigan State University;
Vidgis Torsvik, University of Bergen;
Hans Truper, University of Bonn;
Anne Vidaver, University of Nebraska;
David White, University of Tennessee;
George Zavarzin, Russian Academy of Sciences.


CME is interested in any comments you may have about the contents of this report. Please
contact tiedjej@msu.edu with any questions or comments you may have.

The printed version of the report may be obtained from the Center for Microbial Ecology,
Michigan State University, East Lansing, MI 48824, Email: plinel@msu.edu.


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