Cover Article
The Undiscovered Planet
Microbial science illuminates a world of astounding diversity.
by Jonathan Shaw
All images courtesy of Roberto Kolter, unless otherwise noted
Copernicus, Kepler, Galileo, Newton—these are familiar names. During a 150-year span in the sixteenth and seventeenth centuries, they led the scientific revolution that placed the sun, rather than the earth, at the center of things astronomical. But have you ever heard of Carl Woese? He set in motion a scientific revolution in biology that, in its repudiation of anthropocentric views of life, is proving no less profound.
In 1977, Woese (pronounced “woes”), a professor at the University of Illinois at Urbana-Champaign, drew a terrestrial family tree that showed the genetic relatedness of all living things on this planet. Using modern tools of molecular biology, he sampled the known single-celled, microscopic organisms we call microbes, and also the denizens of the human-scale world with which we are familiar: the flowers, trees, and shrubs; the animals; and the fungi. His map of all this new information revealed that taxonomists of ages past had been looking at the world through the wrong end of a telescope. The formerly great “kingdoms” of Plantae, Animalia, and Fungi almost disappeared, shrinking to fit on a small, trifurcating branch of his tree. In their place were three vast “domains”: Bacteria (single-celled microorganisms that lack a distinct nucleus and organelles); Archaea, or Archaebacteria (similar in appearance and simplicity to bacteria, but with notably different molecular organization); and Eukarya (all organisms whose cells have a distinct nucleus—or, simply put, everything else). Life on Earth, Woese’s model showed, is overwhelmingly microbial. In fact, the extent of microbial diversity is so great that scientists have difficulties estimating its actual size. Some estimates place the number of microbial species in the range of billions, exceeding the number of species of “large” organisms by several orders of magnitude.
The anthropocentric five-kingdom system classified all unicellular organisms lacking nuclei (archaea and bacteria) as Monera. The nucleated eukaryotes comprising plants, animals, and fungi were thought to represent the bulk of biological diversity. All other nucleated eukaryotes were grouped in a grab-bag classification known as Protista.
The modern “tree of life,” based on genetic analysis, shows that the bulk of Earth’s biodiversity resides among the Archaea, Bacteria, and that portion of the Eukarya that does not include plants, animals, and fungi.
In light of this new understanding of life, scientists with advanced research tools are focusing anew on microbes, which, following the great discoveries of penicillin and other antibiotics in the mid twentieth century, had largely been consigned to the confines of pharmaceutical research.
“Our planet has been shaped by an invisible world,” says Roberto Kolter, a professor of microbiology and molecular genetics at Harvard Medical School (HMS). He and Jeffrey professor of biology Colleen Cavanaugh of the Faculty of Arts and Sciences (FAS) together co-direct Harvard’s Microbial Sciences Initiative, which serves as a focal point for researchers in the field from all over the University. “Microbes mediate all the important element cycles on Earth, and have played a defining role in the development of the planet,” says Kolter. They form clouds, break down rocks, deposit minerals, fertilize plants, condition soils, and clean up toxic waste. Among their ranks, explains Cavanaugh, are the photosynthetic “primary producers” that use sunlight, water, and carbon dioxide to form the broad base of the food chain, and together with plants make up the earth’s largest source of biomass. The earliest life on our planet was entirely microbial, and if life exists on other planets, it is surely microbial there as well.
In terms of gene content, humans and potatoes are more closely related than these two bacteria are to each other—one measure of bacterial diversity. On the left, Vibrio cholerae; on the right, Mycobacterium tuberculosis.
From the billions of bacteria in a soil sample, these few cells landed on a nutrient medium where they could grow and form colonies. “There is so much beauty everywhere we look,” says microbiologist Roberto Kolter.
A strain of Streptomyces that produces several antibiotics widely used in medicine and agriculture. When starved, these bacteria take on a “hairy” appearance as they initiate growth of aerial structures where protective spores develop. The pigmented areas consist of small molecules, often with antibiotic properties.
In the presence of the antibiotic streptomycin, colorful antibiotic-resistant mutants of Streptomyces coelicolor spring up and form colonies.
In the realm of human health, microbes help us digest food and produce vitamins, protect us against infection, and are the main source of antibiotic medicines. The human cells in your body number 10 trillion, but that pales by comparison to the estimated 100 trillion microbial cells that live in and on you. “Without them, you would be in trouble,” Kolter says: animals experience abnormal growth and become sick if deprived of their microflora during development. Although a few microbes are known to cause disease, the precise role played by the vast majority is essentially unknown.
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