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FALL 2005
Putting Organisms in Their Places
by Carole VanSickle

Scientists who systematically classify living things are themselves a threatened species. A major federal program aims to reverse this trend.

In 1997, when frogs at the National Zoo in Washington, D.C., were contracting grotesque skin deformities and dying, a taxonomist — a scientist who focuses on the classification of living organisms — fingered the culprit.

Investigators in the case had been stymied until a technician noticed that a microorganism under the dead frogs’ skin resembled something he’d studied in college. So he snapped some pictures and sent them to two former professors: Mel Fuller, a retired botanist from the University of Georgia, and Joyce Longcore, a taxonomist at the University of Maine. The two identified the organism as an aquatic fungus called a chytrid.

“Longcore was one of the few people in the world who could have identified that organism,” said David Porter, professor of plant biology at UGA. But because the number of scientists being trained as taxonomists (also known as systematists) has been steadily declining, the next mystery like the chytrids could long remain unsolved.

“We’re losing experts in groups of organisms and in taxonomy in general,” said James Rodman, program director of the National Science Foundation’s Directorate for Biological Sciences, “and new ones aren’t being trained.”

That’s why the NSF introduced PEET (Partnerships for Enhancing Expertise in Taxonomy) grants in 1995 and has been awarding them to coalitions of taxonomists to investigate new or understudied organisms. These scientists catalog species, train the next generation of experts and share their findings via Internet databases. Of the 25 active grants across the country, UGA has three: a partnership between Porter, Longcore and University of Alabama researchers to analyze chytrids; a study of microscopic organisms called euglenoids by cellular biologist Mark Farmer; and a beetle study by entomologist Joe McHugh.

Although the chytrid stir at the National Zoo has died down, ailing frogs from Panama to Australia continue to be diagnosed with the problem. So the basic question for scientists is: Why now? After all, chytrids aren’t new to the amphibian scene — they date as far back as the Precambrian Age (some four billion years ago). So if chytrids have been dwelling in frog skin for eons, what is causing them to multiply now at such a dramatic and problematic rate?

“Chytrids can live almost anywhere there is water,” Porter said, “although they do not multiply so wildly under all conditions.” But when the environment is right, chytrids can wreak havoc.

These “die-offs” — massive and relatively sudden deaths in isolated frog populations — have serious ecological effects. Forests that once rang with the calls of scores of frog species now are nearly silent. For example, only “three very sick frogs” were found in one day on a recent stream survey in Central America, Longcore said.

“It’s important to recognize and understand even the minutest aspects of our environment,” she noted. “It will be a dull world someday if all we have are dandelions and a bunch of resistant insects because we did not understand the checks and balances within the biota of the earth, and why and how they influence each other.”

Part of that challenge is to distinguish harmless microorganisms from any pathogenic cousins, identify the conditions that unleash the destructiveness, and understand the possible effects on the environment and on humans.

“As the amount of information about organisms continues to grow, it will become imperative for people to know not only what they are working with specifically but also what its ‘friends and relatives’ can do,” said Farmer, who directs the UGA Center for Advanced Ultrastructural Research. Farmer and colleagues at the University of Michigan study euglenoids, tiny one-celled swimmers most commonly recognized by high-school biology students as “the little green things that glide around under a microscope,” he said.

“Euglenoids have a very ancient evolutionary history,” Farmer said. “The more we know about different euglenoids, the more we can learn not only about present-day organisms but also about the ancestor cell that is the origin of life on earth.” His team focuses largely on comparative taxonomy, which involves distinguishing certain physical traits within families of organisms.

Using research derived from the results of his PEET-related work, and collaborating with many other systematists from around the world, Farmer also has developed and published a new classification system to replace the Linnaean system, which uses the traditional groupings of kingdom, phylum, order, family, genus and species. Farmer’s system (see sidebar p. 11) groups all living things around a central ancestor so that different groupings of organisms resemble the petals on a flower. The farther apart the petals, the more divergent are the species within the groups.

“Knowing how organisms differ from each other can be very important for the development of medicinal treatments,” Farmer said. “When groups have totally different evolutionary histories, you may be able to find unique molecular targets that can lead to medicines that will impact an organism without hurting its host.”

Take, for example, Chagas disease and African sleeping sickness, which combined affect more than 18 million people a year. A single epidemic can infect 50,000 people or more at a time and often result in nearly that many fatalities, according to the National Institutes of Health. These cardiac and neural infections are caused by an organism closely related to euglenoids and very distantly related to humans, so conditions and treatments that affect Farmer’s organisms indicate possible medical approaches to these deadly parasites.

As the amount of new information about organisms’ genetic workings increases, institutions such as the Joint Genome Institute (JGI), a U.S. Department of Energy coalition managed by the University of California, are discovering how the organization of an organism’s genes and proteins relates to its structure and function.

“Taxonomy’s value has increased as high-volume DNA sequencing clarifies and expedites the identification process,” said Ari Patrinos, associate director for biological and environmental research at the DOE, whose office supports and funds JGI.

High-volume sequencing also permits scientists to sequence vast amounts of DNA from undocumented origins — a practice known as “prospecting” [see sidebar p. 13].

“Gene prospectors” look for signature sequences that are unique to groups of organisms with a common ancestry. Once they have identified these sequences, a taxonomist can use the information to help place newly discovered organisms in the right groups. Also, the volume of sequences in a sample can indicate what an organism’s role is in a particular environment.

“If you isolate gene sequences from 100 organisms and 95 percent of them are from Dr. Porter’s chytrids, then you know that chytrids are major players in that environment even if you don’t know exactly which ones they are yet,” Farmer said. “It helps you know where to look and what to look for.”

Such research is not limited to analyzing pathogenicity, but it also can contribute to positive new applications. “As investigations by JGI are shedding light on the cellular machinery of microbes,” Patrinos said, “they may be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere and produce potentially important sources of energy.”

Not all organisms of concern to taxonomists — and to society — are microorganisms. For example, UGA’s McHugh and his students have identified 56 new beetle species in the past two years. Working with colleagues at Brigham Young University and Louisiana State University, the group analyzes the relationships between species to improve the classification system and to better understand any single organism’s environmental effects.

McHugh devotes his efforts largely to one beetle “superfamily” called Cucujoidea, which harbors a vast assortment of new species of stomach yeasts that McHugh helped discover. The yeast aids the beetles with digestion and may play a role in the species’ evolution as well, he said. Most of his work, however, focuses on identifying and classifying new beetles, and he travels all over the world to find them. “One in every five known species on Earth is a beetle,” he said. “This kind of work is exactly what I love to do.”

This kind of work also can have great practical value. “In a port like Savannah,” McHugh said, “if a ship arrives with insects on board, the inspectors need to know whether that ship should be allowed to enter the United States, be fumigated or be turned away. If there is no one who can identify the insects, we cannot know if the strange critters may ultimately wipe out North American forests.”

Although most chytrids are not pathogens, most euglenoids are not killers, and most beetles will not deforest the continental United States, understanding the ways in which organisms interact with each other, as well as with their environment, may help understand potential threats and solutions.

“Knowing something about an organism’s evolutionary history can help us understand and work with its present biology, which is what we hope to do with euglenoids and related organisms,” Farmer said. “The relatively gentle euglena from high-school science class may hold the key to the cures for diseases that infect millions of people each year.”

For more information on this article and on the national PEET conference at UGA in September 2006, contact Mark Farmer at farmer@cb.uga.edu, Joe McHugh at jmchugh@bugs.ent.uga.edu, or David Porter at porter@plantbio.uga.edu.