Exploring the Microbial World

Mono Lake, Courtesy of Jonathan P. Zehr, University of California, Santa Cruz They are the oldest forms of life, and by sheer quantity, they dominate the planet. But how bacteria and archaea interact with each other and their environment is essentially unknown. "It's really difficult to understand how the natural world functions if we don't know its most abundant and diverse component," says Matthew Kane, who runs the National Science Foundation's microbial program. Ninety-nine percent of the world's species of bacteria and archaea are "unknown to science, because we don't know the particular laboratory conditions in which to grow them and isolate them into pure cultures and describe them." In 1999 the NSF set out to answer these questions. The program, officially called Microbial Observatories, focuses on discovering and characterizing microorganisms, their genomes, activities, and just about anything else that can help researchers understand the microbes' interactions and their techniques for thriving and survival. "We're promoting the discovery of unknown microbial diversity," Kane says. Between 1999 and 2002, the agency spent $17 million (US) to fund 31 observatories. In the coming year, says Kane, NSF plans to fund an additional eight to 10 projects. Current ventures include studying Silicibacter pomeroyi and its effect on climate; nitrogen fixation; and bacterial degradation of the pollutant naphthalene. One project reported last year that the bacterioplankton SAR 11 (named for the Sargasso Sea, where part of the study took place) dominates ocean surface bacterioplankton communities.1 SAR 11 accounts for one-third of the cells in ocean waters. "Incredibly successful," is how one researcher describes this clade. TINY WEATHER INDICATORS Mary Ann Moran spends time in a salt marsh in Georgia. Moran, associate professor of marine sciences, University of Georgia, is also interested in S. pomeroyi, which she says may contribute to the understanding of climate changes. These bacteria produce organic sulfur, in the form of dimethyl sulfide (DMS), during their day-to-day existence. "Organic sulfur plays a role in cloud formation, in how much solar radiation is scattered back into the atmosphere," she says. Scientists do not know the conditions that determine when these bacteria make that sulfur. "But it makes a big difference in understanding how much sulfur is coming off the surface of the ocean. So if we could find those bacteria, look at their enzymes, then we could understand more about how that global process works," she says. The bacteria actually process the sulfur, which is turned out by marsh plants such as Spartina. "In some cases it becomes volatile DMS and it fluxes to the atmosphere, and in some cases it doesn't. We'd love to understand the role bacteria play in that," she asserts. BACTERIAL MYSTERIES IN MONO LAKE Researchers are focusing their efforts on another body of water, Mono Lake in California. James Hollibaugh, director of the School of Marine Programs, University of Georgia, Jonathan Zehr, professor of ocean sciences, University of California, Santa Cruz, and their colleagues want to understand what role bacteria plays in another major biochemical process--nitrogen fixation. Nitrogen-fixing bacteria remove nitrogen from the atmosphere, create ammonia, and then use this nutrient to fuel plant growth, notes Hollibaugh. This process occurs when there is inadequate, naturally occurring nitrogen in the water to nourish plants. The surface of Mono Lake, notes Zehr, is believed to have limited amounts of nitrogen at certain times during the year. Researchers would then expect to see bacteria in the water actually taking nitrogen from the air, which entered through normal gas exchange, but that has not been noted. So are the bacteria there? And if they are, what regulates their activity? One explanation being explored, says Hollibaugh, is that certain metals--those needed for the enzyme nitrogenase to facilitate nitrogen fixation--are not in Mono Lake. "We're trying to address that by looking at mRNA to see whether nitrogenase is even being expressed by these organisms. If it's being expressed but is not resulting in an active protein, that suggests that there is a control outside of gene control," Hollibaugh says. DINING AND STICKING Natural environments such as lakes and oceans aren't the only sites of microbial observatories. A contaminated aquifer in northern New York is where Eugene Madsen, associate professor of microbiology at Cornell University, is focusing his efforts to understand how bacteria degrade the pollutant naphthalene. He has found that enzymes coded for genes that are horizontally transferred are responsible for the degradation. He recently reported that different alleles involved in degrading naphthalene are found in bacteria located in sites that have different degrees of contamination.2 In the areas that Madsen investigated, he found that these alleles are transferred to diverse bacteria. "These results provide ... evidence that lateral transfer is important in the degradation of contaminants in polluted field sites," he wrote. Furthermore, they can help with "the development of new technologies and management strategies" in cleaning up pollution. Such practical outcomes are also a goal of the NSF program. Kane notes that antibiotics such as penicillin and useful enzymes such as Taq polymerase--vital for PCR--have come from studying microbes. "So one must assume that we've only scratched the surface of the potentially useful products these organisms make in nature for use by scientists and society," says Kane. In Yellowstone National Park, Gill Geesey's microbial observatory is partially dedicated to developing a highly practical product, an underwater adhesive, from the hot springs there. A microbiology professor at Montana State University and a fellow at the Idaho National Engineering and Environmental Laboratory, Geesey is studying microbial mats. "These mats [clumps of bacteria] are anchored to the mineral substratum by polymers that are excreted by these mat communities, and so if we could get a handle on how to culture these organisms, we might be able to recreate the conditions in these hot springs that encourage these microorganisms to produce these materials," he says. That could lead to the commercial production of marine adhesives to replace the currently used adhesives, which release pollutants and are made from nonrenewable resources. The US Navy, he says, is interested in underwater glue, for example. Courtesy of Rolf Schauder, Microbial Diversity, MBL, USA COMMUNITY TIES: Microbial community composed of photosynthetic bacteria and cyanobacteria growing in hot springs on the shore of Paoha Island in Mono Lake. INSET: Microbial mats. TECHNOLOGY'S ROLE Technology, of course, factors into finding the proper cultures for reproducing these microbes. Microarrays are vital, notes Antarctica researcher Alison Murray, research assistant professor at the Desert Research Institute in Reno, Nev. "It gives us a lot of things we can't recreate in the lab. My hope is that we can have microarrays that have representative genes on them from Antarctic microorganisms. ... Then we can come down here at different times of the year and see how gene expression changes from collecting fresh messenger RNA straight out of the ocean, then hybridize that to the microarrays. That gives us an idea of what genes are actually being expressed in the environment at the time of collection," she says. She gathers microorganisms from the ocean by filtering seawater (bacteria and archaea are larger than 0.2 microns). The cells are then broken open, and the DNA, reduced to 40 to 50 1000-base pair fragments, is cloned. Zehr is also using gene chips to understand when genes are active. It's a bit different from the way most researchers use such chips. "Most people put the whole genome of an organism on a chip," Zehr says. "What we're doing is having each spot on a chip representing the same gene from a different organism. So simultaneously we'd be able to watch for the expression of that particular gene by a thousand different organisms." Thus, he and his colleagues can determine, for example, when certain species express specific nitrogenase genes. Stephen Giovannoni, director of the Molecular and Cellular Biology program at Oregon State University, has developed another means of culturing bacteria that is producing numbers large enough to study.3 He isn't sure why they are growing, but they are. The researchers "reduced the size of the culture, the number of cells, by about 1000-fold" to replicate their environmental conditions. In the oceans, he says, the organisms live in an environment in which the nutrient level is "way, way, way below what we work within our labs. The whole idea is instead [to] devise technology that lets us study organisms at the low-cell densities, low substrate concentrations that are typical of the environment." It's hard not to think of investigators in the microbial observatories program as latter-day explorers of a new world, one populated by the "most diverse, abundant, and least known and understood organisms on our planet," says Kane. "There is an incredible wealth of untapped diversity." Harvey Black (hblack@chorus.net) is a freelance writer in Madison, Wis. References 1. R.M. Morris et al., "SAR 11 clade dominates ocean surface bacterioplankton," Nature, 420:806-10, Dec. 19, 2002. 2. M.S. Wilson, "Horizontal transfer of dissimilar dioxygenase genes within phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent but physically distinct environments," Appl Environ Microbiol, in press. 3. S.A. Connon, S.J. Giovannoni, "High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates," Appl Environ Microbiol, 68:3878-85, 2002.

Exploring the Microbial World

Interested in reading more?

Become a Member of