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| U N I V E R S E M A G A Z I N E - F A L L 1 9 9 7 | THE SMELL OF FRESHLY PLOWED SOIL: A Natural History of the Underground MILLIONS AND MILLIONS OF MICROBES Microorganisms require a different way of thinking about diversity. Ann Kennedy hands me a petri dish that an assistant has just brought into the room. I lift the lid. What greets my nose is a dark, familiar smell of earth, rich and dank and ripe. The smell brings back warm spring evenings and freshly plowed midwestern soil. This is the smell of healthy soil—it can actually be traced to a compound, geosmin, produced by the crusty little globs in the petri dish of actinomycetes. Actinomycetes are microorganisms that are a sort of transitional group between bacteria and fungi. Like fungi, they produce tendril-like hyphae. But they also have cell walls, like bacteria. Actinomycetes are intriguing characters. They are able to decompose some fairly complex organic compounds. They eat tough substances such as cellulose and chitins. They also produce antibiotics. Streptomycin, for example, comes from a strain of actinomycetes. Although actinomycetes give healthy soil one of its signature smells, they are merely part of an enormous cast of colorful characters. It has been estimated that there are 10 times the amount of living bacteria in the Earth's soils than in the combined weight of all the Earth's humans, other mammals, and birds. If you add in the other soil organisms such as protozoa, arthropods, earthworms, fungi, and algae, the proportion becomes 50 to one. A single gram of soil from the root zone of plants may contain a billion bacterial cells, representing four to five thousand bacterial types. It has also been estimated that only 13 percent of the earth's microbial populations have been identified, writes Kennedy. The number of known microbial species totals over 110,000, but only a fraction of the species have been identified. Even fewer are being studied or are present in culture collections. However, microorganisms require a different way of thinking in terms of diversity. Cultivated soils, for example, often have more microbial diversity than do native grassland soils. Whereas in undisturbed soil, microbes tend to develop pockets and communities, in tilled soils they become evenly distributed. When we till soil, we think we're doing the right thing, says Kennedy. But what's happening is the community is going berserk. She cites fellow ARS soil scientist Bob Papendick's analogy—the effect of tillage on the microbial community is like earthquake followed by fire. When some kind of stress is imposed on that system—the addition of chemicals, for example, or tillage—the bacteria immediately start adapting to the new conditions. There are also minor players on the periphery of the system. When that system is disturbed, they also shift and might play a much different role. "It's not like they're going to be completely different," says Kennedy, "but enough to live under that stress." This adaptability leads to bacteria within the same species having completely different traits. In fact, because they are so adaptable and quick to mutate, the concept of "species" has limited usefulness when it comes to thinking about microorganisms. For example, both Kennedy and USDA plant pathologist Jim Cook study Pseudomonas fluorescens. Some strains will stress wheat, producing a compound that inhibits lipid synthesis in certain wheat seed. The strain that Cook studies is antifungal. But here's the key to what this difference, this diversity, is all about: "Had we not been looking for wheat inhibition or antifungal qualities," says Kennedy, "no one would ever have known" there were different strains of P. fluorescens that had different characteristics. In other words, not only are there lots of different strains, the characteristics do not necessarily define a strain's total character. Much of what we think we know about the microbial world, suggests Kennedy, is simply due to our perspective. One example is the redundancy many researchers attribute to microorganisms. They infer this redundancy simply because so many organisms do the same thing. "That's because humans are limiting what they're thinking about how a microorganism functions," says Kennedy. "We're not letting the microbe tell us what its function is. "Maybe this guy can degrade residue." But its real function in the soil might be completely different. The idea of redundancy is simply a human mindset. What's exciting about this realization, Kennedy says, is that, for purposes of biocontrol, for example, you can just decide what characteristic you want and "let's go look for it." One of those things that Kennedy goes looking for is a "deleterious rhizobial bacteria." These DRBs produce toxins that are often plant-species- and cultivar-specific and can dramatically alter plant growth. Why DRBs produce these suppressing toxins is unclear, though Kennedy again suggests that lack of clarity is simply a result of not thinking in terms of the total system. DRBs are not pathogens, says Kennedy. They are much smarter. They do not kill the plant, but simply reduce its growth. "This sort of slight inhibition," says Kennedy, "may be more what life is all about than pathogens that are so visual." Some time ago crops and soils department head Tom Lumpkin went to Turkey and brought back soil samples. Cheatgrass, a dramatically invasive weed and major crop competitor in the American West, is indigenous to Turkey. (See Universe, Spring 1997, p. 13, Spring 1996, p. 30.) Kennedy's lab isolated organisms in the soil. Normally, about 50 percent of organisms isolated in this country are inhibitory to cheatgrass, wheat, and other grasses. About 6 percent are inhibitory to cheatgrass, but not to wheat. In the soils from Turkey, 99 percent of the isolates were inhibitory to cheatgrass. At one point in her thinking, Kennedy had not liked the idea of bringing in foreign species as biocontrols for invaders. Her thought was, we have all these billions of organisms in soil, let's find something among them to control the invader. Now she thinks differently, convinced that the DRBs are species-specific. Through their influence on soil nutrients, plants may also select the bacteria and fungi that will populate their rhizospheres. The feedback loops, both within the system and in the evolutionary sense, are likely many and complex. "What we're trying to figure out in our community work is what's peaceful coexistence? What is it in the community that's needed to function?" Agricultural communities, she says, are artificial. Even Frank Lange's no-till field is far from a natural ecosystem. The benefits of no-till are obvious. However, as he puts it, no-till would not be possible without "Roundup," the kill-all herbicide developed by Monsanto. What Kennedy has in mind is developing in the no-till system a microbial community that resists weed takeover and keeps pathogens down, but lets the crop grow. She has already targeted one DRB that stunts cheatgrass. DRBs have been studied for only 15 years or so. "Every one we see produces something different," says Kennedy. "We don't really know why." She ventures a conjecture: "The only thing I can think of, if they really like to eat wheat roots more than they like to eat downy brome roots, then they produce this [suppressant] on purpose. But say they want more wheat roots to grow...then it doesn't really make sense." Maybe, she says, we're making it too teleological. But whether Nature has a final cause or not, She is certainly ironic. We're struck by a simple observation that Niles Eldredge makes in his recent book, Dominion: "Cultural invention lay behind our ability to spread around the globe. But the real break with tradition, the invention that really changed our position in the natural world, was the advent of agriculture some 10,000 years ago. Taking control over production of our own food supply, we became the first species in the 3.5-billion-year history of life to live outside the confines of the local ecosystem." The problem with our mobility, however, is that pathogens and invasive species travel right along with us, and the new territory is ready for neither us nor our foreign companions. Highly evolved as we think of ourselves, and though our success is likely due to our intellectual adaptation, we do not readily adapt physiologically to our specific environment. But the vast underground and invisible population of microbes does, readily, and we are now just figuring out how to adapt the way we grow our food to compensate. | U N I V E R S E M A G A Z I N E H O M E | |
