Tales From The Underground

A Natural History Of Subterranean Life


By David Wolfe

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There are over one billion organisms in a pinch of soil, yet we know much more about deep space than about the universe below. In Tales from the Underground, Cornell ecologist David Wolfe takes us on a tour through current scientific knowledge of the subterranean world. We follow the progress of discovery from Charles Darwin’s experiments with earthworms, to Lewis and Clark’s first encounter with prairie dogs, to the use of new genetic tools that are revealing an astonishingly rich ecosystem beneath our feet. Wolfe plunges us deep into the earth’s rocky crust, where life may have begun-a world devoid of oxygen and light but safe from asteroid bombardment. Primitive microbes found there are turning our notion of the evolutionary tree of life on its head: amazingly, they represent perhaps a full third of earth’s genetic diversity. As Wolfe explains, creatures of the soil can work for us, by providing important pharmaceuticals and recycling the essential elements of life, or against us, by spreading disease and contributing to global climate change. The future of our species may well depend on how we manage our living soil resources. Tales from the Underground will forever alter our appreciation of the natural world around-and beneath-us.





A Natural History of Subterranean Life



I am pleased to have an opportunity to thank publicly the many friends, family members, and colleagues who have contributed to this book. I doubt that I would have had the stamina to complete this project without the unwavering and enthusiastic support of Terry Kristensen, who also carefully read through the earliest, sometimes long and tedious, drafts of each chapter and provided many comments that greatly improved the book’s tone and readability. I am very grateful to my editor, Amanda Cook, who believed early on that these “tales” were worth telling and who championed the project. In addition to providing many detailed suggestions that improved the prose, Amanda’s skillful guidance regarding the structure of individual chapters and the book as a whole was invaluable. I would also like to thank the others at Perseus Books who have contributed in various ways, and Tamara Clark for her wonderful illustrations.

This book is broad in scope, encompassing soil science, microbiology, biogeochemistry, ecology, human and plant pathology, animal behavior, genetics, and evolutionary biology. To tackle all of this, I called on many of my scientist colleagues for help, particularly Dean Biggins, Tom Eisner, Bill Ghiorse, Gary Harman, Bob Howarth, George Hudler, Ken Mudge, Aly Naguib, Janice Thies, Lynne Trulio, and Carl Woese. I thank them for being so very generous with their time, openly sharing their expertise and personal experiences, and reviewing portions of the manuscript. I was not able to incorporate all of their suggestions and had to make difficult decisions regarding what to leave in and what to leave out. The responsibility for any serious omissions or errors in the final product is completely mine.

I feel fortunate to work at an institution—Cornell University— that has a long history of encouraging faculty to communicate scientific information to the general public. I benefited from access to the outstanding collection of resources maintained at Cornell’s Mann Library and from the exceptional service of the dedicated staff who work there. Some of this book was written while on a sabbatical leave at the University of Nevada at Reno. I would like to thank Jeff Seemann of the Department of Biochemistry for providing me with a comfortable environment in which to work while I was there.

Special thanks to Diane Ackerman for some useful advice early on about writing and publishing. Thanks to Alan and Laura Falk for letting me use their lake house as a hideaway at a time when I most needed it. Finally, I thank all of my friends, my daughter, Alexis, and other family members for their cheerful understanding during long periods of neglect as I completed this ambitious project.



Man and man’s earth are unexhausted
and undiscovered.
Wake and listen!
Verily, the earth shall yet be a source of recovery.


ONE DOESN’T HAVE TO VENTURE FAR INTO THE UNDERGROUND for new discoveries. Step out into the backyard, for example, push your thumb and index finger into the root zone of a patch of grass, and bring up a pinch of earth. You will likely be holding close to one billion individual living organisms, perhaps ten thousand distinct species of microbes, most of them not yet named, cataloged, or understood. Interwoven with the thousands of wispy root hairs of the grass would be coils of microscopic, gossamer-like threads of fungal hyphae, the total length of which would best be measured in miles, not inches. That’s in just a pinch of earth. In a handful of typical healthy soil there are more creatures than there are humans on the entire planet, and hundreds of miles of fungal threads.

Some zealous soil ecologists have recruited small armies of graduate students and marched them into forests and grasslands to compile a complete inventory of subterranean life. Within a dimension of one square yard (about one square meter), they typically uncover billions of microscopic roundworms called nematodes, anywhere from a dozen to several hundred of the much larger earthworms, and 100,000 to 500,000 insects and other arthropods (species with hard exoskeletons). And that’s in addition to the astronomical numbers of fungi, single-celled bacteria and protozoa, and other creatures that don’t fall into these major groups. Many of the arthropods are very tiny and can be spotted only with a magnifying lens. Some defy classification; they simply have never been seen before. Even in well-studied areas, new arthropods and other multicellular species of unknown function are routinely encountered.

The numbers are staggering, the biodiversity fascinating, and the potential for discovery unsurpassed by any other habitat on Earth. Yet we have spent more time and effort examining small patches on the surface of the moon and Mars than exploring the subterranean habitat of our own planet. The words of Leonardo da Vinci ring as true today as they did five hundred years ago: “We know more about the movement of celestial bodies than about the soil underfoot.” Even in modern laboratories, scientists are lucky if they can come up with the right nutrient mix to culture and study 1 percent of the microbes found in a typical soil sample. This poor success rate is due in part to the complex interdependence between subterranean organisms. They can’t survive when isolated from their neighbors. Until very recently, we knew next to nothing about the 99 percent of soil microbes that we could not raise in captivity except what their rotting cellular remains looked like under a microscope.

NEW TOOLS, HOWEVER, have opened a window to the underground, ushering in a cornucopia of subterranean discovery. Many of these tools have been borrowed from the tool chests of molecular biologists. The same molecular techniques that allow modern crime labs to detect a fragment of the genetic material left by a suspect at a crime scene allow modern soil labs to probe for evidence of specific organisms or characterize the full range of microbial diversity in a pinch of soil or a rock sample from the deep Earth. This still leaves many questions unanswered, such as the function of the many genetic types found. However, by identifying similarities in the genetic codes of newly discovered organisms and those we are already familiar with, scientists are often able to determine the ecological role played by previously unknown genetic types. At this point, the scientific community is grateful simply to have an opportunity to begin to quantify and catalog all that we have been missing.

In addition to the revolutionary breakthroughs in molecular biology, advances in engineering are providing scientists with new tools for reaching the remote habitats of creatures of the underground. New specialized drilling equipment and sterile techniques have been designed to tunnel into microbial habitats more than 10,000 feet (3,000 meters) below the rocky continental crust and seafloor, and retrieve samples that are completely free of microbial contamination from the surface and soils above. Such explorations have verified the existence of independent ecosystems that thrive in these deep subsurface habitats without sunlight, oxygen, or traditional carbon food sources, and at temperatures often exceeding the boiling point of water. On another front, advances in fiber optics, camera miniaturization, and radio tracking devices have given scientists unprecedented opportunities to study the behavior of burrowing animals within their subterranean habitats. Ecologists have gained valuable information for protecting species at risk, such as the black-footed ferret. Such information can also be used to develop humane control procedures for burrowing animals that have become agricultural pests.

Every venture into the underground using these new technologies takes us into unexplored territory filled with unexpected delights. The comment of Alice as she wandered through Wonderland—“curiouser and curiouser”—comes to mind. The textbooks can’t begin to catch up. Our old notions of biology are being turned topsy-turvy. We are beginning to realize what “surface chauvinists” we have been in our myopic vision of life on the planet, blind to all but the most obvious of subterranean creatures. The latest scientific data suggest that the total biomass of the life beneath our feet is much more vast than all that we observe aboveground. Despite the preponderance of new evidence, our overreliance on visual experience to define our sense of reality makes this notion almost impossible to accept. We see the density of a rain forest, or the enormity of a giant redwood tree, and can only shake our heads incredulously at the possibility of another living world, a hidden subterranean biosphere, more immense than the grand scale of life aboveground.

With each new subterranean discovery, it becomes more apparent that the niche occupied by Homo sapiens is more fragile and much less central than we once thought. Just as the astronomical discoveries of Copernicus forever changed our notion of our physical place in the universe, our new knowledge of the magnitude and genetic diversity of Earth’s subterranean world will forever change how we think about our place in the evolutionary “tree of life.” This revolution began inauspiciously in microbiology and soil ecology but has now spread to encompass the much broader disciplines of evolution and biology. And we have already benefited in practical ways from this revolution. For example, we are putting soil microbes to work for us to combat plant and human diseases, and to help in the cleanup of our toxic wastes.

THE STATUS OF SUBSURFACE biology today is reminiscent of where marine biology was fifty years ago, when Jacques Cousteau was first perfecting his Aqua-lung for exploration of another hidden realm—the oceans. It might sound odd, but my own experience with scuba diving was the spark that motivated me to write this book. Since taking up the sport just a few years ago, I have been awestruck by the scenic beauty and diversity of underwater life. I will always be grateful to the professional dive masters who have taken me and my friends on guided underwater tours. While we nervously stare at our gauges and try to avoid kicking each other with our fins, one of the guides will tap on his or her air tank and point—whoa! It’s a giant tarpon here, a manta ray there, or some other spectacular pelagic swimming below. Then, with hand signals, the guide herds us over to a coral formation and has us hover until we see what he or she has spotted— perhaps some tiny sea creatures doing a ritual underwater mating dance.

In my professional life as an ecologist, I have had the rare pleasure of exploring and learning about a realm—the subterranean world— that is just as diverse and fascinating as the oceans, but even less well known. It has also been exciting to bear witness to a scientific revolution in progress. I don’t think I exaggerate when I say that what I have discovered of the mysterious underworld of our planet not only adds tremendously to my enjoyment of the outdoors and appreciation for the full scope of Earth’s biodiversity, but enhances the quality of my day-to-day life. As a university professor and teacher, my natural inclination is to want to share this.

Knowledge of the incredible beauty, diversity, and activity of the subterranean world completely alters one’s perception of the landscape. Gazing out over a barren plain becomes an experience similar to that of gazing out at a wide expanse of turquoise sea. On my frequent walks along the trails of the Ellis Hollow woods near my home in upstate New York, I get the best of both worlds. There is, of course, the surface life to enjoy—the grassy meadows, the stands of maple, beech, and hemlock trees, the deer and scurrying rabbits being chased by my Labrador retriever companion. But I know this is just the icing on the cake. I am keenly aware of all that I cannot see—the thriving communities of unusual life forms beneath my feet, some of them perhaps several thousand feet below, playing their role in the cycling of the elements and other functions important to all life on the planet. Only hints of subterranean activities are revealed at the surface: The “earthy” perfume of soil bacteria known as actinomycetes, the small mounds of digested soil or “casts” left behind by earthworms, and the openings to the burrows of larger animals.

My doctoral training was in ecology and plant biology. My research program within an agriculture department at Cornell University for the past fifteen years has followed up, more or less, on that experience. Not surprisingly, my interest in soil organisms began with those that affect soil fertility and plant health, and in particular those that form mutually beneficial partnerships with plants. Professional interest evolved into a more personal interest as I was exposed, via scientific journal articles and discussions with colleagues in other disciplines, to the growing excitement generated by the revolutionary developments in many other aspects of soil biology. Writing this book has given me the opportunity to delve into those areas peripheral to my own research much more thoroughly and to discuss the details with scientists who have been at the center of the most exciting discoveries.

This book is by no means intended as a comprehensive treatment of the subject of soil ecology. My goals are modest: To introduce you to a few of the most intriguing creatures of the underground, and to the sometimes equally intriguing scientists and explorers who have studied them, from Charles Darwin and Lewis and Clark to those whose names may be less familiar. You may be surprised to learn of the many ways in which the diverse subsurface biosphere is relevant to our everyday lives and to the environmental issues we will be confronting in the twenty-first century. I hope to serve as a subterranean “dive guide” of sorts as we take a journey together into a mysterious world we are just beginning to comprehend.

As humans, we are a particularly “subterranean-impaired” bunch. We are oversized, solar- and oxygen-dependent, and genetically programmed to think in two-dimensional surface-space. These characteristics tend to exclude us from entering or fully appreciating the most fascinating habitats of the underground. What an adventure it would be if we could become microscopic spelunkers for a day in order to search for new life forms in the dark damp caverns of our backyard soil. Imagine rappelling our way down through a spectacular array of clay crystal formations, the beams from our hard-hat headlamps crisscrossing wildly as we try to catch glimpses of bizarre creatures scurrying about between the particles of sand and silt as big as giant boulders. We would get another perspective entirely if we could hop inside a microscopic submersible to join the unusual aquatic creatures that swim the narrow water channels of the upper soil horizons. If we could dive deep enough to roam the cold dark aquifers, or deeper still into the steamy zones heated by magma upwellings from the Earth’s mantle layer, even stranger worlds would be revealed. Such a “fantastic voyage” is impossible, of course, but with some imagination, there is nothing to stop us from taking an initial dip into the underground for an overview of what can be found there.

The subterranean is not one world but many. It is filled with many unique habitats, and the denizens of these habitats range in size from the microscopic bacteria to the easily visible earthworms and burrowing animals (figure I.1). Over evolutionary time, the activities of this diverse flora and fauna transformed the uppermost layer of the Earth from one of sterile, pulverized rocks and minerals to one that could sustain life both above- and below-ground.

When soil scientists visualize their subject of study they do not imagine a loose pile of dirt, any more than a doctor would imagine his or her patients as a pile of body parts. Soil scientists think in terms of soil “profiles,” which define the complex organic whole—the pattern of horizons or layers of minerals, organic matter, and living organisms as one ventures down from the surface toward bedrock. Soil profiles are used like fingerprints to classify soils in terms of their physical and biological composition and the history of their formation. Soils are referred to by taxonomic names based on their profiles, just as biologists use the binomial genus-species classification system to identify organisms. For those who know the taxonomy, a soil profile’s name immediately reveals what type of rock “parent” material the soil was formed from, details of its biological and climate history over geological time, the topography of the region, and its suitability for farming, skyscraper construction, or other uses.

FIGURE I.1 Soil biodiversity within the root zone. Depicted in the upper diagram are: (1) buried seeds, (2) water bears, (3) springtails, (4) mites, (5) insect larvae, and (6) ants. Depicted in the lower, magnified view are: (7) clay particles, (8) silt, (9) sand, (10) protozoa, (11) fungi, (12) bacteria, and (13) nematode. Illustration by Tamara Clark.

I’ll never forget my experience at a soil-judging contest when I was a graduate student at the University of California at Davis. I had accompanied a friend who was working toward his Ph.D. in soil science and was representing our school in a finals competition against other major land-grant universities. We could easily have been at a more conventional sporting event: The atmosphere was tense, and the contestants were focused, their adrenaline flowing. Soil pits about six feet deep had been dug in several locations in a meadow and up along a hillside to expose the profiles. Teams of students were in these pits with color charts, reference books, and meter sticks to measure the width of various horizons. The goal was to classify correctly the soils in each location. Winner take all. I was just an observer, so I listened while the Davis students debated in a fevered pitch among themselves. “Look, look at the cambic horizon; this has to be post-glacial.” “An Inceptisol!” one of them yelled out, pointing to one of the layers. “No way!” another grumbled. “See the shallow penetration of humus, and that argillic-like horizon? This is an Alfisol if I ever saw one.” I realized then that this special language of the underground, and a fascination with profiles, played a role in attracting many to this field of study.

Although my soil scientist friends would cringe at the notion of a typical soil profile, for purposes of introduction I have attempted one in figure I.2. The upper “O” (for “Organic”) horizon is not truly a soil by most people’s definition because it lacks the mineral components of soil—sand, silt, and clay. Commonly referred to as the “litter layer,” it may be composed of newly fallen plant debris, decaying logs, insect and animal carcasses at the top, and rich, partially decomposed organic matter and earthworm casts near the bottom. This layer can be several inches thick in a temperate forest or grassland, or almost nonexistent in a desert or tundra environment. The O horizon is the interface between the surface and subsurface realms, and many of the creatures one finds here inhabit both worlds. Familiar arthropods such as ants, sowbugs (“rolly-pollies” we called them as kids), millipedes, and beetles are among this group.

The larger burrowing animals also fall into the category of part-time soil dwellers. This group includes moles, ground squirrels, prairie dogs, ferrets, burrowing owls, rabbits, aardvarks, and foxes, to name a few. Many of them spend a lot of their time within the litter layer searching for food items such as fallen fruit, nuts, and tasty earthworms and insects. Others spend most of their time belowground feeding on plant roots. Still others are predators near the top of the food chain that roam the surface or the tunnels below in search of small prey. The burrowing animals as a group are among the most intelligent creatures of the underground, and many live in communities with a complex social structure. Prairie dog colonies often contain thousands of members and spread over an area of several square miles or more.

FIGURE I.2 Typical soil profile showing the primary soil layers, or “horizons.” Illustration by Tamara Clark.

Fortunately for soil ecologists, the vast majority of activity takes place within the litter layer and the top layer of actual soil just below it, called the A horizon. The A horizon is typically four to sixteen inches (ten to forty centimeters) deep. It often contains the highest densities of plant roots and soil organisms of the entire soil profile. It is also often rich in decomposed organic matter as well as a mixture of sand, silt, and clay minerals. Much farm labor is devoted to managing this “plow layer” zone which is so important to crop productivity.

We tend to think of plants, whether crops, wildflowers, or gigantic trees, primarily in terms of their aboveground foliage displays. This is only half the story, of course. Plants are in fact unique in that they equally and simultaneously inhabit both the surface and subsurface worlds. They are the great mediators between the two realms. Their leaves gather carbon and energy through the process of photosynthesis, while their roots drill for water and mine the soil for essential nutrients. Plants eventually are eaten or die and decompose, serving as the base of the food chain for both surface and subsurface ecosystems.

The soil zone immediately around plant roots is a unique, highly populated habitat because it is rich in sugars and other nutrients that leak out from living roots or become available as small root hairs die and decompose. The roots themselves account for much of soil biomass. If we could magically take an upside-down stroll through the underground, we would experience a dark “forest” of roots as dense as the aboveground display of tree trunks, branches, and leaves.

The roots of most plants do not work alone in their quest for water and nutrients. They are helped by beneficial types of soil fungi, collectively called mycorrhizal fungi, that attach to roots and often form a below-ground network between plants of different species. Not all fungi are so helpful; some cause plant diseases, while others parasitize neighboring soil organisms. But the majority of fungal species are harmless and live strictly off of decaying wood and other organic debris, playing an important role in decomposition and nutrient cycling. The threads of fungi of all types that crisscross throughout the O and A soil horizons provide an added benefit for soils by sewing small soil particles together into aggregates. This improves soil “tilth,” or structure, improving drainage and aeration of the subsurface.

The thousands of species of bacteria found in the top two soil horizons play a vital role in the biogeochemical cycling of elements that is important to the sustainability of all life on the planet. Many break down organic matter to basic nutrients that can be absorbed by roots of plants or used by other soil organisms. There are very few waste products, pollutants, or toxins that cannot serve as food to one bacterial species or another. A few bacterial species found in the upper soil zones are pathogenic to plants, animals, or even humans. (Yes, Mother was right, you should wash your hands after playing in the dirt.) But others form important, mutually beneficial symbiotic relationships, such as the very important nitrogen-fixing bacteria that attach to roots and supply the plant with nitrogen in exchange for sugars.


On Sale
Apr 28, 2009
Page Count
256 pages
Basic Books

David Wolfe

About the Author

David W. Wolfe is Associate Professor of Plant Ecology in the Department of Horticulture at Cornell University, and a member of Cornell’s Biogeochemistry Program. Much of his research is focused on soil conservation, and the impact of climate change on plants and soils. He has published many journal articles and academic papers. Tales from the Underground is his first book.

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