GEOBIOLOGY: Exploring the Interface Between the Biosphere and the Geosphere This report is based on a colloquium sponsored by the American Academy of Microbiology held December 1-3, 2000, in Tucson, Arizona.

The American Academy of Microbiology wishes to express its gratitude for the generous support of this project from the following organizations:

A MERICAN S OCIETY FOR M ICROBIOLOGY

N ATIONAL S CIENCE F OUNDATION

U.S. DEPARTMENT OF E NERGY

U.S. GEOLOGICAL S URVEY

The opinions expressed in this report are those solely of the colloquium participants.

Copyright© 2001 American Academy of Microbiology 1752 N Street, N.W. Washington, DC 20036 www.asmusa.org geobiology • A Report from the American Academy of Microbiology GEOBIOLOGY: Exploring the Interface Between the Biosphere and the Geosphere

KENNETH NEALSON, WILLIAM A. GHIORSE, AND EVELYN STRAUSS

A Report from the American Academy of Microbiology Board of Governors, Colloquium Steering Committee American Academy of Microbiology Kenneth Nealson, Ph.D. (Co-Chair) Eugene W. Nester, Ph.D. (Chair) University of Southern California University of Washington William C. Ghiorse, Ph.D. (Co-Chair) Joseph M. Campos, Ph.D. Cornell University Children’s National Medical Center, Washington, DC Edward F. Delong, Ph.D. R. John Collier, Ph.D. Monterey Bay Aquarium Research Institute, Monterey, CA Harvard Medical School Abigail A. Salyers, Ph.D. Marie B. Coyle, Ph.D. University of Illinois Harborview Medical Center, University of Washington James T. Staley, Ph.D. James E. Dahlberg, Ph.D. University of Washington University of Wisconsin, Madison

Julian E. Davies, Ph.D. Cubist Pharmaceuticals, Inc., Vancouver, BC, Canada

Arnold L. Demain, Ph.D. Drew University

Lucia B. Rothman-Denes, Ph.D. University of Chicago

ii Ann M. Skalka, Ph.D. Fox Chase Cancer Center, Philadelphia, PA

Abraham L. Sonenshein, Ph.D. Tufts University Medical Center

David A. Stahl, Ph.D. University of Washington

geobiology • A Report from the American Academy of Microbiology Colloquium Participants James K. Fredrickson, Ph.D. Battelle Pacific Northwest National Lab, Richland, WA Ariel Anbar, Ph.D. University of Rochester E. Imre Friedmann, Ph.D. Florida State University Enriqueta Barrera, Ph.D. National Science Foundation Thomas L. Kieft, Ph.D. New Mexico University of Technology Dennis A. Bazylinski, Ph.D. Iowa State University William W. Metcalf, Ph.D. University of Illinois Terrance J. Beveridge, Ph.D. University of Guelph, Ontario, Canada Alison E. Murray, Ph.D. Desert Research Institute, Reno, CA Gordon E. Brown, Jr., Ph.D. Stanford University Kenneth Nealson, Ph.D. University of Southern California Pan Conrad, Ph.D. NASA-Jet Propulsion Laboratory, Pasadena, CA Eugene W. Nester, Ph.D. University of Washington Edward F. Delong, Ph.D. Monterey Bay Aquarium Research Institute Charles Paull, Ph.D. Monterey Bay Aquarium Research Institute, David Des Marais, Ph.D. Monterey, CA NASA Ames Research Center, Moffett Field, CA Abigail A. Salyers, Ph.D. Suzanne Douglas, Ph.D. University of Illinois NASA-Jet Propulsion Laboratory, Pasadena, CA Staff iii David A. Stahl, Ph.D. Katrina J. Edwards, Ph.D. University of Washington Carol A. Colgan, Director Woods Hole Oceanographic Institute, Woods Hole, MA American Academy of Microbiology James T. Staley, Ph.D. F. Grant Ferris, Ph.D. University of Washington Elizabeth Huston, Program Assistant University of Toronto, Ontario, Canada American Academy of Microbiology Bradley M. Tebo, Ph.D. Steven E. Finkel, Ph.D. Scripps Institute of Oceanography, La Jolla, CA University of Southern California Alexandre Tsapin, Ph.D. Science writer Bruce W. Fouke, Ph.D. NASA-Jet Propulsion Laboratory and University of Illinois California Institute of Technology, Evelyn Strauss, Ph.D. Pasadena, CA Santa Cruz, CA

geobiology • A Report from the American Academy of Microbiology geobiology • A Report from the American Academy of Microbiology Executive Summary

A colloquium was convened by the American Academy remedying some of these problems and for enhancing of Microbiology to deliberate issues relating to the inter- the quality of life on our planet in other ways as well. secting fields of biological and geological sciences. The colloquium was held in Tucson, Arizona, December 1—3, The new discipline of geobiology will provide a plethora 2000. The principal findings of the colloquium are of exciting intellectual and practical rewards. summarized below. Geobiologists hope, for example, to discern how life began and how it evolved. Furthermore, they aim to A wide chasm may seem to divide the living from the identify how environmental conditions influenced these non-living. On closer inspection, however, these two processes and, in turn, were altered by life. Under- realms do not perch on separate ridges, but knit together standing the past will equip us to predict the future. The to form a single lush domain. Geological and biological Earth has already conducted many experiments over the activities are integrated, and they influence each other in course of its evolution, but, because of the complexity of profound ways. This interplay has shaped the Earth and geobiological interactions, we are unable at present to all creatures on it. Studies of geobiology—the present and decipher our planet’s lab notebook. Current and future past interactions between life and inanimate matter— investigations will improve our ability to read the promise to reveal the secrets of life, its origins and relevant records, interpret them, and make predictions evolution, and its present functions on our planet. Such based on past results. studies hold enormous practical potential as well. Many geobiological processes affect environmental Long ago, life arose from chemicals. As new creatures quality and impact human health, which in turn influ- evolved, their activities changed the environment. The ence the economy and work force. As a result, critical altered surroundings in turn invited different types of public and science policy issues require input from this organisms, which again altered the world around them. field. The study of geobiology offers significant payoffs Geobiological interactions have created the gases we that touch society in many ways. To exploit the possibili- breathe and the soil in our forests. They contribute to ties, we need to focus diverse resources on this rapidly global warming and some forms of pollution, yet knowl- growing and tremendously promising new field. edge of geobiological processes offers strategies for 1

geobiology • A Report from the American Academy of Microbiology Introduction

Living creatures and the inanimate worlds they inhabit through the inanimate world. Bacteria, algae, and, Furthermore, we may devise ways to apply geobiological dance an intimate tango. As each partner steps to eventually, plants pumped oxygen into the air, for phenomena in our search for solutions to some of our Nature’s tune, the other responds in harmony. Organisms instance, profoundly changing the composition of the environmental problems. Some interactions between alter their surroundings as part of their normal activities, atmosphere and supporting the development of living creatures and matter are enhancing the quality of and in turn, the changed surroundings nurture different creatures that breathe this gas. Microbes in the soil life for other creatures, for example, and point toward types of life and altered modes of living. This interplay captured critical nitrogen minerals from rocks and further inventions that might build upon these natural of Life with Earth has shaped our present environment. packaged them into forms that other creatures could use success stories. Many microbes transform poisons, such Indeed, Life and Earth, through this “Geobiological to make essential molecules such as proteins. Such activi- as heavy metals, into harmless compounds, or repackage Tango,” continue to choreograph the co-evolution of the ties changed the environment, rendering habitats more them so they are physiologically unavailable. Others biosphere and the geosphere. Understanding the detailed comfortable for some organisms and harsher for others. degrade organic pollutants, restore key nutrients to history and workings of these interactions will provide The resulting fluxes of species and their specialized depleted soil, or act as a sink for greenhouse gases, such insight into the origins and evolution of the geobiolog- biochemical activities in turn registered effects on the as carbon dioxide, from the atmosphere. Understanding ical world. Learning the choreographic design of the surroundings. In such ways, the interactive cycle both biology and geology is critical to solutions aimed at tango will help us to better manage environmental between living things and their geological surroundings many major societal issues, including groundwater affairs and shed light along the path to their future. never ceases. For example, geological materials have quality, environmental contamination, the loss of served as energy sources (electron donors) for productive agricultural lands, and global warming. The environment has been spawning innovations in lithotrophic metabolism and as electron acceptors for biology ever since it sparked life itself. Early on our anaerobic respiration of many types. This often results in Geobiological studies may produce other benefits as planet, the line between life and non-life was much inadvertent dissolution and/or formation of minerals. well. Many microbes produce chemicals of practical use, thinner than it seems today. At some point, inanimate Organisms—especially the more complex eukaryotic such as ethanol, which directly affects the price of chemicals and physical forces interacted in new ways to organisms—have developed exquisite abilities to create gasoline, more cheaply or leanly than do industrial provide compounds and reactions that made life structural materials, such as calcite, silicates, cellulose, processes. Some produce unique complex compounds possible. As biology stirred, its activities sent ripples and chitin. These “biominerals” have served to allow that cannot, as yet, be synthesized by industry, and organisms to become large three-dimensional structures, others make compounds with special properties that e.g., to thwart gravity, to increase predatory efficiency, lend themselves to particular engineering demands. and to be used as protective structures from other preda- Greater understanding of geomicrobiological processes tors. Perhaps of equal importance, they have supplied us could easily lead to new products. 2 with a fossil record detailing much of the recent history of life on our planet. While scientists can cite many isolated examples of biology influencing the environment and vice versa, they Studies of geobiology will reveal these events and eluci- do not fully grasp how these interactions have changed date their details. Increased knowledge in this area will over time or how they all fit together. Furthermore, large enhance our comprehension of how the planet Earth has gaps riddle our understanding of critical past events, and evolved and continues to evolve. In addition to uncov- gargantuan holes confound our ability to explain what ering the underlying designs of natural processes that forces drove particular occurrences or why certain organ- have shaped Earth, we will learn the details and environ- isms and communities responded to their circumstances mental consequences of current human activity. Such in the ways they did. In order to interpret Earth’s past insights will allow us to modify certain activities in ways history or to predict its future, scientists must expose the that will heal and maintain our environment. story of how the geosphere and the biosphere co-evolved. By studying present day geobiology, scientists hope to fill in its history and better predict Earth’s trajectory into the future.

geobiology • A Report from the American Academy of Microbiology Geobiology’s Value/Vision for the Future

This colloquium was organized to devise plans that will The past, the present, the future, environmental perturbations? How do the biological outline the challenges faced by the nascent field of and the possibility of changes caused by environmental perturbations affect geobiology, to devise plans that will address the extraterrestrial life the regional geochemistry? And how will these answers challenges, and to propose some solutions. Although the The field of geobiology offers clues to a wide range of change over time? dominions of geology and biology have independently practical and philosophical enigmas. It has the poten- matured, the intersection of these two areas remains tial to profoundly change both the quality and our The study of geobiology allows us to look backward as relatively immature and underdeveloped. Under the understanding of life. Findings in this area will influ- well as forward. In its infancy, conditions on Earth did influence of heightened interest in life in remote and ence the health of all life on Earth and the planet not welcome life. In order to understand the planet’s extreme environments, the boundaries of geobiology are itself. The field promises tremendous ecological, eco- continued evolution, we must understand its past. A expanding rapidly. The breadth and scope of this nomic, and intellectual rewards. clear picture of how life arose and prospered will expanding discipline need to be more clearly defined and undoubtedly lead us toward answers about how to directed. Intellectual, economic, social, and educational While microbes have historically exerted the largest successfully maintain life on this planet. issues associated with advances in the field must be effect on the Earth, humans are now making a huge anticipated, identified, and analyzed to create a plan of impact. Society today faces challenging questions about Since the beginning of scientific inquiry, people have action. A list of urgent scientific questions needs to be how to counteract some of the damage that we are wondered how life began and how the zoo of complex compiled and evaluated to direct and adequately fund inflicting. Humans are encroaching on natural habitats creatures on our planet arose from our simple predeces- scientific inquiry. Critical intervention at this time by and rapidly polluting and depleting the environment sors. Pondering these issues while surveying the night sky experts in the intersecting and allied fields should help through activities such as mineral mining, oil and gas evokes the question of whether life has arisen elsewhere to guide the development of the field and usher it to its production, large-scale farming, logging, and industrial in the universe. The study of geobiology will undoubt- full promise. production of toxic waste. This damage encompasses the edly provide insights into this question as well. Earth’s continents, as indicated by, for example, the Interactions between the microbial and geological worlds increasing evidence of global atmospheric and oceanic represent a large swath from the cloth of interactions warming. But we also have the opportunity to Geobiology’s potential between living organisms and the geosphere they inhabit. counteract some of the destructive by-products of an Interactions between living creatures and inanimate Thus, most of the examples in this document focus on urbanized civilization. Humanity can aim its technology matter have shaped Earth and its inhabitants since life geomicrobiology. While it was well recognized that in more constructive directions. In addition, we have arose from our comparatively simple ancestors. Yet, animals and plants interact in significant ways with the many valuable natural resources derived from geobiolog- we have just begun to appreciate the extent of its geosphere, colloquium participants concentrated on ical processes. Microbes, for example, perform a influence. A vast repertoire of diverse microbial talent 3 geomicrobiology two reasons: (i) it reflected their exper- multitude of biogeochemical feats that can be put to has eluded scientists until recently. Researchers have tise, and (ii) the time period over which the geosphere good use, from cycling carbon, nitrogen, and sulfur to found microbes in remote places, such as deep-sea and biosphere have co-evolved is known to be over- transforming toxic chemicals, including heavy metals. In thermal vents, which at first were considered too hos- whelmingly dominated by microbes. The more complex the future, we must devise more schemes that respon- tile to support life. Organisms that survive and even eukaryotic organisms have evolved relatively recently. sibly exploit the opportunities that present themselves in thrive in these extremes of temperature, pressure, or Colloquium participants recognize that the activities of the complex natural world. unusual chemical environment, also perform unusual animals, plants, and other complex organisms have and and, in many cases, unanticipated biochemical feats. will continue to exert an enormous impact on the Scientists must tease apart the complexity of contribu- Many of these involve geochemical reactions—making geobiosphere. They project and hope that future geobio- tions from different organisms and reactions and use this or breaking minerals, transforming elements from one logical research will encompass increasing contributions information to predict how the environment is changing. form into another, producing compounds that dra- from the scientific disciplines that deal with more To meet this challenge, we must learn all that we can matically alter the immediate surroundings, and, thus, complex organisms. In the meantime, examples from the about how geology and biology interact. For example, affect the entire local community of organisms, or realm of geomicrobiology handily illustrate the power how do temperature fluctuations impact living things? that build up in the atmosphere and impact the and potential of geobiology as a whole. How do microbes respond to long- and short-term entire planet.

geobiology • A Report from the American Academy of Microbiology The discovery of such microbes and the study of their harmful metals, such as uranium, chromium, selenium, produce enormous amounts of methane gas. Scientists activities have forced scientists to broaden their ideas arsenic, technetium, and plutonium. In some cases—for estimate that this methane store amounts to about twice about life’s capabilities, limits, and effects. While the list uranium, chromium, and technetium—these activities that of the recoverable gas, oil, and coal deposits on the of unusual microbiological activities grows longer with produce reduced metals that are insoluble, effectively entire planet. As such, it represents a tremendous poten- every discovery, each “surprising” finding hints at a removing them from exposure to the food chain. In tial energy resource. Furthermore, the trapped gas, which lengthening list of unknown ones. We have only begun others, undesirable effects occur. For example, iron and exists in crystalline form combined with water in the to dig into the wealth of this information and to gain manganese oxides are scavengers of toxic transition form of “methane hydrates,” holds other importance. tantalizing glimpses of its significance. (copper, nickel, cobalt, zinc), radioactive (uranium, Formation and decomposition of methane hydrates can platinum, technetium), and heavy (lead, mercury) alter the sediment’s stability, with potentially devastating Microbes influence the geosphere in myriad ways, metals. When microbial reduction of iron effects. Many scientists think that methane hydrates especially through influences on the cycling of elements, or manganese occurs, the dire consequences might mean have played a role in generating some of the huge which affect the quality of all life on this planet; yet that these toxic metals are set free, effectively concen- landslides that occur under the ocean next to continents. critical features controlling the elemental cycles remain trated in the environment due to metal oxide scavenging. elusive. Keys to global warming, for example, are likely to Knowing what can—and will—happen will require exten- Some scientists, therefore, suggest that building oil lie inside microbial cells, because multitudes of these sive knowledge of the iron and manganese oxides, the platforms on top of methane hydrate pockets is risky. tiny creatures emit and deplete enormous amounts of extent of toxic load they are carrying, and the abilities Pumping hydrocarbons generates heat, and raising the gases, such as carbon dioxide and methane, that trap heat of the microbes in the environment (or of those that temperature melts methane hydrates, which weakens around the Earth. Despite the importance of such physi- might be added to a polluted system). sediments and may trigger submarine landslides. In ological processes, huge holes in our knowledge foil addition to dramatic effects on the ocean (and under- attempts to assemble the relevant pieces. Microbes and In addition to repackaging or dissolving minerals, water oil rigs), such bursts might release huge amounts plants transform carbon dioxide, the most abundant microbes can produce them. Magnetotactic bacteria, of methane into the ocean and perhaps the atmosphere greenhouse gas, from the air into sugars and other for example, manufacture tiny magnetite crystals as well. Indeed, scientists propose that increases in organic molecules, or solid carbonate structural elements. forming microbial compasses. These tiny crystals display temperature might provoke a cascade of global warming. Other organisms consume organic chemicals, and in the properties that may render them particularly useful in Indeed, even more methane is trapped, frozen, in huge process of breaking them down for energy, spit out the electronics or microchip construction. Other bacteria peat deposits of the Canadian and Russian Arctic. As the carbon in the form of carbon dioxide. While these events construct extractable crystalline surfaces (S-layers) that Earth heats up, methane—itself a potent greenhouse gas— provide a satisfying qualitative view of the carbon cycle, are amenable to forming nanoscale electrical circuits vaporizes, escapes, and pushes temperatures further 4 they don’t explain all aspects quantitatively. For example, once “doped” with metal atoms. Some bacteria even upward. Events such as these may have exerted strong it has been impossible so far to balance the carbon cycle produce a compound, crystalline cellulose, which has effects on global climate over the Earth’s development. on the global scale. Somewhere on the planet is a unusual acoustic characteristics. Engineers have already Despite the tremendous potential impact of microbially substantial sink for carbon dioxide that is not yet discov- incorporated this material into stereo speakers. These produced methane hydrates on human welfare and the ered and, therefore, not understood. Understanding the examples underscore not only the ability of microbes environment, many important questions remain about sources and sinks of carbon, and the fluxes into and out to produce substances of great practical use, but also its generation and dissipation, as well as its possible use of these boxes, is key to understanding and intelligently illustrate their ability to leave distinct geobiological as an energy source and its hazardous potential. dealing with the issues of global climate. Similar informa- signatures. The magnetotactic bacteria, for example, tion for the cycling of other elements with key geological produce ultrafine-grain magnetite particles with unique While many geobiological phenomena result from and biological roles is also missing and of great interest. shapes and magnetic properties that have been invoked natural processes, others are by-products of industrial- as evidence for past life on Mars. ized civilization. For example, mining operations release The geological and biological worlds interact in many toxic heavy metals, such as chromium, copper, zinc, other ways as well. Recent studies have established that Tiny microbial cells can affect large—even global— arsenic, lead, and mercury, into local and regional some microbes obtain energy for growth by transferring environments, as well as local ones. For example, environments. Such operations bring ore to the Earth’s electrons to a wide range of toxic or environmentally microbes in organic-rich sediments under the ocean floor surface and vastly increase the surface area of these

geobiology • A Report from the American Academy of Microbiology minerals through crushing and milling. These processes I Harnessing microbes to detoxify industrially Finally, we look beyond Earth. The finding of life on expose them to air and make them react more quickly produced poisons, such as PCBs, that contaminate another planet would represent the greatest scientific and with water, thus increasing the acidity of the environ- water, soil, and other parts of the environment. ultimately societal event of this century, and perhaps of all ment and releasing toxic heavy metals into natural Scientists already know that some microorganisms time. The discoveries of microbes that thrive in extreme bodies of water, soil, and the atmosphere. are capable of converting the offending chemical environments has expanded notions about how life began groups in these compounds into harmless products. on Earth and strengthened the possibility that similar These examples hint at the wide extent of interactive However, we don’t yet know how best to harness microbes may live on other planets. effects that occur at the intersection of the biosphere these capabilities. and the geosphere. If we uncover and understand the full range of these possibilities, we will stand in a I The ability to recycle, which is a fundamental Seizing the moment position to use these natural processes to benefit activity of microbes, should be utilized to increase Many scientists from a broad range of disciplines are humankind and, possibly, to rejuvenate the planet. the efficiency and specificity of recycling human- thinking expansively about geobiology and its potential. generated waste materials. Geochemistry, geohydrology, oceanography, astrobiology, There are many potential practical and intellectual microbiology, environmental studies, ecology, molecular benefits that might arise from the study of geobiology, I Understanding how particular geobiological biology, genomics, paleobiology, and mineralogy repre- including: processes may create environments that support or sent only some of the specialties falling under the broad suppress the growth of emerging, and potentially canopy of geobiology. This tremendous span begins to I Cleaning up oil spills and other environmental dangerous, microbes. provide a glimpse at the vast field and implications of hazards with microbes. geobiology. Certainly this discipline is greater than the I Cleaning up toxic mine tailing leachates. While sum of its parts. I Producing useful substances in easier and cleaner daunting, such situations might offer a positive side. ways, as compared with conventional engineering For example, the right methodologies—perhaps ones Fruitful new endeavors and groundbreaking research will approaches. that include special talents of particular microbes— likely lead and challenge those from these overlapping might recover valuable metals from such cleanups. disciplines. Much research in the basic sciences is moving I Providing information about why water supplies We need to develop methodologies to turn environ- toward interdisciplinary research, and the field of geobi- in many areas are dwindling. It would be useful to mental disasters into economic prosperity. ology is poised to lead this movement and set precedents know what roles microbes are playing in such events, for the future of collaborative research that bridges and to discern whether they can be used as indicators I Understanding better how microbes are involved in diverse specialties. Compelling questions are already 5 of water sources and quality. energy production. launching researchers in fruitful directions, with enthu- siasm fueling the progress. The appropriate recognition I Understanding the conditions that result in the I Understanding Earth’s history, including the origin and support for this growing field promise to provide a dissolution and precipitation of economically of life and the evolution of global biogeochemical model for other emerging, interdisciplinary scientific important minerals. cycles. disciplines at the same time that it addresses key environ- mental and basic science topics that have huge impacts on I Protecting from various sorts of corrosion in a I A greater appreciation for how life survives at social and economic issues. cost-effective manner by modifying or exploiting nutritional, chemical, and physical extremes. microbial communities. Both biological and non- biological phenomena erode and otherwise damage I Improving our knowledge of how cell-to-cell commu- buildings, roads, sewer systems, ships, and even nications and microbial community interactions can sculptures. control global biogeochemical processes.

geobiology • A Report from the American Academy of Microbiology Current Status

Microorganisms have lived at the Earth’s surface for humans are trying to cope with, our lack of under- This progress represents some of the first steps toward most (about 85%) of Earth’s age, and the importance of standing might foil our efforts; perhaps we are not understanding how living things and their environ- microbial activity in shaping the Earth’s oceans and incorporating all of the relevant considerations and ments influence each other and promises to help rectify atmospheres has long been accepted. Only recently, components into our plans. many environmental problems. However, many however, have geologists, geohydrologists, and challenges remain. geochemists recognized the broad consequences of Technological and scientific advances in the last decade microbial activity. Microbes impact and are impacted by have fostered interdisciplinary alliances between the Although analysis of genetic sequences has revealed the virtually all geochemical processes that occur at the earth and life sciences and have allowed scientists to existence of microorganisms that have not previously Earth’s surface, as well as deep within its subsurface. probe geobiological interactions in ways that previously been grown in the laboratory, this information doesn’t were not possible. For example, now scientists can detect establish what biochemical tricks these microbes can Our ignorance represents possible hazards and lost trace elements that previously would have gone perform or what environmental conditions trigger these opportunities. The economic potential of understanding unnoticed and observe microbes that cannot be grown in feats. Furthermore, although we now know that scien- how microorganisms function in the geosphere is the lab in their natural habitats. Progress in light and tists grossly underestimated the extent of microbial tremendous. Although this area is receiving increased electron microscopy is permitting quantitative studies of diversity, most microbes and their functions still have attention, it remains largely untapped. Currently hidden microbial interactions at the community level in not been identified. For example, while decades of metabolic processes might present us with new options biofilms and with mineral surfaces at the atomic scale. intense study have provided information about how for transforming one substance into another or for Breakthroughs in molecular biology and, in particular, living things—especially microorganisms—interact with utilizing other useful activities. In order to harness the revelations about the genomic content of many different organic compounds in the environment, a view into potential of microbes, we must better understand their organisms have spurred an explosion of information interactions with inorganic compounds is only now natural capabilities. Furthermore, major unknown about the capabilities of living things. For the most part, beginning to crack open. metabolic activities could be exerting huge effects on the high-temperature geology explains what we know about geochemistry of the planet. If these unknown the cycling of rocks and minerals, because, at high Other tasks loom large as well. For example, scientists phenomena touch upon geobiological systems that temperatures, the rocks melt. At low temperatures need tools and research programs that more precisely characteristic of the surface and near subsurface, where document geobiological processes as they occur. geological processes are slow, life intervenes and speeds Improvements in detection methods and monitoring up the reactions to its own benefit. tools are needed. In this area, particular problems arise: how to study extremely slow-growing or dormant life, 6 As such techniques improve, the complexity and for example, and how to recognize and understand the richness of the geobiological world are coming into focus meaning of subtle microbial signatures in rocks. on the canvas of the globe. Fuzzy ideas are sharpening as scientists exploit better tools and develop new Countless other examples exist of questions that hypotheses. These insights are revealing ever deeper ties can only be answered by knowledge and technology between the biological and geological worlds. The currently unavailable. In order to exploit the great methodological improvements have allowed scientists to potential of geobiology, new methodologies and intellec- more accurately assess the geochemical and ecological tual frameworks that address all such issues must be consequences of perturbations to the environment developed. To achieve this goal, scientists and engineers sparked by both natural biological processes and the might need to exploit and adapt technologies from technological activities of human beings. other disciplines than their own.

geobiology • A Report from the American Academy of Microbiology Challenges and Opportunities

Scientists from different disciplines are forging research The field of geobiology faces many challenges and I What were the physical conditions on Earth before alliances to delve into the growing field of geobiology, opportunities as it attempts to address key fundamental life arose? (Was there water? How hot was it?) but education in this area is insufficient. Geologists are questions. Of course, these challenges represent research not generally trained in biology and vice versa. In isola- opportunities that will help to set the research agenda for I How deeply entwined were the bio- and geospheres tion, these fields can be expected to mature in their own this new field. Some of the questions discussed at the on the primitive Earth and has this dependence directions, but they will not merge on their own. Now is colloquium are: altered over time? the time to bring them together. The discipline of geobi- ology needs the concerted efforts of the scientific and I What role do living things play in the cycling of I How did life begin? From where did early life collect informed lay communities to identify the important “geological” substances? There is increasing recognition chemical energy? (The atmosphere? Extraterrestrial problems and knowledge gaps and then to devise novel that microorganisms are important agents in planetary sources?) By what biochemical means did the original approaches to resolve them. Results from geobiological scale processes such as carbon cycling (which relates inhabitants extract energy? Where on today’s earth studies will positively impact global change, illuminate to a number of phenomena that include climate can we find proxies for early metabolism? the deep biosphere, demystify astrobiology, unravel the change and food production), oxygen levels in the complexities of extreme environments, and elucidate the atmosphere, and weathering and precipitation of rocks I How and when did the processes of photosynthesis processes of evolution. This will be reflected in new job and minerals. Yet we know relatively little about the and respiration evolve? What drove the change to opportunities at all levels. Thus, the field needs to recruit microbial mechanisms involved, the rates and extents oxygen-based respiratory energy extraction from food? and prepare students to meet this demand. of these processes on a global scale, and how humankind may be irreversibly altering them. I Did distinctly more complex life forms originate due With a growing appreciation for the magnitude of geo- to environmental, climate, and nutrient pressures or biological effects and improved technology, scientists in a I How do reactions on surfaces and at interfaces from purely random evolution? How did the rise of wide variety of disciplines are poised to achieve tremen- contribute to geobiological events? Interfaces occur these organisms impact the simpler creatures that dous gains in this area. Available funds, however, currently on both small and large scales. Cell surfaces, for had existed until that time? How did these organ- are too limited to support the kinds of interdisciplinary example, are very reactive and can spur minerals isms impact their surroundings and how were these research programs that need to be launched and sustained. to precipitate and dissolve. Some microbial communi- changes preserved in the geological record? Future investigations should not only delve deeper into ties exist as structured “biofilms,” which are highly questions that have already been explored, but should organized communities with different physical, I Can we correlate major climatic effects with rapid expand into areas that have experienced relatively less chemical, and biological characteristics in different evolutionary branching? What evidence would examination. Our biases have directed us more strongly in regions of their matrices. Transition zones on larger we seek? 7 some directions than others. For example, we have interro- scales include, for example, the areas between gated outer space more diligently than the sea floor or freshwater and saltwater. These regions typically I What was the impact of increasing or decreasing deep beneath the Earth’s surface. nurture a wide array of life forms. This abundance temperature events on the evolution of microbial of life reflects a healthy ecosystem and can serve communities? We stand at a unique time in history. Humans are as a source of novel biological products and capabili- impacting the environment in significant negative ways, ties. Details of events at all of these (and other) I Did the types and populations of living things but our technological and cognitive capabilities allow us natural boundaries remain largely unknown and increase dramatically when the atmosphere first to alter conditions for the future. At the moment, a huge untapped, both practically and conceptually. acquired significant amounts of oxygen? scientific chasm separates us from a full understanding of our planet and its deep reservoirs of biochemical and There were also questions about the origins and evolu- I How do microbes respond to environmental change, geobiological reactions, which may affect Earth in ways tion of life on Earth. Many of these questions may be how rapidly do they respond, and how do these that we don’t currently comprehend and can’t predict. asked about the origins and evolution of life on other changes affect geochemistry? This wide zone of ignorance compels exploration to the planets and the conditions that could support life next frontier of knowledge. elsewhere in the universe.

geobiology • A Report from the American Academy of Microbiology Key Issues and Potential Solutions

Another set of questions was raised about life in deep Cataloging the capabilities Finally, many microbiological scientists study physiology, subsurface regions of the Earth’s crust where, until of living things but fail to put their findings in the context of the evolu- recently, life was not thought to exist. We have only begun to chart the diversity and potential tion of the planet. The feedback between Earth’s history of the Earth’s most abundant and diverse biological and microbial metabolism is important to understanding I What is the extent of the biosphere that exists deep resources, the microorganisms. They compose more than the development of both life and the environment, how below the Earth’s surface? When and how did it half of all living matter on Earth, yet we have identified organisms are currently keeping the Earth’s systems in evolve? How much biomass lies there? less than one percent of all the predicted microbial balance, and how to anticipate—and even impact—future species. In order to tap natural communities for events and trends. I From where do organisms that are trapped inside economic or social benefit, we will need to monitor and rocks or in sediments below the Earth’s surface develop new means to more deeply probe the natural These challenges can be overcome in numerous ways. derive their energy? Do these organisms employ very activities of microorganisms. Such an achievement Strong support should encourage new genomics efforts, slow metabolic rates and how important is the should help establish links between processes associated particularly those aimed at linking biogeological phenomenon of slow metabolism? How long do with life and its inanimate surroundings. function with sequence data. Funding agencies and these microbes live and for what do they use energy professional organizations should encourage collabora- in unknown ways to maintain their cells? What kind The genetic content—or genome—of an organism can be tions between genomics experts and others from diverse of selective forces act on microbes under the severe used to predict its biochemical and physiological poten- earth science fields. For example, projects that explore starvation conditions of the deep subsurface? tials, or lack thereof. For this reason, the genomic geobiological questions in novel ways by crossing sequence provides a wealth of information about ways in conventional specialty lines or by employing unconven- I How do subsurface microbes affect rock weathering? which a living creature can influence the planet. tional methods to answer geobiological questions should Are subsurface processes similar to those involved Technological advances in this area have led to a situa- be fostered. in soil formation? How do subsurface microbes tion in which the amount of DNA sequence information compare to the soil microbes that contribute to greatly exceeds our understanding of its meaning. Major Geomicrobiologists should be encouraged to move that process? work is needed to connect physiological functions with beyond descriptive surveys and move toward more the ever-accumulating masses of sequence data. mechanistic understanding of geobiological phenomena. Special emphasis should be put on efforts to culture Scientists must find new ways to capture the potential of novel microbes so that their biogeochemical functions species diversity in genetic terms. To this end, they must can be investigated. In this regard, geochemists should 8 develop new means for uncovering biological processes collaborate with microbiologists in elucidating geochem- and continue to decipher the genetic sequences that ical reactions that microbes might be employing. dictate these behaviors. Reaching this goal requires advances in laboratory and computational technology associated with sequence and functional analysis. This Analytic techniques requirement calls for interdisciplinary research and tools. Despite decades of study, basic information about funda- For example, computer scientists must grasp the relevant mental biological and geological processes is missing. For biological questions to create software that exploits the example, while scientists realize that some microbes can sequence and functional data, and biologists must learn to persist for extended periods of time, many mechanisms of navigate new software that is developed. Biologists must long-term survival remain mysterious. No one knows reach beyond traditional ground and extend ways to whether or how organisms endure the apparent absence study, for example, organisms that don’t grow under of an energy source or whether apparently entombed conventional laboratory conditions. Geologists and biolo- microbes gain energy by very slow metabolism of a source gists must collaborate in ventures that explore the impact that is not readily apparent. Hydrogen gas can be a major of particular microbes on the environment and vice versa. energy source and perhaps some long-lived organisms are

geobiology • A Report from the American Academy of Microbiology exploiting this substance for energy—yet the mechanisms and exploiting such microbial sensing phenomena, we can Methods for analyzing environmental samples at the of hydrogen gas production and distribution in geological use microbiology to tell us about geochemistry. nano- or microscale include conventional, fluorescence, samples remain murky. and laser scanning light microscopy; ion microprobe The field also needs to develop sensors that can be analysis; scanning probe microscopy; scanning and/or The ecological and geological importance of such “slow” deployed and used remotely to make environmental transmission electron microscopy; electron spectroscopic metabolism remains similarly obscure. Most microbiolo- measurements on a real-time or near-real-time basis in imaging and energy dispersive X-ray spectroscopy; gists are trained to conduct experiments with rapidly areas of the planet that have been understudied or are electron energy loss spectroscopy; selected area electron growing cells in the laboratory or even in the field over relatively inaccessible. Some programs aimed at devel- diffraction; and X-ray imaging using synchrotron radia- periods of hours or months or years; conventional scien- oping such tools exist, but much more development in tion. These tools serve as probes and chemical analyzers tific grants fund 3- to 5-year investigations. Studying this area is needed. of the microscopic world, providing detailed biological microbes that live at a very slow pace will be essential for and geological information on the scale of microns to understanding geobiological processes, the microbes that nanometers. These techniques need to be improved and catalyze them, and the function of environments in Observation on small expanded in order to conduct these “single-cell” experi- which they are important, such as the deep subsurface. and large physical scales ments because their capabilities are currently limited to The environmental influence of such slow-living organ- In order to document the interplay between organisms only a very few dedicated facilities and because of instru- isms and their associated biochemical activities may be and their surroundings, scientists must measure chemical mental limitations. Many promising nano- and very significant over long periods of time, but only reactions and products on spatial scales that range from microscale techniques are not yet well developed. They become apparent after decades or longer. Only by long- distances between molecules to those between mountain are still clumsy and inefficient. Furthermore, they gener- term studies will we determine how gradual changes in ranges. Tools exist for accomplishing this task under ally employ large expensive instruments that cannot the local environment may lead to the gain of an ecolog- some circumstances, but not all, and for some purposes, routinely be used in the field. ical advantage or how to identify the potential energy but not others. sources in an environment and discern how the energy While many of these tools allow scientists to outline available is used or to discover whether the resident Analyses of individual microbial cells can identify organ- pieces of the geobiological puzzle, many pieces remain microbes actually can evolve under starvation conditions. isms and the chemicals that they are consuming and hazy. Sensors are needed that can measure a broader producing. Furthermore, by taking a small step backward array of chemicals and other microenvironmental The hydrogen example above illustrates a general from single cells and looking at their neighbors and their factors—such as pH, temperature, and light—central to principle that affects many domains of geobiological immediate surroundings, scientists can also examine the the interplay between life and non-living matter. study: scientists don’t have reliable ways to measure consequences of microbial processes as reflected in the Development of such methodologies faces multiple 9 many critical processes that they would like to measure. local microenvironment. Bulk measurements provide challenges, such as detecting and quantifying the target Beyond quantification, there is an urgent need to only averages over large volumes and many cells, factors in natural environments, where other conditions develop better techniques for detecting specific however, while the real action happens at the level of the (the presence of minerals, for example) can interfere processes and determining how they are occurring. individual microbial cell or small groups of microbial with measurements. Furthermore, key geobiological cells. Sometimes, for instance, two or more specific processes frequently occur at hard-to-reach locations— Microbes themselves may serve as environmental sensors. organisms in close physical association must collaborate within sediments and rocks or deep in the ocean, for For example, some organisms respond in predictable ways to accomplish a particular biogeochemical transforma- example. New technologies are needed that permit three- to particular chemical or physical conditions; many tion. The details of such processes can be measured only dimensional detection and mapping of microbes, bacteria move toward nutrients and away from poisons. at the level of individual cells or small groups of cells. minerals, chemical compounds, and their associated Microbes possess sophisticated systems for detecting and The problem is similar to trying to understand the basic processes in all locations of interest. responding to chemicals in the environment. With mechanisms of forest ecology using only satellite enough ingenuity and application of new molecular and pictures without examining the individual trees or In addition, scientists must extend their insights gained analytical microscopic techniques that are available today, groups of trees. The tools to address these problems of from such Lilliputian observations and extract we should be able to learn their secrets. By understanding scale are only now coming on line. meaningful information to be applied at much larger

geobiology • A Report from the American Academy of Microbiology scales. Equally important as concentrations of a partic- But imprints of shelled or otherwise hard-bodied understanding of the past and our ability to predict the ular compound around an individual microbe are the creatures deposited in rocks are just one kind of fossil future. Furthermore, an improved catalog of life’s finger- levels of its products in the environment. Indeed some and provide only a partial record of former life. Soft- prints will enhance our ability to detect life if it exists bantam scale processes—greenhouse gas formation and bodied organisms, including microbes, leave more subtle elsewhere in the universe. destruction by microbes, for example—can impact the traces, and scientists have a great interest in uncovering entire planet. Global warming almost certainly results in these clues. Just as certain shapes and structures reveal large part from gases that are controlled by microbiolog- what types of animals were alive at particular times and Searching for extraterrestrial life ical activities. In addition to utilizing microscopy, under particular conditions, the presence of certain To ensure that we can detect life on other planets if it scientists must collect tools and perspectives that allow molecules can belie the existence of living creatures and exists, we must hone our ability to uncover its hallmarks them to integrate the effects of the microscale processes provide information about their properties. For example, here on Earth. But the search for extraterrestrial life on a global scale. They must expand the repertoire of some chemicals—e.g., isoprenoids or phytanyl-based must incorporate the idea that living creatures on other available methods and develop tools that integrate obser- lipids—in ancient sediments might reveal how cell planets may be fabricated and look and act differently vations from very small or very large scales. membranes were constructed, while others provide clues from those on Earth. It would be foolish to restrict our about other biological characteristics and processes that definitions of life to Earth-based constraints. Scientists occurred as life evolved. Further investigation into need to keep their minds open and entertain the idea Observation over long micropaleontology, in conjunction with studies of that, for example, the chemical basis of life could be periods of time present day microbe-mineral interactions, will provide different on other planets. Studies of geobiology on this To construct an accurate depiction of how our planet additional biogeochemical signatures that can be used planet should include consideration of the fundamental evolved, we must measure geobiological interactions for detecting which types of microbial activity were constraints on life here that could help us define or throughout Earth’s history. Scientists must find ways to important, not only in paleoenvironments on ancient look for it elsewhere. Investigations at the extremes will identify what types of metabolism were present in Earth, but in other poorly understood and difficult to aid these endeavors by cataloging the permutations of different time periods, how populations swelled and sample modern environments. life in a wide a variety of environments that we can dwindled, and why. Geobiologists are particularly inter- probe here on Earth. ested in cataloguing changes in life forms as they relate Similarly, such molecular and chemical fingerprints, or to alterations in the environmental character of the biomarkers, should allow scientists to infer details about Earth. Most species that have ever lived on Earth are now the environmental conditions at the time a particular Informatics tools extinct. The geologic record provides the only window organism lived. The development of new and more sensi- To advance the field of geobiology, scientists require an 10 into the broad physiological variation that evolution has tive methods that detect fingerprints of life and understanding of a wide array of processes in a large produced. Buried organic matter, rocks, fossils, and corresponding geological processes are needed to probe number of organisms on tremendous scales of space and trapped gases (which can reveal what ancient organisms the environments where life flourished and floundered time. Progress depends on the development, manipula- ate and breathed) provide the best record of ancient and to discern how this was changed by the chemical tion, and integration of huge data sets. Computational biological activities. and physical surroundings. Furthermore, scientists need tools must allow researchers to combine information these improved analytical tools to reveal high-resolution from a variety of sources. These include databases that Fossils also provide the only direct avenue for under- absolute and relative ages for events and species that can be used to map microbes, minerals, geological forma- standing the environmental conditions present at times extend back through the last three billion years. tions, and temperatures to particular locations on the of major biological innovation and mass extinction. The planet, to compare genomic DNA sequences, and to material that holds the remains of an organism provides Current analytical tools do not adequately look compile information about the cycling of particular information about the environment at the time that backward, which limits scientists’ ability to look forward. chemical elements, for example. This informatics creature died. Because rocks reveal their age by their Biologists would like to uncover diagnostic microbial technology also needs to be powerful enough and user chemical composition, any biological material that gets signatures in rocks and to enhance their ability to friendly enough to assist scientists as they explore what preserved in them can also be dated. examine microbes and biogeochemical events on a tiny kind of life existed where and under what conditions scale. Improving these methodologies will enhance our and time periods. It should thus help researchers

geobiology • A Report from the American Academy of Microbiology document the fossil record, provide tools for analyzing Information from sequencing efforts is a high-profile Culturing techniques these data, and link this information to other relevant piece of the geobiology puzzle. In order to assemble the The ability to grow microorganisms in the laboratory biological and geological databases. New informatics full picture, scientists would like to overlay physical and is the only way to directly test hypotheses about their technology should facilitate recognition of and help chemical data on the genomic sequencing data. In an physiological and biochemical potential. Currently, it is establish connections, trends, and patterns that might imaginary example, they would construct maps that estimated that greater than 99 % of all microbes cannot otherwise go unnoticed. Furthermore, it should fuel showed the types of organisms that inhabit specific areas be cultivated in the laboratory. This number must be researchers’ findings by raising queries and providing of the globe and that allowed one to easily “see” the corre- reduced. Because the diversity of microbes that are answers that would be impossible without substantial sponding environments. In addition, there would be a important in geobiological processes is enormous, geobi- computing power. tool that showed critical information about the content ologists can make a big difference in solving this of solids, liquids, and gases in a particular location, and problem. While techniques for identifying microorgan- Scientists are rapidly uncovering genetic secrets of large there would be data about, for example, specific isms and their biological capabilities in the absence of numbers of organisms by sequencing their genomes. chemical constituents, temperature, and pressure. pure cultures (such as deciphering and comparing their Comparisons of these sequences can highlight both Furthermore, the fantasy computer tools would map this genetic sequence) are blossoming, geobiologists will also shared and unique features of microbes, which can information over time so scientists could examine how need to make special efforts to grow specific microbes in reveal clues about their physiological capabilities. DNA the various parameters are changing, and thus develop the laboratory. sequences present in all life forms, for example, point hypotheses about how components in complex geobio- toward basic functions, while those carried only by logical webs are influencing each other. They could also Dedicated funding is needed to develop new culturing organisms that convert one obscure compound into learn about how species, or even specific genetic techniques. Scientists need to make significant headway on another or that squeeze nutrients out of rocks point sequence variations, correlate with changes in tempera- expanding culture methods to include more organisms. Of toward specific biochemical talents and help link DNA ture, chemicals in the environment, and so forth. particular interest would be culture methods for studying sequence with function. Although seemingly simple, the interactive groups, or consortia (not just individual task can require enormous computing power because of In order to achieve such imaginative goals, investigators microbes), under conditions that mimic the natural the huge number of genes and organisms being studied. need new ways to integrate the relevant data. This will environment as closely as possible. This goal presents The scientific community requires new and improved require manipulating and combining huge data sets from informatics tools to handle even this type of seemingly different sources. To accomplish this task, new and more straightforward analysis. powerful informatics tools need to be forged and honed as more information and more questions arise. In addition, researchers have recently set their sights on 11 much more ambitious goals. Some are collecting not only Finally, the entire scientific community will benefit sequences of individual organisms, but also sets of when these data and tools are available to everyone and sequences that represent whole microbial communities when the tools are easily usable by scientists with a from particular environments. By considering the added variety of backgrounds and training. Currently, there is complexity of comparing entire communities, it is even no central site that serves as a hub and storehouse for easier to appreciate the tremendous need for powerful geobiological information. This situation can lead to computing tools. inefficiency and duplication of efforts. Care must also be taken to set up systems by which the data in the databases are easily accessed and manipulated by members of all sections of the geobiology community.

geobiology • A Report from the American Academy of Microbiology special challenges because microbial communities consist Another major challenge is the environmental relevance products of purely geochemical processes from those of many different microbes, each with a different function of a particular geobiological process. Just because a with strictly biological origins. In addition to defining in the community. The challenges are that each individual process is observed does not mean it is a major process in life’s signatures, we also need methods to detect the may require different conditions for growth in the labora- the environment, or that it operates to any extent in the diagnostic signs of life at distant locations. tory and that, in the consortium, the requirements may be natural setting. Geobiologists must devise strategies to different from those for any individual microbe. determine whether the geobiological processes they observe are occurring in the same way under observation Model systems as they are in their undisturbed natural contexts. While the major emphasis will be on understanding Sampling technologies geobiological processes in natural environments, labora- Researchers require new ways to sample organisms and The examples given above illustrate just a few of the tory experiments designed to isolate and test the effects their surroundings from the environment to discover challenges posed by remote sampling endeavors for of individual physical, chemical, and biological and monitor biogeochemical processes. These challenges geobiological research. Special technologies will be phenomena will continue to play an important role in are particularly acute in remote or extreme environ- required to probe other planets for their geobiological geobiological research programs. This is the only way to ments, where life and its associated processes have not potential. We need small and easily portable machines probe specific hypotheses about the interplay between been adequately explored or mapped. New technologies that require minimal maintenance. Furthermore, devices life and matter. To extend these types of investigations, are required that both increase access to these areas and for sampling other planets must not only collect samples, new technologies are needed for accurate laboratory address combined biological and geological objectives. but also must analyze them on the spot, e.g., in situ. In simulation of environmental conditions. Such tools When developing such methodologies, scientists and some cases, existing survey technology may be adaptable should also simulate conditions thought to exist in the engineers face unique problems. for geobiological surveys. For example, radar that early era of life on Earth, which will enable scientists to penetrates the ground can detect subterranean liquid test scenarios of how life began. Pulling up material for geobiological studies from a lake or water on Earth and will be useful for surveying other the ocean or beneath the Earth’s surface requires care to planets remotely for water from satellites. Likewise, Scientists would like to test possible pathways that led to avoid contamination by microbes and chemical remote drilling methods must be developed to access the chemistry of life. The big question is how pre-biotic compounds on the surface and to detect such adulteration environments and retrieve geobiological samples from chemistry gave rise to reproducing organisms. A big if it occurs. Sampling strategies have been worked out for underneath the surface of other planets. experimental challenge is inherent to these studies. At most of these near-surface environments, although this point in the planet’s development, the Earth is so improvements are still required. Improved methods are A major issue for geobiologists who study extraterrestrial steeped in life that it is very difficult to subtract biolog- 12 also required for sampling and analyzing extreme and sites is whether or not life exists there, and, if it does, ical products. This situation poses difficulties in remote locations (such as deep sea hydrothermal vents or what is it like, and if it does not, why doesn’t it? To simulating conditions of a much younger Earth. While the subsurface of Mars) to identify organisms and geobio- answer these questions, scientists need to figure out how very simple renditions might be possible, others are more logical processes. Analytical devices that operate inside they will identify such life if it is present. This problem difficult. For example, some scientists propose that deep boreholes, for example, will facilitate subsurface consists partly of finding potential life forms and partly certain clays may have provided the physical structure monitoring of geobiological processes. However, the of recognizing such life forms if they are present. If a on which pre-biotic chemicals met and reacted. But at peculiarities of some microbes may not allow them to spaceship makes contact with entities that obviously eat, this point, clays interact so strongly with existing natural hold up well under conditions at Earth’s surface. Microbes move, breathe, and reproduce, we will know that they biomolecules that they cannot be easily cleansed of their that have evolved at high temperatures and pressure or are living aliens. But more likely, life on other planets will organic matter for accurate pre-biotic experimentation. under other special environmental conditions might die be in the form of microbes, which are by definition on their journey to the environment that we consider invisible to the unaided eye and are most easily observed normal. Similarly, gases that are maintained under high by their indirect effects and signatures they leave in their pressure (and the microbes that metabolize them) might environment. Controversy is currently raging about escape (or die) unless transferred under appropriate what exactly constitutes life’s molecular signatures. pressurized conditions. Improved methods are required for distinguishing

geobiology • A Report from the American Academy of Microbiology Field studies The choice of field sites is also important. Established traditional geology and biology faculties work together While model systems allow scientists to perform field sites are valuable because they allow scientists to and to create a new geobiology vocabulary that they controlled experiments that probe specific questions, conduct long-term studies and to exploit documented and their students can agree on. Geobiology training field studies are necessary to study the natural environ- geobiological history. However, colloquium participants programs might branch out to include, for example, ment. Such endeavors reveal how different communities also stressed the importance of branching out and in-depth exposure to mathematics, numerical modeling, interact with each other and their environments in the exploring new areas and types of environments. and computational techniques. In addition to the need real world. Studying complex ecosystems can elucidate for people with strong mathematical and quantitative activities that would remain obscure by analyzing skills, there is also a need for improvement of observa- individual organisms or sets of interactions in the labora- Ethical issues tional skills and a return to the approaches of traditional tory. For example, microbial consortia collaborate to The pursuit of geobiological studies requires ethical, as naturalists. Both quantitative and qualitative approaches perform tasks and impact the environment in ways that well as technological and theoretical, consideration. Some are necessary. The new field will benefit from cross- single microbes do not. studies may perturb natural populations or processes, trained specialists with background and experience in which could result in undesired consequences. It is diffi- both areas. At present, tools to accomplish this goal are lacking. In cult to predict what problems might arise from, for order to describe natural communities and habitats in example, transporting samples from a relatively To introduce quality control and uniformity to this field, detail, scientists face formidable challenges. Organisms sequestered environment to another, more exposed one. recommendations about what might ideally constitute and chemicals may be present at concentrations so low For this reason, effort should be directed toward devel- degree requirements should be developed for universi- that they are difficult to detect, and identifying oping guidelines for handling material from remote ties. Furthermore, strong recruitment efforts at the individual molecules or microbial species can be tricky sampling sites, such as the deep underground zones that undergraduate and graduate levels will stimulate interest when they are immersed in a soup with others. have not been exposed to the Earth’s surface. Similarly, among young scientists. Currently, jobs in this field Furthermore, such systems are not static; behaviors and we must entertain the possibility that we could contami- outnumber applicants. This is true for both academia chemical reactions can change over minutes, days, or nate other planets with life from Earth as we explore and industry. seasons. Because the natural environment contains a rich them; along the same lines, we run a risk of introducing array of chemicals and life, in situ analytic techniques foreign life forms from other planets when we return While educational programs will groom students and must be honed so that they measure the entity of them to Earth. Such possibilities must be considered postdoctoral fellows for full participation in this interest—at the scale of interest—without interference. when developing geobiological research programs and emerging field, other efforts must be made to allow Scientists need improved micro-sensors that can detect new methodologies. Scientists, lawmakers, and the public established investigators to reach across disciplines. small amounts of chemicals over small spatial scales. should engage in discussions about the stewardship of Geobiology encompasses a variety of different fields and 13 Such sensors will allow for determination of processes the natural universe and decide how best to care for it addresses questions that span spatial and temporal scales that play key roles in microbe-microbe and microbe- during these investigations. in nontraditional ways. Such interdisciplinary and mineral interactions. Furthermore, these devices must unconventional science is not necessarily compatible operate under a wide variety of conditions, including at with academic infrastructure, such as promotion and hard-to-reach or harsh locations deep beneath the Earth’s Education, personnel, and training tenure of faculty, design of undergraduate and graduate surface or at the bottom of the ocean. Scientists will require diverse backgrounds to traverse degree programs, and federal and state funding of the traditionally non-overlapping fields that comprise academic institutions. Like other new and emerging Such tools must also be able to sample on a micro-scale the new discipline of geobiology. In addition to the disciplines, this one requires special attention at all levels and map findings relative to each other. Key geobiolog- conventional biological and geological university courses, of administration. ical processes frequently occur unevenly within new cross-disciplinary courses in geobiology must be sediments and rocks, for example. Tools that document developed. This will be best achieved by fostering Efforts should be made to foster working collaborations the presence of microbes and their associated activities collaborations between teaching faculty, as well as and establish a common language between fields so and geological consequences in three dimensions, on fine research faculty and students. Departmental and experts from diverse specialties can communicate effec- scale but over broad areas, would be extremely valuable. institutional leaders must make special efforts to help tively to state and solve problems. Better integration is

geobiology • A Report from the American Academy of Microbiology needed between basic research scientists in relevant disci- Professional societies are actively supporting geobiology. concepts of geobiology. Furthermore, some of the basic plines and between scientists and engineers for This is a positive trend, and they should be encouraged questions of geobiology—how living things and the development of appropriate conceptual and practical to continue fostering special educational programs, environment influence each other and how life strategies to tackle problems in geobiology. Various focused sessions at meetings, collaborations between evolved—may well hold appeal for children and may approaches might build bridges between investigators members, and so on. International societies in particular promote curiosity and interest in science in general. who do not usually interact. Career opportunities and should continue and increase support for conference incentives, for example, might foster interdisciplinary sessions and other activities that nurture geobiology. ties, training opportunities, and education in geobiology. More interdisciplinary journals might be useful. To Support for research and training ensure the field’s success, the lay public, as well as the In order to tackle the challenges and realize the goals While colloquium participants stressed the need for scientific community, need to recognize geobiology as an discussed by colloquium participants, there is a strong strengthening the breadth of scientific training, some identifiable scientific discipline that promises practical need for funding for educational, research, and techno- were also concerned about the demise of microbiologists benefits and insight into the basic processes that shape the logical development. This support will ensure with deep roots in microbial physiology. Strong support environment and its life forms. establishment of programs that promote geobiological is needed for robust research efforts aimed at under- training and investigations at the graduate and postgrad- standing the physiological and biochemical repertoire of Colloquium participants suggested organizing an uate levels. Furthermore, it will attract and educate high microorganisms. To this end, those with training in outreach program to communicate the power and school and undergraduate students. Financial support is conventional microbiology will continue to play critical promise of this field to the general public. People needed for seminars, workshops, short courses, and roles. They should be encouraged to delve into research involved in this project might, for example, pitch story conferences. Interdisciplinary grants that promote collab- questions outside the traditional arenas of medical and ideas to media outlets or develop Internet resources that orations between specialists in different fields will be industrial microbiology and, as much as possible, to apply convey how biology and geology fit together. especially important to stimulate the field of geobiology, their well-developed microbiological sciences to relevant as would those directed toward development of new geobiological issues. Finally, education should start early. Young (K-12) analytical and computer tools. In short, while limited students need to learn about the relationship between funding has supported some special, short-term Earth and its inhabitants, especially with microbes. programs, more financing is needed to sustain long-term Environmental issues may particularly interest children projects, training, and vigorous development of the field. and could be used to illustrate some of the general

14

geobiology • A Report from the American Academy of Microbiology Specific Recommendations

Specific Recommendations I Develop informatics systems and computer • Organize national and international scientific I Foster development of geobiology at appropriate technology infrastructure for: meetings in the field of geobiology. institutions by providing support for innovative, cross-disciplinary teaching, research, and outreach • Easily accessible electronic databases to store • Foster cross-pollination among subdisciplines of programs. geobiological information. geobiology and between geobiologists and engineers.

I Support and encourage basic research and • Management and comparison of geobiological data • Encourage continuing support for “classical” fields of engineering programs in geobiology, stressing the key resources that range over wide scales of observations microbiology, physiology, taxonomy, and metabolic issues in this report. and across vast stretches of time and space. diversity, while expanding their repertoires to include the less conventional areas that crossover into earth I Establish more field laboratories for geobiological • Computational tools that can integrate geobiological science disciplines. research and continue to support existing field information from genomics to global cycles of laboratories. the elements.

I Support laboratory studies of basic biological I Support geobiology education at all levels: sciences, especially microbial diversity, physiology, and genomics, which represent the basic science • Develop systems to educate the general public as backbone of the field. well as scientists about the potential benefits of studying geobiology. Organize an outreach system that I Improve methods for defining and detecting communicates the power and promise of this field. chemical signatures and other biomarkers that indicate the presence of past and present life. • Establish a central repository for information about geobiology on the World Wide Web. I Support efforts to catalog the diversity microorgan- isms, including their biogeochemical capabilities and • Introduce interdisciplinary issues on geobiology into their geobiological importance. undergraduate level courses in biology and geology. Encourage programs that grant minor degrees in I Establish and support centralized culture collections geobiology, with major degrees in a primary biological 15 for organisms important to the field. or geological discipline.

I Encourage further exploration of how human beings • Develop summer field courses that will spread interac- might exploit the geobiological capabilities of tions and communications through a broad audience microbes for society’s benefit, such as in cleaning up and enrich the experiences of graduate students, polluted areas or extracting valuable resources from postdoctoral fellows, and principal investigators. the environment. Courses similar to the Woods Hole summer course series and Cold Spring Harbor courses represent good I Improve analytical tools for observation and models for this enterprise. measurements on small (microscopic) and large (planetary) physical scales and that operate at • Provide travel and research support for investigators inaccessible sites remote from the Earth’s surface. to branch out into other areas for cross-training and to bring new expertise and insight into the field of geobiology.

geobiology • A Report from the American Academy of Microbiology Bibliography

Amy, PS, and DL Haldemann. 1997. The microbiology of the terrestrial deep subsurface. CRC Press, Boca Raton, FL.

Banfield, JF, and CR Marshall. 2000. Genomics and the geosciences. Science 287:605-606.

Banfield, JF, and KH Nealson (Eds.). 1997. Geomicrobiology: interactions between microbes and minerals. Review in Mineralogy. Mineralogical Society of America, Washington, DC.

Ehrlich, HL. 1995. Geomicrobiology. Marcel Dekker, New York, NY.

Nealson, KH, and PG Conrad. 1999. Life: past, present and future. Philosophical Trans. R. Soc. London B. 354:1923-1939.

Romig, PR, Chair (with 18 committee members). 2000. Seeing into the Earth: non-invasive techniques for characterization of the shallow subsurface for environ- mental and engineering applications. National Research Council, National Academy Press, Washington, DC.

16

geobiology • A Report from the American Academy of Microbiology