GEOBIOLOGY - SENR Geobiology Report 2001.pdfIntroduction. This colloquium was organized to devise...

GEOBIOLOGY:Exploring the Interface Between the Biosphere and the Geosphere

This report is based on a colloquium sponsored by the American Academy ofMicrobiology held December 1-3, 2000, in Tucson, Arizona.

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

A M E R I C A N S O C I E T Y F O R M I C R O B I O L O G Y

N AT I O N A L S C I E N C E F O U N D AT I O N

U. S . D E PA R T M E N T O F E N E R G Y

U. S . G E O L O G I C A L S U R V E Y

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

Copyright© 2001American Academy of Microbiology

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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


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Board of Governors, American Academy of Microbiology

Eugene W. Nester, Ph.D. (Chair)University of Washington

Joseph M. Campos, Ph.D.Children’s National Medical Center, Washington, DC

R. John Collier, Ph.D.Harvard Medical School

Marie B. Coyle, Ph.D.Harborview Medical Center, University of Washington

James E. Dahlberg, Ph.D.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

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

Colloquium Steering Committee

Kenneth Nealson, Ph.D. (Co-Chair)University of Southern California

William C. Ghiorse, Ph.D. (Co-Chair)Cornell University

Edward F. Delong, Ph.D.Monterey Bay Aquarium Research Institute, Monterey, CA

Abigail A. Salyers, Ph.D.University of Illinois

James T. Staley, Ph.D.University of Washington


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Colloquium Participants

Ariel Anbar, Ph.D.University of Rochester

Enriqueta Barrera, Ph.D.National Science Foundation

Dennis A. Bazylinski, Ph.D.Iowa State University

Terrance J. Beveridge, Ph.D.University of Guelph, Ontario, Canada

Gordon E. Brown, Jr., Ph.D.Stanford University

Pan Conrad, Ph.D.NASA-Jet Propulsion Laboratory, Pasadena, CA

Edward F. Delong, Ph.D.Monterey Bay Aquarium Research Institute

David Des Marais, Ph.D.NASA Ames Research Center, Moffett Field, CA

Suzanne Douglas, Ph.D.NASA-Jet Propulsion Laboratory, Pasadena, CA

Katrina J. Edwards, Ph.D.Woods Hole Oceanographic Institute, Woods Hole, MA

F. Grant Ferris, Ph.D.University of Toronto, Ontario, Canada

Steven E. Finkel, Ph.D.University of Southern California

Bruce W. Fouke, Ph.D.University of Illinois

James K. Fredrickson, Ph.D.Battelle Pacific Northwest National Lab, Richland, WA

E. Imre Friedmann, Ph.D.Florida State University

Thomas L. Kieft, Ph.D.New Mexico University of Technology

William W. Metcalf, Ph.D.University of Illinois

Alison E. Murray, Ph.D.Desert Research Institute, Reno, CA

Kenneth Nealson, Ph.D.University of Southern California

Eugene W. Nester, Ph.D.University of Washington

Charles Paull, Ph.D.Monterey Bay Aquarium Research Institute, Monterey, CA

Abigail A. Salyers, Ph.D.University of Illinois

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

James T. Staley, Ph.D.University of Washington

Bradley M. Tebo, Ph.D.Scripps Institute of Oceanography, La Jolla, CA

Alexandre Tsapin, Ph.D.NASA-Jet Propulsion Laboratory and California Institute of Technology,Pasadena, CA

Staff

Carol A. Colgan, DirectorAmerican Academy of Microbiology

Elizabeth Huston, Program AssistantAmerican Academy of Microbiology

Science writer

Evelyn Strauss, Ph.D.Santa Cruz, CA


A colloquium was convened by the American Academyof Microbiology to deliberate issues relating to the inter-secting fields of biological and geological sciences. Thecolloquium was held in Tucson, Arizona, December 1—3,2000. The principal findings of the colloquium aresummarized below.

A wide chasm may seem to divide the living from thenon-living. On closer inspection, however, these tworealms do not perch on separate ridges, but knit togetherto form a single lush domain. Geological and biologicalactivities are integrated, and they influence each other inprofound ways. This interplay has shaped the Earth andall creatures on it. Studies of geobiology—the present andpast interactions between life and inanimate matter—promise to reveal the secrets of life, its origins andevolution, and its present functions on our planet. Suchstudies hold enormous practical potential as well.

Long ago, life arose from chemicals. As new creaturesevolved, their activities changed the environment. Thealtered surroundings in turn invited different types oforganisms, which again altered the world around them.Geobiological interactions have created the gases webreathe and the soil in our forests. They contribute toglobal warming and some forms of pollution, yet knowl-edge of geobiological processes offers strategies for

remedying some of these problems and for enhancingthe quality of life on our planet in other ways as well.

The new discipline of geobiology will provide a plethoraof exciting intellectual and practical rewards.Geobiologists hope, for example, to discern how lifebegan and how it evolved. Furthermore, they aim toidentify how environmental conditions influenced theseprocesses and, in turn, were altered by life. Under-standing the past will equip us to predict the future. TheEarth has already conducted many experiments over thecourse of its evolution, but, because of the complexity ofgeobiological interactions, we are unable at present todecipher our planet’s lab notebook. Current and futureinvestigations will improve our ability to read therelevant records, interpret them, and make predictionsbased on past results.

Many geobiological processes affect environmentalquality and impact human health, which in turn influ-ence the economy and work force. As a result, criticalpublic and science policy issues require input from thisfield. The study of geobiology offers significant payoffsthat touch society in many ways. To exploit the possibili-ties, we need to focus diverse resources on this rapidlygrowing and tremendously promising new field.

Executive Summary

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Living creatures and the inanimate worlds they inhabitdance an intimate tango. As each partner steps toNature’s tune, the other responds in harmony. Organismsalter their surroundings as part of their normal activities,and in turn, the changed surroundings nurture differenttypes of life and altered modes of living. This interplayof Life with Earth has shaped our present environment.Indeed, Life and Earth, through this “GeobiologicalTango,” continue to choreograph the co-evolution of thebiosphere and the geosphere. Understanding the detailedhistory and workings of these interactions will provideinsight into the origins and evolution of the geobiolog-ical world. Learning the choreographic design of thetango will help us to better manage environmentalaffairs and shed light along the path to their future.

The environment has been spawning innovations inbiology ever since it sparked life itself. Early on ourplanet, the line between life and non-life was muchthinner than it seems today. At some point, inanimatechemicals and physical forces interacted in new ways toprovide compounds and reactions that made lifepossible. As biology stirred, its activities sent ripples

through the inanimate world. Bacteria, algae, and,eventually, plants pumped oxygen into the air, forinstance, profoundly changing the composition of theatmosphere and supporting the development ofcreatures that breathe this gas. Microbes in the soilcaptured critical nitrogen minerals from rocks andpackaged them into forms that other creatures could useto make essential molecules such as proteins. Such activi-ties changed the environment, rendering habitats morecomfortable for some organisms and harsher for others.The resulting fluxes of species and their specializedbiochemical activities in turn registered effects on thesurroundings. In such ways, the interactive cyclebetween living things and their geological surroundingsnever ceases. For example, geological materials haveserved as energy sources (electron donors) forlithotrophic metabolism and as electron acceptors foranaerobic respiration of many types. This often results ininadvertent dissolution and/or formation of minerals.Organisms—especially the more complex eukaryoticorganisms—have developed exquisite abilities to createstructural materials, such as calcite, silicates, cellulose,and chitin. These “biominerals” have served to alloworganisms to become large three-dimensional structures,e.g., to thwart gravity, to increase predatory efficiency,and to be used as protective structures from other preda-tors. Perhaps of equal importance, they have supplied uswith a fossil record detailing much of the recent historyof life on our planet.

Studies of geobiology will reveal these events and eluci-date their details. Increased knowledge in this area willenhance our comprehension of how the planet Earth hasevolved and continues to evolve. In addition to uncov-ering the underlying designs of natural processes thathave shaped Earth, we will learn the details and environ-mental consequences of current human activity. Suchinsights will allow us to modify certain activities in waysthat will heal and maintain our environment.

Furthermore, we may devise ways to apply geobiologicalphenomena in our search for solutions to some of ourenvironmental problems. Some interactions betweenliving creatures and matter are enhancing the quality oflife for other creatures, for example, and point towardfurther inventions that might build upon these naturalsuccess stories. Many microbes transform poisons, suchas heavy metals, into harmless compounds, or repackagethem so they are physiologically unavailable. Othersdegrade organic pollutants, restore key nutrients todepleted soil, or act as a sink for greenhouse gases, suchas carbon dioxide, from the atmosphere. Understandingboth biology and geology is critical to solutions aimed atmany major societal issues, including groundwaterquality, environmental contamination, the loss ofproductive agricultural lands, and global warming.

Geobiological studies may produce other benefits aswell. Many microbes produce chemicals of practical use,such as ethanol, which directly affects the price ofgasoline, more cheaply or leanly than do industrialprocesses. Some produce unique complex compoundsthat cannot, as yet, be synthesized by industry, andothers make compounds with special properties thatlend themselves to particular engineering demands.Greater understanding of geomicrobiological processescould easily lead to new products.

While scientists can cite many isolated examples ofbiology influencing the environment and vice versa, theydo not fully grasp how these interactions have changedover time or how they all fit together. Furthermore, largegaps riddle our understanding of critical past events, andgargantuan holes confound our ability to explain whatforces drove particular occurrences or why certain organ-isms and communities responded to their circumstancesin the ways they did. In order to interpret Earth’s pasthistory or to predict its future, scientists must expose thestory of how the geosphere and the biosphere co-evolved.By studying present day geobiology, scientists hope to fillin its history and better predict Earth’s trajectory intothe future.


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Introduction

This colloquium was organized to devise plans that willoutline the challenges faced by the nascent field ofgeobiology, to devise plans that will address thechallenges, and to propose some solutions. Although thedominions of geology and biology have independentlymatured, the intersection of these two areas remainsrelatively immature and underdeveloped. Under theinfluence of heightened interest in life in remote andextreme environments, the boundaries of geobiology areexpanding rapidly. The breadth and scope of thisexpanding discipline need to be more clearly defined anddirected. Intellectual, economic, social, and educationalissues associated with advances in the field must beanticipated, identified, and analyzed to create a plan ofaction. A list of urgent scientific questions needs to becompiled and evaluated to direct and adequately fundscientific inquiry. Critical intervention at this time byexperts in the intersecting and allied fields should helpto guide the development of the field and usher it to itsfull promise.

Interactions between the microbial and geological worldsrepresent a large swath from the cloth of interactionsbetween living organisms and the geosphere they inhabit.Thus, most of the examples in this document focus ongeomicrobiology. While it was well recognized thatanimals and plants interact in significant ways with thegeosphere, colloquium participants concentrated ongeomicrobiology two reasons: (i) it reflected their exper-tise, and (ii) the time period over which the geosphereand biosphere have co-evolved is known to be over-whelmingly dominated by microbes. The more complexeukaryotic organisms have evolved relatively recently.Colloquium participants recognize that the activities ofanimals, plants, and other complex organisms have andwill continue to exert an enormous impact on thegeobiosphere. They project and hope that future geobio-logical research will encompass increasing contributionsfrom the scientific disciplines that deal with morecomplex organisms. In the meantime, examples from therealm of geomicrobiology handily illustrate the powerand potential of geobiology as a whole.

The past, the present, the future,and the possibility of extraterrestrial lifeThe field of geobiology offers clues to a wide range ofpractical and philosophical enigmas. It has the poten-tial to profoundly change both the quality and ourunderstanding of life. Findings in this area will influ-ence the health of all life on Earth and the planetitself. The field promises tremendous ecological, eco-nomic, and intellectual rewards.

While microbes have historically exerted the largesteffect on the Earth, humans are now making a hugeimpact. Society today faces challenging questions abouthow to counteract some of the damage that we areinflicting. Humans are encroaching on natural habitatsand rapidly polluting and depleting the environmentthrough activities such as mineral mining, oil and gasproduction, large-scale farming, logging, and industrialproduction of toxic waste. This damage encompasses theEarth’s continents, as indicated by, for example, theincreasing evidence of global atmospheric and oceanicwarming. But we also have the opportunity tocounteract some of the destructive by-products of anurbanized civilization. Humanity can aim its technologyin more constructive directions. In addition, we havemany valuable natural resources derived from geobiolog-ical processes. Microbes, for example, perform amultitude of biogeochemical feats that can be put togood use, from cycling carbon, nitrogen, and sulfur totransforming toxic chemicals, including heavy metals. Inthe future, we must devise more schemes that respon-sibly exploit the opportunities that present themselves inthe complex natural world.

Scientists must tease apart the complexity of contribu-tions from different organisms and reactions and use thisinformation to predict how the environment is changing.To meet this challenge, we must learn all that we canabout how geology and biology interact. For example,how do temperature fluctuations impact living things?How do microbes respond to long- and short-term

environmental perturbations? How do the biologicalchanges caused by environmental perturbations affectthe regional geochemistry? And how will these answerschange over time?

The study of geobiology allows us to look backward aswell as forward. In its infancy, conditions on Earth didnot welcome life. In order to understand the planet’scontinued evolution, we must understand its past. Aclear picture of how life arose and prospered willundoubtedly lead us toward answers about how tosuccessfully maintain life on this planet.

Since the beginning of scientific inquiry, people havewondered how life began and how the zoo of complexcreatures on our planet arose from our simple predeces-sors. Pondering these issues while surveying the night skyevokes the question of whether life has arisen elsewherein the universe. The study of geobiology will undoubt-edly provide insights into this question as well.

Geobiology’s potentialInteractions between living creatures and inanimatematter have shaped Earth and its inhabitants since lifearose from our comparatively simple ancestors. Yet,we have just begun to appreciate the extent of itsinfluence. A vast repertoire of diverse microbial talenthas eluded scientists until recently. Researchers havefound microbes in remote places, such as deep-seathermal vents, which at first were considered too hos-tile to support life. Organisms that survive and eventhrive in these extremes of temperature, pressure, orunusual chemical environment, also perform unusualand, in many cases, unanticipated biochemical feats.Many of these involve geochemical reactions—makingor breaking minerals, transforming elements from oneform into another, producing compounds that dra-matically alter the immediate surroundings, and, thus,affect the entire local community of organisms, orthat build up in the atmosphere and impact the entire planet.

Geobiology’s Value/Vision for the Future


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The discovery of such microbes and the study of theiractivities have forced scientists to broaden their ideasabout life’s capabilities, limits, and effects. While the listof unusual microbiological activities grows longer withevery discovery, each “surprising” finding hints at alengthening list of unknown ones. We have only begunto dig into the wealth of this information and to gaintantalizing glimpses of its significance.

Microbes influence the geosphere in myriad ways,especially through influences on the cycling of elements,which affect the quality of all life on this planet; yetcritical features controlling the elemental cycles remainelusive. Keys to global warming, for example, are likely tolie inside microbial cells, because multitudes of thesetiny creatures emit and deplete enormous amounts ofgases, such as carbon dioxide and methane, that trap heataround the Earth. Despite the importance of such physi-ological processes, huge holes in our knowledge foilattempts to assemble the relevant pieces. Microbes andplants transform carbon dioxide, the most abundantgreenhouse gas, from the air into sugars and otherorganic molecules, or solid carbonate structural elements.Other organisms consume organic chemicals, and in theprocess of breaking them down for energy, spit out thecarbon in the form of carbon dioxide. While these eventsprovide a satisfying qualitative view of the carbon cycle,they don’t explain all aspects quantitatively. For example,it has been impossible so far to balance the carbon cycleon the global scale. Somewhere on the planet is asubstantial sink for carbon dioxide that is not yet discov-ered and, therefore, not understood. Understanding thesources and sinks of carbon, and the fluxes into and outof these boxes, is key to understanding and intelligentlydealing with the issues of global climate. Similar informa-tion for the cycling of other elements with key geologicaland biological roles is also missing and of great interest.

The geological and biological worlds interact in manyother ways as well. Recent studies have established thatsome microbes obtain energy for growth by transferringelectrons to a wide range of toxic or environmentally

harmful metals, such as uranium, chromium, selenium,arsenic, technetium, and plutonium. In some cases—foruranium, chromium, and technetium—these activitiesproduce reduced metals that are insoluble, effectivelyremoving them from exposure to the food chain. Inothers, undesirable effects occur. For example, iron andmanganese oxides are scavengers of toxic transition(copper, nickel, cobalt, zinc), radioactive (uranium,platinum, technetium), and heavy (lead, mercury)metals. When microbial reduction of iron or manganese occurs, the dire consequences might meanthat these toxic metals are set free, effectively concen-trated in the environment due to metal oxide scavenging.Knowing what can—and will—happen will require exten-sive knowledge of the iron and manganese oxides, theextent of toxic load they are carrying, and the abilities of the microbes in the environment (or of those thatmight be added to a polluted system).

In addition to repackaging or dissolving minerals,microbes can produce them. Magnetotactic bacteria, for example, manufacture tiny magnetite crystalsforming microbial compasses. These tiny crystals displayproperties that may render them particularly useful inelectronics or microchip construction. Other bacteriaconstruct extractable crystalline surfaces (S-layers) thatare amenable to forming nanoscale electrical circuitsonce “doped” with metal atoms. Some bacteria evenproduce a compound, crystalline cellulose, which hasunusual acoustic characteristics. Engineers have alreadyincorporated this material into stereo speakers. Theseexamples underscore not only the ability of microbes to produce substances of great practical use, but alsoillustrate their ability to leave distinct geobiologicalsignatures. The magnetotactic bacteria, for example,produce ultrafine-grain magnetite particles with uniqueshapes and magnetic properties that have been invokedas evidence for past life on Mars.

Tiny microbial cells can affect large—even global—environments, as well as local ones. For example,microbes in organic-rich sediments under the ocean floor

produce enormous amounts of methane gas. Scientistsestimate that this methane store amounts to about twicethat of the recoverable gas, oil, and coal deposits on theentire planet. As such, it represents a tremendous poten-tial energy resource. Furthermore, the trapped gas, whichexists in crystalline form combined with water in theform of “methane hydrates,” holds other importance.Formation and decomposition of methane hydrates canalter the sediment’s stability, with potentially devastatingeffects. Many scientists think that methane hydrateshave played a role in generating some of the hugelandslides that occur under the ocean next to continents.

Some scientists, therefore, suggest that building oilplatforms on top of methane hydrate pockets is risky.Pumping hydrocarbons generates heat, and raising thetemperature melts methane hydrates, which weakenssediments and may trigger submarine landslides. Inaddition to dramatic effects on the ocean (and under-water oil rigs), such bursts might release huge amountsof methane into the ocean and perhaps the atmosphereas well. Indeed, scientists propose that increases intemperature might provoke a cascade of global warming.Indeed, even more methane is trapped, frozen, in hugepeat deposits of the Canadian and Russian Arctic. As theEarth heats up, methane—itself a potent greenhouse gas—vaporizes, escapes, and pushes temperatures furtherupward. Events such as these may have exerted strongeffects on global climate over the Earth’s development.Despite the tremendous potential impact of microbiallyproduced methane hydrates on human welfare and theenvironment, many important questions remain aboutits generation and dissipation, as well as its possible use as an energy source and its hazardous potential.

While many geobiological phenomena result fromnatural processes, others are by-products of industrial-ized civilization. For example, mining operations releasetoxic heavy metals, such as chromium, copper, zinc,arsenic, lead, and mercury, into local and regionalenvironments. Such operations bring ore to the Earth’ssurface and vastly increase the surface area of these


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minerals through crushing and milling. These processesexpose them to air and make them react more quicklywith water, thus increasing the acidity of the environ-ment and releasing toxic heavy metals into naturalbodies of water, soil, and the atmosphere.

These examples hint at the wide extent of interactiveeffects that occur at the intersection of the biosphereand the geosphere. If we uncover and understand thefull range of these possibilities, we will stand in aposition to use these natural processes to benefithumankind and, possibly, to rejuvenate the planet.

There are many potential practical and intellectualbenefits that might arise from the study of geobiology,including:

n Cleaning up oil spills and other environmentalhazards with microbes.

n Producing useful substances in easier and cleanerways, as compared with conventional engineeringapproaches.

n Providing information about why water supplies in many areas are dwindling. It would be useful toknow what roles microbes are playing in such events,and to discern whether they can be used as indicatorsof water sources and quality.

n Understanding the conditions that result in the dissolution and precipitation of economically important minerals.

n Protecting from various sorts of corrosion in a cost-effective manner by modifying or exploitingmicrobial communities. Both biological and non-biological phenomena erode and otherwise damagebuildings, roads, sewer systems, ships, and even sculptures.

n Harnessing microbes to detoxify industriallyproduced poisons, such as PCBs, that contaminatewater, soil, and other parts of the environment.Scientists already know that some microorganisms are capable of converting the offending chemicalgroups in these compounds into harmless products.However, we don’t yet know how best to harnessthese capabilities.

n The ability to recycle, which is a fundamental activity of microbes, should be utilized to increase the efficiency and specificity of recycling human-generated waste materials.

n Understanding how particular geobiologicalprocesses may create environments that support orsuppress the growth of emerging, and potentiallydangerous, microbes.

n Cleaning up toxic mine tailing leachates. Whiledaunting, such situations might offer a positive side.For example, the right methodologies—perhaps onesthat include special talents of particular microbes—might recover valuable metals from such cleanups.We need to develop methodologies to turn environ-mental disasters into economic prosperity.

n Understanding better how microbes are involved inenergy production.

n Understanding Earth’s history, including the originof life and the evolution of global biogeochemicalcycles.

n A greater appreciation for how life survives at nutritional, chemical, and physical extremes.

n Improving our knowledge of how cell-to-cell commu-nications and microbial community interactions cancontrol global biogeochemical processes.

Finally, we look beyond Earth. The finding of life onanother planet would represent the greatest scientific andultimately societal event of this century, and perhaps of alltime. The discoveries of microbes that thrive in extremeenvironments has expanded notions about how life beganon Earth and strengthened the possibility that similarmicrobes may live on other planets.

Seizing the moment Many scientists from a broad range of disciplines arethinking expansively about geobiology and its potential.Geochemistry, geohydrology, oceanography, astrobiology,microbiology, environmental studies, ecology, molecularbiology, genomics, paleobiology, and mineralogy repre-sent only some of the specialties falling under the broadcanopy of geobiology. This tremendous span begins toprovide a glimpse at the vast field and implications ofgeobiology. Certainly this discipline is greater than thesum of its parts.

Fruitful new endeavors and groundbreaking research willlikely lead and challenge those from these overlappingdisciplines. Much research in the basic sciences is movingtoward interdisciplinary research, and the field of geobi-ology is poised to lead this movement and set precedentsfor the future of collaborative research that bridgesdiverse specialties. Compelling questions are alreadylaunching researchers in fruitful directions, with enthu-siasm fueling the progress. The appropriate recognitionand support for this growing field promise to provide amodel for other emerging, interdisciplinary scientificdisciplines at the same time that it addresses key environ-mental and basic science topics that have huge impacts onsocial and economic issues.


Microorganisms have lived at the Earth’s surface formost (about 85%) of Earth’s age, and the importance ofmicrobial activity in shaping the Earth’s oceans andatmospheres has long been accepted. Only recently,however, have geologists, geohydrologists, andgeochemists recognized the broad consequences ofmicrobial activity. Microbes impact and are impacted byvirtually all geochemical processes that occur at theEarth’s surface, as well as deep within its subsurface.

Our ignorance represents possible hazards and lostopportunities. The economic potential of understandinghow microorganisms function in the geosphere istremendous. Although this area is receiving increasedattention, it remains largely untapped. Currently hiddenmetabolic processes might present us with new optionsfor transforming one substance into another or forutilizing other useful activities. In order to harness thepotential of microbes, we must better understand theirnatural capabilities. Furthermore, major unknownmetabolic activities could be exerting huge effects on thegeochemistry of the planet. If these unknownphenomena touch upon geobiological systems that

humans are trying to cope with, our lack of under-standing might foil our efforts; perhaps we are notincorporating all of the relevant considerations andcomponents into our plans.

Technological and scientific advances in the last decadehave fostered interdisciplinary alliances between theearth and life sciences and have allowed scientists toprobe geobiological interactions in ways that previouslywere not possible. For example, now scientists can detecttrace elements that previously would have goneunnoticed and observe microbes that cannot be grown inthe lab in their natural habitats. Progress in light andelectron microscopy is permitting quantitative studies ofmicrobial interactions at the community level inbiofilms and with mineral surfaces at the atomic scale.Breakthroughs in molecular biology and, in particular,revelations about the genomic content of many differentorganisms have spurred an explosion of informationabout the capabilities of living things. For the most part,high-temperature geology explains what we know aboutthe cycling of rocks and minerals, because, at hightemperatures, the rocks melt. At low temperaturescharacteristic of the surface and near subsurface, wheregeological processes are slow, life intervenes and speedsup the reactions to its own benefit.

As such techniques improve, the complexity andrichness of the geobiological world are coming into focuson the canvas of the globe. Fuzzy ideas are sharpening asscientists exploit better tools and develop newhypotheses. These insights are revealing ever deeper tiesbetween the biological and geological worlds. Themethodological improvements have allowed scientists tomore accurately assess the geochemical and ecologicalconsequences of perturbations to the environmentsparked by both natural biological processes and thetechnological activities of human beings.

This progress represents some of the first steps towardunderstanding how living things and their environ-ments influence each other and promises to help rectifymany environmental problems. However, manychallenges remain.

Although analysis of genetic sequences has revealed theexistence of microorganisms that have not previouslybeen grown in the laboratory, this information doesn’testablish what biochemical tricks these microbes canperform or what environmental conditions trigger thesefeats. Furthermore, although we now know that scien-tists grossly underestimated the extent of microbialdiversity, most microbes and their functions still havenot been identified. For example, while decades ofintense study have provided information about howliving things—especially microorganisms—interact withorganic compounds in the environment, a view intointeractions with inorganic compounds is only nowbeginning to crack open.

Other tasks loom large as well. For example, scientistsneed tools and research programs that more preciselydocument geobiological processes as they occur.Improvements in detection methods and monitoringtools are needed. In this area, particular problems arise:how to study extremely slow-growing or dormant life,for example, and how to recognize and understand themeaning of subtle microbial signatures in rocks.

Countless other examples exist of questions that can only be answered by knowledge and technologycurrently unavailable. In order to exploit the great potential of geobiology, new methodologies and intellec-tual frameworks that address all such issues must bedeveloped. To achieve this goal, scientists and engineersmight need to exploit and adapt technologies from other disciplines than their own.

Current Status


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Challenges and Opportunities

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Scientists from different disciplines are forging researchalliances to delve into the growing field of geobiology,but education in this area is insufficient. Geologists arenot generally trained in biology and vice versa. In isola-tion, these fields can be expected to mature in their owndirections, but they will not merge on their own. Now isthe time to bring them together. The discipline of geobi-ology needs the concerted efforts of the scientific andinformed lay communities to identify the importantproblems and knowledge gaps and then to devise novelapproaches to resolve them. Results from geobiologicalstudies will positively impact global change, illuminatethe deep biosphere, demystify astrobiology, unravel thecomplexities of extreme environments, and elucidate theprocesses of evolution. This will be reflected in new jobopportunities at all levels. Thus, the field needs to recruitand prepare students to meet this demand.

With a growing appreciation for the magnitude of geo-biological effects and improved technology, scientists in awide variety of disciplines are poised to achieve tremen-dous gains in this area. Available funds, however, currentlyare too limited to support the kinds of interdisciplinaryresearch programs that need to be launched and sustained.Future investigations should not only delve deeper intoquestions that have already been explored, but shouldexpand into areas that have experienced relatively lessexamination. Our biases have directed us more strongly insome directions than others. For example, we have interro-gated outer space more diligently than the sea floor ordeep beneath the Earth’s surface.

We stand at a unique time in history. Humans areimpacting the environment in significant negative ways,but our technological and cognitive capabilities allow usto alter conditions for the future. At the moment, a hugescientific chasm separates us from a full understandingof our planet and its deep reservoirs of biochemical andgeobiological reactions, which may affect Earth in waysthat we don’t currently comprehend and can’t predict.This wide zone of ignorance compels exploration to thenext frontier of knowledge.

The field of geobiology faces many challenges and opportunities as it attempts to address key fundamentalquestions. Of course, these challenges represent researchopportunities that will help to set the research agenda forthis new field. Some of the questions discussed at thecolloquium are:

n What role do living things play in the cycling of“geological” substances? There is increasing recognitionthat microorganisms are important agents in planetaryscale processes such as carbon cycling (which relates to a number of phenomena that include climatechange and food production), oxygen levels in theatmosphere, and weathering and precipitation of rocksand minerals. Yet we know relatively little about themicrobial mechanisms involved, the rates and extentsof these processes on a global scale, and howhumankind may be irreversibly altering them.

n How do reactions on surfaces and at interfacescontribute to geobiological events? Interfaces occuron both small and large scales. Cell surfaces, forexample, are very reactive and can spur minerals to precipitate and dissolve. Some microbial communi-ties exist as structured “biofilms,” which are highlyorganized communities with different physical,chemical, and biological characteristics in differentregions of their matrices. Transition zones on largerscales include, for example, the areas between freshwater and saltwater. These regions typicallynurture a wide array of life forms. This abundance of life reflects a healthy ecosystem and can serve as a source of novel biological products and capabili-ties. Details of events at all of these (and other)natural boundaries remain largely unknown anduntapped, both practically and conceptually.

There were also questions about the origins and evolu-tion of life on Earth. Many of these questions may beasked about the origins and evolution of life on otherplanets and the conditions that could support lifeelsewhere in the universe.

n What were the physical conditions on Earth beforelife arose? (Was there water? How hot was it?)

n How deeply entwined were the bio- and geosphereson the primitive Earth and has this dependencealtered over time?

n How did life begin? From where did early life collectchemical energy? (The atmosphere? Extraterrestrialsources?) By what biochemical means did the originalinhabitants extract energy? Where on today’s earthcan we find proxies for early metabolism?

n How and when did the processes of photosynthesisand respiration evolve? What drove the change tooxygen-based respiratory energy extraction from food?

n Did distinctly more complex life forms originate dueto environmental, climate, and nutrient pressures orfrom purely random evolution? How did the rise ofthese organisms impact the simpler creatures thathad existed until that time? How did these organ-isms impact their surroundings and how were thesechanges preserved in the geological record?

n Can we correlate major climatic effects with rapidevolutionary branching? What evidence would we seek?

n What was the impact of increasing or decreasingtemperature events on the evolution of microbialcommunities?

n Did the types and populations of living thingsincrease dramatically when the atmosphere firstacquired significant amounts of oxygen?

n How do microbes respond to environmental change,how rapidly do they respond, and how do thesechanges affect geochemistry?


Another set of questions was raised about life in deepsubsurface regions of the Earth’s crust where, untilrecently, life was not thought to exist.

n What is the extent of the biosphere that exists deepbelow the Earth’s surface? When and how did itevolve? How much biomass lies there?

n From where do organisms that are trapped insiderocks or in sediments below the Earth’s surfacederive their energy? Do these organisms employ veryslow metabolic rates and how important is thephenomenon of slow metabolism? How long dothese microbes live and for what do they use energyin unknown ways to maintain their cells? What kindof selective forces act on microbes under the severestarvation conditions of the deep subsurface?

n How do subsurface microbes affect rock weathering?Are subsurface processes similar to those involved in soil formation? How do subsurface microbescompare to the soil microbes that contribute to that process?

Cataloging the capabilities of living thingsWe have only begun to chart the diversity and potentialof the Earth’s most abundant and diverse biologicalresources, the microorganisms. They compose more thanhalf of all living matter on Earth, yet we have identifiedless than one percent of all the predicted microbialspecies. In order to tap natural communities foreconomic or social benefit, we will need to monitor anddevelop new means to more deeply probe the naturalactivities of microorganisms. Such an achievementshould help establish links between processes associatedwith life and its inanimate surroundings.

The genetic content—or genome—of an organism can beused to predict its biochemical and physiological poten-tials, or lack thereof. For this reason, the genomicsequence provides a wealth of information about ways inwhich a living creature can influence the planet.Technological advances in this area have led to a situa-tion in which the amount of DNA sequence informationgreatly exceeds our understanding of its meaning. Majorwork is needed to connect physiological functions withthe ever-accumulating masses of sequence data.

Scientists must find new ways to capture the potential ofspecies diversity in genetic terms. To this end, they mustdevelop new means for uncovering biological processesand continue to decipher the genetic sequences thatdictate these behaviors. Reaching this goal requiresadvances in laboratory and computational technologyassociated with sequence and functional analysis. Thisrequirement calls for interdisciplinary research and tools.For example, computer scientists must grasp the relevantbiological questions to create software that exploits thesequence and functional data, and biologists must learn tonavigate new software that is developed. Biologists mustreach beyond traditional ground and extend ways tostudy, for example, organisms that don’t grow underconventional laboratory conditions. Geologists and biolo-gists must collaborate in ventures that explore the impactof particular microbes on the environment and vice versa.

Finally, many microbiological scientists study physiology,but fail to put their findings in the context of the evolu-tion of the planet. The feedback between Earth’s historyand microbial metabolism is important to understandingthe development of both life and the environment, howorganisms are currently keeping the Earth’s systems inbalance, and how to anticipate—and even impact—futureevents and trends.

These challenges can be overcome in numerous ways.Strong support should encourage new genomics efforts,particularly those aimed at linking biogeologicalfunction with sequence data. Funding agencies andprofessional organizations should encourage collabora-tions between genomics experts and others from diverseearth science fields. For example, projects that exploregeobiological questions in novel ways by crossingconventional specialty lines or by employing unconven-tional methods to answer geobiological questions shouldbe fostered.

Geomicrobiologists should be encouraged to movebeyond descriptive surveys and move toward moremechanistic understanding of geobiological phenomena.Special emphasis should be put on efforts to culturenovel microbes so that their biogeochemical functionscan be investigated. In this regard, geochemists shouldcollaborate with microbiologists in elucidating geochem-ical reactions that microbes might be employing.

Analytic techniques Despite decades of study, basic information about funda-mental biological and geological processes is missing. Forexample, while scientists realize that some microbes canpersist for extended periods of time, many mechanisms oflong-term survival remain mysterious. No one knowswhether or how organisms endure the apparent absenceof an energy source or whether apparently entombedmicrobes gain energy by very slow metabolism of a sourcethat is not readily apparent. Hydrogen gas can be a majorenergy source and perhaps some long-lived organisms are

Key Issues and Potential Solutions


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exploiting this substance for energy—yet the mechanismsof hydrogen gas production and distribution in geologicalsamples remain murky.

The ecological and geological importance of such “slow”metabolism remains similarly obscure. Most microbiolo-gists are trained to conduct experiments with rapidlygrowing cells in the laboratory or even in the field overperiods of hours or months or years; conventional scien-tific grants fund 3- to 5-year investigations. Studyingmicrobes that live at a very slow pace will be essential forunderstanding geobiological processes, the microbes thatcatalyze them, and the function of environments inwhich they are important, such as the deep subsurface.The environmental influence of such slow-living organ-isms and their associated biochemical activities may bevery significant over long periods of time, but onlybecome apparent after decades or longer. Only by long-term studies will we determine how gradual changes inthe local environment may lead to the gain of an ecolog-ical advantage or how to identify the potential energysources in an environment and discern how the energyavailable is used or to discover whether the residentmicrobes actually can evolve under starvation conditions.

The hydrogen example above illustrates a generalprinciple that affects many domains of geobiologicalstudy: scientists don’t have reliable ways to measuremany critical processes that they would like to measure.Beyond quantification, there is an urgent need todevelop better techniques for detecting specificprocesses and determining how they are occurring.

Microbes themselves may serve as environmental sensors.For example, some organisms respond in predictable waysto particular chemical or physical conditions; manybacteria move toward nutrients and away from poisons.Microbes possess sophisticated systems for detecting andresponding to chemicals in the environment. Withenough ingenuity and application of new molecular andanalytical microscopic techniques that are available today,we should be able to learn their secrets. By understanding

and exploiting such microbial sensing phenomena, we canuse microbiology to tell us about geochemistry.

The field also needs to develop sensors that can bedeployed and used remotely to make environmentalmeasurements on a real-time or near-real-time basis inareas of the planet that have been understudied or arerelatively inaccessible. Some programs aimed at devel-oping such tools exist, but much more development inthis area is needed.

Observation on small and large physical scalesIn order to document the interplay between organismsand their surroundings, scientists must measure chemicalreactions and products on spatial scales that range fromdistances between molecules to those between mountainranges. Tools exist for accomplishing this task undersome circumstances, but not all, and for some purposes,but not others.

Analyses of individual microbial cells can identify organ-isms and the chemicals that they are consuming andproducing. Furthermore, by taking a small step backwardfrom single cells and looking at their neighbors and theirimmediate surroundings, scientists can also examine theconsequences of microbial processes as reflected in thelocal microenvironment. Bulk measurements provideonly averages over large volumes and many cells,however, while the real action happens at the level of theindividual microbial cell or small groups of microbialcells. Sometimes, for instance, two or more specificorganisms in close physical association must collaborateto accomplish a particular biogeochemical transforma-tion. The details of such processes can be measured onlyat the level of individual cells or small groups of cells.The problem is similar to trying to understand the basicmechanisms of forest ecology using only satellitepictures without examining the individual trees orgroups of trees. The tools to address these problems ofscale are only now coming on line.

Methods for analyzing environmental samples at thenano- or microscale include conventional, fluorescence,and laser scanning light microscopy; ion microprobeanalysis; scanning probe microscopy; scanning and/ortransmission electron microscopy; electron spectroscopicimaging and energy dispersive X-ray spectroscopy;electron energy loss spectroscopy; selected area electrondiffraction; and X-ray imaging using synchrotron radia-tion. These tools serve as probes and chemical analyzersof the microscopic world, providing detailed biologicaland geological information on the scale of microns tonanometers. These techniques need to be improved andexpanded in order to conduct these “single-cell” experi-ments because their capabilities are currently limited toonly a very few dedicated facilities and because of instru-mental limitations. Many promising nano- andmicroscale techniques are not yet well developed. Theyare still clumsy and inefficient. Furthermore, they gener-ally employ large expensive instruments that cannotroutinely be used in the field.

While many of these tools allow scientists to outlinepieces of the geobiological puzzle, many pieces remainhazy. Sensors are needed that can measure a broaderarray of chemicals and other microenvironmentalfactors—such as pH, temperature, and light—central tothe interplay between life and non-living matter.Development of such methodologies faces multiplechallenges, such as detecting and quantifying the targetfactors in natural environments, where other conditions(the presence of minerals, for example) can interferewith measurements. Furthermore, key geobiologicalprocesses frequently occur at hard-to-reach locations—within sediments and rocks or deep in the ocean, forexample. New technologies are needed that permit three-dimensional detection and mapping of microbes,minerals, chemical compounds, and their associatedprocesses in all locations of interest.

In addition, scientists must extend their insights gainedfrom such Lilliputian observations and extractmeaningful information to be applied at much larger


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scales. Equally important as concentrations of a partic-ular compound around an individual microbe are thelevels of its products in the environment. Indeed somebantam scale processes—greenhouse gas formation anddestruction by microbes, for example—can impact theentire planet. Global warming almost certainly results inlarge part from gases that are controlled by microbiolog-ical activities. In addition to utilizing microscopy,scientists must collect tools and perspectives that allowthem to integrate the effects of the microscale processeson a global scale. They must expand the repertoire ofavailable methods and develop tools that integrate obser-vations from very small or very large scales.

Observation over long periods of timeTo construct an accurate depiction of how our planetevolved, we must measure geobiological interactionsthroughout Earth’s history. Scientists must find ways toidentify what types of metabolism were present indifferent time periods, how populations swelled anddwindled, and why. Geobiologists are particularly inter-ested in cataloguing changes in life forms as they relateto alterations in the environmental character of theEarth. Most species that have ever lived on Earth are nowextinct. The geologic record provides the only windowinto the broad physiological variation that evolution hasproduced. Buried organic matter, rocks, fossils, andtrapped gases (which can reveal what ancient organismsate and breathed) provide the best record of ancientbiological activities.

Fossils also provide the only direct avenue for under-standing the environmental conditions present at timesof major biological innovation and mass extinction. Thematerial that holds the remains of an organism providesinformation about the environment at the time thatcreature died. Because rocks reveal their age by theirchemical composition, any biological material that getspreserved in them can also be dated.

But imprints of shelled or otherwise hard-bodiedcreatures deposited in rocks are just one kind of fossiland provide only a partial record of former life. Soft-bodied organisms, including microbes, leave more subtletraces, and scientists have a great interest in uncoveringthese clues. Just as certain shapes and structures revealwhat types of animals were alive at particular times andunder particular conditions, the presence of certainmolecules can belie the existence of living creatures andprovide information about their properties. For example,some chemicals—e.g., isoprenoids or phytanyl-basedlipids—in ancient sediments might reveal how cellmembranes were constructed, while others provide cluesabout other biological characteristics and processes thatoccurred as life evolved. Further investigation intomicropaleontology, in conjunction with studies ofpresent day microbe-mineral interactions, will provideadditional biogeochemical signatures that can be usedfor detecting which types of microbial activity wereimportant, not only in paleoenvironments on ancientEarth, but in other poorly understood and difficult tosample modern environments.

Similarly, such molecular and chemical fingerprints, orbiomarkers, should allow scientists to infer details aboutthe environmental conditions at the time a particularorganism lived. The development of new and more sensi-tive methods that detect fingerprints of life andcorresponding geological processes are needed to probethe environments where life flourished and flounderedand to discern how this was changed by the chemicaland physical surroundings. Furthermore, scientists needthese improved analytical tools to reveal high-resolutionabsolute and relative ages for events and species thatextend back through the last three billion years.

Current analytical tools do not adequately lookbackward, which limits scientists’ ability to look forward.Biologists would like to uncover diagnostic microbialsignatures in rocks and to enhance their ability toexamine microbes and biogeochemical events on a tinyscale. Improving these methodologies will enhance our

understanding of the past and our ability to predict thefuture. Furthermore, an improved catalog of life’s finger-prints will enhance our ability to detect life if it existselsewhere in the universe.

Searching for extraterrestrial lifeTo ensure that we can detect life on other planets if itexists, we must hone our ability to uncover its hallmarkshere on Earth. But the search for extraterrestrial lifemust incorporate the idea that living creatures on otherplanets may be fabricated and look and act differentlyfrom those on Earth. It would be foolish to restrict ourdefinitions of life to Earth-based constraints. Scientistsneed to keep their minds open and entertain the ideathat, for example, the chemical basis of life could bedifferent on other planets. Studies of geobiology on thisplanet should include consideration of the fundamentalconstraints on life here that could help us define orlook for it elsewhere. Investigations at the extremes willaid these endeavors by cataloging the permutations oflife in a wide a variety of environments that we canprobe here on Earth.

Informatics toolsTo advance the field of geobiology, scientists require anunderstanding of a wide array of processes in a largenumber of organisms on tremendous scales of space andtime. Progress depends on the development, manipula-tion, and integration of huge data sets. Computationaltools must allow researchers to combine informationfrom a variety of sources. These include databases thatcan be used to map microbes, minerals, geological forma-tions, and temperatures to particular locations on theplanet, to compare genomic DNA sequences, and tocompile information about the cycling of particularchemical elements, for example. This informaticstechnology also needs to be powerful enough and userfriendly enough to assist scientists as they explore whatkind of life existed where and under what conditionsand time periods. It should thus help researchers


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document the fossil record, provide tools for analyzingthese data, and link this information to other relevantbiological and geological databases. New informaticstechnology should facilitate recognition of and helpestablish connections, trends, and patterns that mightotherwise go unnoticed. Furthermore, it should fuelresearchers’ findings by raising queries and providinganswers that would be impossible without substantialcomputing power.

Scientists are rapidly uncovering genetic secrets of largenumbers of organisms by sequencing their genomes.Comparisons of these sequences can highlight bothshared and unique features of microbes, which canreveal clues about their physiological capabilities. DNAsequences present in all life forms, for example, pointtoward basic functions, while those carried only byorganisms that convert one obscure compound intoanother or that squeeze nutrients out of rocks pointtoward specific biochemical talents and help link DNAsequence with function. Although seemingly simple, thetask can require enormous computing power because ofthe huge number of genes and organisms being studied.The scientific community requires new and improvedinformatics tools to handle even this type of seeminglystraightforward analysis.

In addition, researchers have recently set their sights onmuch more ambitious goals. Some are collecting not onlysequences of individual organisms, but also sets ofsequences that represent whole microbial communitiesfrom particular environments. By considering the addedcomplexity of comparing entire communities, it is eveneasier to appreciate the tremendous need for powerfulcomputing tools.

Information from sequencing efforts is a high-profilepiece of the geobiology puzzle. In order to assemble thefull picture, scientists would like to overlay physical andchemical data on the genomic sequencing data. In animaginary example, they would construct maps thatshowed the types of organisms that inhabit specific areasof the globe and that allowed one to easily “see” the corre-sponding environments. In addition, there would be atool that showed critical information about the contentof solids, liquids, and gases in a particular location, andthere would be data about, for example, specificchemical constituents, temperature, and pressure.Furthermore, the fantasy computer tools would map thisinformation over time so scientists could examine howthe various parameters are changing, and thus develophypotheses about how components in complex geobio-logical webs are influencing each other. They could alsolearn about how species, or even specific geneticsequence variations, correlate with changes in tempera-ture, chemicals in the environment, and so forth.

In order to achieve such imaginative goals, investigatorsneed new ways to integrate the relevant data. This willrequire manipulating and combining huge data sets fromdifferent sources. To accomplish this task, new and morepowerful informatics tools need to be forged and honedas more information and more questions arise.

Finally, the entire scientific community will benefitwhen these data and tools are available to everyone andwhen the tools are easily usable by scientists with avariety of backgrounds and training. Currently, there isno central site that serves as a hub and storehouse forgeobiological information. This situation can lead toinefficiency and duplication of efforts. Care must also betaken to set up systems by which the data in thedatabases are easily accessed and manipulated bymembers of all sections of the geobiology community.

Culturing techniquesThe ability to grow microorganisms in the laboratoryis the only way to directly test hypotheses about theirphysiological and biochemical potential. Currently, it isestimated that greater than 99 % of all microbes cannotbe cultivated in the laboratory. This number must bereduced. Because the diversity of microbes that areimportant in geobiological processes is enormous, geobi-ologists can make a big difference in solving thisproblem. While techniques for identifying microorgan-isms and their biological capabilities in the absence ofpure cultures (such as deciphering and comparing theirgenetic sequence) are blossoming, geobiologists will alsoneed to make special efforts to grow specific microbes inthe laboratory.

Dedicated funding is needed to develop new culturingtechniques. Scientists need to make significant headway onexpanding culture methods to include more organisms. Ofparticular interest would be culture methods for studyinginteractive groups, or consortia (not just individualmicrobes), under conditions that mimic the naturalenvironment as closely as possible. This goal presents


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special challenges because microbial communities consistof many different microbes, each with a different functionin the community. The challenges are that each individualmay require different conditions for growth in the labora-tory and that, in the consortium, the requirements may bedifferent from those for any individual microbe.

Sampling technologiesResearchers require new ways to sample organisms andtheir surroundings from the environment to discoverand monitor biogeochemical processes. These challengesare particularly acute in remote or extreme environ-ments, where life and its associated processes have notbeen adequately explored or mapped. New technologiesare required that both increase access to these areas andaddress combined biological and geological objectives.When developing such methodologies, scientists andengineers face unique problems.

Pulling up material for geobiological studies from a lake orthe ocean or beneath the Earth’s surface requires care toavoid contamination by microbes and chemicalcompounds on the surface and to detect such adulterationif it occurs. Sampling strategies have been worked out formost of these near-surface environments, althoughimprovements are still required. Improved methods arealso required for sampling and analyzing extreme andremote locations (such as deep sea hydrothermal vents orthe subsurface of Mars) to identify organisms and geobio-logical processes. Analytical devices that operate insidedeep boreholes, for example, will facilitate subsurfacemonitoring of geobiological processes. However, thepeculiarities of some microbes may not allow them tohold up well under conditions at Earth’s surface. Microbesthat have evolved at high temperatures and pressure orunder other special environmental conditions might dieon their journey to the environment that we considernormal. Similarly, gases that are maintained under highpressure (and the microbes that metabolize them) mightescape (or die) unless transferred under appropriatepressurized conditions.

Another major challenge is the environmental relevanceof a particular geobiological process. Just because aprocess is observed does not mean it is a major process inthe environment, or that it operates to any extent in thenatural setting. Geobiologists must devise strategies todetermine whether the geobiological processes theyobserve are occurring in the same way under observationas they are in their undisturbed natural contexts.

The examples given above illustrate just a few of thechallenges posed by remote sampling endeavors forgeobiological research. Special technologies will berequired to probe other planets for their geobiologicalpotential. We need small and easily portable machinesthat require minimal maintenance. Furthermore, devicesfor sampling other planets must not only collect samples,but also must analyze them on the spot, e.g., in situ. Insome cases, existing survey technology may be adaptablefor geobiological surveys. For example, radar thatpenetrates the ground can detect subterranean liquidwater on Earth and will be useful for surveying otherplanets remotely for water from satellites. Likewise,remote drilling methods must be developed to accessenvironments and retrieve geobiological samples fromunderneath the surface of other planets.

A major issue for geobiologists who study extraterrestrialsites is whether or not life exists there, and, if it does,what is it like, and if it does not, why doesn’t it? Toanswer these questions, scientists need to figure out howthey will identify such life if it is present. This problemconsists partly of finding potential life forms and partlyof recognizing such life forms if they are present. If aspaceship makes contact with entities that obviously eat,move, breathe, and reproduce, we will know that theyare living aliens. But more likely, life on other planets willbe in the form of microbes, which are by definitioninvisible to the unaided eye and are most easily observedby their indirect effects and signatures they leave in theirenvironment. Controversy is currently raging aboutwhat exactly constitutes life’s molecular signatures.Improved methods are required for distinguishing

products of purely geochemical processes from thosewith strictly biological origins. In addition to defininglife’s signatures, we also need methods to detect thediagnostic signs of life at distant locations.

Model systemsWhile the major emphasis will be on understandinggeobiological processes in natural environments, labora-tory experiments designed to isolate and test the effectsof individual physical, chemical, and biologicalphenomena will continue to play an important role ingeobiological research programs. This is the only way toprobe specific hypotheses about the interplay betweenlife and matter. To extend these types of investigations,new technologies are needed for accurate laboratorysimulation of environmental conditions. Such toolsshould also simulate conditions thought to exist in theearly era of life on Earth, which will enable scientists totest scenarios of how life began.

Scientists would like to test possible pathways that led tothe chemistry of life. The big question is how pre-bioticchemistry gave rise to reproducing organisms. A bigexperimental challenge is inherent to these studies. Atthis point in the planet’s development, the Earth is sosteeped in life that it is very difficult to subtract biolog-ical products. This situation poses difficulties insimulating conditions of a much younger Earth. Whilevery simple renditions might be possible, others are moredifficult. For example, some scientists propose thatcertain clays may have provided the physical structureon which pre-biotic chemicals met and reacted. But atthis point, clays interact so strongly with existing naturalbiomolecules that they cannot be easily cleansed of theirorganic matter for accurate pre-biotic experimentation.


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Field studiesWhile model systems allow scientists to perform controlled experiments that probe specific questions, field studies are necessary to study the natural environ-ment. Such endeavors reveal how different communitiesinteract with each other and their environments in the real world. Studying complex ecosystems can elucidateactivities that would remain obscure by analyzingindividual organisms or sets of interactions in the labora-tory. For example, microbial consortia collaborate toperform tasks and impact the environment in ways thatsingle microbes do not.

At present, tools to accomplish this goal are lacking. Inorder to describe natural communities and habitats indetail, scientists face formidable challenges. Organismsand chemicals may be present at concentrations so lowthat they are difficult to detect, and identifyingindividual molecules or microbial species can be trickywhen they are immersed in a soup with others.Furthermore, such systems are not static; behaviors andchemical reactions can change over minutes, days, orseasons. Because the natural environment contains a richarray of chemicals and life, in situ analytic techniquesmust be honed so that they measure the entity ofinterest—at the scale of interest—without interference.Scientists need improved micro-sensors that can detectsmall amounts of chemicals over small spatial scales.Such sensors will allow for determination of processesthat play key roles in microbe-microbe and microbe-mineral interactions. Furthermore, these devices mustoperate under a wide variety of conditions, including athard-to-reach or harsh locations deep beneath the Earth’ssurface or at the bottom of the ocean.

Such tools must also be able to sample on a micro-scaleand map findings relative to each other. Key geobiolog-ical processes frequently occur unevenly withinsediments and rocks, for example. Tools that documentthe presence of microbes and their associated activitiesand geological consequences in three dimensions, on finescale but over broad areas, would be extremely valuable.

The choice of field sites is also important. Establishedfield sites are valuable because they allow scientists toconduct long-term studies and to exploit documentedgeobiological history. However, colloquium participantsalso stressed the importance of branching out andexploring new areas and types of environments.

Ethical issuesThe pursuit of geobiological studies requires ethical, aswell as technological and theoretical, consideration. Somestudies may perturb natural populations or processes,which could result in undesired consequences. It is diffi-cult to predict what problems might arise from, forexample, transporting samples from a relativelysequestered environment to another, more exposed one.For this reason, effort should be directed toward devel-oping guidelines for handling material from remotesampling sites, such as the deep underground zones thathave not been exposed to the Earth’s surface. Similarly,we must entertain the possibility that we could contami-nate other planets with life from Earth as we explorethem; along the same lines, we run a risk of introducingforeign life forms from other planets when we returnthem to Earth. Such possibilities must be consideredwhen developing geobiological research programs andnew methodologies. Scientists, lawmakers, and the publicshould engage in discussions about the stewardship ofthe natural universe and decide how best to care for itduring these investigations.

Education, personnel, and trainingScientists will require diverse backgrounds to traversethe traditionally non-overlapping fields that comprisethe new discipline of geobiology. In addition to theconventional biological and geological university courses,new cross-disciplinary courses in geobiology must bedeveloped. This will be best achieved by fosteringcollaborations between teaching faculty, as well asresearch faculty and students. Departmental andinstitutional leaders must make special efforts to help

traditional geology and biology faculties work togetherand to create a new geobiology vocabulary that theyand their students can agree on. Geobiology trainingprograms might branch out to include, for example,in-depth exposure to mathematics, numerical modeling,and computational techniques. In addition to the needfor people with strong mathematical and quantitativeskills, there is also a need for improvement of observa-tional skills and a return to the approaches of traditionalnaturalists. Both quantitative and qualitative approachesare necessary. The new field will benefit from cross-trained specialists with background and experience inboth areas.

To introduce quality control and uniformity to this field,recommendations about what might ideally constitutedegree requirements should be developed for universi-ties. Furthermore, strong recruitment efforts at theundergraduate and graduate levels will stimulate interestamong young scientists. Currently, jobs in this fieldoutnumber applicants. This is true for both academiaand industry.

While educational programs will groom students andpostdoctoral fellows for full participation in thisemerging field, other efforts must be made to allowestablished investigators to reach across disciplines.Geobiology encompasses a variety of different fields andaddresses questions that span spatial and temporal scalesin nontraditional ways. Such interdisciplinary andunconventional science is not necessarily compatiblewith academic infrastructure, such as promotion andtenure of faculty, design of undergraduate and graduatedegree programs, and federal and state funding ofacademic institutions. Like other new and emergingdisciplines, this one requires special attention at all levelsof administration.

Efforts should be made to foster working collaborationsand establish a common language between fields soexperts from diverse specialties can communicate effec-tively to state and solve problems. Better integration is

needed between basic research scientists in relevant disci-plines and between scientists and engineers fordevelopment of appropriate conceptual and practicalstrategies to tackle problems in geobiology. Variousapproaches might build bridges between investigatorswho do not usually interact. Career opportunities andincentives, for example, might foster interdisciplinaryties, training opportunities, and education in geobiology.

While colloquium participants stressed the need forstrengthening the breadth of scientific training, somewere also concerned about the demise of microbiologistswith deep roots in microbial physiology. Strong supportis needed for robust research efforts aimed at under-standing the physiological and biochemical repertoire ofmicroorganisms. To this end, those with training inconventional microbiology will continue to play criticalroles. They should be encouraged to delve into researchquestions outside the traditional arenas of medical andindustrial microbiology and, as much as possible, to applytheir well-developed microbiological sciences to relevantgeobiological issues.

Professional societies are actively supporting geobiology.This is a positive trend, and they should be encouragedto continue fostering special educational programs,focused sessions at meetings, collaborations betweenmembers, and so on. International societies in particularshould continue and increase support for conferencesessions and other activities that nurture geobiology.More interdisciplinary journals might be useful. Toensure the field’s success, the lay public, as well as thescientific community, need to recognize geobiology as anidentifiable scientific discipline that promises practicalbenefits and insight into the basic processes that shape theenvironment and its life forms.

Colloquium participants suggested organizing anoutreach program to communicate the power andpromise of this field to the general public. Peopleinvolved in this project might, for example, pitch storyideas to media outlets or develop Internet resources thatconvey how biology and geology fit together.

Finally, education should start early. Young (K-12)students need to learn about the relationship betweenEarth and its inhabitants, especially with microbes.Environmental issues may particularly interest childrenand could be used to illustrate some of the general

concepts of geobiology. Furthermore, some of the basicquestions of geobiology—how living things and theenvironment influence each other and how lifeevolved—may well hold appeal for children and maypromote curiosity and interest in science in general.

Support for research and trainingIn order to tackle the challenges and realize the goalsdiscussed by colloquium participants, there is a strongneed for funding for educational, research, and techno-logical development. This support will ensureestablishment of programs that promote geobiologicaltraining and investigations at the graduate and postgrad-uate levels. Furthermore, it will attract and educate highschool and undergraduate students. Financial support isneeded for seminars, workshops, short courses, andconferences. Interdisciplinary grants that promote collab-orations between specialists in different fields will beespecially important to stimulate the field of geobiology,as would those directed toward development of newanalytical and computer tools. In short, while limitedfunding has supported some special, short-termprograms, more financing is needed to sustain long-termprojects, training, and vigorous development of the field.


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Specific Recommendations


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Specific Recommendationsn Foster development of geobiology at appropriate

institutions by providing support for innovative,cross-disciplinary teaching, research, and outreachprograms.

n Support and encourage basic research andengineering programs in geobiology, stressing the keyissues in this report.

n Establish more field laboratories for geobiologicalresearch and continue to support existing fieldlaboratories.

n Support laboratory studies of basic biologicalsciences, especially microbial diversity, physiology,and genomics, which represent the basic sciencebackbone of the field.

n Improve methods for defining and detectingchemical signatures and other biomarkers thatindicate the presence of past and present life.

n Support efforts to catalog the diversity microorgan-isms, including their biogeochemical capabilities andtheir geobiological importance.

n Establish and support centralized culture collectionsfor organisms important to the field.

n Encourage further exploration of how human beingsmight exploit the geobiological capabilities ofmicrobes for society’s benefit, such as in cleaning uppolluted areas or extracting valuable resources fromthe environment.

n Improve analytical tools for observation andmeasurements on small (microscopic) and large(planetary) physical scales and that operate atinaccessible sites remote from the Earth’s surface.

n Develop informatics systems and computertechnology infrastructure for:

• Easily accessible electronic databases to store geobiological information.

• Management and comparison of geobiological dataresources that range over wide scales of observationsand across vast stretches of time and space.

• Computational tools that can integrate geobiologicalinformation from genomics to global cycles ofthe elements.

n Support geobiology education at all levels:

• Develop systems to educate the general public as well as scientists about the potential benefits ofstudying geobiology. Organize an outreach system thatcommunicates the power and promise of this field.

• Establish a central repository for information aboutgeobiology on the World Wide Web.

• Introduce interdisciplinary issues on geobiology intoundergraduate level courses in biology and geology.Encourage programs that grant minor degrees in geobiology, with major degrees in a primary biologicalor geological discipline.

• Develop summer field courses that will spread interac-tions and communications through a broad audienceand enrich the experiences of graduate students,postdoctoral fellows, and principal investigators.Courses similar to the Woods Hole summer courseseries and Cold Spring Harbor courses represent goodmodels for this enterprise.

• Provide travel and research support for investigators to branch out into other areas for cross-training and to bring new expertise and insight into the field of geobiology.

• Organize national and international scientificmeetings in the field of geobiology.

• Foster cross-pollination among subdisciplines of geobiology and between geobiologists and engineers.

• Encourage continuing support for “classical” fields ofmicrobiology, physiology, taxonomy, and metabolicdiversity, while expanding their repertoires to includethe less conventional areas that crossover into earth science disciplines.


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Bibliography

GEOBIOLOGY - SENR Geobiology Report 2001.pdfIntroduction. This colloquium was organized to devise...

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