15CHAPTERISIGNIFICANCE,HISTORY,AND CHALLENGESOF ENVIRONMENTALMICROBIOLOGYTable 1.5 ContinuedSubject matter and contribution toDisciplineReferencesEnvironmental MicrobiologyFundamental reactions of aqueous inorganic andStummand Morgan,Aquatic chemistry1996:Millero,2001;organicchemistryandtheirquantificationbasedSchwarzenbach eton thermodynamics, equilibrium, and kineticsal.,2002GeochemistryChemical basis for rock-water interactionsAlbarede,2003;involving thermodynamics,mineral equilibria,Andrews,2004and solid-,liquid-,and vapor-phasereactionsSoil scienceBrady and Weil, 1999Study of the intrinsic properties of soils andexamination ofphysical,chemical,and bioticprocesses that lead to soil formation;the crucialroleofsoils inagricultureand ecosystemsLimnologyWetzel and Likens,Thestudyoffreshwaterecosystems,especiallylakes and streams2000;Wetzel,2001OceanographyThestudy of saltwater ecosystems,especiallySverdrup et al., 2003oceansHydrogeologyThe study of the physical flow and migration ofFetter,1994wateringeological systemsAnalytical chemistryFifield, 2000;Christian,Methodsandtechnologiesfordetecting,separating2003andidentifyingmolecularstructuresof organicand inorganiccompoundsCivil andPhysical, chemical, hydraulic, and biologicalRittmann and McCarty,environmentalprinciples applied to the quantitative design of2001;Tchobanoglousetal.,2002engineeringwater supply,wastewater,and other engineeringneedsEcologyIntegration of relationships between the biosphereRickleffs and Miller,and its inhabitants, with emphases on evolution,2000;Krebs,2001;trophicdynamics,and emergentpropertiesChapin et al.,2002EnvironmentalMultidisciplinary study of how the Earth functions,Miller,2004sciencewith emphasis on human influences on lifesupportsystemsmicrobial ecology (Figure 1.5).Both disciplines (spheres in Figure 1.5)seek to understand highly complexand underexplored systems.Each dis-cipline currently consists of a significantbody of facts and principles (greeninnerareasofspheresinFigure1.5),withexpandingzonesofresearch(pinkbands).Butthechancesarehighthatinformationawaitingdiscovery(blue areas)greatly exceeds currentknowledge.For example,nearly allcurrent informationaboutprokaryoticmicroorganismsisbaseduponmeas-urements performed on less than 6500 isolated species.These cultivatedspecies representapproximately0.1%of the total estimated diversity ofmicroorganism in the biosphere (see Sections 5.1-5.7).The exciting newdiscoveriesin environmental microbiology emerge by examining how
microbial ecology (Figure 1.5). Both disciplines (spheres in Figure 1.5) seek to understand highly complex and underexplored systems. Each discipline currently consists of a significant body of facts and principles (green inner areas of spheres in Figure 1.5), with expanding zones of research (pink bands). But the chances are high that information awaiting discovery (blue areas) greatly exceeds current knowledge. For example, nearly all current information about prokaryotic microorganisms is based upon measurements performed on less than 6500 isolated species. These cultivated species represent approximately 0.1% of the total estimated diversity of microorganism in the biosphere (see Sections 5.1–5.7). The exciting new discoveries in environmental microbiology emerge by examining how CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY 15 Fundamental reactions of aqueous inorganic and organic chemistry and their quantification based on thermodynamics, equilibrium, and kinetics Chemical basis for rock–water interactions involving thermodynamics, mineral equilibria, and solid-, liquid-, and vapor-phase reactions Study of the intrinsic properties of soils and examination of physical, chemical, and biotic processes that lead to soil formation; the crucial role of soils in agriculture and ecosystems The study of freshwater ecosystems, especially lakes and streams The study of saltwater ecosystems, especially oceans The study of the physical flow and migration of water in geological systems Methods and technologies for detecting, separating, and identifying molecular structures of organic and inorganic compounds Physical, chemical, hydraulic, and biological principles applied to the quantitative design of water supply, wastewater, and other engineering needs Integration of relationships between the biosphere and its inhabitants, with emphases on evolution, trophic dynamics, and emergent properties Multidisciplinary study of how the Earth functions, with emphasis on human influences on life support systems Stumm and Morgan, 1996; Millero, 2001; Schwarzenbach et al., 2002 Albaréde, 2003; Andrews, 2004 Brady and Weil, 1999 Wetzel and Likens, 2000; Wetzel, 2001 Sverdrup et al., 2003 Fetter, 1994 Fifield, 2000; Christian, 2003 Rittmann and McCarty, 2001; Tchobanoglous et al., 2002 Rickleffs and Miller, 2000; Krebs, 2001; Chapin et al., 2002 Miller, 2004 Table 1.5 Continued Subject matter and contribution to Discipline Environmental Microbiology References Aquatic chemistry Geochemistry Soil science Limnology Oceanography Hydrogeology Analytical chemistry Civil and environmental engineering Ecology Environmental science 9781405136471_4_001.qxd 1/15/08 9:21 Page 15
16CHAPTERISIGNIFICANCE,HISTORY,ANDCHALLENGESOFENVIRONMENTALMICROBIOLOGYEnvironmentalscienceMicrobialecologyNaturally occurring microorganismsBiospherehabitats (waters,in waters, sediments,and soilssediments, and soils)CurrentfrontiersAwaitingAwaitingCurrent knowledgediscoverydiscoveryMicroorganism-habitatinteractionsResources and selectiveNew informationPhysiological and geneticcapabilitiespressureformicroorganismsBiochemical,genetic,and.Processesare expressedeachComplex,poorlyunderstoodevolutionarymechanismsthatphysical,geochemical,andbioticdayasbiochemicalreactionsthatmaintainecosystemscharacteristicsmaintainthebiosphere·KnowledgethatcanimproveHeterogenousand dynamicin.Selectivepressures arehumanity's abilityto manage thetimeandspaceintegrated intothegenomesofbiosphereandexpandGradientsofreduced andcontemporarymicroorganismsbiotechnologicalproductsandoxidizedmaterialswhosereactionsAwaiting discovery:oftheservicesallowmicroorganismstoproduceestimatedglobaldiversityATPandgrow(-5millionmicroorganisms)Awaitingdiscovery:organiconly6500havebeencultivatedand>100.000havebeengeochemistry,colloidscience,kineticcontrolsofreactions,documentedbybiomarkersmicro-andnanoscaleprocesses(suchas16SrRNAgenes)Figure1.5 Conceptual representation of how the disciplines of environmental science (left sphere)and microbial ecology (right sphere)interacttoallownewdiscoveriesatthe interface betweenmicroorganisms and theirhabitats.Information in eachdiscipline is depicted asa combination ofcurrentknowledge,currentfrontiers,andknowledgeawaiting discovery.Microbial EcologyandEnvironmentalMicrobiologyhaveconsiderabledisciplinaryoverlap(seeTable1.5);nonetheless,advancements inthelatterarerepresentedbythe central,downwardarrow.(Reproduced andmodified withpermissionfromNatureReviewsMicrobiology,fromMadsen,E.L.2005.Identifyingmicroorganismsresponsiblefor ecologicallysignificantbiogeochemical processes.NatureRev.Microbiol.3:439-446.MacmillanMagazinesLtd,www.nature.com/reviews.)microorganisms interact with theirhabitats (central downward arrow inFigure 1.5).Thus, the path toward progress in environmental microbiology in-volvesmultidisciplinaryapproaches,assemblingconvergentlinesofinde-pendentevidence,andtestingalternativehypotheses.Ongoingintegrationof new methodologies (e.g.,from environmental science,microbial eco-logyand other disciplines listed in Table1.5)into environmental micro-biologyensures thatthenumber of linesand therobustness of boththeirconvergenceandtheirtestswillincrease.Aconceptualparadigmthatgraphicallydepictsthesynergisticrelationshipbetweenmicrobiologicalprocessesinfield sites,reductionisticbiological disciplines,and iterativemethodo-logical linkages between these disciplines is presented in Figure 1.6
microorganisms interact with their habitats (central downward arrow in Figure 1.5). Thus, the path toward progress in environmental microbiology involves multidisciplinary approaches, assembling convergent lines of independent evidence, and testing alternative hypotheses. Ongoing integration of new methodologies (e.g., from environmental science, microbial ecology and other disciplines listed in Table 1.5) into environmental microbiology ensures that the number of lines and the robustness of both their convergence and their tests will increase. A conceptual paradigm that graphically depicts the synergistic relationship between microbiological processes in field sites, reductionistic biological disciplines, and iterative methodological linkages between these disciplines is presented in Figure 1.6. 16 CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY Resources and selective pressure for microorganisms Biosphere habitats (waters, sediments, and soils) Environmental science Microbial ecology Naturally occurring microorganisms in waters, sediments, and soils • Complex, poorly understood physical, geochemical, and biotic characteristics • Heterogenous and dynamic in time and space • Gradients of reduced and oxidized materials whose reactions allow microorganisms to produce ATP and grow • Awaiting discovery: organic geochemistry, colloid science, kinetic controls of reactions, micro- and nanoscale processes New information Current frontiers Awaiting discovery Awaiting discovery Current knowledge Microorganism–habitat interactions • Biochemical, genetic, and evolutionary mechanisms that maintain ecosystems • Knowledge that can improve humanity’s ability to manage the biosphere and expand biotechnological products and services Physiological and genetic capabilities • Processes are expressed each day as biochemical reactions that maintain the biosphere • Selective pressures are integrated into the genomes of contemporary microorganisms • Awaiting discovery: of the estimated global diversity (~5 million microorganisms) only 6500 have been cultivated and 100,000 have been documented by biomarkers (such as 16S rRNA genes) Figure 1.5 Conceptual representation of how the disciplines of environmental science (left sphere) and microbial ecology (right sphere) interact to allow new discoveries at the interface between microorganisms and their habitats. Information in each discipline is depicted as a combination of current knowledge, current frontiers, and knowledge awaiting discovery. Microbial Ecology and Environmental Microbiology have considerable disciplinary overlap (see Table 1.5); nonetheless, advancements in the latter are represented by the central, downward arrow. (Reproduced and modified with permission from Nature Reviews Microbiology, from Madsen, E.L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Rev. Microbiol. 3:439–446. Macmillan Magazines Ltd, www.nature.com/reviews.) 9781405136471_4_001.qxd 1/15/08 9:21 Page 16
17CHAPTERISIGNIFICANCE,HISTORY,ANDCHALLENGESOF ENVIRONMENTALMICROBIOLOGYIn situ gene diversity. expression:MICROBIOLOGICALPROCESSES INFIELD SITESidentification of microorganisms(SOILS,SEDIMENTS,WATERS)responsible for geochemical change￥Biogeochemical activity in laboratory-incubated samplesYField methodsPure cultures in the laboratoryMicroscopic examination ofcells and cell structures, isotope+fractionation, field deploymentGrowth, energy yields..-ofchambers documentingfluxesPhysiologyenzymatic mechanismsof physiological gases:+Extraction of cell components.Enzymes, metabolic pathways.--- Biochemistry -spectrophotometric and GC/MScell constituentsanalyses, enzyme activity.microscopic and immunoassaysYfor enzymes and metabolitesMutation, recombination.geneGeneticsregulationNucleotide sequences forMolecular biologygenes providingNucleic acid extraction, Southern-"phylogenetic insights andand northern blots, detection andcoding for geochemical - - sequencing of genes and transcripts,catalysisPCR, RT-PCR, in situ PCRmicroscopy in combination withfluorescent probes,microarray analyses, genomics.transcriptomics,proteomics.metabolomicsFigureI.6Paradigmfor how theintegration of disciplinesandtheirrespectivemethodologiescan extend knowledge of environmental microbiology.Relationships between microorganismsresponsibleforfield biogeochemical processes, reductionistic disciplines,and their application tomicroorganisms in field sites are depicted. The three different types of arrows indicate sequentialrefinementsinbiologicaldisciplines(largedownward-pointingsolidarrows),resultantinformation(small arrows pointing to the right),and innovative methodological applications to naturallyoccurringmicrobial communities (dashedarrows).Gc/Ms,gas chromatography/mass spectrometry:PCR, polymerase chain reaction; RT, reverse transcriptase. (Reprinted and modified withpermissionfromMadsen,E.L.1998.Epistemologyofenvironmentalmicrobiology.Environ.Sci.Technol.32:429-439.Copyright 1998, American Chemical Society.)Observations of microorganisms in natural settings instigate a series ofprocedures progressing through mixed cultures, pure cultures, and physi-ological,biochemical,genetic,and molecular biological inquiries thateach stand alone scientifically.Butappreciablenewknowledgeof natu-rallyoccurringmicroorganismsisgainedwhenadvancementsfromthepure biological sciences are directed back to microorganisms in their field
Observations of microorganisms in natural settings instigate a series of procedures progressing through mixed cultures, pure cultures, and physiological, biochemical, genetic, and molecular biological inquiries that each stand alone scientifically. But appreciable new knowledge of naturally occurring microorganisms is gained when advancements from the pure biological sciences are directed back to microorganisms in their field CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY 17 In situ gene diversity, expression; identification of microorganisms responsible for geochemical change Field methods Microscopic examination of cells and cell structures, isotope fractionation, field deployment of chambers documenting fluxes of physiological gases Extraction of cell components, spectrophotometric and GC/MS analyses, enzyme activity, microscopic and immunoassays for enzymes and metabolites Nucleic acid extraction, Southern and northern blots, detection and sequencing of genes and transcripts, PCR, RT-PCR, in situ PCR, microscopy in combination with fluorescent probes, microarray analyses, genomics, transcriptomics, proteomics, metabolomics MICROBIOLOGICAL PROCESSES IN FIELD SITES (SOILS, SEDIMENTS, WATERS) Biogeochemical activity in laboratory-incubated samples Pure cultures in the laboratory Physiology Growth, energy yields, enzymatic mechanisms Enzymes, metabolic pathways, cell constituents Mutation, recombination, gene regulation Nucleotide sequences for genes providing phylogenetic insights and coding for geochemical catalysis Biochemistry Genetics Molecular biology Figure 1.6 Paradigm for how the integration of disciplines and their respective methodologies can extend knowledge of environmental microbiology. Relationships between microorganisms responsible for field biogeochemical processes, reductionistic disciplines, and their application to microorganisms in field sites are depicted. The three different types of arrows indicate sequential refinements in biological disciplines (large downward-pointing solid arrows), resultant information (small arrows pointing to the right), and innovative methodological applications to naturally occurring microbial communities (dashed arrows). GC/MS, gas chromatography/mass spectrometry; PCR, polymerase chain reaction; RT, reverse transcriptase. (Reprinted and modified with permission from Madsen, E.L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32:429–439. Copyright 1998, American Chemical Society.) 9781405136471_4_001.qxd 1/15/08 9:21 Page 17
18CHAPTERISIGNIFICANCE,HISTORY.ANDCHALLENGESOFENVIRONMENTALMICROBIOLOGYhabitats.Thesemethodological advancements (shown as dashed arrowsin Figure 1.6; see Chapter 6 for methodologies and their impacts)andtheknowledgetheygenerateaccruewitheach newcyclefromfield obser-vationstomolecularbiologyand back.Thus,integration ofmanydiscip-lines is thepathforward in environmental microbiology.STUDYQUESTIONS1 Core concept 1 presumes a two-dimensional house like thatdrawn on paper by school chil-dren. If you were to expand the concept to three dimensions, then two more walls would berequired to keep the"house of environmental microbiology"from falling down.Whattwodisciplineswouldyouaddand why?(Hint:forsuggestionsseeTable1.5.)2 Core concept 3 uses the phrase"mechanistic series of linkages between our planet's habitatdiversity and what is recorded in the genomes of microorganisms found in the world today".This is a hypothesis.If you wanted to test thehypothesis by completing measurementsandassembling a data set, what would you do? Specifically,what experimental design would read-ily test the hypothesis? And what would you measure? What methodological barriers mighthamper assembling a useful data set?Howmight these be overcome?(Hint: Sections 3.2 and3.3discussesgenomictools.Answerthis question beforeand afterreading Chapter3.)3Manynames ofmicroorganismsaredesignedtorecognizeindividual microbiologists whohavecontributed to the discipline.For instance,the genera Pasteurella, Thauera, and Shewanella arenamed after people.Similarly,the speciesdesignations in Vibrio harveyi,Desulfomoniletiedjei,Thermotoga jannaschii,Nitrobacterwinogradkyi,and Acetobacterium woodii are also named for peo-ple.Use theworld wide web or a resource like Bergey's Manual of Systematic Bacteriology or theInternational Journal of Systematicand Evolutionary Microbiology to discoverthe legacyof atleastonepersonmemorializedinthenameofamicroorganism4 Go fora walk outsideto visita forest,agricultural field,garden, orpond, stream or otherbodyof water.Sit down and examine (literally,and aided byyour imagination)thebiotic and abi-otic components of a cubicmeter of water, sediment, or soil.This cubicmeter definesa studysystem. What to you see? Divide a piece of paper into six columns with the headings"Materials and energy entering and leaving","Inorganic materials","Organic materials","Organisms","Interactions between system components",and"Biological processes".Addatleastfive entries under each column heading.Then imagine how each entry would change overthe course of ayear.Compare and contrast what you compiled in your listing with informa-tion in Figures 1.3-1.6and Tables1.2and 1.4.REFERENCESAdrian,L.,U.Szewyk,J.Wecke,andH.Gorisch.Alexander,M.1999.Biodegradation and Biore-2000.Bacterial dehalorespiration with chlorin-mediation,2nd edn.AcademicPress,San DiegoCA.atedbenzenes.Nature408:580-583Albarede,F.2003.Geochemistry:An introduction.Amann, R.I., W. Ludwig, and K.-H. Schleifer. 1995.CambridgeUniversityPress,NewYork.Phylogenetic identification and in situ detection
STUDY QUESTIONS 1 Core concept 1 presumes a two-dimensional house like that drawn on paper by school children. If you were to expand the concept to three dimensions, then two more walls would be required to keep the “house of environmental microbiology” from falling down. What two disciplines would you add and why? (Hint: for suggestions see Table 1.5.) 2 Core concept 3 uses the phrase “mechanistic series of linkages between our planet’s habitat diversity and what is recorded in the genomes of microorganisms found in the world today”. This is a hypothesis. If you wanted to test the hypothesis by completing measurements and assembling a data set, what would you do? Specifically, what experimental design would readily test the hypothesis? And what would you measure? What methodological barriers might hamper assembling a useful data set? How might these be overcome? (Hint: Sections 3.2 and 3.3 discusses genomic tools. Answer this question before and after reading Chapter 3.) 3 Many names of microorganisms are designed to recognize individual microbiologists who have contributed to the discipline. For instance, the genera Pasteurella, Thauera, and Shewanella are named after people. Similarly, the species designations in Vibrio harveyii, Desulfomonile tiedjei, Thermotoga jannaschii, Nitrobacter winogradkyi, and Acetobacterium woodii are also named for people. Use the world wide web or a resource like Bergey’s Manual of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology to discover the legacy of at least one person memorialized in the name of a microorganism. 4 Go for a walk outside to visit a forest, agricultural field, garden, or pond, stream or other body of water. Sit down and examine (literally, and aided by your imagination) the biotic and abiotic components of a cubic meter of water, sediment, or soil. This cubic meter defines a study system. What to you see? Divide a piece of paper into six columns with the headings “Materials and energy entering and leaving”, “Inorganic materials”, “Organic materials”, “Organisms”, “Interactions between system components”, and “Biological processes”. Add at least five entries under each column heading. Then imagine how each entry would change over the course of a year. Compare and contrast what you compiled in your listing with information in Figures 1.3–1.6 and Tables 1.2 and 1.4. 18 CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY REFERENCES Adrian, L., U. Szewyk, J. Wecke, and H. Görisch. 2000. Bacterial dehalorespiration with chlorinated benzenes. Nature 408:580–583. Albaréde, F. 2003. Geochemistry: An introduction. Cambridge University Press, New York. Alexander, M. 1999. Biodegradation and Bioremediation, 2nd edn. Academic Press, San Diego, CA. Amann, R.I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection habitats. These methodological advancements (shown as dashed arrows in Figure 1.6; see Chapter 6 for methodologies and their impacts) and the knowledge they generate accrue with each new cycle from field observations to molecular biology and back. Thus, integration of many disciplines is the path forward in environmental microbiology. 9781405136471_4_001.qxd 1/15/08 9:21 Page 18
19CHAPTERISIGNIFICANCE,HISTORY,AND CHALLENGESOFENVIRONMENTAL MICROBIOLOGYof individual microbial cells without cultivation.Dalsgaard,T.,D.E.Canfield,J.Petersen,B.Microbiol.Rev.59:143-169.Thamdrup and J.Acufia-Gonzalez.2003.N2pro-Amann, R., N.Springer, w.Ludwig, H.-D. Gortz, andduction bytheanammox reaction in theanoxicK.-H. Schleifer. 1991. Identification in situ andwater column of Golfo Culce,Costa Rica.Naturephylogeny of uncultured bacterial endosym-422:606-608.Deeb, R.A., K.-H. Chu, T. Shih, et al. 2003.MTBEbionts.Nature351:161-164.Andrews,J.E.2004.AnIntroductiontoEnvironmentaland other oxygenates:Environmental sources,Chemistry.Blackwell Science,Oxford.analysis, occurrence, and treatment. Environ.Eng.Atlas, R.M.and R.Bartha.1998.Microbial Ecology:Sci.20:433-447.Devlin,T.M.(ed.)2001.TextbookofBiochemistrywithFundamentalsandapplications,4thedn.BenjaminCummings, Menlo Park, CA.Clinical Correlations,5thedn.WileyandSons,NewBaxevanis,A.D.and B.F.F.Ouellette.2ool.Bio-York.Edwards, K.J., P.L.Bond, T.M. Gihrling, and J.Finformatics:A practical guide to the analysis of genesand proteins, 2nd edn.wiley Interscience, NewBanfield.2000.An archaeal iron-oxidizing extremeYork.acidophile important in acid mine drainage.Bitton,G.E.1999.WastewaterMicrobiology,2ndedn.Science287:1796-1799.Wiley Liss, New York.Ehrlich, H.L.2002.Geomicrobiology,4th edn.MarcelBoetius, A.,K.Ravenschlag,C.J.Schubert, et al.2000.Dekker, New York.Amarinemicrobial consortium apparentlymedi-Esteve-Nunez,A.,A. Caballero,and J.L.Ramos.ating anaerobic oxidation of methane.Nature2001.Biological degradation of 2,4,6-trinitro-407:623-626toluene.Microbiol.Molec.Biol.Rev.65:335-352.Boxall, A.B.A., C.J. Sinclair, K. Fenner, D. Kolpin,Fenchel, T.,G.M.King,and T.H.Blackburn.1998and S.J.Maund.2004.When synthetic chemicalsBacterialBiogeochemistry:Theecophysiologyofmineraldegrade in the environment.Environ. Sci.Technol.cycling.AcademicPress,SanDiego,CA.38:368A-375AFetter,G.W.1994.Applied Hydrogeology.PrenticeBrady,N.C. and R.R. Weil. 1999. The Nature andHall, UpperSaddleRiver, NJ.Properties of Soils, 12th edn.Prentice Hall, UpperFifield,F.W.2000.Principles and Practice of AnalyticalSaddle River, NJChemistry,5th edn.Blackwell Science, Oxford.Brock,T.D.1961.Milestones inMicrobiology.PrenticeFord,T.E.(ed.)1993.Aquatic Microbiology:An eco-Hall,Englewood Cliffs, NJ.logical approach.Blackwell Scientific Publications,Oxford.Bull, I.D.,N.R.Parekh,G.H.Hall, P.Ineson,and R.PEvershed.2ooo.Detectionand classificationofFred.E.B..LL,Baldwin,andE.McCoy.1932.Rooatmospheric methane oxidizing bacteria in soil.NoduleBacteriaandLeguminousPlants.UniversityofNature405:175-178.Wisconsin Studies of ScienceNo.5.University ofBurlage, R., R. Atlas, D. Stahl, G. Geesey, and G.Wisconsin, Madison, wI.Sayler (eds)1998.Techniques in Microbial Ecology.Glick,B.R.and J.J.Pasternack.2003.MolecularOxfordUniversityPress,NewYorkBiotechnology:Principles and application of recombin-Chapin,F.S.,P.A.Matson,and H.A.Mooney.2o02ant DNA,3rd edn. American Society of Micro-biologyPress,Washington,DC.Principles of Terrestrial Ecosystem Ecology.SpringerVerlag, New York.Gottschalk,G.1986.Bacterial Metabolism,2nd edn.Christian,G.D.2003.AnalyticalChemistry.6thednSpringer-Verlag,New York.Habicht, K.S. and D.E. Canfield. 1996. Sulphur iso-Wiley and Sons, New York.Coates,J.D.and L.A.Achenbach.2o04.Microbial per-tope fractionation inmodern microbial mats andchlorate reduction: rocket-fuelled metabolism.theevolutionofthesulphur cycle.Nature25:342-343.NatureRev.Microbiol.2:569-580.Conrad,R.1996.Soil microorganismsascontrollersHaggblom,M.andL.D.Bossert(eds)2003.Dehalogena-ofatmospheric tracegases (H2,co, CHa,os,N,tion:Microbialprocessesandenvironmentalapplications.KluwerAcademicPublications,Boston,MA.andNO).Microbiol.Rev.60:609-640
of individual microbial cells without cultivation. Microbiol. Rev. 59:143–169. Amann, R., N. Springer, W. Ludwig, H.-D. Görtz, and K.-H. Schleifer. 1991. Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature 351:161–164. Andrews, J.E. 2004. An Introduction to Environmental Chemistry. Blackwell Science, Oxford. Atlas, R.M. and R. Bartha. 1998. Microbial Ecology: Fundamentals and applications, 4th edn. Benjamin Cummings, Menlo Park, CA. Baxevanis, A.D. and B.F.F. Ouellette. 2001. Bioinformatics: A practical guide to the analysis of genes and proteins, 2nd edn. Wiley Interscience, New York. Bitton, G.E. 1999. Wastewater Microbiology, 2nd edn. Wiley Liss, New York. Boetius, A., K. Ravenschlag, C.J. Schubert, et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626. Boxall, A.B.A., C.J. Sinclair, K. Fenner, D. Kolpin, and S.J. Maund. 2004. When synthetic chemicals degrade in the environment. Environ. Sci. Technol. 38:368A–375A. Brady, N.C. and R.R. Weil. 1999. The Nature and Properties of Soils, 12th edn. Prentice Hall, Upper Saddle River, NJ. Brock, T.D. 1961. Milestones in Microbiology. Prentice Hall, Englewood Cliffs, NJ. Bull, I.D., N.R. Parekh, G.H. Hall, P. Ineson, and R.P. Evershed. 2000. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405:175–178. Burlage, R., R. Atlas, D. Stahl, G. Geesey, and G. Sayler (eds) 1998. Techniques in Microbial Ecology. Oxford University Press, New York. Chapin, F.S., P.A. Matson, and H.A. Mooney. 2002. Principles of Terrestrial Ecosystem Ecology. Springer Verlag, New York. Christian, G.D. 2003. Analytical Chemistry, 6th edn. Wiley and Sons, New York. Coates, J.D. and L.A. Achenbach. 2004. Microbial perchlorate reduction: rocket-fuelled metabolism. Nature Rev. Microbiol. 2:569–580. Conrad, R. 1996. Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol. Rev. 60:609–640. CHAPTER I SIGNIFICANCE, HISTORY, AND CHALLENGES OF ENVIRONMENTAL MICROBIOLOGY 19 Dalsgaard, T., D.E. Canfield, J. Petersen, B. Thamdrup and J. Acu1a-González. 2003. N2 production by the anammox reaction in the anoxic water column of Golfo Culce, Costa Rica. Nature 422:606–608. Deeb, R.A., K.-H. Chu, T. Shih, et al. 2003. MTBE and other oxygenates: Environmental sources, analysis, occurrence, and treatment. Environ. Eng. Sci. 20:433–447. Devlin, T.M. (ed.) 2001. Textbook of Biochemistry with Clinical Correlations, 5th edn. Wiley and Sons, New York. Edwards, K.J., P.L. Bond, T.M. Gihrling, and J.F. Banfield. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796–1799. Ehrlich, H.L. 2002. Geomicrobiology, 4th edn. Marcel Dekker, New York. Esteve-Núñez, A., A. Caballero, and J.L. Ramos. 2001. Biological degradation of 2,4,6-trinitrotoluene. Microbiol. Molec. Biol. Rev. 65:335–352. Fenchel, T., G.M. King, and T.H. Blackburn. 1998. Bacterial Biogeochemistry: The ecophysiology of mineral cycling. Academic Press, San Diego, CA. Fetter, G.W. 1994. Applied Hydrogeology. Prentice Hall, Upper Saddle River, NJ. Fifield, F.W. 2000. Principles and Practice of Analytical Chemistry, 5th edn. Blackwell Science, Oxford. Ford, T.E. (ed.) 1993. Aquatic Microbiology: An ecological approach. Blackwell Scientific Publications, Oxford. Fred, E.B., I.L. Baldwin, and E. McCoy. 1932. Root Nodule Bacteria and Leguminous Plants. University of Wisconsin Studies of Science No. 5. University of Wisconsin, Madison, WI. Glick, B.R. and J.J. Pasternack. 2003. Molecular Biotechnology: Principles and application of recombinant DNA, 3rd edn. American Society of Microbiology Press, Washington, DC. Gottschalk, G. 1986. Bacterial Metabolism, 2nd edn. Springer-Verlag, New York. Habicht, K.S. and D.E. Canfield. 1996. Sulphur isotope fractionation in modern microbial mats and the evolution of the sulphur cycle. Nature 25:342– 343. Haggblom, M. and I.D. Bossert (eds) 2003. Dehalogenation: Microbial processes and environmental applications. Kluwer Academic Publications, Boston, MA. 9781405136471_4_001.qxd 1/15/08 9:21 Page 19