《水处理生物学》课程教学资源（书籍文献）《Environmental Microbiology》书籍PDF电子书 From genomes to biogeochemistry（Eugene L. Madsen）.pdf_P31-P35

after Earth was struck by another planet about the size of Mars. Bombardment diminished perhaps by 4.2–4.0 × 109 years ago. The scale of geologic time, from planet formation to the present, is shown in Figure 2.2. The influence of ancient atmospheres upon surface conditions was critical. Abundances of greenhouse and other gases (especially CO2, NH3, H2O, CO, CH4, HCN, N2) were probably highly dynamic. In combination with variations in solar radiation, atmospheric conditions may have contributed to periods of high surface temperatures (~100°C) that perhaps alternated with low-temperature (glaciated) periods. Clearly, conditions on prebiotic Earth were turbulent – characterized by fluctuating temperatures, aqueous reactions with magma, input of materials from meteorites (including organic carbon), electrical discharges from the atmosphere, and reduced (nonoxidizing) gases in the atmosphere. CHAPTER 2 FORMATION OF THE BIOSPHERE: KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTS 25 Table 2.1 Key event and conditions of early Earth Time (109 years before present) 4.6 4.2 4.0 3.8 3.5–3.4 2.7 2.4 1.4 0.6 0.4 0.1 Events • Colliding planetisemals • Earth formed • Moon formed • Loss of water and hydrogen from atmosphere • Volcanism • Cooling of surface • Faint young Sun? • Glaciation? • Bombardment ceased (?) • RNA world, iron/sulfur world • Last universal common ancestor • Anoxygenic photosynthesis • Fossils resembling bacterial filaments on stromatolite microbial mats • Biomarker for cyanobacteria • Biomarker for primitive eukaryotes • Signs of oxygen at low concentration in atmosphere • Nucleated eukaryotic algae • Cambrian explosion of eukaryotic diversity • Dinosaurs, higher plants, mammals Conditions • Heat • Meteor bombardment and impacts • Lightning • UV radiation • Hot oceans followed each bombardment • Atmosphere: N2, CO2, CO, H2, NH3, CH4, HCN • Ocean chemistry: H2S, Fe2+ , heavy metals • Banded iron geologic formations • Red bed geologic formations • Oxygen in atmosphere ~1% • Ozone shield • Oxygen in atmosphere ~21% 9781405136471_4_002.qxd 1/15/08 8:47 Page 25

26CHAPTER2FORMATIONOFTHEBIOSPHERE:KEYBIOGEOCHEMICALAND EVOLUTIONARY EVENTSTable 2.2Scientific tools providing information about Earth history and evolutionToolDisciplineInsightsGeologyGlobal surveys of terrestrialSedimentary,igneous,and metamorphicand oceanic rocksformationsreveal tectonicand otherprocesses governing Earth's evolutionNuclear chemistryRadioisotopic datingAges of rocks,minerals,and theircomponents are revealedPaleontologyFossil recordOrganism structurespreserved in stratifiedsedimentsproviderecordsofevolutionAnalytical chemistryAnalytical determinationMolecular remnants of biomoleculesofbiomarkersof biomolecules via(membranes,pigments, cell walls,etc.)chromatography anddocument ancient biotamassspectrometryAnalytical chemistryEnzyme reactions favor substrate moleculesIsotoperatiomassspectrometryof isotopicratioscomposedof lighteratoms.Biomassassimilatesthelighterisotopeandtheremaining isotopic pool becomes"heavier"foragiven processExperimentalModel systems that simulateDiscovery of precursors of cellular structuresancient Earthbiochemistryand their self-assembling propertiesMolecular phylogenySequencing and analysis ofAlignment of sequences from DNA,proteins,informational biomoleculesand other molecules allow evolutionaryinferencestobedrawn,especiallyregarding the three domains of lifeMineralogy andX-ray diffraction and wet-Chemicalreactionsandreactantsofpastchemical analysis of rocksages can be inferred from the compositiongeochemistryand oxidation/reduction status of ancientsedimentsBiochemistryComparative biochemistry ofTrends in evolutionary relatedness amongand between members of Bacteria,cellular materialsArchaea,and Eukarya2.3DIDLIFEREACHEARTHFROMMARS?There is a general consensus that stable isotopic ratios (see Tables 2.1,2.2and Box2.2) in graphite isolated from the Isua supracrustal belt (WestGreenland; see Figure 2.1)prove that life,manifest as anoxygenic photo-synthesis,was present 3.8×10°years ago (Nisbetand Sleep,2001).BeforefocusinguponaplausiblescenarioofhowlifeevolvedonEarth,analter-native,perhaps equally plausible,hypothesismustbrieflybe consid-ered:Panspermia.Intheearlyhistoryofoursolar system,Earth,Venus,and Mars, close neighbors,were simultaneously undergoing planetary

2.3 DID LIFE REACH EARTH FROM MARS? There is a general consensus that stable isotopic ratios (see Tables 2.1, 2.2 and Box 2.2) in graphite isolated from the Isua supracrustal belt (West Greenland; see Figure 2.1) prove that life, manifest as anoxygenic photosynthesis, was present 3.8 × 109 years ago (Nisbet and Sleep, 2001). Before focusing upon a plausible scenario of how life evolved on Earth, an alternative, perhaps equally plausible, hypothesis must briefly be considered: Panspermia. In the early history of our solar system, Earth, Venus, and Mars, close neighbors, were simultaneously undergoing planetary 26 CHAPTER 2 FORMATION OF THE BIOSPHERE: KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTS Table 2.2 Scientific tools providing information about Earth history and evolution Discipline Geology Nuclear chemistry Paleontology Analytical chemistry of biomarkers Analytical chemistry of isotopic ratios Experimental biochemistry Molecular phylogeny Mineralogy and geochemistry Biochemistry Tool Global surveys of terrestrial and oceanic rocks Radioisotopic dating Fossil record Analytical determination of biomolecules via chromatography and mass spectrometry Isotope ratio mass spectrometry Model systems that simulate ancient Earth Sequencing and analysis of informational biomolecules X-ray diffraction and wetchemical analysis of rocks Comparative biochemistry of cellular materials Insights Sedimentary, igneous, and metamorphic formations reveal tectonic and other processes governing Earth’s evolution Ages of rocks, minerals, and their components are revealed Organism structures preserved in stratified sediments provide records of evolution Molecular remnants of biomolecules (membranes, pigments, cell walls, etc.) document ancient biota Enzyme reactions favor substrate molecules composed of lighter atoms. Biomass assimilates the lighter isotope and the remaining isotopic pool becomes “heavier” for a given process Discovery of precursors of cellular structures and their self-assembling properties Alignment of sequences from DNA, proteins, and other molecules allow evolutionary inferences to be drawn, especially regarding the three domains of life Chemical reactions and reactants of past ages can be inferred from the composition and oxidation/reduction status of ancient sediments Trends in evolutionary relatedness among and between members of Bacteria, Archaea, and Eukarya 9781405136471_4_002.qxd 1/15/08 8:47 Page 26

27CHAPTER2FORMATIONOFTHEBIOSPHERE:KEYBIOGEOCHEMICAL AND EVOLUTIONARY EVENTSBox 2.1TheageoftheEarthandbiotaRadioactivedecayinrocksMeasurements performed on rock containing radioactive elements (nuclides)can reveal theageof therock.For example,238u (half-life=4.5×1o°years)decays tohelium and 206pb.Each atom of 238U that decomposes forms eight atoms of helium (with total mass 32) leav-ing one atom of 206pb. In 4.5 x 10° years, 1 g of 238pb becomes 0.5000 g of 238U and 0.174 gof He and 0.326 g of 20pb. If analyses document nuclides present in the rock in the aboveratios,theage would be 4.5x1o°years.Other radioactiveelements havetheirown char-acteristichalf-livesand decayproducts; thus,ratios of235U/207Pb,232Th/208pb,40K/40Ar,and87Rb/s7s arealso insightful fordeterminingtheages of rocks.Thepresent estimateof theage of Earth and the other inner planets in our solar system is 4.6 × 1oyears.Carbon dating of lifeAbout one in every 1o12 carbon atoms on Earth is radioactive (14c)and has a half-life of576oyears.Carbondioxide,radioactiveandnonradioactivealike,isabsorbedbyplantsandincorporatedintothebiotathatconsumeplants.Whenaplantoranimaldies,its14Catomsbeginundergoingradioactive decay.After 11,52o years(twohalf-lives),onlyone-quarterof the original radioactivity is left.Accordingly,by determining the i4c radioactivity of asample of carbon from wood, flesh, charcoal, skin,horn,or other plantor animal remains,thenumber of yearsthat have passed sincethecarbon was removed from atmospheric inputofi4ccanbedeterminedBox2.2BiomarkersandisotopicfractionationBiomarkersBiomarker compounds are molecules of known biosynthetic origin. As such, their detectioningeologicsamples(ancientburied soils,rocks,sediments)associates thebiosyntheticpath-way and/orits host organism with the source material.Biomarker geochemistry has beenroutinely applied to petroleum exploration and also has been insightful in analyzing rocks(e.g.,2.7x1o°-year-old shales from northwestern Australia; Brocks et al.,1999).Examplesofbiomarkersthathavebeenextractedfromrocksare2-methyl-hopanes(derivedfrom2-methyl-bacteriohopane polyols,which aremembranelipids synthesized bycyanobacteria)andpyrrolemolecules,essential buildingblocks ofthephotosynthetic (chlorophyll)and res-piratory(cytochrome)apparatus

CHAPTER 2 FORMATION OF THE BIOSPHERE: KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTS 27 Box 2.1 The age of the Earth and biota Radioactive decay in rocks Measurements performed on rock containing radioactive elements (nuclides) can reveal the age of the rock. For example, 238U (half-life = 4.5 × 109 years) decays to helium and 206Pb. Each atom of 238U that decomposes forms eight atoms of helium (with total mass 32) leaving one atom of 206Pb. In 4.5 × 109 years, 1 g of 238Pb becomes 0.5000 g of 238U and 0.174 g of He and 0.326 g of 206Pb. If analyses document nuclides present in the rock in the above ratios, the age would be 4.5 × 109 years. Other radioactive elements have their own characteristic half-lives and decay products; thus, ratios of 235U/207Pb, 232Th/208Pb, 40K/40Ar, and 87Rb/87S are also insightful for determining the ages of rocks. The present estimate of the age of Earth and the other inner planets in our solar system is 4.6 × 109 years. Carbon dating of life About one in every 1012 carbon atoms on Earth is radioactive (14C) and has a half-life of 5760 years. Carbon dioxide, radioactive and nonradioactive alike, is absorbed by plants and incorporated into the biota that consume plants. When a plant or animal dies, its 14C atoms begin undergoing radioactive decay. After 11,520 years (two half-lives), only one-quarter of the original radioactivity is left. Accordingly, by determining the 14C radioactivity of a sample of carbon from wood, flesh, charcoal, skin, horn, or other plant or animal remains, the number of years that have passed since the carbon was removed from atmospheric input of 14C can be determined. Box 2.2 Biomarkers and isotopic fractionation Biomarkers Biomarker compounds are molecules of known biosynthetic origin. As such, their detection in geologic samples (ancient buried soils, rocks, sediments) associates the biosynthetic pathway and/or its host organism with the source material. Biomarker geochemistry has been routinely applied to petroleum exploration and also has been insightful in analyzing rocks (e.g., 2.7 × 109 -year-old shales from northwestern Australia; Brocks et al., 1999). Examples of biomarkers that have been extracted from rocks are 2-methyl-hopanes (derived from 2- methyl-bacteriohopane polyols, which are membrane lipids synthesized by cyanobacteria) and pyrrole molecules, essential building blocks of the photosynthetic (chlorophyll) and respiratory (cytochrome) apparatus. 9781405136471_4_002.qxd 1/15/08 8:47 Page 27

28 CHAPTER 2 FORMATION OF THE BIOSPHERE: KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTS Box 2.2 Continued Isotopic fractionation Many chemical elements on Earth occur as mixtures of atoms with differing numbers of neutrons in their nuclei. For instance, the natural abundance of stable (nonradioactive) carbon with six neutrons and six protons (12C) is 98.9%, while ~1.1% of the total carbon pool has seven neutrons (13C). Enzymes involved in photosynthesis show subtle selectivity in acting on their substrate (CO2) when it is composed of the lighter (12C) carbon isotope. Photosynthesis fixes atmospheric CO2 into biomass; therefore, the biomass is enriched in 12C – it is “light”. Correspondingly, as 12C-CO2 is removed from the atmosphere, the remaining pool is enriched in 13C-CO2 – it becomes “heavy”. Such shifts in isotopic ratios can be detected in carbon and other elements (especially sulfur) extracted from ancient rocks. Because enzymatic selectivity is the only known mechanism for such shifts, these constitute evidence for biological processes. As listed in Table 2.2, carbon isotopic ratios are determined using an analytical technique known as isotope ratio mass spectrometry. The means of expressing the ratio uses a “del 13C” value, which contrasts the 13C/12C ratio in a sample with that of a standard: δ13C = × 1000 Note that the δ13C value becomes negative (“light”) if the sample is depleted in 13C, relative to the standard. Extensive surveys of carbon pools found in nature have been cataloged. This compilation of characteristic values (Grossman, 2002) allows the origin of many carbon pools to be ascertained: Pool of carbon Range of δ13C Marine carbonate −5 to +8 Atmospheric CO2 −8 to −5 Calvin cycle plants (C3) −27 to −21 C4 plants −17 to −9 Petroleum −32 to −22 Thermogenic methane −48 to −34 Microbial methane −90 to −48 Cyanobacteria −30 to −18 Purple sulfur bacteria −35 to −20 Green sulfur bacteria −20 to −9 Recent marine sediments −35 to −10 ( 13C/12C sample) − ( 13C/12C standard) 13C/12C standard 9781405136471_4_002.qxd 1/15/08 8:47 Page 28

29CHAPTER 2FORMATION OFTHEBIOSPHERE:KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTSdevelopment.Mars,inparticular,featured an abundance of waterIsuaand other geochemical conditionsthat may have been favorable for,andledtothedevelopmentof,life.Meteor bombardmentwas ram-pant in the early solar system.Such collisions transferred materi-Redbedsals between planets.Microbial lifeburiedwithintheintersticesofMartian rocks may have survivedWarrawoonatransit to Earth and landed inPilbaraseas capable of supporting growth.BarbertonOnce seeded,Earth-specificevolu-tionaryforceswouldhave takenhold.The discussion below on theFigure2.1Map of theworld showinglocationsof rockformations thatprovide insights into the coevolution of lifepossible origin of life applies toand theEarth.Earth, as well as other planets.2.4 PLAUSIBLESTAGESINTHEDEVELOPMENTOFEARLYLIFEAmonglife'smanyattributesisthecreationof order out of disorder.TheSecond Law of Thermodynamics mandates that order be created at theexpenseof energy and theproduction ofentropy.Mechanisticallylifeismanifest as the synthesis ofmolecular structures that facilitatemetabolicand genetic processes.Such structures are antientropic-requiringenergy for synthesis and assemblyFortunately.abundant physicalenergy sources prevailed in sterile,prebiotic Earth: these included heat,UVradiation,andelectricaldischarges(lightning).InvestigationsbyS.Millerinthe195Osprovedthataminoacidscanbechemicallvsvnthesizedunderconditionssimulating ancientseas.Thisdenovo synthesisoforganiccom-pounds,supplementedwithonesborneonmeteorites,leaveslittledoubtthatan organicgeochemical broth developed.The transition from a soup of life's primitivepotential buildingblocksto advanced cellular life is thoughtto have proceeded through many stagesof increasingcomplexity(Figures2.2,2.3).Thefundamentalconceptualfoundation in developing and testing theories about the origin of life is"getting herefrom there".Weneed to define"here",define"there",anddoourbestindevisingfeasible,continuousconnectionsbetweenthetwo."Here"referstothehighlycomplexcharacteristicsofmoderncellularlife:heredity(DNA),transcription(RNA),translation (ribosomes),catalysis(pro-teins),compartmentalization (membrane-enclosed cells and organelles),metabolic energy production [e.g.,electron transport, adenosine triphos-phate(ATP),and ATP synthasel,and biosynthesis (using energy for

development. Mars, in particular, featured an abundance of water and other geochemical conditions that may have been favorable for, and led to the development of, life. Meteor bombardment was rampant in the early solar system. Such collisions transferred materials between planets. Microbial life buried within the interstices of Martian rocks may have survived transit to Earth and landed in seas capable of supporting growth. Once seeded, Earth-specific evolutionary forces would have taken hold. The discussion below on the possible origin of life applies to Earth, as well as other planets. 2.4 PLAUSIBLE STAGES IN THE DEVELOPMENT OF EARLY LIFE Among life’s many attributes is the creation of order out of disorder. The Second Law of Thermodynamics mandates that order be created at the expense of energy and the production of entropy. Mechanistically, life is manifest as the synthesis of molecular structures that facilitate metabolic and genetic processes. Such structures are antientropic – requiring energy for synthesis and assembly. Fortunately, abundant physical energy sources prevailed in sterile, prebiotic Earth: these included heat, UV radiation, and electrical discharges (lightning). Investigations by S. Miller in the 1950s proved that amino acids can be chemically synthesized under conditions simulating ancient seas. This de novo synthesis of organic compounds, supplemented with ones borne on meteorites, leaves little doubt that an organic geochemical broth developed. The transition from a soup of life’s primitive potential building blocks to advanced cellular life is thought to have proceeded through many stages of increasing complexity (Figures 2.2, 2.3). The fundamental conceptual foundation in developing and testing theories about the origin of life is “getting here from there”. We need to define “here”, define “there”, and do our best in devising feasible, continuous connections between the two. “Here” refers to the highly complex characteristics of modern cellular life: heredity (DNA), transcription (RNA), translation (ribosomes), catalysis (proteins), compartmentalization (membrane-enclosed cells and organelles), metabolic energy production [e.g., electron transport, adenosine triphosphate (ATP), and ATP synthase], and biosynthesis (using energy for CHAPTER 2 FORMATION OF THE BIOSPHERE: KEY BIOGEOCHEMICAL AND EVOLUTIONARY EVENTS 29 Isua Red beds Barberton Warrawoona Pilbara Figure 2.1 Map of the world showing locations of rock formations that provide insights into the coevolution of life and the Earth. 9781405136471_4_002.qxd 1/15/08 8:47 Page 29