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Systems Microbiology20.106J (1.084J) Lecture: MW 9:30-11
Prereq:5.111, 5.112 or 3.091; 7.012/7.013/7.014 Units: 3-0-9
Modern microbiology from a systems perspective
Professors David Schauer & Ed DeLong
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Systems Microbiology20.106 LOGISTICS
TEXT: Biology of Microorganisms
Mike Madigan and John Martinko
Grading based on: Grade %
Problem sets : ~ 1 every 2 weeks 25 %
Midterms : I - Monday October 17 20 %
II - Monday, November 14 20 %
Final Exam : Date TBD 35 %
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Microsopic photograph of microbes removed due to copyright restrictions.
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•• MICROBIAL DIVERSITY & the BIOSPHEREMICROBIAL DIVERSITY & the BIOSPHERE
•• ENERGY & ENVIRONMENTENERGY & ENVIRONMENT
•• HUMAN HEALTHHUMAN HEALTH
•• BIOLOGICAL ENGINEERINGBIOLOGICAL ENGINEERING
MICROBIAL BIOLOGYMICROBIAL BIOLOGY
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MICROBIALMICROBIAL DIVERSITY &DIVERSITY &
THE BIOSPHERETHE BIOSPHERE
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Photographs of extreme cold and warm microbial habitats removed due to copyright restrictions.
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Relative Voltage Relative Voltage
FUELS (EAT) OXIDANTS (BREATHE)MICROBIALMICROBIALMETABOLICMETABOLIC DIVERSITYDIVERSITY
Microbes can
eat & breathe just
about anything !
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4
+ 6
+ 8
+ 10
+ 12
+ 14
Organic Carbon
H2
H2S So
Fe(II)
NH4 +
Mn(II)
A
B
Photoreductants -10
- 8
- 6
- 4
- 2
0
+ 2
+ 4
+ 6
+ 8
+ 10
+ 12
+ 14
CO2 =SO4
AsO43-
FeOOH
SeO3 -NO2 -NO3
MnO2
NO3-/N2
O2
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ENERGYENERGY AND THEAND THE
ENVIRONMENTENVIRONMENT
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The Global Importance of MicrobesThe Global Importance of Microbes
The only form of life on Earth for over 2-3 billion yearsThe only form of life on Earth for over 2-3 billion years
Encompass most of the diversity of genes and biochemistryEncompass most of the diversity of genes and biochemistry
Represent > 50% of the biomass in the open oceanRepresent > 50% of the biomass in the open ocean
Control all elemental cycles that shape EarthControl all elemental cycles that shape Earth’’s habitabilitys habitability
They can live without usThey can live without us…………
but we canbut we can’’t live without themt live without them
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Life on Earth: The FoundationLife on Earth: The Foundation
COCO22 ++ HH22OOcarbon watercarbon waterdioxidedioxide
CC66HH1212OO66 ++
PlantsPlantsPhytoplanktonPhytoplankton
PhotosynthesisPhotosynthesisSolar energySolar energy
ChemicalChemicalenergy or heatenergy or heat
N,P,S,FeN,P,S,Fe……..carboncarbon
AnimalsAnimalsBacteriaBacteria
RespirationRespiration
OO22organic oxygenorganic oxygen
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The Global Carbon Cycle (GtC)Accumulation in atmosphere +3.2/year+3.2/year
5.35.3Combustion
0.6-2.60.6-2.6Land use changes
Plant
90-12090-120Respiration
Intake100-120100-120 100-115100-115
Gas exchange 100-115100-115
between air and ocean
Net accumulation in ocean 1.6-2.41.6-2.4
Biological pump
Circulation Geological reservoir
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from SeaWiFs Project website
PRODUCTS and OUTPUTS
THE ANTHROPOCENTRIC PERSPECTIVE
ENERGY
Photograph of an oil drill ship removed due to copyright restrictions.
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from SeaWiFs Project website
Atmospheric Carbon Dioxide (Mauna Loa)
WinterWinterR > PR > P
SummerSummerP > RP > R
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MICROBES &MICROBES &HUMAN HEALTHHUMAN HEALTH
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in
THE POPULAR VIEW OF “BUGS”
Flesh Bug Kills Drug BossDaily Record | Dec 26, 2003ONE-EYED gangster Gerry ''Cyclops'' Carbin has died after being struck down by a flesh-eating bug.
Flesh-Eating Bananas from Costa RicaInside Costa Rica | Apr 15, 2005Warning: Several shipments of bananas from Costa Rica have been infected with necrotizing fasciitis, otherwise known as flesh eating bacteria
Flesh-Eating Bacteria Claims Teen's LegWJXT | Jan 4, 2005A Central Florida teen is recovering Tuesday after a flesh-eating bacteria forced doctors to amputate most of his leg, according to WKMG-TV
Man Loses Battle With Gulf Bacteria KPRC Houston | Aug 16, 2004A Houston dentist has died after flesh-eating bacteria invaded a cut on his leg while he was fishing near Port O'Connor about a month ago
(Streptococcus pyrogenes. - > Necrotizing fasciitis)
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Host-Bacterial Mutualism in the Human IntestineBäckhed,*Ley,*Sonnenburg, Peterson, Gordon SCIENCE 307:1915 (2005)
Diagram from Backhed, Ley, Sonnenburg, and Peterson removed due to copyright restrictions.
Firmicutes
OD1
Actino
bacte
ria
Proteobacteria
ABY1
OP9
SR1
WS6
SC3WS5Termite Group 1
TM7BD1-5
Coprothermobacter
Dictyoglomus OP1
OP 11
Synergistes
Guaymas1
0.05
SC4
to the Archaea
EM3
TM6
KSB1
OP3
WS2
WS3BRC1
SBR1093NKB19
OP5Fusobacteri
a
Spiro
chae
ates
Fibr
obac
tere
s
Cya
noba
cter
iaG
reen
Non
Sul
fur
Deinococcus-Thermus
OS-K
OP8
Acidobacteria
Plantomycetales
Chlamiydiae
CFB
Chlorobi
Nitrospira Verrucomicrobi
VadinBE9 7
Marine Group ANC10
Gemm
atimonadetes
Deferribacter
Aquifacae
Desulfo
bacte
ria
OP10Thermotogae
Thermodesulfobacteria
Figure by MIT OCW.
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E. coli 0157:H7 = Jack in the Box food poisoning incident
UROPATHOGENIC & ENTEROHAEMORRHAGIC “HOT-SPOTS” Welch, R. A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 17020-17024
5857.6%
MG1655 (K-12)Non-Pathogenic
CFT073 Uropathogenic
EDL933 (O157:H7)Enterohaemorrhagic
5146.7%
2042.6%
162321.2%
134617.6%
1932.5%
299639.2%
Total proteins = 76382996 (39.2%) in all 3911 (11.9%) in 2 out of 33554 (46.5%) in 1 out of 3
100 Kb aspV
aspV
thrW
serX
serXserW
serU
serU
argW
argW
ssrA
ssrA
metV
selC (pap)pheU
selC(LEE)
leuX
leuX
(pap-hly)pheV
pheV
asnT,V
thrW
**
*
* * * * * **
100 Kb
CFT073
EDL933
Figures by MIT OCW.
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Vibrio cholerae
Movement
Movement Movement(random reorientation)
Counter-clockwiserotation
Counter-clockwiserotation
Helical bundle
Tumbling-random reorientation Clockwise rotation
Clockwise rotation
a) Peritrichous Flagella
b) Monotrichous Flagellum
Figure by MIT OCW.
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Planktonic V. cholerae
Human HostEnvironmental Reservoirs
Surface Biofilms Cyanobacteria Copepods Chironomid Egg Masses
Figure by MIT OCW.
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BIOTECHNOLOGYBIOTECHNOLOGY&&
BIOLOGICALBIOLOGICALENGINEERINGENGINEERING
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ANTIBIOTIC BIOSYNTHESIS
Organization of 6-deoxyerythronolide B synthase and erythromycin A biosynthesis
S S S S S S SO O
Loading Module 1 Module 2 Module 3 Module 4 Module 5 Module 6
Termination/Cyclization
O O O O
O
O
OO
OHOHO
HOHO
HO
HO
HOHO
HO
OH
OH
OH
OH
OHOH
OHOH
OH
OHOH
HO
HO
HOHO
HO
HOCH3 CH3 CH3
CH3
CH3
CH3
CH3
CH3 CH3 CH3CH3CH3CH3CH3CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3CH3
CH3
CH3
CH3
CH3
CH3CH3
CH3CH3
R1CH3
CH3
CH3N(CH3)2
OR2
CH3
CH3 CH3
CH3
CH3
CH3CH3
6-deoxyerythronolide B(6-dEB)
3 -mycarosylerythronolide B
Organization of 6-deoxyerythronolide B synthase and erythromycin A biosynthesis
CH3CH3CH3CH3
CH3
CH3H3C
H3C
erythromycin A(R1=OH, R2=CH3)
H3CH3C
H3CH3C
H3C
ANTIBIOTIC BIOSYNTHESIS
AT ACP I KS AT KR ACP I KS AT KR ACP I KS AT ACP I KS AT DH/ER/KR ACP I KS AT KR ACP I KS AT KR ACP I TE
O O
OOO
OO
O
O
O
O
O
O
erythromycin D (R1, R2=H)erythromycin B (R1=H, R2=CH3)erythromycin C (R1=OH, R2=H)
O
O
Figure by MIT OCW.
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Rhodopsin functional diversityH+
H+
H+
Asp-96
Asp-85
Arg-82
Glu-204
Glu-194
Retinal
Figures by MIT OCW.
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Professor Drew Endy
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LIFE ON EARTH :LIFE ON EARTH :
HOW DID WE GET FROM THERE,TO HERE?HOW DID WE GET FROM THERE,TO HERE?(OR, LESSONS IN GEOBIOLOGICAL ENGINEERING)(OR, LESSONS IN GEOBIOLOGICAL ENGINEERING)
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Microbes thrive at the extreme rangesof temperature, salinity, pH,pressure, water activity …..
Whats needed for life Energy (light, oxidants, reductants)Water (liquid)Basic elements :C, H, N, O, P, S + trace metals
Microbial life thrives wherever these are found …
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THE EARLY EARTH SYSTEM
1) The formation of the Earth 2) Early Earth physical and chemical conditions 3) Atmospheric and ocean “evolution” 4) The evolution of life 5) The evolution of photosynthesis
THE EVIDENCE 1) Isotopic record 2) Rocks and Microfossils 3) Organic Geochemical Record (“molecular fossils”) 4) Molecular Evolution
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D. J. Des Marais
Science, Vol 289, Issue 5485, 1703-1705 , 8 September 2000
Humans
Origin of Earth
Life
Billions of Years Ago
MammalsVascular plants
Shelly invertebrates
Algal kingdoms
?Phototrophic bacteria
Cyanobacteria plusother phototrophs
Macroscopic eukaryotes
PrecambrianPaieozoic
Mesozoic
Cenozoic
1
2 3
4
Figure by MIT OCW.
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What was the early Earth really like ????1) Was the early Earth hot or cold?2) Was there lots of NH3, hydrogen and methane in Earth’s atmosphere?3) What was the redox potential of the ocean and atm ?
Image removed due to copyright restrictions.
The Early days … (first few million years)1. Accretion. Impacting bodies bombard the Earth and convert their energy of motion (kinetic energy) into heat. In recent years we also learned that anearly collision with a very large object was responsible for the "extraction" of the Moon from Earth.
2. Self-compression. As the Earth gets bigger, the extra gravity forces the mass to contract into a smaller volume, producing heat (just like a bicyclepump gets hot on compression).
3. Differentiation. Conversion of gravitational potential energy to heat during core formation
3. Short-lived radiogenic isotopes. The surrounding material absorbs the energy released in radioactivity, heating up.
AtmosphereOceanCrust
Mantle
Outer core (liquid)
Inner core (solid)
Figure by MIT OCW.
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So, how did life originally arise on Earth ???1) In situ, or panspermia ???
2) Oparin ocean scenario, or hydrothermal vents ?
3) Geo-template, or solution chemistry ?
Images removed due to copyright restrictions.
eon
eraeriod
Haden Archean Proterozoic *Phanerozoic*Meso-zoic
Cz
Paleo-zoic
Neoproterozoic
E-d
Cryog-enian
Ton-ian
Sten-ian
Ecta-sian
Calym-mian
Stath-erian
Oro-sirian
Rhya-cian
Sid-erian
Neo-archean
Meso-archean
Paleo-archean
Eoar-chean
Paleoproterozoic Mesoproterozoic
-4500 -4000 -3500 -3000 -2500 -2000 -1500 -1000 -500 0
Figure by MIT OCW.
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Formation conditions
Initial Composition - Probably H2, He These gases are relatively rare on Earth compared to other places in theuniverse and were probably lost to space early in Earth's history because Earth's gravity was not strong enough to holdlighter gases. Earth still did not have a differentiated core (solid inner/liquid outer core) which creates Earth's magneticfield (magnetosphere = Van Allen Belt) which deflects solar winds. Once the core differentiated the heavier gases couldbe retained.“First” Atmosphere
Probably produced by volcanic out gassing. Gases produced were likely similar to those created by modern volcanoes (H2O,CO2, SO2, CO, S2, Cl2, N2, H2) and NH3 (ammonia) and CH4 (methane).
Used to think mostly this in early atm !
(Note: Mildly reducing, not strongly reducing …) But more of the other gases in volcanicEmmissions, and these detstroyed by UV& UV hydrolysis.
No free atmospheric O2 in the Early Earth !!! (not found in volcanic gases)
Present day volcanic gases • Water Vapor 50--60% • Carbon Dioxide 24% • Sulfur 13% • Nitrogen 5.7% • Argon 0.3% • Chlorine 0.1%
Atmospheric composition on the early Earth - still largely guesswork
Water
Hydrogen escapes
Nitrogen
To atmosphereWater
To oceans
Oxygen
Oxygen
Erosional debris
Volcano
Sun
Radiant energy
Hydrogen escapes
Photo-synthesis
Carbon dioxide
Figure by MIT OCW.
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Atmosphere of Earth and its planetary neighbors -
Why so different ?
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Summary of data on the probable chemical composition of the atmosphere over time
Stage 1 (Early Earth) Stage 2 (~2 x 109 years ago) Stage 3 (Today)
Major components (p > 10-2 atm)
CO2 (10 bar)
CO2 (10-3 bar)CO2
SO2
O2CO
CONO
(CO?)
N2 (1 bar) N2
H2 (?)
H2S (?)
NH3 (?)
H2O
H2SNH3
CH4 CH4
H2O H2O
O2 (?)
O2 (10-13 bar)
H2 (?) / CH4
N2
Minor components ( 10-2 > p > 10-6 atm )
Argon
ArgonArgon
Trace components ( p < 10-6 atm )
HeHe HeNe Ne
Ne
Table: the probable chemical composition of the atmosphere over time
Figure by MIT OCW.
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Summary of some of the early Earth conditions
Lots of bolide impacts, volcanic activity
Much warmer average global temperature than today (80°C ?)
Mildly reducing conditions in the atmosphere (CO,CO2, N2,H2O,CH4)
Oceans formed > 3.8 bya (condensation from atm as Earth cooled)
No free oxygen (O2) !!!
Image removed due to copyright restrictions
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Proto-ocean (?)
pH = 2.0 (initial); T = 80oCCO2 and SO2 not very soluble
HCL provides acidityInitially weak content of cations, but increasing to Ca2+, 115 mM; Mg2+, 95 mM; Na+, 120 mM; K+, 60 mM
Redox potential around - 0.5 to 0.0 volts
Early OceanpH = 8.0; T = 55oC
pH = 8.0; T = 25oC
HCO3 (CO2) high; SO4 low; H2S high
Ca2+ > 10 mM
Fe2+, 1 mM; Zn2+ < 10-10 M
Redox potential > 0.0 rising to < 0.4volts
Late Ocean (today)
HCO3 (CO2) high, and SO4 (not H2S) presentAverage concentrations of cations are Ca2+, 10 mM; Mg2+, 105 mM; Na+, 470 mM; K+, 10mM Redox potential up to 0.80 volts at surface (O2)Fe3+, 10-17M
_
_
_
_
2-
2-
The Characteristics of the Ocean on Early Earth and Today
Figure by MIT OCW.
Elements Present
Elements Largely Absent
Fe2+, Mn2+, (Mo6+), V4+, (Ni2+), W6+, (Co2+), Se as H2Se
Cu2+, Cd2+, Zn2+, Cr3+, Ti3+
Some Trace Elements In The Early Sea*
*The assumption is that the pH > 5 and the amount of H2S kept the sea as a reducing medium. The concentration of Mo6+ may have been lower than that of W6+ as Mo is precipitated as MoS2 at low pH.
_
Figure by MIT OCW.
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Diagram removed due to copyright restrictions. See Figure 11-8 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
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THE EARLY EARTH SYSTEM
1) The formation of the Earth 2) Early Earth physical and chemical conditions 3) Atmospheric and ocean “evolution” 4) The evolution of life 5) The evolution of photosynthesis
THE EVIDENCE 1) Isotopic record 2) Rocks and Microfossils 3) Organic Geochemical Record (“molecular fossils”) 4) Molecular Evolution
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1920s. The Oparin-Haldane model Under strongly reducing conditions (theorized to have been present in the atmosphere of the early earth), inorganicmolecules could spontaneously form organic molecules (simple sugars and amino acids).
Inorganic materials - > organic materials
Strongly reducing gases Miller Urey experimentCH4, H2, NH4, H20
E
CH3-CH(NH2)-COOH
amino acids,sugars, etc …å
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Diagrams removed due to copyright restrictions. See Figures 11-11 and 11-5 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
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THE EARLY EARTH SYSTEM
1) The formation of the Earth 2) Early Earth physical and chemical conditions 3) Atmospheric and ocean “evolution” 4) The evolution of life 5) The evolution of photosynthesis
THE EVIDENCE 1) Isotopic record 2) Rocks and Microfossils 3) Organic Geochemical Record (“molecular fossils”) 4) Molecular Evolution
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THE EVIDENCE
Microfossils Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life
J. William SchopfScience, New Series, Vol. 260, No. 5108. (Apr. 30, 1993), pp. 640-646
Diagram removed due to copyright restrictions.
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Image removed due to copyright restrictions. See Figure 11-3 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
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Images of "macrofossils" removed due to copyright restrictions.
Ozark Precambrian
Microbes that make“macrofossils”
Stromatolites
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STROMATOLITES
Stromatolites are formed through the activity of primitive unicellular organisms: cyanobacteria
(which used to be called blue-green algae) and other algae. These grow through sediment and
sand, binding the sedimentary particles together, resulting in successive layers which, over a long
period of time, harden to form rock. For at least three-quarters of the earth's history stromatolites were the main reef building organisms, constructing large masses of calcium carbonate.
Images of stromatolites removed due to copyright restrictions. See Figure 11-2 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 1th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
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STABLE ISOTOPE ANALYSIS, ORGANIC GEOCHEMISTRY,AND THE HISTORY OF LIFE ON EARTH
Internal structure of an atom
Z = number of protons, the number of electrons, the “atomic number” N = number of neutrons, the “neutron number”
A = Z + N the “mass number”
Ex: mass number
14C6 has 6 protons, 6 electrons, and 14-6=8 neutrons
atomic number
Ad-hoc definition of atomic weights
12C has 6 protons and 6 neutrons = 12 subatomic particles with appreciable mass
So … one atom 12C = 12.000000 amu
1 atomic mass unit (amu) = 1/12 the mass of 12C
And … one mole of 12C = 12.000000 g, one mole = 6.022e23 atoms
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Stable isotope abundancesELEMENT
HYDROGEN (Z=l)
CARBON (Z=6)
NITROGEN (Z=7)
OXYGEN (Z=8)
ISOTOPE ATOMIC WEIGHT (amu) ABUNDANCE (atom %)
1.0079 lH (Protium) 1.007825 99.985 2H (D, for Deuterium) 2.014102 0.015
12.011 12C 12 98.9 13C 13.00335 1.1
14.0067 14N 14.003074 99.63 15N 15.00109 0.37
15.9994 16O 15.994915 99.76 17O 16.999131 0.04 18O 17.99916 0.2
From Walker et al. (1989) Nuclides and Isotopes
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ISOTOPE RATIOS, R
ALWAYS: R = HEAVY ISOTOPE/ LIGHT ISOTOPE
THAT IS: R = RARE ISOTOPE / ABUNDANT ISOTOPE
e.g. D/H, 13C/12C, 15N/14N , 18O/16O, 34S/32S
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€
The delta value δ − comparing isotope ratios
In practice, stable isotope measurements are made by massspectroscopy, comparing isotopic ratios of a given sample to
those of a known standard.
Hence use δ-value:-
δx = 1000 Rx − Rstd
Rstd
‰ (permil)
Written δD (δ2H), δ13C, δ15N etc.
δx>0 ⇒ Rx “heavier” than Rstd (δx<0 ⇒ Rx “lighter” than Rstd)
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Non-Equilibrium FractionationKinetic Isotope Effects
Bonds involving “light” isotopes break more readily than those involving “heavy” isotopes.
Rate determining step which includes breaking of bond dictates isotopic fractionation of entire process
Typical of processes which are unidirectional and irreversible
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Biological Fractionation ! Example: Breathing - we use 16O preferentially for respiration, so 17O and 18O become progressively more abundant in lung air and exhaled air)
Example: During photosynthesis, green plants “fix” CO2 1. Primary step is diffusion of CO2 atm into stomata
Photograph of stomata removed due to copyright restrictions.
2. Preferential utilization of “light” carbon by CO2-fixing enzymes Preferential incorporation of 12C in CO2 fixing plants -passed on to herbivores and up the food chain
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Photosynthetic microbial mats in the 3,416-Myr-old oceanMICHAEL M. TICE AND DONALD R. LOWE Nature 431, 549 - 552 (30 September 2004)
Buck Reef Chert a) 3.4 billion years old
b) Laminated mat-like structures
c) Stable carbon isotope signaturesuggests CO2 fixation : δ 13C = -35 o/oo
d) Normal marine sediment Images removed due to copyright restrictions.
(not hydrothermal) δ 13C = -35 o/oo
d) Evidence for photosynthesis> 3.4 Bya ???
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“Molecular fossils” - organic geochemical markers Archaean Molecular Fossils and the Early Rise of Eukaryotes Jochen J. Brocks, Graham A. Logan, Roger Buick, Roger E. Summons (EAPS @ MIT) Science, Vol 285, Issue 5430, 1033-1036 , 13 August 1999
Organic biomarkers from2.7 billion year old shales
A) Steranes (cholestane) - eukaryotes
B) 2-methyl hopanes - cyanobacteria
Lots of care has to be taken Graphs removed due to copyright restrictions.To ensure organics are derivedfrom the rock was buried - andnot contaminating material.Hard stuff to do !!!
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BANDED IRON FORMATIONS Geochemical evidence
Photographs removed due to copyright restrictions.
Banded iron formations are very large bodies of sedimentary rock laid down Fe2+ very soluble some 2.5 - 1.8 billion years ago. Fe3+ insoluble, precipitates from solution
BIF formation seems to require anoxic deep waters for formation. Thus, if deep-sea O2 became abundant, it could inhibit BIF formation (By formation of Fe-oxyhyriddes, and removal of Fe2+ from solution, precluding its transport to BIF formation zones.)
(BUT, alternative theory suggests Fe-sulfides can also highly insoluble. Was it oxygen or sulfide, that ended BIF deposition ??????)
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Something BIG happened ~2.5 bya !!!
“Red beds” Photographs removed due to copyright restrictions. 900 Ma - 150 Ma
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Time before Present (Ga)
P O2 (a
tm)
1
0.1
0.01
0.001
0.0001
0.00001 4.5 4 3.5 3 2.5 2 1.5 1 0.5 0
Multi-cell Life
Man
ProkaryoteWorld
First Eukaryotes
First Invertebrates
LifeLife’’s History on Earths History on Earth
GREAT OXIDATION EVENT - 2.5 BILLION YEARS AGO