Geobiology Spring 2009

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1 MIT OpenCourseWare Geobiology Spring 2009 For information about citing these materials or our Terms of Use, visit:

2 Geobiology 2009 Lecture 6 Biogeochemical Tracers #1 COMMON TRACERS: Elemental abundances Redfield ratio Isotopes See below Biominerals Pyrite, carbonates, silica Isotopics #1: C and S Biological Marker Compounds, Biomarkers See later in the course Acknowledgements: John Hayes, Yanan Shen, Steve Macko, John Hedges

3 Biogeochemical Tracers #1 Isotopics #1: C and S Need to Know: Isotopic nomenclature; definition of atm%, ratio, α, δ, ε How to do simple isotopic calculations including mass balance Names of the CHNOS standards, what they are and the forms that are prepared for analysis What processes cause isotopic fractionation including C, H & N in OM and C & O in limestones; S in pyrite and sulfate

4 Geobiology 2009 Lecture 6 Biogeochemical Tracers #1 Isotopics #1: C and S Assigned Reading for this week and C-cycle Stanley 2 nd Ed Chapter 10, pp The Earth System, Lee R. Kump, James F. Kasting & Robert G. Crane Prentice Hall, Upper Saddle River, NJ, 2004).Chap. 7 Hayes, Introduction to Isotopic Calculations Hayes, J. M., Strauss, H. & Kaufman, A. J. (1999) The abundance of 13C in marine organic matter and isotopic fractionation in the global biogeochemical cycle of carbon during the past 800 Ma Chem. Geol. 161, Other readings Hayes JM 2001 Fractionation of the isotopes of carbon and hydrogen in biosynthetic processes. Reviews in Mineralogy Stable Isotopic Geochemistry, John W. Valley and David R. Cole (eds.) S Ono et al. New insights into Archean sulfur cycle from mass-independent sulfur isotope records from the Hamersley Basin, Australia. Earth and Planetary Science Letters 213 (2003) Y Shen et al., Isotopic evidence for microbial sulphate reduction in the early Archaean era. NATURE VOL 410, 1 MARCH 2001, p77

5 Light isotope abundances Isotope Atom% 1 H H (D) C C N N O O O S S S S 0.014

6 Some concepts about isotope chemistry 13 C Atom percent 13 C = X % 13 C + 12 C 13 C Fractional abundance 13 C = 13 F = 13 C + 12 C Carbon isotope ratio = 13 C 12 C = 13 R R sample -R std The delta value δ in = X 1000 R std 0.00 VPDB 13R = = VPDB

7 Terminology R = X heavy δx heavy = R spl - R std x 1000 X light Rstd Primary Standards Standard mean ocean water Isotope Ratios Ratios x H/ 1 H O/ 16 O O/ 16 O 373 PeeDee belemnite (PDB) 13 C/ 12 C Air 15 N/ 14 N Canyon Diablo meteorite (CDT) 32 S/ 34 S NB Standard for δ 18 O/ 16 O in carbonates is PDB

8 Relationship between an isotope effect and the occurrence of isotopic fractionation R P + Q An Isotope Effect causes a physical phenomenon arising from the mass difference between two isotopes Fractionation an observable quantity

9 Isotope Effects Equilibrium Kinetic Mass Independent Fractionation

10 Origins of Mass Dependent Isotopic Fractionation Equilibrium in a reversible reaction, where the heavier isotope concentrated in the more strongly bonded form: 13 CO 2 (g) + H 12 CO 3 -(aq) = 12 CO 2 (g) + H 13 CO 3 -(aq) Different rates of diffusive transport where: 12 CO 2 diffuses ~1% faster than 13 CO 2 Different rates of reaction in kinetically controlled conversions - the light isotope tends to react faster: most biochemistry

11 Example of equilibrium isotope effects 13 CO 2 (g) + H 12 CO 3- (aq) 12 CO 2 (g) + H 13 CO 3- (aq) K = (0 o C) (30 o C) An equilibrium isotope effects will cause the heavy isotope to accumulate in a particular component to a system at equilibrium Fractionation factor α HCO3-/CO2 = ( 13 C/ 12 C) HCO3 ( 13 C/ 12 C) CO2 It is numerically equal to the equilibrium constant

12 Example of equilibrium isotope effects 13 CO 2 (g) + H 12 CO 3- (aq) 12 CO 2 (g) + H 13 CO 3- (aq) The rule: the heavy isotope goes preferentially to the chemical compound in which the element is bound most strongly Thus, 13 C accumulates in the bicarbonate ion ε = δ CO2 δ HCO (α-1) ~ 7.9

13 Some equilibrium isotope effects Reaction Isotope α equilib* ε CO 2 (g) CO 2 (aq) 13 C CO 2 (g) CO 2 (aq) 18 O CO 2 + H 2 O HCO - 3 +H + 13 C O 2 (g) O 2 (aq) 18 O H 2 O (s) H 2 O (l) 18 O H 2 O (s) H 2 O (l) 2 H NH + 4 NH 3 + H + 15 N * Measured for C except phase transition of water

14 Kinetic Isotope Effect (KIE) KIE occurs when the rate of a chemical reaction is sensitive to atomic mass at a particular position in one of the reacting species The rule: A normal KIE is one which the species containing the lighter isotope tend to react more rapidly

15 Terminology dx h,p /X h,s α = is the kinetic fractionation factor = dx l,p /X l,s Where p is product, s is substrate, h is heavy and l is light. Written precisely this is α = [(δ R ) / (δ P )] ε = 10 3 (α-1) A general approximation is ε = δ P δ R or δ P = δ R ε ε is also called the isotope effect or epsilon!! Equilibrium isotope effects are simply related to kinetic effects by α = k2/k1

16 Example of Kinetic Isotope Effects (KIE) NAD+ NADH + H H 3 C-C-CO 2 H H 3 C-C-SCoA + CO 2 O CoASH O Pyruvate Dehydrogenase ( 12 K/ 13 K) C-2 = The species containing carbon-12 at position 2 reacts times more rapidly that the species containing carbon-13 at that position It is termed a 23 isotope effect

17 Biological carbon fixation (Park & Epstein, GCA 21: ) CO 2(external) 1 2 CO 2(internal) Organic molecule Step 1: the uptake and intracellular diffusion of CO 2 Step 2: the biosynthesis of cellular components

18 Autotrophy CO 2 Fixation Photosynthate (C3-C6 carbohydrates) Biosynthesis Proteins Carbohydrates Lipids Nucleic Acids Hayes, Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes

19 Heterotrophy Organic material, food Assimilation Metabolic intermediates (C3-C6 acids and carbohydrates) Biosynthesis Proteins Carbohydrates Lipids Nucleic Acids Hayes, Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes

20 Carbon fixation (C3 pathway) RuBP Rubisco: ribulose-1,5-bisphosphate carboxylase oxygenase Rubisco catalyzes the carboxylation of RuBP, a 5-carbon molecule. A 6-carbon product is formed as a transient intermediate, but the first stable products are two molecules of PGA, 3 phosphoglyceric acid, C3H7O7P. The carbon number gives its name: C3 photosynthesis ε = 29.4 (O leary, Guy, 1987)

21 Carbon fixation (C4 & CAM pathways) Formation of oxaloacetate from PEP (Phosphoenolpyruvate) catalysed by PEP carboxylase Mesophyll cell Bundle-Sheath cell ATM CO 2 oxaloacetate Æ malate HCO 3 - PEP Å pyruvate Æ malate Å pyruvate CO 2 Calvin cycle CAM (Crassulacean acid metabolism): Use both C3 and C4 metabolism

22 The flow of carbon in the Calvin cycle Rubisco C 5 C 5 C 5 CO 2 CO 2 CO 2 Fixation PGA PGA PGA PGA PGA PGA 6NADPH+6H + Reduction 6NADP + C 3 C 3 C 3 C 3 C 3 C 3 C 5 : RuBP C 3 : threecarbon carbohydrate C 7 C 4 C 6 C 5 Rearrangement (no oxidation or reduction of carbon involved) Net product C 5 C 5 3C 5 + 3CO 2 6C 3 3C 5 + C 3

23 Fractionation of C-Isotopes during Autotrophy Pathway, enzyme C3 Rubisco1 Rubisco2 PEP carboxylase PEP carboxykinase CO 2 +PEP oxaloacetate plants & algae C4 and CAM This could be the basis for a good exam 2-15 question! PEP carboxylase HCO - 3 +PEP CO 2 oxaloacetate 2 plants & Rubisco1 +RUBP 3-PGA x 2 30 algae (C4) Acetyl-CoA CO dehydrog Pyruvate synthase PEP carboxylase PEP carboxykinase Reductive or reverse TCA 3-hydroxypropionate React & substr CO 2 +RUBP CO 2 +RUBP HCO 3 - +PEP CO 2 + 2H+ CoASH CO2 + Ac-CoA HCO 3 - +PEP CO 2 +PEP CO2 + succinyl- CoA (+ others) HCO acetylcoa Product 3-PGA x 2 3-PGA x 2 oxaloacetate AcSCoA pyruvate oxaloacetate Oxaloacetate α- ketoglutarate Malonyl-CoA ε Organisms plants & algae cyanobacteria plants & algae bacteria Bacteria esp green sulfur Green non-s

24 Schematic representation of sample-preparation procedures Combustion (excess O 2 ) Sample sample Reduction H 2 O H 2 CO 2 (MS for 13 C) (MS for 2 H) N 2 (MS for 15 N) Pyrolysis Conversion CO CO 2 excess C (+?) (MS for 18 O)

25 Standard requirements Be used worldwide as the zero point Be homogeneous in composition Be available in relatively large amounts Be easy to handle for chemical preparation and isotope measurements Have an isotope ratio near the middle of the natural variation range

26 Isotopic compositions of primary standards Primary Standards Standard mean ocean water Isotope Ratios Ratios x H/ 1 H O/ 16 O O/ 16 O 373 PeeDee belemnite (PDB) 13 C/ 12 C Air 15 N/ 14 N Canyon Diablo meteorite (CDT) 34 S/ 32 S 22.22

Principles of Isotopic Measurement Mass Analyser Electromagnet Focussing Plates Ion Source Collector Array of Farady cups for simultaneous measurement of all

27 Principles of Isotopic Measurement Mass Analyser Electromagnet Focussing Plates Ion Source Collector Array of Farady cups for simultaneous measurement of all ions of interest Inlet Either a pure gas via a duel inlet system for sample and standard Or a stream of gas containing sample slugs interspersed with standard slugs

28 Natural variability in bulk C-isotopes Marine carbonate Marine bicarbonate Atmospheric CO2 C3 vascular plants C4 vascular plants Eukarotic Algae Photosynthetic bacteria Methanogenic bacteria C, o / oo

29 Organismal variability in bulk C-isotopes 13 C, o/oo Fractions of a marine plankton Pectin Protein Hemicellulose Total Carbohydrate Total Organic Matter Cellulose Lignin-like material Lipids Marine Sediment Degens, 1969

32 Isotopic Mass Balance of Crustal Carbon Reservoirs Image removed due to copyright restrictions. (Des Marais, 2002)

33 Reprise to Evidence of Early Life

34 13 C Evidence for Antiquity of Earthly Life + 5 C carb Recent marine carbonate Marine bicarbonate ± 0 ± 0 5a CO Isua meta sediments -10 ( 3.8x10 9 yr) 6c 3 6d δ 13 C 0 0 Approximate mean Corg 1 5b 6a 6b Fortescue group ( 2.7x10 9 yr) Francevillian series ( 2.1x10 9 yr) Archaean Proterozoic Phanerozoic autotrophs sediments Figure by MIT OpenCourseWare. Time Ga Span of modern values

35 S.J.Mojzsis et al., Evidence for life on Earth before 3,800 million years ago based on isotopically light carbon in graphite in apatite.. Image removed due to copyright restrictions. Cover of Nature, Volume 384, Issue 6604, November But.. Sano et al. 99 report the apatite had U/Pb and Pb/Pb ages of only ~ 1.5 Ga. And.

36 Tracing Life in the Earliest Terrestrial Rock Record, Eos Trans. AGU, 82(47), Fall Meet. Suppl., Abstract P22B-0545, 2001 Lepland, A., van Zuilen, M., Arrhenius, G Text removed due to copyright restrictions. References: Mojzsis,S.J,.Arrhenius,G., McKeegan, K.D.,.Harrison, T.M.,.Nutman, A.P \& C.R.L.Friend.,1996. Nature 384: 55 Schidlowski, M., Appel, P.W.U., Eichmann, R. \& Junge, C.E., Geochim. Cosmochim. Acta 43:

37 13 C Evidence for Antiquity of Earthly Life + 5 C carb Recent marine carbonate Marine bicarbonate ± 0 ± 0 5a CO Isua meta sediments -10 ( 3.8x10 9 yr) 6c 3 6d δ 13 C 0 0 Approximate mean Corg 1 5b 6a 6b Fortescue group ( 2.7x10 9 yr) Francevillian series ( 2.1x10 9 yr) Archaean Proterozoic Phanerozoic sediments Time Ga Figure by MIT OpenCourseWare. Span of modern values

38 Sulfur forms and their oxidation state Compound Formula Oxidation state Sulfide S Polysulfide S 2- n -2, 0 Sulfur S 8 0 Hyposulfite (dithionite) S 2 O Sulfite SO Thiosulfate S 2 O , +6

39 Sulfur forms and their oxidation state Compound Formula Oxidation state Dithionate S 2 O Trithionate S 3 O , +6 Tetrathionate S 4 O , +6 Pentathionate S 5 O , +6 Sulfate SO

40 Abundances of stable sulfur isotopes (MacNamara & Thode, Phys. Rev.) 32 S: 95.02% 33 S: 0.75% 34 S: 4.21% 36 S: 0.02% However, the abundances of stable isotopes may vary from their average values as a result of biological and inorganic reactions, Involving the chemical transformation of sulfur compounds.

41 δ notation δ 34 S = ( 34 S/ 32 S) sample -( 34 S/ 32 S) standard X 1000 ( 34 S/ 32 S) standard Standard: I: troilite (FeS) from the Cañon Diablo meteorite, CDT II: IAEA-S-1 (Ag 2 S), V-CDT

42 Multiple sulfur isotopes 33 S 34 S 36 S 32 S δ 36 S δ 34 S δ 33 S Mass-dependent Fractionation: δ 33 S=0.515δ 34 S, δ 36 S=1.91δ 34 S

43 Dissimilatory sulfate reduction - SO CH 2 O H 2 S + HCO 3 SO H 2 H 2 S + H 2 O 32 S-O bond easier to break than 34 S-O Sulfides become enriched in 32 S and depleted in 34 S

44 Sulfur isotope fractionation The partitioning of isotopes between two substances (H 2 S and SO 4 ) with different isotope ratios Fractionation (ε SR ) = δ 34 S SO4 δ 34 S H2S

45 Biochemical pathway of dissimilatory SR SO 4 2- (out) SO 4 2- (in) APS SO 3 2 H 2 S cell wall Fractionation

46 Tree of Biological Sulfur Cycle SO SO 2 4 SO 4 S 4 O 2 SO S 2 O 2 H 3 2 S S 4 O 2-6 S 2 O 2 S 3 2 O 2-3 S 0 S 0 organic sulfur SO 4 H 2 S 2 H 2 S reduction oxidation disproportionation

47 Empirical Measurements of S-isotopic fractionation during sulfate reduction (Shen and Buick, Earth-Sci. Rev.) Number of occurrences pure cultures natural populations Non-limiting sulfate Fractionation ( ) Courtesy Elsevier, Inc., Used with permission.

48 Pyrite formation and S-isotope preservation Fe 2+ H 2 S SO 4 2- H 2 S FeS FeS 2 S 0 little fractionation (<1 ) Therefore, δ 34 S of pyrites in sedimentary rocks provide indication: I: the activity of SRB (Life) II: conditions of sulfide formation (Environment)

49 Typical δ 34 S values of some geological material (relative to CDT) ocean water sedimentary rocks metamorphic rocks granitic rocks basaltic rocks δ 34 S ( )

50 Isotopic evidence for microbial sulfate reduction 1. Isotope signature is primary from sedimentary rocks 2. δ 34 S values are distinctly shifted to the negative values. 3. Fairly large spread of δ 34 S values for sulfides, and thus large fractionations.

51 The oldest terrestrial S-isotopic records (~3.8 Ga) from the Isua Superacrustal Belt, Greenland (Monster et al., GCA) Narrow range δ 34 S (ave. 0.5±0.9 ) Similar to those of magmatic sulfides

52 Models for low fractionation of 0±5 (~3.8 Ga 2.7 Ga) (Paytan, Science) Non-biological fractionation Low sulphate concentration High SRR Closed system effect Low po 2 po 2 =10-12 atm po 2 = atm po 2 = atm Low SO 2 4 SO 2-4 <1mM SO 2-4 >10mM SO 2-4 >10mM SRB not active SRB active SRB active SRB active T ~ 40 0 C SR Rates> diffusion rates

53 I: Sedimentary stage (~3.47 Ga) (Greatly simplified from Groves et al., Sci. Am.) Evaporation pumice gypsum Archean Ocean BASALT

54 II: Hydrothermal alteration BASALT BaSO 4 BASALT Ba 2+ CaSO 4 2H 2 O BASALT Pb 2+ Si 2+ NO SULFATE

55 Images removed due to copyright restrictions. Photographs of different basalts.

56 macroscopic py Images removed due to copyright restrictions. sulfate microscopic py

57 The δ 34 S of sulfur species from the North Pole barite, northwestern Australia (Shen et al., Nature 410: ) 14 Number of occurrences pyrite barite δ 34 S ( )

58 Isotopic evidence for microbial sulphate reduction in the early Archaean era Yanan Shen*, Roger Buick² & Donald E. Canfield* NATURE VOL MARCH 2000p79-81 Figure by MIT OpenCourseWare. After Shen, Buick and Canfield, Figure 3 The secular trends in the isotopic composition of seawater sulphate and sulphide over geological time. Data within the oval are from this work, the other data are from refs 2, 29. The band (double line) in the upper part of the figure represents the isotopic composition of seawater sulphate through time. The single line in the lower part of the figure is displaced from the seawater sulphate trend by 55per mil, representing themaximum fractionation between sulphate and sulphide through the past 600 million years. Before 1.7 Gyr ago, constraints on the isotopic composition of seawater sulphateare sparse.

59 Mass Independent Fractionation Detectable when there are >2 isotopes fractionated by different mechanisms Seems to apply to gas phase chemistry (eg atmospheric processes in Nature) Examples occur in O 3, O 2, CO 2, CO, N 2 O, H 2 O 2 and sulfate aerosols. The isotopic anomalies are apparently linked to photochemical reactions A well-known example is the transfer, in the stratosphere, of 17 O and 18 O from molecular oxygen to CO 2 via ozone. Oxygenated sulfur species undergo gas phase reactions leading to MIF in the absence of O 2 This is the origin of MIF in Archean sulfur species (eg Farquhar et al) although the precise mechanisms are still to be elucidated

60 Mass Independent Fractionation Fig. 3. A conceptual model of Archean sulfur cycle. Photochemistry in the atmosphere causes MIF in sulfur isotopes, and aerosols of S 8 and H 2 SO 4 carry sulfur with positive (*S) and negative (#S) v33s signatures, respectively. The preservation of MIF signatures in the sediments implies incomplete oxidation of S8 in the ocean (dashed arrow). Courtesy Elsevier, Inc., Used with permission.

61 Mass Independent Fractionation Pyrite MFL 2 Average 1 Values Barite Data from Ga sedimentary sulfides and sulfates. All Phanerozoic sulfides and sulfates plot along the MFL line. Figure by MIT OpenCourseWare. After Farquhar et al., Mass-Independent Fractionation of Sulfur Isotopes in Archean Sediments: Strong Evidence for an Anoxic Archean Atmosphere A.A. PAVLOV and J.F. KASTING ASTROBIOLOGY Volume 2, Number 1, 2002

Mass Independent (Anomalous) Fractionation of O-isotopes in Atmospheric Gases http://www.igac.

A three-isotope plot showing the mass dependent line and the most important deviations for CO

Figure 1. The distribution of ozone isotopomers measured by using enriched mixtures.

62 Mass Independent (Anomalous) Fractionation of O-isotopes in Atmospheric Gases Figure 3. A three-isotope plot showing the mass dependent line and the most important deviations for CO 2, CO, and tropospheric O3. Stratospheric ozone (not shown here) is further enriched. Figure 1. The distribution of ozone isotopomers measured by using enriched mixtures. The asymmetric molecules are formed preferentially. Numbers next to bars indicate molecular Figures courtesy of IGAC. composition, e.g., "667" = 16O16O17O.

63 Summary The wide spread of δ 34 S values of microscopic pyrites aligned along growth faces of former gypsum crystals in the North Pole barite deposit demonstrate that sulfate-reducing prokaryotes had evolved by 3.47 Ga. The large S-isotopic fractionations in this localized and sulfate-rich environment imply that Archean ocean was low in sulfate, and, by implication, low oxygen in the atmosphere.

Geobiology 2013 Lecture 4 Biogeochemical Tracers #1

Geobiology 2013 Lecture 4 Biogeochemical Tracers #1 Isotopics #1: C and S COMMON TRACERS of BIOLOGY: Fossils Elemental abundances Redfield ratio Isotopes See below Biominerals Pyrite, carbonates, silica