Tracing Carbon Fluxes: Resolving Complexity Using Isotopes

  • H. Schnyder
  • U. Ostler
  • C. Lehmeier
  • M. Wild
  • A. Morvan-Bertrand
  • R. Schäufele
  • F. A. Lattanzi
Chapter
Part of the Ecological Studies book series (ECOLSTUD, volume 220)

Abstract

Cells, organisms and ecosystems are interconnected and interdependent metabolic networks, which are operated by carbon substrate fluxes. Isotope methodologies are useful tools for tracing these fluxes. A large diversity of tracer approaches is available for such investigations, ranging from uses of position-labelled 13C substrates in steady-state systems to tracing of natural alterations of isotopic signals in natural conditions. We discuss general principles of different carbon isotope tracer methodologies and specifics of their use in studies of processes at various time frames and scales of biological complexity. Furthermore, we show how “compartmental modelling” can help to characterise the structure and kinetic features of metabolic systems.

Keywords

Metabolic Network Compartmental Modelling Metabolic Flux Analysis Compartmental Analysis Tracer Kinetic 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Allen DK, Libourel IGL, Shachar-Hill Y (2009) Metabolic flux analysis in plants: coping with complexity. Plant Cell Environ 32:1241–1257PubMedCrossRefGoogle Scholar
  2. Atkins GL (1969) Multicompartment models in biological systems. Methuen, LondonGoogle Scholar
  3. Austin RB, Ford MA, Edrich JA (1976) Some effects of leaf posture on photosynthesis any yield in wheat. Ann Appl Biol 83:425–446CrossRefGoogle Scholar
  4. Bahn M, Schmitt M, Siegwolf R, Richter A, Brüggemann N (2009) Does photosynthesis affect grassland soil-respired CO2 and its carbon isotope composition on a diurnal timescale? New Phytol 182:451–460PubMedCrossRefPubMedCentralGoogle Scholar
  5. Bassham JA, Benson AA, Calvin M (1950) The path of carbon in photosynthesis. 8. The role of malic acid. J Biol Chem 185:781–787PubMedGoogle Scholar
  6. Bassham JA, Benson AA, Kay LD, Harris AZ, Wilson AT, Calvin M (1954) The path of carbon in photosynthesis, 21. The cyclic regeneration of carbon dioxide acceptor. J Am Chem Soc 76:1760–1770CrossRefGoogle Scholar
  7. Bender MM (1971) Variations in 13C/12C ratios of plants in relation to pathway of photosynthetic carbon dioxide fixation. Phytochemistry 10:1239–1244CrossRefGoogle Scholar
  8. Benson AA (1951) The identification of Ribulose in 14CO2 photosynthesis products. J Am Chem Soc 73:2971–2972CrossRefGoogle Scholar
  9. Bird MI, Chivas AR, Head J (1996) A latitudinal gradient in carbon turnover times in forest soils. Nature 381:143–146CrossRefGoogle Scholar
  10. Bock M, Glaser B, Millar N (2007) Sequestration and turnover of plant- and microbially derived sugars in a temperate grassland soil during 7 years exposed to elevated atmospheric pCO2. Glob Change Biol 13:478–490CrossRefGoogle Scholar
  11. Bol R, Poirier N, Balesdent J et al (2009) Molecular turnover time of soil organic matter in particle-size fractions of an arable soil. Rapid Commun Mass Spectrom 23:2551–2558PubMedCrossRefGoogle Scholar
  12. Broecker WS, Peng TH, Ostlund G, Stuiver M (1985) The distribution of bomb radiocarbon in the ocean. J Geophys Res Oceans 90(C4):6953–6970CrossRefGoogle Scholar
  13. Buchmann NN, Ehleringer JR (1998) CO2 concentration profiles, and carbon and oxygen isotopes in C3 and C4 crop canopies. Agric Forest Meteorol 89:45–58CrossRefGoogle Scholar
  14. Carbone MS, Trumbore SE (2007) Contribution of new photosynthetic assimilates to respiration by perennial grasses and shrubs: residence times and allocation patterns. New Phytol 176:124–135PubMedCrossRefGoogle Scholar
  15. Carbone MS, Czimczik CI, McDuffee KE, Trumbore SE (2007) Allocation and residence time of photosynthetic products in a boreal forest using a low-level 14C pulse-chase labeling technique. Glob Change Biol 13:466–477CrossRefGoogle Scholar
  16. Cernusak LA, Tcherkez G, Keitel C, Cornwell WK, Santiago LS, Knohl A, Barbour MM, Williams DG, Reich PB, Ellsworth DS, Dawson TE, Griffiths HG, Farquhar GD, Wright IJ (2009) Viewpoint: why are non-photosynthetic tissues generally 13C enriched compared with leaves in C3 plants? Review and synthesis of current hypotheses. Funct Plant Biol 36:199–213CrossRefGoogle Scholar
  17. Ciais P, Tans PP, White JWC, Trolier M, Francey RJ, Berry JA, Randall DR, Sellers PJ, Collatz JG, Schimel DS (1995) Partitioning of ocean and land uptake of CO2 as inferred by δ13C measurements from the NOAA climate monitoring and diagnostics laboratory global air sampling network. J Geophys Res Atmos 100:5051–5070CrossRefGoogle Scholar
  18. De Groot PA (ed) (2004) Handbook of stable isotope analytical techniques, vol I. Elsevier, AmsterdamGoogle Scholar
  19. De Groot PA (ed) (2008) Handbook of stable isotope analytical techniques, vol II. Elsevier, AmsterdamGoogle Scholar
  20. Deines P (1980) The isotopic composition of reduced organic carbon. In: Fritz P, Fontes JC (eds) Handbook of environmental isotope geochemistry, vol 1. The terrestrial environment A. Elsevier, Amsterdam, pp 329–406Google Scholar
  21. Deléens E, Pavlides D, Queiroz O (1983) Natural 13C abundance as a tracer for the determination of leaf matter turn-over in C3 plants. Physiologie Végétale 21:723–729Google Scholar
  22. DeNiro MJ, Epstein S (1977) Mechanisms of carbon isotope fractionation associated with lipid synthesis. Science 197:261–263PubMedCrossRefGoogle Scholar
  23. Ehleringer JR, Buchmann N, Flanagan LB (2000) Carbon isotope ratios in belowground carbon cycle processes. Ecol Appl 10:412–422CrossRefGoogle Scholar
  24. Farquhar GD, Ehleringer JR, Hubick KT (1989) Carbon isotope discrimination and photosynthesis. Annu Rev Plant Physiol Plant Mol Biol 40:503–537CrossRefGoogle Scholar
  25. Fung I, Field CB, Berry JA, Thompson MV, Randerson JT, Malmstrom CM, Vitousek PM, Collatz GJ, Sellers PJ, Randall DA, Denning AS, Badeck F, John J (1997) Carbon 13 exchanges between the atmosphere and biosphere. Glob Biogeochem Cycles 11:507–533CrossRefGoogle Scholar
  26. Gamnitzer U, Schäufele R, Schnyder H (2009) Observing 13C labelling kinetics in CO2 respired by a temperate grassland ecosystem. New Phytol 184:376–386PubMedCrossRefGoogle Scholar
  27. Gamnitzer U, Moyes AB, Bowling DR, Schnyder H (2011) Measuring and modelling the isotopic composition of soil respiration: insights from a grassland tracer experiment. Biogeosciences 8:1333–1350CrossRefGoogle Scholar
  28. Gebbing T, Schnyder H (1999) Pre-anthesis reserve utilization for protein and carbohydrate synthesis in grains of wheat. Plant Physiol 121:871–878PubMedCrossRefPubMedCentralGoogle Scholar
  29. Gebbing T, Schnyder H, Kühbauch W (1998) Carbon mobilization in shoot parts and roots of wheat during grain filling: assessment by 13C/12C steady-state labelling, growth analysis and balance sheets of reserves. Plant Cell Environ 21:301–313CrossRefGoogle Scholar
  30. Geiger DR (1980) Measurement of translocation. Methods Enzymol 69:561–571CrossRefGoogle Scholar
  31. Geiger DR, Fondy BR (1979) Methods for continuous measurement of export from a leaf. Plant Physiol 64:361–365PubMedCrossRefPubMedCentralGoogle Scholar
  32. Geiger DR, Swanson CA (1965) Sucrose translocation in sugar beet. Plant Physiol 40:685–690PubMedCrossRefPubMedCentralGoogle Scholar
  33. Ghashghaie J, Badeck FW, Lanigan G, Nogues S, Tcherkez G, Deléens E, Cornic G, Griffiths H (2003) Carbon isotope fractionation during dark respiration and photorespiration in C3 plants. Phytochem Rev 2:145–161CrossRefGoogle Scholar
  34. Glaser B, Millar N, Blum H (2006) Sequestration and turnover of bacterial- and fungal-derived carbon in a temperate grassland soil under long-term elevated atmospheric pCO2. Glob Change Biol 12:1521–1531CrossRefGoogle Scholar
  35. Gleixner G, Schmidt H-L (1997) Carbon isotope effects on the fructose-1,6-bisphosphate aldolase reaction, origin for non-statistical 13C distributions in carbohydrates. J Biol Chem 272:5382–5387PubMedCrossRefGoogle Scholar
  36. Grams TEE, Werner H, Kuptz D, Ritter W, Fleischmann F, Andersen CP, Matyssek R (2011) A free-air system for long-term stable carbon isotope labeling of adult forest trees. Trees 25:187–198CrossRefGoogle Scholar
  37. Gregory PJ, Atwell BJ (1991) The fate of carbon in pulse-labelled crops of barley and wheat. Plant Soil 136:205–213CrossRefGoogle Scholar
  38. Grimoldi AA, Kavanova M, Lattanzi FA, Schäufele R, Schnyder H (2006) Arbuscular mycorrhizal colonization on carbon economy in perennial ryegrass: quantification by 13CO2/12CO2 steady-state labelling and gas exchange. New Phytol 172:544–553PubMedCrossRefGoogle Scholar
  39. Hanson PJ, Edwards NT, Garten CT, Andrews JA (2000) Separating root and soil microbial contributions to soil respiration: a review of methods and observations. Biogeochemistry 48:115–146CrossRefGoogle Scholar
  40. Haupt-Herting S, Klug K, Fock HP (2001) A new approach to measure gross CO2 fluxes in leaves. Gross CO2 assimilation, photorespiration, and mitochondrial respiration in the light in tomato under drought stress. Plant Physiol 126:388–396PubMedCrossRefPubMedCentralGoogle Scholar
  41. Heinemeyer A, Ineson P, Ostle N, Fitter AH (2006) Respiration of the external mycelium in the arbuscular mycorrhizal symbiosis shows strong dependence on recent photosynthates and acclimation to temperature. New Phytol 171:159–170PubMedCrossRefGoogle Scholar
  42. Hobbie EA, Werner RA (2004) Intramolecular, compound-specific, and bulk carbon isotope patterns in C3 and C4 plants: a review and synthesis. New Phytol 161:371–385CrossRefGoogle Scholar
  43. Högberg P, Högberg MN, Göttlicher SG, Betson NR, Keel SG, Metcalfe DB, Campbell C, Schindlbacher A, Hurry V, Lundmark T, Linder S, Nasholm T (2008) High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms. New Phytol 177:220–228PubMedGoogle Scholar
  44. Jacquez J (1996) Compartmental analysis in biology and medicine. Elsevier, AmsterdamGoogle Scholar
  45. Jahnke S, Stöcklin G, Willenbrink J (1981) Translocation profiles of 11C-assimilates in the petiole of Marsilea quadrifolia L. Planta 153:56–63PubMedCrossRefGoogle Scholar
  46. Johnson D, Leake JR, Ostle N, Ineson P, Read DJ (2002) In situ 13CO2 pulse-labelling of upland grassland demonstrates a rapid pathway of carbon flux from arbuscular mycorrhizal mycelia to the soil. New Phytol 153:327–334CrossRefGoogle Scholar
  47. Jones DA, Smith AM, Woolhouse HW (1983) An apparatus for pulse and pulse-chase experiments with 14CO2 on attached leaves with known, steady-state rates of photosynthesis. Plant Cell Environ 6:161–166CrossRefGoogle Scholar
  48. Keel SG, Siegwolf RTW, Körner C (2006) Canopy CO2 enrichment permits tracing the fate of recently assimilated carbon in a mature deciduous forest. New Phytol 172:319–329PubMedCrossRefGoogle Scholar
  49. Kilian MR, van Geel B, van der Plicht J (2000) 14C AMS wiggle matching of raised bog deposits and models of peat accumulation. Quat Sci Rev 19:1011–1033CrossRefGoogle Scholar
  50. Kodama N, Barnard RL, Salmon Y, Weston C, Ferrio JP, Holst J, Werner RA, Saurer M, Rennenberg H, Buchmann N, Gessler A (2008) Temporal dynamics of the carbon isotope composition in a Pinus sylvestris stand: from newly assimilated organic carbon to respired carbon dioxide. Oecologia 156:737–750PubMedCrossRefGoogle Scholar
  51. Kouchi H, Yoneyama T (1984) Dynamics of carbon photosynthetically assimilated in nodulated soya bean-plants under steady-state conditions. 1. Development and application of 13CO2 assimilation system at a constant 13C abundance. Ann Bot 53:875–882Google Scholar
  52. Kruger NJ, Ratcliffe RG (2009) Insights into plant metabolic networks from steady-state metabolic flux analysis. Biochimie 91:697–702PubMedCrossRefGoogle Scholar
  53. Kruger NJ, Le Lay P, Ratcliffe RG (2007) Vacuolar compartmentation complicates the steady-state analysis of glucose metabolism and forces reappraisal of sucrose cycling in plants. Phytochemistry 68:2189–2196PubMedCrossRefGoogle Scholar
  54. Kuptz D, Fleischmann F, Matyssek R, Grams TEE (2011) Seasonal patterns of carbon allocation to respiratory pools in 60-yr-old deciduous (Fagus sylvatica) and evergreen (Picea abies) trees assessed via whole-tree stable carbon isotope labeling. New Phytol. doi: 10.1111/j.1469-8137.2011.03676.x
  55. Kuzyakov Y (2006) Sources of CO2 efflux from soil and review of partitioning methods. Soil Biol Biochem 38:425–448CrossRefGoogle Scholar
  56. Lattanzi FA, Schnyder H, Thornton B (2005) The sources of carbon and nitrogen supplying leaf growth. Assessment of the role of stores with compartmental models. Plant Physiol 137:383–395PubMedCrossRefPubMedCentralGoogle Scholar
  57. Lattanzi FA, Ostler U, Wild M, Morvan-Bertrand A, Decau M-L, Lehmeier CA, Meuriot F, Prud’homme M-P, Schäufele R, Schnyder H (2012) Fluxes in central carbohydrate metabolism of source leaves in a fructan-storing C3 grass – rapid turnover and futile cycling of sucrose in continuous light under contrasted nitrogen nutrition status. J Exp Bot. doi: 10.1093/jxb/ers020
  58. Leavitt SW, Paul EA, Kimball BA, Hendrey GR, Mauney JR, Rauschkolb R, Rogers H, Lewin KF, Nagy J, Pinter PJ Jr, Johnson HB (1994) Carbon isotope dynamics of free-air CO2-enriched cotton and soils. Agric Forest Meteorol 70:87–101CrossRefGoogle Scholar
  59. Lehmeier CA, Lattanzi FA, Schäufele R, Wild M, Schnyder H (2008) Root and shoot respiration of perennial ryegrass are supplied by the same substrate pools: assessment by dynamic 13C labeling and compartmental analysis of tracer kinetics. Plant Physiol 148:1148–1158PubMedCrossRefPubMedCentralGoogle Scholar
  60. Libourel IGL, Shachar-Hill Y (2008) Metabolic flux analysis in plants: from intelligent design to rational engineering. Annu Rev Plant Biol 59:625–650PubMedCrossRefGoogle Scholar
  61. Loreto F, Delfine S, Di Marco G (1999) Estimation of photorespiratory carbon dioxide recycling during photosynthesis. Aust J Plant Physiol 26:733–736CrossRefGoogle Scholar
  62. Ludwig LJ, Canvin DT (1971) An open gas-exchange system for simultaneous measurement of CO2 and 14CO2 fluxes from leaves. Can J Bot 49:1299–1313CrossRefGoogle Scholar
  63. Meharg AA (1994) A critical review of labeling techniques used to quantify rhizosphere carbon-flow. Plant Soil 166:55–62CrossRefGoogle Scholar
  64. Melzer E, Schmidt HL (1987) Carbon isotope effects on the pyruvate-dehydrogenase reaction and their importance for relative carbon-13 depletion in lipids. J Biol Chem 262:8159–8164PubMedGoogle Scholar
  65. Minchin PEH, Thorpe MR (2003) Using the short-lived isotope 11C in mechanistic studies of photosynthate transport. Funct Plant Biol 30:831–841CrossRefGoogle Scholar
  66. O’Leary MH (1981) Carbon isotope fractionation in plants. Phytochemistry 20:553–567CrossRefGoogle Scholar
  67. Ostle N, Ineson P, Benham D, Sleep D (2000) Carbon assimilation and turnover in grassland vegetation using an in situ 13CO2 pulse labelling system. Rapid Commun Mass Spectrom 14:1345–1350PubMedCrossRefGoogle Scholar
  68. Paterson E, Midwood AJ, Millard P (2009) Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance. New Phytol 184:19–33PubMedCrossRefGoogle Scholar
  69. Pollock CJ, Cairns AJ (1991) Fructan metabolism in grasses and cereals. Annu Rev Plant Physiol Plant Mol Biol 42:77–101CrossRefGoogle Scholar
  70. Randerson JT, Thompson MV, Field CB (1999) Linking 13C-based estimates of land and ocean sinks with predictions of carbon storage from CO2 fertilization of plant growth. Tellus B Chem Phys Meteorol 51:668–678CrossRefGoogle Scholar
  71. Ratcliffe RG, Shachar-Hill Y (2006) Measuring multiple fluxes through plant metabolic networks. Plant J 45:490–511PubMedCrossRefGoogle Scholar
  72. Richter DD, Markewitz D, Trumbore SE, Wells CG (1999) Rapid accumulation and turnover of soil carbon in a re-establishing forest. Nature 400:56–58CrossRefGoogle Scholar
  73. Ryle GJA, Cobby JM, Powell CE (1976) Synthetic and maintenance respiratory losses of 14CO2 in uniculm barley and maize. Ann Bot 40:571–586Google Scholar
  74. Sauer U (2006) Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2:62PubMedCrossRefPubMedCentralGoogle Scholar
  75. Schimel DS (1995) Terrestrial ecosystems and the carbon-cycle. Glob Change Biol 1:77–91CrossRefGoogle Scholar
  76. Schnyder H (1992) Long-term steady-state labelling of wheat plants by use of natural 13CO2/12CO2 mixtures in an open, rapidly turned-over system. Planta 187:128–135PubMedCrossRefGoogle Scholar
  77. Schnyder H, de Visser R (1999) Fluxes of reserve-derived and currently assimilated carbon and nitrogen in perennial ryegrass recovering from defoliation. The regrowing tiller and its component functionally distinct zones. Plant Physiol 119:1423–1435PubMedCrossRefPubMedCentralGoogle Scholar
  78. Schnyder H, Lattanzi FA (2005) Partitioning respiration of C3-C4 mixed communities using the natural abundance 13C approach – testing assumptions in a controlled environment. Plant Biol 7:592–600PubMedCrossRefGoogle Scholar
  79. Schnyder H, Schäufele R, Lötscher M, Gebbing T (2003) Disentangling CO2 fluxes: direct measurements of mesocosm-scale natural abundance 13CO2/12CO2 gas exchange, 13C-discrimination, and labelling of CO2 exchange flux components in controlled environments. Plant Cell Environ 26:1863–1874CrossRefGoogle Scholar
  80. Schuetz R, Kuepfer L, Sauer U (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3:119PubMedCrossRefPubMedCentralGoogle Scholar
  81. Schwender J (ed) (2009) Plant metabolic networks. Springer, Dordrecht, 331 pGoogle Scholar
  82. Spalding KL, Arner E, Westermark PO et al (2008) Dynamics of fat cell turnover in humans. Nature 453:783–787PubMedCrossRefGoogle Scholar
  83. Stenhouse MJ, Baxter MS (1977) Bomb 14C as a biological tracer. Nature 267:828–832PubMedCrossRefGoogle Scholar
  84. Sweetlove LJ, Fell D, Fernie AR (2008) Getting to grips with the plant metabolic network. Biochem J 409:27–41PubMedCrossRefGoogle Scholar
  85. Tcherkez G, Farquhar GD (2005) Carbon isotope effect predictions for enzymes involved in the primary carbon metabolism of plant leaves. Funct Plant Biol 32:277–291CrossRefGoogle Scholar
  86. Tcherkez G, Hodges M (2008) How stable isotopes may help to elucidate primary nitrogen metabolism and its interaction with (photo)respiration in C3 leaves. J Exp Bot 59:1685–1693PubMedCrossRefGoogle Scholar
  87. Tcherkez G, Nogues S, Bleton J, Cornic G, Badeck F, Ghashghaie J (2003) Metabolic origin of carbon isotope composition of leaf dark-respired CO2 in French Bean. Plant Physiol 131:237–244PubMedCrossRefPubMedCentralGoogle Scholar
  88. Tcherkez G, Mahe A, Gauthier P, Mauve C, Gout E, Bligny R, Cornic G, Hodges M (2009) In folio respiratory fluxomics revealed by 13C isotopic labeling and H/D isotope effects highlight the noncyclic nature of the tricarboxylic acid “cycle” in illuminated leaves. Plant Physiol 151:620–630PubMedCrossRefPubMedCentralGoogle Scholar
  89. Thorpe MR, Minchin PEH (1991) Continuous monitoring of fluxes of photoassimilate in leaves and whole plants. J Exp Bot 42:461–468CrossRefGoogle Scholar
  90. Trumbore SE (2006) Carbon respired by terrestrial ecosystems – recent progress and challenges. Glob Change Biol 12:141–153CrossRefGoogle Scholar
  91. Trumbore SE (2009) Radiocarbon and soil carbon dynamics. Annu Rev Earth Planet Sci 37:47–66CrossRefGoogle Scholar
  92. Vargas R, Detto M, Baldocchi DD, Allen MF (2010) Multiscale analysis of temporal variability of soil CO2 production as influenced by weather and vegetation. Glob Change Biol 16:1589–1605CrossRefGoogle Scholar
  93. Wild M (2010) The carbon and nitrogen supply systems of leaf growth in perennial ryegrass – characterization by dynamic 15N and 13C labelling and compartmental analysis of tracer influx into the leaf growth zone. Doctoral thesis, Technische Universität MünchenGoogle Scholar
  94. Yakir D, Wang XF (1996) Fluxes of CO2 and water between terrestrial vegetation and the atmosphere estimated from isotope measurements. Nature 380:515–517CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • H. Schnyder
    • 1
  • U. Ostler
    • 1
  • C. Lehmeier
    • 1
  • M. Wild
    • 1
  • A. Morvan-Bertrand
    • 2
  • R. Schäufele
    • 1
  • F. A. Lattanzi
    • 1
  1. 1.Lehrstuhl für GrünlandlehreTechnische Universität MünchenFreisingGermany
  2. 2.UMR INRA-UCBN 950 EVA Ecophysiologie Végétale, Agronomie and Nutritions NCSUniversité de Caen Basse-NormandieCaen CedexFrance

Personalised recommendations