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The Symbiontic Nature of Metabolic Evolution

  • S. A. L. M. Kooijman
  • R. Hengeveld

Abstract

We discuss evolutionary aspects of metabolism, right from the beginning of life to the present day at various levels of organization, thereby including quantitative aspects on the basis of the Dynamic Energy Budget (DEB) theory. We propose a scheme for the evolution of the central metabolism with archaeal as well as eubacterial roots. After an extended initial phase of prokaryotic diversification, cycles of exchange of metabolites between partners in a symbiosis, integration of partners into new individuals and new specializations led to forms of symbiosis of various intensity ranging from loosely living together in species aggregates to several forms of endosymbiosis. While the prokaryotic metabolism evolved into a considerable chemical diversity, the eukaryotic metabolic design remained qualitatively the same but shows a large organizational diversity. Homeostasis of biomass evolved, introducing stoichiometric constraints on production and excretion of products that can be re-utilized; carbohydrates and inorganic nitrogen being the most important ones. This stimulates the formation of symbioses, since most are based on syntrophy, which is probably the basis of the huge biodiversity. A remarkable property of DEB theory for metabolic organization is that organisms of two species that exchange products, and thereby follow the DEB rules, can together follow a symbiogenic route such that the symbiosis behaves as a new organism that itself follows the DEB rules. This property of the reserve dynamics in the DEB theory also explains a possible evolutionary route to homeostasis. The reserve dynamics in DEB theory also plays a key role in linking the kinetics of metabolic pathways to needs of metabolites at the cellular level. Moreover, reserve kinetics, in combination with other DEB elements, explains how metabolic performance depends on body size and why such relationships work out differently within and between species. Apart from the key role of reserves, the dynamic interaction between surface areas and volumes is a basic feature of the DEB theory at all levels of organization (molecules, individuals, ecosystems). The explicit mass and energy balances of the DEB theory facilitates ecosystem modelling as it depends on nutrient exchange. The theoretical interest in this topic concerns the huge range in space-time scales that is involved in understanding the significance of the actions of life within the context of metabolic organization.

Keywords

Anaerobic Ammonium Oxidation Calvin Cycle Domoic Acid Central Metabolism Metabolic Organization 
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.

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References

  1. Alberts, B., A. Johnson, J. Leweis, M. Raff, K. Robert and P. Walter (2002). Molecular Biology of the Cell. Garland Science, New York.Google Scholar
  2. Amend, J. P. and E. L. Shock (2001). Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiological Reviews 25: 175–243.Google Scholar
  3. Anbar, A. D. and A. H. Knoll (2002). Proterozoic ocean chemistry and evolution: A bioinorganic bridge? Science 297: 1137–1142.CrossRefGoogle Scholar
  4. Andersson, J. O. and A. J. Roger (2002). A cyanobacterial gene in nonphotosybthetic protests — an early chloroplast acquisition in eukaryotes? Current Biology 12: 115–119.CrossRefGoogle Scholar
  5. Andersson, S. G. E., A. Zomorodipour, J. O. Andersson, T. Sicheritz-Pontén, U. C. M. Alsmark, R.M. Podowski, A. K. Nälund, A.-S. Eriksson, H. H. Winkler and C. G. Kurland (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396: 133–143.CrossRefGoogle Scholar
  6. Bakker, B. (1998). Control and Regulation of Glycolysis in Trypanosoma brucei. PhD Thesis, Vrije Universiteit, Amsterdam.Google Scholar
  7. Baltscheffsky, H. (1996). Energy conversion leading to the origin and early evolution of life: did inorganic pyrophosphate precede adenosine triphosphate? In: Baltscheffsky, H. (Ed.). Origin and Evolution of Biological Energy Conversion. VCH Publishers, Cambridge. pp. 1–9.Google Scholar
  8. Baltscheffsky, M., A. Schultz and H. Baltscheffsky (1999). H+-P pases: a tightly membrane-bound family. FEBS Letters 457: 527–533.CrossRefGoogle Scholar
  9. Barth, F. G. (1991). Insects and Flowers. Princeton University Press, Princeton.Google Scholar
  10. Bengtson, S. (1994). Early Life on Earth. Columbia University Press, New York.Google Scholar
  11. Bernard, C, A. G. B. Simpson and D. J. Patterson (2000). Some free-living flagellates (Protista). from anoxic habitatats. Ophelia 52: 113–142.Google Scholar
  12. Bigay, J., P. Guonon, S. Robineau and B. Antonny (2003). Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer urvature. Nature 426: 563–566.CrossRefGoogle Scholar
  13. Birky, C. W. (2001). The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms, and models. Annual Review of Genetics 35: 125–148.CrossRefGoogle Scholar
  14. Bjerrum, C. J. and D. E. Canfield (2002). Ocean productivity before about 1.9 Gyr ago limited by phosphorus adsorption onto iron oxides. Nature 417: 159–162.CrossRefGoogle Scholar
  15. Blankenship, R. E. and H. Hartman (1992). Origin and early evolution of photosynthesis. Photosynthesis Research 33: 91–111.CrossRefGoogle Scholar
  16. Blankenship, R. E. and H. Hartman (1998). The origin and evolution of oxygenic photosynthesis. Trends in Biochemical Sciences 23: 94–97.CrossRefGoogle Scholar
  17. Boyce, A. J., M. L. Coleman and M. J. Russell (1983). Formation of fossil hydrothermal chimneys and mounds from Silvermines, Ireland. Nature 306: 545–550.CrossRefGoogle Scholar
  18. Brandt, B. W. (2002). Realistic Characterizations of Biodegradation. PhD Thesis. Vrije Universiteit, Amsterdam.Google Scholar
  19. Brandt, B. W. and S. A. L. M. Kooijman (2000). Two parameters account for the flocculated growth of microbes in biodegradation assays. Biotechnology and Bioengineering 70: 677–684.CrossRefGoogle Scholar
  20. Brandt, B. W., I. M. M. van Leeuwen and S. A. L. M. Kooijman (2003). A general model for multiple substrate biodegradation. Application to co-metabolism of non structurally analogous compounds. Water Research 37: 4843–4854.CrossRefGoogle Scholar
  21. Brocks, J. J., G. A. Logan, G. A. Logan, R. Buick and R. E. Summons (1999). Archean molecular fossils and the early rise of eukaryotes. Science 285: 1033–1036.CrossRefGoogle Scholar
  22. Cairns-Smith, A. G., A. J. Hall and M. J. Russell (1992). Mineral theories of the origin of life and an iron sulphide example. Origins Life and Evolution of the Biosphere 22: 161–180.CrossRefGoogle Scholar
  23. Cavalier-Smith, T. A. (1987a). The simulataneous origin of mitochondria, chloroplasts and microbodies. Annals of the New York Academy of Sciences 503: 55–71.Google Scholar
  24. Cavalier-Smith, T. A. (1987b). The origin of cells, a symbiosis between genes, catalysts and membranes. Cold Spring Harbor Symposia on Quantitative Biology 52: 805–824.Google Scholar
  25. Cavalier-Smith, T. A. (1998). A revised six-kingdom system of life. Biological Reviews 73: 203–266.Google Scholar
  26. Cavalier-Smith, T. A. (2000). Membrane heredity and early chloroplast evolution. Trends in Plant Sciences 5: 174–182.CrossRefGoogle Scholar
  27. Cavalier-Smith, T. A. (2002a). Chloroplast evolution: Secondary symbiogenesis and multiple losses. Current Biology 12: R62–64.CrossRefGoogle Scholar
  28. Cavalier-Smith, T. A. (2002b). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52: 297–354.Google Scholar
  29. Chela-Flores, J. (1998). First step in eukaryogenesis: Physical phenomena in the origin and evolution of chromosome structure. Origins of Life and Evolution of the Biosphere 28: 215–225.CrossRefGoogle Scholar
  30. Dalsgaard, T., D. E. Canfield, J. Petersen, B. Thamdrup and J. Acuna-Gonzalez (2003). N-2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422: 606–608.CrossRefGoogle Scholar
  31. de Duve, C. (1984). A Guided Tour of the Living Cell. Scientific American Library, New York.Google Scholar
  32. Deamer, D. W. and R. M. Pashley (1989). Amphiphilic components of the Murchison carbonaceous chondrite; surface properties and membrane formation. Origins of Life and Evolution of the Biosphere 19: 21–38.CrossRefGoogle Scholar
  33. DeLuca, T. H., O. Zackrisson, M.-C. Nilsson and A. Sellstedt (2002). Quantifying nitrogen-fixation in feather moss carpets of boreal forests. Nature 419: 917–920.CrossRefGoogle Scholar
  34. Delwiche, C. F. (1999). Tracing the thread of plastid diversity through the tapestry of life. American Naturalist 154: S164–S177.CrossRefGoogle Scholar
  35. Dennis, C. (2003). Close encounters of the jelly kind. Nature 426: 12–14.CrossRefGoogle Scholar
  36. Derelle, E., C. Ferraz, P. Lagoda, S. Eychenié, R. Cooke, F. Regad, X. Sabau, C. Courties, M. Delseny, J. Demaille, A. Picard and H. Moreau (2002). DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): the smallest free-living eukaryotic cell. Journal of Phycology 38: 1150–1156.CrossRefGoogle Scholar
  37. Dillon, J. G. and R. W. Castenholz (1999). Scytonemin, a cyanobacterial sheath pigment, protects against UVC Radiation: implications for early photosynthetic life. Journal of Phycology 35: 673–681.CrossRefGoogle Scholar
  38. Dismukes, G. C., V. V. Klimov, S. V. Baranov, Yu. N. Kozlov, J. DasGupta and A. Tyryshkin (2001). The origin of atmospheric oxygen on earth: the innovation of oxygenic photosynthesis. Proceedings of the National Academy of Sciences of the USA 98: 2170–2175.CrossRefGoogle Scholar
  39. Dixon, P. S. (1973). Biology of the Rhodophyta. Oliver and Boyd, Edinburgh.Google Scholar
  40. Doolittle, W. F. (1999). Phylogenetic classification and the universal tree. Science 284: 2124–2128.CrossRefGoogle Scholar
  41. Dubilier, N., C. Mulders, T. Felderman, D. de Beer, A. Pernthaler, M. Klein, M. Wagner, C. Erséus, F. Thiermann, J. Krieger, O. Giere and R. Amann (2001). Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature 411: 298–302.CrossRefGoogle Scholar
  42. Dworkin, M. (1985). Developmental Biology of the Bacteria. Benjamin-Cummings Publishing Company, California.Google Scholar
  43. Elser, J. J. (2004). Biological stoichiometry: a theoretical framework connecting ecosystem ecology, evolution, and biochemistry for application in astrobiology. International Journal of Astrobiology: to appear.Google Scholar
  44. Embley, T. M. and R. P. Hirt (1998). Early branching eukaryotes? Current Opinion in Genetics and Development 8: 624–629.CrossRefGoogle Scholar
  45. Fenchel, T. (2002). Origin and Early Evolution of Life. Oxford University Press, Oxford.Google Scholar
  46. Fenchel, T. and B. L. Finlay (1995). Ecology and Evolution in Anoxic Worlds. Oxford University Press, Oxford.Google Scholar
  47. Forterre, P. and H. Philippe (1999). Where is the root of the universal tree of life? BioEssays 21: 871–879.CrossRefGoogle Scholar
  48. Forterre, P., A. Bergerat, P. Lopez-Garvia (1996). The unique DNA topology and DNA topoisomerase of hyperthermophilic archaea. FEMS Microbiology Reviews 18: 237–248.Google Scholar
  49. Fuhrman, J. (2003). Genome sequences from the sea. Nature 424: 1001–1002.CrossRefGoogle Scholar
  50. Gruenberg, J. (2001). The endocytic pathway: a mosaic of domains. Nature Reviews 2: 721–730.CrossRefGoogle Scholar
  51. Guerrero, R. (1991). Predation as prerequisite to organelle origin: Daptobacter as example. In: Margulis, L. and R. Fester (Eds). Symbiosis as a Source of Evolutionary Innovation. MIT Press, Cambridge, Mass.Google Scholar
  52. Gupta, R. S. (1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiology and Molecular Biology Reviews 62: 1435–1491.Google Scholar
  53. Hartman, H. (1975). Speculations on the origin and evolution of metabolism. Journal of Molecular Evolution 4: 359–370.CrossRefGoogle Scholar
  54. Hartman, H. (1998). Photosythesis and the origin of life. Origins of Life and the Evolution of the Biosphere 28: 515–521.CrossRefGoogle Scholar
  55. Heinrich, B. (1993). The Hot-Blooded Insects. Harvard University Press, Cambridge, Massachusetts.Google Scholar
  56. Heinrich, R. and S. Schuster (1996). The Regulation of Cellular Systems. Chapman and Hall, New York.Google Scholar
  57. Hendrix, R. W., M. C. Smith, R. N. Burns, M. E. Ford and G. F. Hatfull (1999). Evolutionary relationships among diverse bacteriophages: All the world's phage. Proceedings of the National Academy of Sciences of the USA 96: 2192–2197.CrossRefGoogle Scholar
  58. Hengeveld, R. and M. A. Fedonkin (2004). Causes and consequences of eukaryotization through mutualistic endosymbiosis. Acta Biotheoretica 52: 105–154.CrossRefGoogle Scholar
  59. Hibbet, D. S. (2002). When good relationships go bad. Nature 419: 345–346.CrossRefGoogle Scholar
  60. Holland, H. D. (1994). Early proterozoic atmospheric change. In: Bengtson, S. (Ed.). Early life on earth. Columbia University Press, New York: pp 237–244.Google Scholar
  61. Hope, A. B. and N. A. Walker (1975). The Physiology of Giant Algal Cells. Cambridge University Press, Cambridge.Google Scholar
  62. Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer and K. O. Stetter (2002). A new phylum of Archaea represented by nanosized hyperthermophilic symbiont. Nature 417: 63–67.CrossRefGoogle Scholar
  63. Hugenholtz, J. and L. G. Ljungdahl (1990). Metabolism and energy generation in homoacetogenic Clostridia. FEMS Microbiology Reviews 87: 383–389.Google Scholar
  64. Kandler, O. (1998). The early diversification of life and the origin of the three domains: a proposal. In: Wiegel, J. and M. W. W. Adams (Eds). Thermophiles: The keys to molecular evolution and the origin of life. Taylor and Francis, Washington. pp 19–31.Google Scholar
  65. Kasting, J. F. (2001). Earth's early atmosphere. Science 259: 920–925.Google Scholar
  66. Kates, M. (1979). The phytanyl ether-linked polar lipids and isopreniod neutral lipids of extremely halophilic bacteria. Lipids 15: 301–342.Google Scholar
  67. Keefe, A. D., S. L. Miller and G. Bada (1995). Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. Proceedings of the National Academy of Sciences of the USA 92: 11904–11906.Google Scholar
  68. Keeling, P. J. (1998). A kingdom's progress: Archaezoa and the origin of eukaryotes. BioEssays 20: 87–95.CrossRefGoogle Scholar
  69. Kirkpatrick, M. (Ed.). (1993). The evolution of Haploid-Diploid life cycles. Lectures on Mathematics in the Life Sciences 25. American Mathematical Society, Providence, Rhode Island.Google Scholar
  70. Knoll, A. H. (2003). Life on a Young Planet; The First Three Billion Years of Evolution on Earth. Princeton University Press, Princeton.Google Scholar
  71. Koga, Y., T. Kyuragi, M. Nishhihara and N. Sone (1998). Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipids with enantiomeric glycerophosphate backbones caused the separation of the two lines of decent. Journal of Molecular Evolution 46: 54–63.CrossRefGoogle Scholar
  72. Kooi, B. W. and S. A. L. M. Kooijman (2000). Invading species can stabilize simple trophic systems. Ecological Modelling 133: 57–72.CrossRefGoogle Scholar
  73. Kooi, B. W., L. D. J. Kuijper and S. A. L. M. Kooijman (2004). Consequences of symbiosis on food web dynamics in an open system. Journal of Mathematical Biology: to appear.Google Scholar
  74. Kooijman, S. A. L. M. (1986). Energy budgets can explain body size relations. Journal of Theoretical Biology 121: 269–282.Google Scholar
  75. Kooijman, S. A. L. M. (1998). The synthesizing unit as model for the stoichiometric fusion and branching of metabolic fluxes. Biophysical Chemistry 73: 179–188.CrossRefGoogle Scholar
  76. Kooijman, S. A. L. M. (2000). Dynamic Energy and Mass Budgets in Biological Systems. Cambridge University Press, Cambridge.Google Scholar
  77. Kooijman, S. A. L. M. (2001). Quantitative aspects of metabolic organization; a discussion of concepts. Philosophical Transactions of the Royal Society — Series B 356: 331–349.CrossRefGoogle Scholar
  78. Kooijman, S. A. L. M. (2004). On the coevolution of life and its environment. In: Miller, J., P. J. Boston, S. H. Schneider and E. Crist (Eds). Scientists on Gaia: 2000. MIT Press, Cambridge, Massachusetts, Chapter 30, to appear.Google Scholar
  79. Kooijman, S. A. L. M. and L. Segel (2003). How growth affects the fate of metabolites. (to appear).Google Scholar
  80. Kooijman, S. A. L. M., T. R. Andersen and B. W. Kooi (2004). Dynamic energy budget representations of stoichiometric constraints on population dynamics. Ecology 85: 1230–1243.Google Scholar
  81. Kooijman, S. A. L. M., P. Auger, J. C. Poggiale and B. W. Kooi (2003). Quantitative steps in symbiogenesis and the evolution of homeostasis. Biological Reviews 78: 435–463.CrossRefGoogle Scholar
  82. Kroon, D., R. D. Norris and A. Klaus (2001). Western North Atlantic Palaeogene and Cretaceous Palaeoceanography, Geological Society Special Publication 183: 1–319.Google Scholar
  83. Kuijper, L. D. J., T. R. Anderson and S. A. L. M. Kooijman (2003). C and N gross efficiencies of copepod egg production studies using a Dynamic Energy Budget model. Journal of Plankton Research 26: 213–226.CrossRefGoogle Scholar
  84. Kurland, C. G. and S. G. E. Andersson (2000). Origin and evolution of the mitochondrial proteome. Microbiology and Molecular Biology Reviews 64: 786–820.CrossRefGoogle Scholar
  85. Lane, N. (2002). Oxygen, the Molecule that made the World. Oxford University Press, Oxford.Google Scholar
  86. Lee, J. J., G. F. Leedale and P. Bradbury (2000). An Illustrated Guide to the Protozoa. Society of Protozoologists, Lawrence, Kansas.Google Scholar
  87. Leigh, R. A. and D. Sanders (1997). The Plant Vacuole. Academic Press, San Diego.Google Scholar
  88. Lengeler, J. W., G. Drews and H. G. Schlegel (1999). Biology of the Prokaryotes. Thieme Verlag, Stuttgart.Google Scholar
  89. Lindahl, P. A. and B. Chang (2001). The evolution of acetyl-CoA synthase. Origins of Life and Evolution of the Biosphere 31: 403–434.CrossRefGoogle Scholar
  90. Ljungdahl, L. G. (1994). The acetyl-CoA pathway and the chemiosmotic generation of ATP during acetogenesis. In: Drake, H. L. (Ed.). Acetogenesis. Chapman and Hall, New York. pp 63–87.Google Scholar
  91. Madigan, M. T., J. M. Martinko and J. Parker (2000). Brock Biology of Micro-organisms. Prentice Hall International, New Jersey.Google Scholar
  92. Margulis, L. (1970). Origins of Eukaryotic Cells. Freeman, San Francisco.Google Scholar
  93. Martin, M. M. (1987). Invertebrate-Microbial Interactions; Ingested Fungal Enzymes in Arthropod Biology. Comstock Publishers & Associates, Ithaca.Google Scholar
  94. Martin, W. and M. Muller (1998). The hydrogen hypothesis for the first eukaryote. Nature 392: 37–41.CrossRefGoogle Scholar
  95. Martin, W. and M. Russell (2003). On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society — Series B 358: 59–85.CrossRefGoogle Scholar
  96. Martin, W. and C. Schnarrenberger (1997). The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Current Genetics 32: 1–18.CrossRefGoogle Scholar
  97. Martin, W., T. Rujan, E. Richly, A. Hansen, S. Cornelsen, T. Lins, D. Leister, B. Stoebe, M. Hasegawa and D. Penny (2002). Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proceedings of the National Academy of Sciences of the USA 99: 12246–12251.CrossRefGoogle Scholar
  98. McFadden, G. I. (2001). Primary and secondary endosymbiosis and the origin of plastids. Journal of Phycology 37: 951–959.CrossRefGoogle Scholar
  99. Meléndez-Hevia, E. (1990). The game of the pentose phosphate cycle: a mathematical approach to study the optimization in design of metabolic pathways during evolution. Biomedica Biochemica Acta 49: 903–916.Google Scholar
  100. Meléndez-Hevia, E. and A. Isidoro (1985). The game of the pentose phosphate cycle. Journal of Theoretical Biology 117: 251–263.Google Scholar
  101. Michaelis, W., R. Seifert, K. Nauhaus, T. Treude, V. Thiel, M. Blumenberg, K. Knittel, A. Gieseke, K. Peterknecht, T. Pape, A. Boetius, R. Amann, B. B. Jøgensen, F. Widdel, J. Peckmann, N. V. Pimenov and M. B. Gulin (2002). Microbial reefs in the Black Sea fuelled by anaerobic oxidation of methane. Science 297: 1013–1015.CrossRefGoogle Scholar
  102. Misra, J. K. and R. W. Lichtwardt (2000). Illustrated Genera of Trichomycetes; Fungal Symbionts of Insects and Other Arthropods. Science Publishers, Enfield, NH.Google Scholar
  103. Moore, D. (1998). Fungal Morphogenesis. Cambridge University Press, Cambridge.Google Scholar
  104. Morowitz, H. J., J. D. Kostelnik, J. Yang and G. D. Cody (2000). The origin of intermediary metabolism. Proceedings of the National Academy of Sciences of the USA 97: 7704–7708.CrossRefGoogle Scholar
  105. Nisbet, E. G. and C. M. R. Fowler (1999). Archaean metabolic evolution of microbial mate. Proceedings of the Royal Society of London — B — Biological Sciences 266: 2375–2382.CrossRefGoogle Scholar
  106. Nisbet, R. M., E. B. Muller, K. Lika and S. A. L. M. Kooijman (2000). From molecules to ecosystems through Dynamic Energy Budget models. Journal of Animal Ecology 69: 913–926.CrossRefGoogle Scholar
  107. Norris, V. and D. J. Raine (1998). A fission-fusion origin for life. Origins of Life and Evolution of the Biosphere 28: 523–537.CrossRefGoogle Scholar
  108. Olsen, G. J. and C. R. Woese (1996). Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii? Trends in Genetics 12: 377–379.CrossRefGoogle Scholar
  109. Orgel, L. E. (1998). The origin of life — a review of facts and speculations. Trends in Biochemical Sciences 23: 491–495.CrossRefGoogle Scholar
  110. Orgel, L. E. (2000). Self-organizing biochemical cycles. Proceedings of the National Academy of Sciences of the USA 97: 12503–12507.CrossRefGoogle Scholar
  111. Osteryoung, K. W. and J. Nunnari (2003). The division of endosymbiotic organelles. Science 302: 1698–1704.CrossRefGoogle Scholar
  112. Parniske, M. and J. A. Downie (2003). Lock, keys and symbioses. Nature 425: 569–570.CrossRefGoogle Scholar
  113. Patterson, D. J. (1999). The diversity of eukaryotes. American Naturalist 154: S96–S124.CrossRefGoogle Scholar
  114. Proctor, M. and P. Yeo (1973). The Pollination of Flowers. Collins, London.Google Scholar
  115. Rai, A. N., E. Soderback and B. Bergman (2000). Cyanobacterium-plant symbioses. New Phytologist 147: 449–481.CrossRefGoogle Scholar
  116. Raven, J. A. and C. Brownlee (2001). Understanding membrane function. Journal of Phycology 37: 960–967.CrossRefGoogle Scholar
  117. Raven, J. A. and Z. H. Yin (1998). The past, present and future of nitrogenous compounds in the atmosphere, and their interactions with plants. New Phytologist 139: 205–219.CrossRefGoogle Scholar
  118. Rickard, D., I. B. Butler and A. Olroyd (2001). A novel iron sulphide switch and its implications for earth and planetary science. Earth and Planetary Science Letters 189: 85–91.CrossRefGoogle Scholar
  119. Rizzotti, M. (2000). Early Evolution. Birkhauser Verlag, Basel.Google Scholar
  120. Roger, A. J. (1999). Reconstructing early events in eukaryotic evolution. American Naturalist 154: S146–S163.CrossRefGoogle Scholar
  121. Romano, A. H. and T. Conway (1996). Evolution of carbohydrate metabolic pathways. Reseach in Microbiology 147: 448–455.CrossRefGoogle Scholar
  122. Rothenberg, M. E. and Y.-N. Jan (2003). The hyppo hypothesis. Nature 425: 469–470.CrossRefGoogle Scholar
  123. Russell, M. J. and A. J. Hall (1997). The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. Journal of the Geological Society of London 154: 377–402.Google Scholar
  124. Russell, M. J. and A. J. Hall (2002). From geochemistry to biochemistry; chemiosmotic coupling and transition element clusters in the onset of life and photosynthesis. The Geochemical News 133/October: 6–12.Google Scholar
  125. Russell, M. J., R. M. Daniel, A. J. Hall and J. A. Sherringham (1994). A hydrothermally precipitated catalytic iron sulfide membrane as a first step toward life. Journal of Molecular Evolution 39: 231–243.CrossRefGoogle Scholar
  126. Ryan, F. (2003). Darwin's Blind Spot. Texere, New York.Google Scholar
  127. Schalk, J. (2000). A Study of the Metabolic Pathway of Anaerobic Ammonium Oxidation. PhD Thesis, University of Delft.Google Scholar
  128. Schönheit, P. and T. Schafer (1995). Metabolism of hyperthermophiles. World Journal of Microbiology and Biotechnology 11: 26–57.CrossRefGoogle Scholar
  129. Schoonen, M. A. A., Y. Xu and J. Bebie (1999). Energetics and kinetics of the prebiotic synthesis of simple organic and amino acids with the FeS-H2S/FeS2 redox couple as a reductant. Origins of Life and Evolution of the Biosphere 29: 5–32.CrossRefGoogle Scholar
  130. Schoonhoven, L. M., T. Jermy and J. J. A. van Loon (1998). Insect-Plant Biology; From Physiology to Ecology. Chapman and Hall, London.Google Scholar
  131. Schüßler, A. (2002). Molecular phylogeny, taxonomy, and evolution of Geosiphon pyriformis and arbuscular mycorrhizal fungi. Plant and Soil 244: 75–83.CrossRefGoogle Scholar
  132. Segré, D., D. Ben-Eli, D. W. Deamer and D. Lancet (2001). The lipid world. Origins of Life and Evolution of the Biosphere 31: 119–145.CrossRefGoogle Scholar
  133. Selig, M., K. B. Xavier, H. Santos and P. Schönheit (1997). Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyper-thermophilic archaea and the bacterium Thermotoga. Archives of Microbiology 167: 217–232.Google Scholar
  134. Selosse, M.-A. and F. Le Tacon (1998). The land flora: a phototroph-fungus partnership? Trends in Ecology and Evolution 13: 15–20.CrossRefGoogle Scholar
  135. Siegel, J. M. (2003). Why we sleep. Scientific American, Nov. 2003: 72–77.Google Scholar
  136. Simpson, A. G. B. and A. J. Roger (2002). Eukaryotic evolution: getting to the root of the problem. Current Biology 12: R691–693.CrossRefGoogle Scholar
  137. Simpson, P. G. and W. B. Whitman (1993). Anabolic pathways in methanogens. In: Ferry, J. G. (Ed.). Methanogenesis. Chapman and Hall, New York. pp 445–472.Google Scholar
  138. Smith, D. C. and A. E. Douglas (1987). The Biology of Symbiosis. E. Arnold, Baltimore.Google Scholar
  139. Smith, D. J. and G. J. C. Underwood (2000). The production of extracellular carbohydrates by estuarine benthic diatoms: the effects of growth phase and light and dark treatment. Journal of Phycology 36: 321–333.CrossRefGoogle Scholar
  140. Smith, M. L., J. N. Bruhn and J. B. Anderson (1992). The fungus Armillaria bulbosa is among the largest and oldest living organisms. Nature 356: 428–431.CrossRefGoogle Scholar
  141. Snow, B. and D. Snow (1988). Birds and Berries. Poyser, Calton.Google Scholar
  142. Sprent, J. I. (1987). The Ecology of the Nitrogen Cycle. Cambridge University Press, Cambridge.Google Scholar
  143. Staley, J. T., M. P. Bryant, N. Pfennig and J. G. Holt (1989). Bergey's manual of systematic bacteriology. Williams and Wilkins, Baltimore.Google Scholar
  144. Stechmann, A. and T. Cavalier-Smith (2002). Rooting the eukaryote tree by using a derived gene fusion. Science 297: 89–91.CrossRefGoogle Scholar
  145. Stracke, S., C. Kistner, S. Yoshida, L. Mulder, S. Sato, T. Kaneko, S. Tabata, N. Sandal, J. Stougaard, K. Szczyglowski and M. Parniske (2002). A plant receptor-like kinase required for both bacterial and fungal symbiosis Nature 417: 959–962.Google Scholar
  146. Stryer, L. (1988). Biochemistry. W. H. Freeman and Co., New York.Google Scholar
  147. Sullivan, M. B., J. B. Waterbury and S. W. Chisholm (2003). Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424: 1047–1050.CrossRefGoogle Scholar
  148. Taylor, P., T. E. Rummery and D. G. Owen (1979). Reactions of iron monosulfide solids with aqueous hydrogen sulfide up to 160°C. Journal of Inorganic and Nuclear Chemistry 41: 1683–1687.CrossRefGoogle Scholar
  149. Tielens, A. G. M., C. Rotte, J. J. van Hellemond and W. Martin (2002). Mitochondria as we don't know them. Trends in Biochemical Sciences 27: 564–572.CrossRefGoogle Scholar
  150. van den Berg, H. A. (1998). Multiple Nutrient Limitation in Microbial Ecosystems. PhD Thesis, Vrije Universiteit, Amsterdam.Google Scholar
  151. van den Ent, F., L. A. Amos and J. Lowe (2001). Prokaryotic origin of the actin cytoskeleton. Nature 413: 39–44.CrossRefGoogle Scholar
  152. van den Hoek, C., D. G. Mann and H. M. Jahn (1995). Algae; An Introduction to Phycology. Cambridge University Press, Cambridge.Google Scholar
  153. Van Dover, C. L. (2000). The Ecology of Deep-Sea Hydrothermal Vents. Princeton University Press, Princeton.Google Scholar
  154. van Leeuwen, I. M. M. and C. Zonneveld (2001). From exposure to effect: a comparison of modeling approaches to chemical carcinogenesis. Mutations Research 489: 17–45.CrossRefGoogle Scholar
  155. van Leeuwen, I. M. M., F. D. L. Kelpin and S. A. L. M. Kooijman (2002). A mathematical model that accounts for the effects of caloric restriction on body weight and longevity. Biogerontology 3: 373–381.CrossRefGoogle Scholar
  156. van Wensum, J. (1992). Isopods and Pollutants in Decomposing Leaf Litter. PhD Thesis, Vrije Universeit, Amsterdam.Google Scholar
  157. Vánky, K. (1987). Illustrated Genera of Smut Fungi. Cryptogamic Studies Volume 1. Gustav Fischer Verlag, Stuttgart.Google Scholar
  158. Von Dohlen, C. D., S. Kohler, S. T. Alsop and W. R. McManus (2001). Mealybug β — proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412: 433–436.CrossRefGoogle Scholar
  159. Vrede, T. J., D. Dobberfuhl, S. A. L. M. Kooijman and J. J. Elser (2004). The stoichiometry of production — fundamental connections among organism C:N:P stoichiometry, macromolecular composition and growth rate. Ecology 85: 1217–1229.Google Scholar
  160. Wächtershäuser, G. (1988). Pyrite formation, the first energy source for life: A hypothesis. Systematic Applied Microbiology 10: 207–210.Google Scholar
  161. Wächtershäuser, G. (1990). Evolution of the 1st metabolic cycles. Proceedings of the National Academy of Sciences of the USA 87: 200–204.Google Scholar
  162. Waddell, T. G., P. Repovic, E. Melendez-Hevia, R. Heinrich and F. Montero (1997). Optimization of glycolysis: A new look at the efficiency of energy coupling. Biochemical Education 25: 204–205.CrossRefGoogle Scholar
  163. Woese, C. R. (1979). A proposal concerning the origin of life on the planet earth. Journal of Molecular Evolution 12: 95–100.CrossRefGoogle Scholar
  164. Woese, C. R. (2002). On the evolution of cells. Proceedings of the National Academy of Sciences of the USA 99: 8742–8747.CrossRefGoogle Scholar
  165. Wood, R. (1999). Reef Evolution. Oxford University Press, Oxford.Google Scholar
  166. Xiong, J., W. M. Fisher, K. Inoue, M. Nakahara and C. E. Bauer (2000). Molecular evidence for the early evolution of photosynthesis. Science 289: 1724–1730.CrossRefGoogle Scholar
  167. Zachos, J. C., M. W. Wara, S. Bohaty, M. L. Delaney, M. R. Petrizzo, A. Brill, T. J. Bralower and I. Premoli-Silva (2003). A transient rise in tropical sea surface temperature during the Paeocene-Eocene thermal maximum. Science 302: 1551–1554.CrossRefGoogle Scholar
  168. Zubay, G. (2000). Origins of Life on Earth and in the Cosmos. Academic Press, San Diego.Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • S. A. L. M. Kooijman
    • 1
  • R. Hengeveld
    • 2
  1. 1.Department of Theoretical BiologyVrije Universiteit AmsterdamAmsterdam
  2. 2.Department of EcotoxicologyVrije Universiteit AmsterdamAmsterdam

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