Evolution of Metabolism

Treatise on Geochemistry

Volumn 8-9, Issue , 2003, Pages 41-61

  Nealson, K H ^a   Rye, R ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CO-EVOLUTION; COMPLEX MOLECULES; DIRECT INTERACTIONS; ENERGY; MINERAL DISSOLUTION; MINERAL FORMATION; PROPERTY; REDOX METABOLISM;

METABOLISM;

EID: 84942433521     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B0-08-043751-6/08126-3     Document Type: Chapter

References (125)

1. Anbar A.D. Iron isotope biosignatures: promise and progress. EOS, Trans., AGU 2001, 82:173-179.
2. Anbar A.D., Roe J.E., Barling J., Nealson K.H. Nonbiological fractionation of iron isotopes. Science 2000, 288(5463):126-128.
3. Banfield J.F., Nealson K.H. Geomicrobiology: interactions between microbes and minerals. Mineralogical Society of America 1997, vol. 35.
4. Barghoorn E.S., Tyler S.A. Microorganisms from the Gunflint Chert. Science 1965, 147(3658):563-577.
5. Beard B.L., Johnson C.M., Cox L., Sun H., Nealson K.H., Aguilar C. Iron isotope biosignatures. Science 1999, 285(5435):1889-1892.
6. Beard B.L., Johnson C.M., Skulan J.L., Nealson K.H., Cox L., Sun H. Application of Fe isotopes to tracing the geochemical and biological cycling of Fe. Chem. Geol. 2003, (published online 1/8/03).
7. Beaumont V., Robert F. Nitrogen isotopic composition of organic matter from Precambrian cherts: new keys for nitrogen cycle evolution?. Bull. Soc. Geol. Fr. 1998, 169(2):211-220.
8. Beaumont V., Robert F. Nitrogen isotope ratios of kerogens in Precambrian cherts: a record of the evolution of atmosphere chemistry?. Precamb. Res. 1999, 96(1-2):63-82.
9. Benner S.A., Caraco M.D., Thomson J.M., Gaucher E.A. Evolution-Planetary biology-Paleontological, geological, and molecular histories of life. Science 2002, 296(5569):864-868.
10. Bertrand-Sarfati J., Walter M.R. Stromatolite biostratigraphy. Precamb. Res. 1981, 15(3-4):353-371.
11. Beukes N.J., Doland H., Gutzmer J., Nedachi M., Ohmoto H. Tropical laterites, life on land, and the history of atmospheric oxygen in the Paleoproterozoic. Geology 2002, 30(6):491-494.
12. Bjerrum C.J., Canfield D.E. Ocean productivity before about 1.9 Gyr ago limited by phosphorus adsorption onto iron oxides. Nature 2002, 417(6885):159-162.
13. Blankenship R.E. Molecular Mechanisms of Photosynthesis 2002, Blackwell.
14. Blankenship R.E., Hartman H. The origin and evolution of oxygenic photosynthesis. Trends Biochem. Sci. 1998, 23(3):94-97.
15. Boetius A., Ravenschlag K., Schubert C.J., Rickert D., Widdel F., Gieseke A., Amann R., Jorgensen B.B., Witte U., Pfannkuche O. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 2000, 407(6804):623-626.
16. Bottjer D.J., Etter W., Hagadorn J.W., Tang C.M. Exceptional Fossil Preservation: A Unique View on the Evolution of Marine Life 2002, Columbia University Press.
17. Brasier M.D., Green O.R., Jephcoat A.P., Kleppe A.K., Van Kranendonk M.J., Lindsay J.F., Steele A., Grassineau N.V. Questioning the evidence for Earth's oldest fossils. Nature 2002, 416(6876):76-81.
18. Brochier C., Philippe H. Phylogeny-a non-hyperthermophilic ancestor for bacteria. Nature 2002, 417(6886). 244-244.
19. Brocks J.J., Logan G.A., Buick R., Summons R.E. Archean molecular fossils and the early rise of eukaryotes. Science 1999, 285(5430):1033-1036.
20. Buick R. The antiquity of oxygenic photosynthesis: evidence from stromatolites in sulphate-deficient Archaean lakes. Science 1992, 255:74-77.
21. Butler A. Acquisition and utilization of transition metal ions by marine organisms. Science 1998, 281(5374):207-210.
22. Canfield D.E. A new model for Proterozoic ocean chemistry. Nature 1998, 396(6710):450-453.
23. Canfield D.E., Teske A. Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature 1996, 382(6587):127-132.
24. Canfield D.E., Habicht K.S., Thamdrup B. The Archean sulfur cycle and the early history of atmospheric oxygen. Science 2000, 288(5466):658-661.
25. Cloud P. Atmospheric and hydrospheric evolution on the primitive Earth. Science 1968, 160:729-736.
26. Cloud P. Paleoecological significance of the banded iron-formation. Econ. Geol. 1973, 68(7):1135-1143.
27. Cloud P. Oasis in Space: Earth History from the Beginning 1988, W. W. Norton and Company.
28. Coates J.D., Michaelidou U., Bruce R.A., O'Connor S.M., Crespi J.N., Achenbach L.A. Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. Appl. Environ. Microbiol. 1999, 65(12):5234-5241.
29. Cody G.D., Boctor N.Z., Filley T.R., Hazen R.M., Scott J.H., Sharma A., Yoder H.S. Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science 2000, 289(5483):1337-1340.
30. Cohen Y., Jorgensen B.B., Padan E., Shilo M. Sulfide-dependent anoxygenic photosynthesis in cyanobacterium oscillatoria-limnetica. Nature 1975, 257(5526):489-492.
31. Croal L.R., Johnson C.M., Beard B.L., Newman D.K. Iron isotope fractionation by anoxygenic Fe(II)-phototrophic bacteria. Geochim. Cosmochim. Acta 2003, (in press).
32. DeLong E. Microbiology-Archaeal means and extremes. Science 1998, 280(5363):542-543.
33. DesMarais D.J. Tectonic control of the crustal organic-carbon reservoir during the Precambrian. Chem. Geol. 1994, 114(3-4):303-314.
34. DesMarais D.J., Strauss H., Summons R.E., Hayes J.M. Carbon isotope evidence for the stepwise oxidation of the Proterozoic environment. Nature 1992, 359(6396):605-609.
35. Detmers J., Bruchert V., Habicht K.S., Kuever J. Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes. Appl. Environ. Microbiol. 2001, 67(2):888-894.
36. Dimroth E., Kimberley M.M. Precambrian atmospheric oxygen-evidence in sedimentary distributions of carbon, sulfur, uranium, and iron. Can. J. Earth Sci. 1976, 13(9):1161-1185.
37. Doolittle R.F., Feng D.F., Tsang S., Cho G., Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 1996, 271(5248):470-477.
38. Doolittle W.F. Lateral DNA transfer: mechanisms and consequences. Nature 2002, 418(6898):589-590.
39. Ehrenreich A., Widdel F. Anaerobic oxidation of ferrous iron by purple bacteria, a new-type of phototrophic metabolism. Appl. Environ. Microbiol. 1994, 60(12):4517-4526.
40. Farquhar J., Bao H.M., Thiemens M. Atmospheric influence of Earth's earliest sulfur cycle. Science 2000, 289(5480):756-758.
41. Farquhar J., Savarino J., Jackson T.L., Thiemens M.H. Evidence of atmospheric sulphur in the martian regolith from sulphur isotopes in meteorites. Nature 2000, 404(6773):50-52.
42. Farquhar J., Wing B.A., McKeegan K.D., Harris J.W., Cartigny P., Thiemens M.H. Mass-independent sulfur of inclusions in diamond and sulfur recycling on early earth. Science 2002, 298(5602):2369-2372.
43. Fedo C.M., Whitehouse M.J. Metasomatic origin of quartz-pyroxene rock, Akilia, Greenland, and implications for Earth's earliest life. Science 2002, 296(5572):1448-1452.
44. Ford G.C., Harrison P.M., Rice D.W., Smith J.M.A., Treffry A., White J.L., Yariv J. Ferritin-design and formation of an iron-storage molecule. Phil. Trans. Roy. Soc. London Ser. B-Biol. Sci. 1984, 304(1121):551-565.
45. Galtier N., Tourasse N., Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Science 1999, 283(5399):220-221.
46. Grotzinger J.P., Knoll A.H. Stromatolites in Precambrian carbonates: evolutionary mileposts or environmental dipsticks?. Ann. Rev. Earth Planet. Sci. 1999, 27:313-358.
47. Grotzinger J.P., Rothman D.H. An abiotic model for stromatolite morphogenesis. Nature 1996, 383(6599):423-425.
48. Habicht K.S., Gade M., Thamdrup B., Berg P., Canfield D.E. Calibration of sulfate levels in the Archean Ocean. Science 2002, 298(5602):2372-2374.
49. Hartman H. The evolution of photosynthesis and microbial mats: a speculation on the banded iron formations. Microbial Mats: Stromatolites 1984, 449-453. Alan R. Liss. Y. Cohen, R.W. Castenholz, H.O. Halvorson (Eds.).
50. Hayes J.M. Global methanotrophy at the Archean-Proterozoic transition. Early Life on Earth 1994, vol. 84:220-236. Columbia University Press. S. Bengtson (Ed.).
51. Higgins I.J., Best D.J., Hammond R.C., Scott D. Methane-oxidizing microorganisms. Microbiol. Rev. 1981, 45(4):556-590.
52. Holland H.D. The Chemical Evolution of the Atmosphere and Oceans 1984, Princeton University Press.
53. Holland H.D., Beukes N.J. A paleoweathering profile from Griqualand West, South-Africa-evidence for a dramatic rise in atmospheric oxygen between 2.2 and 1.9 By BP. Am. J. Sci. 1990, 290A:1-34.
54. Holland H.D., Rye R. Evidence in pre-2.2 Ga paleosols for the early evolution of atmospheric oxygen and terrestrial biota: Comment. Geology 1997, 25(9):857-858.
55. Jackson B.E., McInerney M.J. Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 2002, 415(6870):454-456.
56. Johnson C.M., Skulan J.L., Beard B.L., Sun H., Nealson K.H., Braterman P.S. Isotopic fractionation between Fe(III) and Fe(II) in aqueous solutions. Earth Planet. Sci. Lett. 2002, 195(1-2):141-153.
57. Kamber B.S., Moorbath S. Initial Pb of the Amitsoq gneiss revisited: implication for the timing of early Archaean crustal evolution in West Greenland. Chem. Geol. 1998, 150(1-2):19-41.
58. Kelley D.S., Karson J.A., Blackman D.K., Fruh-Green G.L., Butterfield D.A., Lilley M.D., Olson E.J., Schrenk M.O., Roe K.K., Lebon G.T., Rivizzigno P. An off-axis hydrothermal vent field near the mid-Atlantic ridge at 30 degrees N. Nature 2001, 412(6843):145-149.
59. Kirkham R.V., Roscoe S.M. Atmospheric evolution and ore deposit formation. Resour. Geol. Spec. Issue 1993, 15:1-17.
60. Konhauser K.O., Hamade T., Raiswell R., Morris R.C., Ferris F.G., Southam G., Canfield D.E. Could bacteria have formed the Precambrian banded iron formations?. Geology 2002, 30(12):1079-1082.
61. Lasaga A.C., Ohmoto H. The oxygen geochemical cycle: dynamics and stability. Geochim. Cosmochim. Acta 2002, 66(3):361-381.
62. Laval B., Cady S.L., Pollack J.C., McKay C.P., Bird J.S., Grotzinger J.P., Ford D.C., Bohm H.R. Modern freshwater microbialite analogues for ancient dendritic reef structures. Nature 2000, 407(6804):626-629.
63. Li C.W., Chen J.Y., Hua T.E. Precambrian sponges with cellular structures. Science 1998, 279(5352):879-882.
64. Lipps J. Fossil Prokaryotes and Protists 1993, Blackwell.
65. Maness P.C., Weaver P.F. Evidence for three distinct hydrogenase activities in Rhodospirillum rubrum. Appl. Microbiol. Biotechnol. 2001, 57(5-6):751-756.
66. Margulis L. Symbiosis in Cell Evolution 1981, W. H. Freeman.
67. Michaelis W., Seifert R., Nauhaus K., Treude T., Thiel V., Blumenberg M., Knittel K., Gieseke A., Peterknecht K., Pape T., Boetius A., Amann R., Jorgensen B.B., Widdel F., Peckmann J.R., Pimenov N.V., Gulin M.B. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 2002, 297(5583):1013-1015.
68. Mojzsis S.J., Harrison T.M. Establishment of a 3.83-Ga magmatic age for the Akilia tonalite (southern West Greenland). Earth Planet. Sci. Lett. 2002, 202(3-4):563-576.
69. Mojzsis S.J., Arrhenius G., McKeegan K.D., Harrison T.M., Nutman A.P., Friend C.R.L. Evidence for life on Earth before 3,800 million years ago. Nature 1996, 384(6604):55-59.
70. Nealson K.H. Sediment bacteria: Who's there, what are they doing, and what's new?. Ann. Rev. Earth Planet. Sci. 1997, 25:403-434.
71. Nealson K.H., Ghiorse W.C. Geobiology: Exploring the Interface between the Biosphere and the Geosphere 2001, American Academy of Microbiology.
72. Nealson K.H., Myers C.R. Iron reduction by bacteria-a potential role in the genesis of banded iron formations. Am. J. Sci. 1990, 290A:35-45.
73. Nealson K.H., Saffarini D. Iron and manganese in anaerobic respiration-environmental significance, physiology, and regulation. Ann. Rev. Microbiol. 1994, 48:311-343.
74. Nealson K.H., Stahl D.A. Microorganisms and biogeochemical cycles: What can we learn from layered microbial communities?. Geomicrobiology: Interactions between Microbes and Minerals 1997, vol. 35.
75. Neilands J.B. Microbial iron compounds. Ann. Rev. Biochem. 1981, 50:715-731.
76. Nisbet E.G., Sleep N.H. The habitat and nature of early life. Nature 2001, 409(6823):1083-1091.
77. Ohmoto H. Evidence in pre-2.2 Ga paleosols for the early evolution of atmospheric oxygen and terrestrial biota: Reply. Geology 1997, 25(9):858-859.
78. Oremland R.S., Hoeft S.E., Santini J.A., Bano N., Hollibaugh R.A., Hollibaugh J.T. Anaerobic oxidation of arsenite in Mono Lake water and by facultative, arsenite-oxidizing chemoautotroph, strain MLHE-1. Appl. Environ. Microbiol. 2002, 68(10):4795-4802.
79. Orphan V.J., House C.H., Hinrichs K.U., McKeegan K.D., DeLong E.F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 2001, 293(5529):484-487.
80. Pace N.R. New perspective on the natural microbial world: molecular microbial ecology. ASM News 1996, 62(9):463-470.
81. Padan E. Facultative anoxygenic photosynthesis in cyanobacteria. Ann. Rev. Plant Physiol. Plant Molecul. Biol. 1979, 30:27-40.
82. Pavlov A.A., Kasting J.F. Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere. Astrobiology 2002, 2:27-41.
83. Pope M.C., Grotzinger J.P., Schreiber B.C. Evaporitic subtidal stromatolites produced by in situ precipitation: textures, facies associations, and temporal significance. J. Sedim. Res. 2000, 70(5):1139-1151.
84. Porter S.M., Knoll A.H. Testate amoebae in the Neoproterozoic Era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon. Paleobiology 2000, 26(3):360-385.
85. Ramdohr P. New observations on the ores of the Witwatersrand in South Africa and their genetic significance. Trans. Geol. Soc. S. Afr. 1958, 61:1-50.
86. Rasmussen B. Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature 2000, 405(6787):676-679.
87. Rasmussen B., Buick R. Redox state of the Archean atmosphere: evidence from detrital heavy minerals in ca. 3,250-2,750 Ma sandstones from the Pilbara Craton, Australia. Geology 1999, 27(2):115-118.
88. Raymond J., Zhaxybayeva O., Gogarten J.P., Gerdes S.Y., Blankenship R.E. Whole-genome analysis of photosynthetic prokaryotes. Science 2002, 298(5598):1616-1620.
89. Reid R.P., Visscher P.T., Decho A.W., Stolz J.F., Bebout B.M., Dupraz C., Macintyre L.G., Paerl H.W., Pinckney J.L., Prufert-Bebout L., Steppe T.F., DesMarais D.J. The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. Nature 2000, 406(6799):989-992.
90. Robb L.J., Davis D.W., Kamo S.L., Meyer F.M. Ages of altered granites adjoining the Witwatersrand Basin with implications for the origin of gold and uranium. Nature 1992, 357:677-680.
91. Roger A.J., Silberman J.D. Cell evolution: mitochondria in hiding. Nature 2002, 418(6900):827-829.
92. Rye R., Holland H.D. Paleosols and the evolution of atmospheric oxygen: a critical review. Am. J. Sci. 1998, 298(8):621-672.
93. Rye R., Holland H.D. Geology and geochemistry of paleosols developed on the Hekpoort basalt, Pretoria Group, South Africa (vol. 300, pp. 85, 2000). Am. J. Sci. 2000, 300(4):344-345.
94. Rye R., Holland H.D. Life associated with the 2.76 billion year old Mt. Roe #2 paleosol, Western Australia. Geology 2000, 28:483-486.
95. Rye R., Kuo P.H., Holland H.D. Atmospheric carbon-dioxide concentrations before 2.2-billion years ago. Nature 1995, 378(6557):603-605.
96. Saier M.H. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Molecul. Biol. Rev. 2000, 64(2):354-411.
97. SchȨfer G., Engelhard M., Muller V. Bioenergetics of the archaea. Microbiol. Molecul. Biol. Rev. 1999, 63(3):570-620.
98. Schink B., Friedrich M. Bacterial metabolism-phosphite oxidation by sulphate reduction. Nature 2000, 406(6791). 37-37.
99. Schink B., Thiemann V., Laue H., Friedrich M.W. Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate. Arch. Microbiol. 2002, 177(5):381-391.
100. Schoell M. The hydrogen and carbon isotopic composition of methane from natural gases of various origins. Geochim. Cosmochim. Acta 1980, 44:649-661.
101. 13C depletion in early Precambrian graphites from Superior Province, Canada. Nature 1981, 290:696-699.
102. Schopf J.W. Cradle of Life: The Discovery of Earth's Earliest Fossils 1999, Princeton University Press, Princeton.
103. Schopf J.W., Klein C. The Proterozoic Biosphere: A Multidisciplinary Study 1992, Cambridge University Press.
104. Schopf J.W., Kudryavtsev A.B., Agresti D.G., Wdowiak T.J., Czaja A.D. Laser-Raman imagery of Earth's earliest fossils. Nature 2002, 416(6876):73-76.
105. Semikhatov M.A., Gebelein C.D., Cloud P., Awramik S.M., Benmore W.C. Stromatolite morphogenesis-progress and problems. Can. J. Earth Sci. 1979, 16(5):992-1015.
106. Shen Y.A., Buick R., Canfield D.E. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 2001, 410(6824):77-81.
107. Shock E.L., McCollom T., Schulte M.D. Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems. Origins Life Evol. Biosphere 1995, 25(1-3):141-159.
108. Smock A.M., Bottcher M.E., Cypionka H. Fractionation of sulfur isotopes during thiosulfate reduction by Desulfovibrio desulfuricans. Arch. Microbiol. 1998, 169(5):460-463.
109. Stolz J.F., Oremland R.S. Bacterial respiration of arsenic and selenium. Fems Microbiol. Rev. 1999, 23(5):615-627.
110. Strous M., Fuerst J.A., Kramer E.H.M., Logemann S., Muyzer G., van de Pas-Schoonen K.T., Webb R., Kuenen J.G., Jetten M.S.M. Missing lithotroph identified as new planctomycete. Nature 1999, 400(6743):446-449.
111. Summons R.E., Jahnke L.L., Hope J.M., Logan G.A. 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 1999, 400(6744):554-557.
112. Svetlitchnyi V., Peschel C., Acker G., Meyer O. Two membrane-associated NiFeS-carbon monoxide dehydrogenases from the anaerobic carbon-monoxide-utilizing eubacterium Carboxydothermus hydrogenoformans. J. Bacteriol. 2001, 183(17):5134-5144.
113. Vadas A., Monbouquette H.G., Johnson E., Schroder I. Identification and characterization of a novel ferric reductase from the hyperthermophilic Archaeon Archaeoglobus fulgidus. J. Biol. Chem. 1999, 274(51):36715-36721.
114. van Zuilen M.A., Lepland A., Arrhenius G. Reassessing the evidence for the earliest traces of life. Nature 2002, 418(6898):627-630.
115. Vargas M., Kashefi K., Blunt-Harris E.L., Lovley D.R. Microbiological evidence for Fe(III) reduction on early Earth. Nature 1998, 395(6697):65-67.
116. Walker J.C.G. Suboxic diagenesis in banded iron formations. Nature 1984, 309(5966):340-342.
117. Walker J.C.G. Was the Archean biosphere upside down. Nature 1987, 329(6141):710-712.
118. Walsh M.M., Lowe D.R. Filamentous microfossils from the 3,500-Myr-old Onverwacht Group, Barberton Mountain Land, South-Africa. Nature 1985, 314(6011):530-532.
119. Weinberg E.D. Iron withholding-a defense against infection and neoplasia. Physiol. Rev. 1984, 64(1):65-102.
120. White D.C. In-situ measurement of microbial biomass, community structure and nutritional-status. Phil. Trans. Roy. Soc. London Ser. A: Math. Phys. Eng. Sci. 1993, 344(1670):59-67.
121. Widdel F., Schnell S., Heising S., Ehrenreich A., Assmus B., Schink B. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 1993, 362(6423):834-836.
122. Woese C.R. Bacterial evolution. Microbiol. Rev. 1987, 51(2):221-271.
123. Xiong J., Fischer W.M., Inoue K., Nakahara M., Bauer C.E. Molecular evidence for the early evolution of photosynthesis. Science 2000, 289(5485):1724-1730.
124. Yang W.B., Holland H.D., Rye R. Evidence for low or no oxygen in the late Archean atmosphere from the ∼2.76 Ga Mt. Roe #2 paleosol, Western Australia: Part 3. Geochim. Cosmochim. Acta 2002, 66(21):3707-3718.
125. Yurkov V.V., Beatty J.T. Aerobic anoxygenic phototrophic bacteria. Microbiol. Molecul. Biol. Rev. 1998, 62(3):695-724.