Biogeochemical signatures through time as inferred from whole microbial genomes

American Journal of Science

Volumn 305, Issue 6-8 SPEC. ISS., 2005, Pages 467-502

  Zerkle, Aubrey L ^a   House, Christopher H ^a   Brantley, Susan L ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOCHEMISTRY; EVOLUTION; GEOLOGICAL RECORD; ORIGIN OF LIFE; PALEOENVIRONMENT;

CYANOBACTERIA; PROKARYOTA;

EID: 32644453530     PISSN: 00029599     EISSN: None     Source Type: Journal    
DOI: 10.2475/ajs.305.6-8.467     Document Type: Review

References (214)

1. Altekar, W., and Rajagopalan, R., 1990, Ribulose biphosphate carboxylase activity in halophilic Archaebacteria: Archives of Microbiology, v. 153, p. 169-174.
2. Anbar, A. D., and Knoll, A. H., 2002, Proterozoic ocean chemistry and evolution: A bioinorganic bridge?: Science, v. 297, p. 1137-1142.
3. Andreesen, J. R., and Gottschalk, G., 1969, The occurrence of a modified Entner-doudoroff pathway in Clostridium aceticum: Archives of Microbiology, v. 69, p. 160-170.
4. Arnold, G. L., Anbar, A. D., Barling, J., and Lyons, T. W., 2004, Molybdenum isotope evidence for widespread anoxia in mid-proterozoic oceans: Science, v. 304, p. 87-90.
5. Bansal, A. K., and Meyer, T. E., 2002, Evolutionary analysis by whole-genome comparisons: Journal of Bacteriology, v. 184, p. 2260-2272.
6. Battistuzzi, F. U., Feijao, A., and Hedges, S. B., 2004, A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land: BMC Evolutionary Biology, v. 4, p. 43.
7. Beaumont, V., and Robert, F., 1999, Nitrogen isotope ratios of kerogens in Precambrian cherts: a record of the evolution of atmosphere chemistry?: Precambrian Research, v. 96, p. 63-82.
8. Beh, M., Strauss, R., Huber, R., Stetter, K. O., and Fuchs, G., 1993, Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archeabacterium Thermoproteus neutrophilus: Archives of Microbiology, v. 160, p. 306-311.
9. Belyaev, S. S., Wolkin, R., Kenealy, W. R., DeNiro, M. J., Epstein, S., and Zeikus, J. G., 1983, Methanogenic bacteria from the Bondyuzhskoe Oil field: general characterization and analysis of stable-carbon isotopic fractionation: Applied and Enviromnental Microbiology, v. 45, p. 691-697.
10. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weisseg, H., Shindyalov, I. N., and Bourne, P. E., 2000, The Protein Data Bank: Nucleic Acids Research, v. 28, p. 235-242.
11. Bertine, K. K., and Turekian, K. K., 1973, Molybdenum in marine deposits: Geochimica et Cosmochimica Acta, v. 48, p. 605-615.
12. Blank, C. E., 2004, Evolutionary timing of the origins of mesophilic sulphate reduction and oxygenic photosynthesis: a phylogenomic dating approach: Geobiology, v. 2, p. 1-20.
13. Bokova, E. N., 1954, Oxidation of ethane an propane by certain species of mycobacteria: Mikrobiologiya, v. 23, p. 15-21.
14. 2 reduction: Organic Geochemistry, v. 25, p. 255-262.
15. Brantley, S. L., Liermann, L., Bau, M., and Wu, S., 2001, Uptake of trace metals and rare earth elements from hornblende by a soil bacterium: Geomicrobiology Journal, v. 18, p. 37-61.
16. Brochier, C., Bapteste, E., Moreira, D., and Philippe, H., 2002, Eubacterial phylogeny based on translational apparatus proteins: Trends in Genetics, v. 18, p. 1-5.
17. Brocks, J.J., Logan, G. A., Buick, R., and Summons, R. E., 1999, Archean molecular fossils and the early rise of eukaryotes: Science, v. 285, p. 1033-1036.
18. Brown, J. R., Donady, C. J., Italia, M. J., Marshall, W. E., and Stanhope, M. J., 2001, Universal trees based on large combined protein sequence data sets: Nature Genetics, v. 28, p. 281-285.
19. Bruland, K. W., 1980, Oceanographic distributions of cadmium, zinc, nickel, and copper in the North Pacific: Earth and Planetary Science Letters, v. 47, p. 176-198.
20. Bruland, K. W., 1989, Complexation of Zinc by Natural Organic-Ligands in the Central North Pacific: Limnology and Oceanography, v. 34, p. 269-285.
21. Bruland, K. W., Donat, J. R., and Hutchins, D. A., 1991, Interactive influences of bioactive trace metals on biological production in oceanic waters: Limnology and Oceanography, v. 36, p. 1555-1577.
22. Burgess, B. K., and Lowe, D. J., 1996, Mechanism of molybdenum nitrogenase: Chemical Review, v. 96, p. 2983-3011.
23. Calder, J. A., and Parker, P. L., 1973, Geochemical implications of induced changes in C13 fractionation by blue-green algae: Geochimica et Cosmochimica Acta, v. 37, p. 133-140.
24. Cameron, V., Zhang, Z., House, C. H., and Brantley, S. L., 2004, A search for hydrothermal tungsten ligands, in Wanty, R., and Seal, R., editors, Proceedings of the 11th International Symposium on Water-Rock Interaction: London, Taylor and Francis Group, p. 1269-1273.
25. Canfield, D. E., 1998, A new model for Proterozoic ocean chemistry: Nature, v. 396, p. 450-453.
26. Canfield, D. E., and Teske, A., 1996, Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies: Nature, v. 382, p. 127-132.
27. Chan, M. Mukund, S., Kletzin, A., Adams, M. W. W., and Rees, D. C., 1995, Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase: Science, v. 267, p. 1462-1469.
28. Clarke, G. D., Beiko, R. G., Ragan, M. A., and Charlebois, R. I., 2002, Inferring genome trees by using a filter to eliminate phylogenetically discord sequences and a distance matrix based on mean normalized BLASTP scores: Journal of Bacteriology, v. 184, p. 2072-2080.
29. Collier, R. W., 1985, Molybdenum in the Northeast Pacific Ocean: Limnology and Oceanography, v. 30, p. 1351-1354.
30. Davis, J. B., Chase, H. H., and Raymond, R. L., 1956, Mycobacterium paraffinicum n. sp., a bacterium isolated from soil: Applied Microbiology, v. 4, p. 310-315.
31. de Bont, J. A., 1976, Oxidation of ethylene by soil bacteria: Antonie van Leeuwenhoek, v. 42, p. 59-71.
32. Delwiche, C. F., and Palmer, J. D., 1996, Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids: Molecular Biology and Evolution, v. 13, p. 873-882.
33. Des Marais, D. J., Strauss, H., Summons, R. E., and Hayes, J. M., 1992, Carbon isotope evidence for the stepwise oxidation of the Proterozoic environment: Nature, v. 359, p. 605-609.
34. D'Hondt, S. L., Jorgensen, B. B., Miller, D. J., et al., 2003, Leg 201 Summary: Proceedings of the Ocean Drilling Program, Initial Reports: College Station, Texas, Ocean Drilling Program, v. 201, p. 1-81.
35. Dismukes, G. C., 1996, Manganese enzymes with binuclear active sites: Chemical Review, v. 96, p. 2909-2926.
36. Donat, J. R., and Bruland, K. W., 1995, Trace Elements in the Oceans, in Salbu, B., and Steinnes, E., editors, Trace Elements in Natural Waters: Boca Raton, CRC Press, p. 247-281.
37. Eady, R. R., 1996, Structure-function relationships of alternative nitrogenases: Chemical Review, v. 96, p. 3013-3030.
38. Eitenger, T., and Friedrich, B., 1997, Microbial nickel transport and incorporation into hydrogenases, in Winkelmann, G., and Carrano, C. J., editors, Transition Metals in Microbial Metabolism: Reading, United Kingdom, Hardwood Academic Publishers, p. 235-256.
39. Emerson, S. R., and Huested, S. S., 1991, Ocean anoxia and the concentrations of molybdenum and vanadium in seawater: Marine Chemistry, v. 34, p. 177-196.
40. Felsenstein, J., 1993, PHYLIP (Phylogeny Inference Package), Distributed by the Author: Department of Genetics, University of Washington, Seattle.
41. Finn, M. W., and Tabita, F. R., 2003, Synthesis of catalytically active form III ribulose 1,5-biphosphate carboxylase/oxygenase in archaea: Journal of Bacteriology, v. 185, p. 3049-3059.
42. Fitz-Gibbon, S. T., and House, C. H., 1999, Whole genome-based phylogenetic analysis of free-living microorganisms: Nucleic Acids Research, v. 27, p. 4218-4222.
43. Fox, G. E., Stackebrandt, E., Hespell, R. B., Gibson, J., Maniloff, J., Dyer, T. A., Wolfe, R. S., Balch, W. E., Tanner, R. S., Magrum, L.J., Zablen, L. B., Blakemore, R. P., Gupta, R. S., Bunsen, L., Lewis, B.J., Stahl, D. A., Luehrsen, K. R., Chen, K. N., and Woese, C. R., 1980, The phylogeny of prokaryotes: Science, v. 209, p. 457-463.
44. Frausto da Silva, J. J. R., and Williams, R. J. P., 2001, The Biological Chemistry of the Elements: New York, Oxford University Press, 575 p.
45. Fu, L. M., and Fu-Liu, C. S., 2002, Is Mycobacterium tuberculosis a closer relative to Gram-positive or Gram-negative bacterial pathogens?: Tuberculosis, v. 82, p. 85-90.
46. Fuchs, G., and Stupperich, E., 1978, Evidence for an incomplete reductive carboxylic acid cycle in Methanobacterium thermoautotrophicum: Archives of Microbiology, v. 118, p. 121-125.
47. Fuchs, G., Thauer, R., Ziegler, H., and Stichler, W., 1979, Carbon isotope fractionation by Methanobacterium thermoautotrohicum: Archives of Microbiology, v. 120, p. 135-139.
48. 2 fixation in Chlorobium limicola. Evidence for the operation of a reductive tricarboxylic acid cycle in growing cells: Archives of Microbiology, v. 151, p. 64-71.
49. Gerstein, M., 1998, Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census: PROTEINS: Structure, Function, and Genetics, v. 33, p. 518-534.
50. Gerstein, M., and Hegyi, H., 1998, Comparing genomes in terms of protein structure: surveys of a finite parts list: FEMS Microbiology Reviews, v. 22, p. 277-304.
51. Gogarten, J. P., Doolittle, W. F., and Lawrence, J. G., 2002, Prokaryotic evolution in light of gene transfer: Molecular Biology Evolution, v. 19, p. 2226-2238.
52. Golubic, S., Sergeev, V. N., and Knoll, A. H., 1995, Mesoproterozoic Archaeoellipsoides: akinetes of heterocystons cyanobacteria: Lethaia, v. 28, p. 285-298.
53. Gordon, R. M., Martin, J. H., and Knauer, G. A., 1982, Iron in north-cast Pacific waters: Nature, v. 299, p. 611-612.
54. Gorlenko, V. M., and Pivovarova, T. A., 1977, On the assignment of the blue-green alga Oscillatoria coerulescens Gicklhorn 1921 to the new genus of Chlorobacteria Oscillochloris nov. gen.: Proceedings of the Academy of Sciences of the Estonian SSR: Biology, v. 3, p. 396-409.
55. Guss, J. M., and Freeman, H., 1983, The blue copper electron transfer proteins: Journal of Molecular Biology, v. 169, p. 521-563.
56. Habicht, K. S., Gade, M., Thamdrup, B., Berg, P., and Canfield, D. E., 2002, Calibration of sulfate levels in the Archean ocean: Science, v. 298, p. 2372-2374.
57. Hallam, S. J., Girguis, P. R., Preston, C. M., Richardson, P. M., and DeLong, E. F., 2003, Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing bacteria: Applied and Environmental Microbiology, v. 69, p. 5483-5491.
58. Hausmann, S., and Martin, W., 2000, Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis: International Journal of Systematic and Evolutionary Microbiology, v. 50, p. 1655-1663.
59. Hanson, R. S., and Hanson, T. E., 1996, Methanotrophic bacteria: Microbiological Reviews, v. 60, p. 439.
60. Hanson, T. E., and Tabita, F. R., 2001, A ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress: Proceedings of the National Academy of Sciences, v. 98, p. 4397-4402.
61. Hausinger, R. P., 1987, Nickel utilization in microorganisms: Microbiological Reviews, v. 51, p. 22-42.
62. Hayes, J. M., 2002, Practice and principles of isotopic measurements in organic geochemistry, revision 2: http://www.nosams.whoi.edu/research/ staff_hayes.html.
63. Hayes, J. M., Kaplan, I. R., and Wedeking, K. W., 1983, Precambrian organic geochemistry, preservation of the record, in Schopf, J. W., editor, Earth's Earliest Biosphere: Princeton, Princeton University Press, p. 93-134.
64. Hayes, J. M., Des Marais, I. B., Lambert, H., Strauss, H., and Summons, R. E., 1992, Proterozoic biogeochemistry, in Schopf, J. W., and Klein, C., editors, The Proterozoic Biosphere: New York, Cambridge University Press, p. 81-134.
65. Hersman, L., Lloyd, T., and Sposito, G., 1995, Siderophore-promoted dissolution of hematite: Geochimica et Cosmochimica Acta, v. 59, p. 3327-3330.
66. Hider, R. C., 1984, Siderophore mediated absorption of Fe, in Clarke, M. J., Ibers, J. A., Mingos, D. M. P., Palmer, G. A., Sadler, P. J., and Williams, R. J. P., editors, Structure and bonding: siderophores from microorganisms and plants: Berlin, Springer-Verlag, v. 58, p. 25-87.
67. Hille, R., 1996, The mononuclear molybdenum enzymes: Chemical Review, v. 96, p. 2757-2816.
68. Holland, H. D., 1973, The Oceans: A possible source of iron in iron-formations: Economic Geology and the Bulletin of the Society of Economic Geologists, v. 68, p. 1169-1172.
69. Holland, H. D., 1984, The Chemical Evolution of the Atmosphere and Oceans: Princeton, New Jersey, Princeton University Press, 560 p.
70. Holland, H. D., and Beukes, N. J., 1990, A paleoweathering profile from Griqualand West, South Africa; evidence for a dramatic rise in atmospheric oxygen between 2.2 and 1.9 yBP: American Journal of Science, v. 290-A p. 1-34.
71. Holm, R. H., Kennepohl, P., and Solomon, E. I., 1996, Structural and functional aspects of metal sites in biology: Chemical Review, v. 96, p. 2239-2314.
72. 2 and acetate: Archives of Microbiology, v. 151, p. 252-256.
73. 2 fixaton of Chloroflexus aurantiacus. Archives of Microbiology, v. 145, p. 173-180.
74. House, C. H., ms, 1999, Carbon isotopic fractionation by diverse extant and fossil prokaryotes and microbial diversity revealed through genomics: Ph.D. Dissertation, The University of California at Los Angeles, 208 p.
75. House, C. H., and Fitz-Gibbon, S. T., 2002, Using homolog groups to create a whole-genomic tree of free-living organisms: An update: Journal of Molecular Evolution, v. 54, p. 539-547.
76. House, C. H., Runnegar, B., and Fitz-gibbon, S. T., 2003b, Geobiological analysis using whole-genome based tree building applied to the Bacteria, Archaea, and Eukarya: Geobiology, v. 1, p. 15-26.
77. House, C. H., Schopf, J. W., McKeegan, K. D., Coath, C. D., Harrison, T. M., and Stetter, K. O., 2000, The carbon isotopic composition of individual Precambrian microfossils: Geology, v. 28, p. 707-710.
78. House, C. H., Schopf, J. W., and Stetter, K. O., 2003a, Carbon isotopic fractionation by Archaeans and other thermophilic prokaryotes: Organic Geochemistry, v. 34, p. 345-356.
79. Howard, J. B., and Rees, D. C., 1996, Structural basis of biological nitrogen fixation: Chemical Review, v. 96, p. 2965-2982.
80. Huber, C., and Wachtershauser, G. 1997, Activated acetic acid by carbon fixation on (Fe, Ni)S under primordial conditions: Science, v. 276, p. 245-247.
81. Hughes, M. N., and Poole, R. K., 1989, Metals and Microorganisms: London, Chapman and Hall, 412 p.
82. 2 fixation pathways in archaea (Crenarchaeota): Archives of Microbiology, v. 179, p. 160-173.
83. 2 and energy metabolism in a thermophilic, aerobic and obligately autotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus strain TK-6: Nippon Nogeikagaku Kaishi, v. 72, p. 1165-1170.
84. Ishii, M. T., Miyake, T., Satoh, T., Sugiyams, H., Oshima, Y., Kodama, T., and Igarashi, Y., 1996, Autotrophic carbon dioxide fixation in Acidianus brierleyi: Archives of Microbiology, v. 166, p. 368-371.
85. Ivanovsky, R. N., Fal, Y. I., Berg, I. A. Ugolkova, N. V., Krasilnikova, E. N., Keppen, O. I., Zakharchuc, L. M., and Zyakun, A. M., 1999, Evidence for the presence of the reductive pentose phosphate cycle in a filamentous anoxygenic photosynthetic bacterium, Oscillochloris trichoides strain DG-6: Microbiology, v. 145, p. 1743-1748.
86. Jahnke, L. L., Eder, W., Huber, R., Hope, J. M., Hinrichs, K. U., Hayes, J. M., Des Marais, D.J., Cady, S. L., and Summons, R. E., 2001, Signature lipids and stable carbon isotope analysis of Octopus Spring hydrothermophilic communities compared with those of Aquificales representatives: Applied and Environmental Microbiology, v. 67, p. 5179-5189.
87. Jahnke, L. L., Summons, R. E., Hope, J. M., and Des Marais, D.J., 1999, Carbon isotope fractionation in lipids from methanotrophic bacteria II: The effects of physiology and environmental parameters on the biosynthesis and isotopic signatures of biomarkers: Geochimica et Cosmochimica Acta, v. 63, p. 79-93.
88. Johnson, M. K., Rees, D. C., and Adams, M. W. W., 1996, Tungstoenzymes: Chemical Review, v. 96, p. 2817-2839.
89. Kalinowski, B. E., Liermann, L. J., Givens, S., and Brantley, S. L., 2000, Rates of bacteria-promoted solubilization of Fe from minerals: a review of problems and approaches: Chemical Geology, v. 169, p. 357-370.
90. Kandler, O., 1994, The early diversification of life, in Benston, S., editor, Early Life on Earth: New York, Columbia University Press, p. 152-160.
91. 2 levels in the Proterozoic atmosphere estimated from analyses of individual microfossils: Nature, v. 425, p. 279-282.
92. Keppen, O. I., Baulina, O. I., and Kondratieva, E. N., 1994, Oscillochloris trichoides neotype strain DG-6: Photosynthesis Research, v. 41, p. 29-33.
93. Keppen, O. I., Tourova, T. P., Kuznetsov, B. B., Ivanovsky, R. N., and Gorlenko, V. M., 2000, Proposal of Oscillochloridaceae fam. nov. on the basis of a phylogenetic analysis of the filamentous anoxygenic phototrophic bacteria, and emended description of Oscillochloris and Oscillochloris trichoides in comparison with further new isolates: International Journal of Systematic Evolutionary Microbiology, v. 50, p. 1529-1537.
94. Kisker, C., Schindelin, H., and Rees, D. C., 1997, Molybdenum-cofactor-containing enzymes: Structure and mechanism: Annual Review in Biochemistry, v. 66, p. 233-267.
95. Klappenback, J. A., and Pierson, B. K., 2004, Phylogenetic and physiological characterization of a filamentous anoxygenic photoautotrophic bacterium 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., recovered from hypersaline microbial mats: Archives of Microbiology, v. 181, p. 17-25.
96. Kletzin, A., Mukund, S., Kelley-Crouse, T. L., Chan, M. K., Rees, D. C., and Adams, M. W. W., 1995, Molecular characterization of the genes encoding the tungsten-containing aldehyde ferredoxin oxidoreductase from Pyrococcus furiosus and formaldehyde ferredoxin oxidoreductase from Thermococcus litoralis. Journal of Bacteriology, v. 177, p. 4817-4819.
97. Knoll, A. H., 2003, The geological consequences of evolution: Geobiology, v. 1, p. 3-14.
98. Knoll, A. H., and Canfield, D. E., 1998, Isotopic inferences on early ecosystems: The Paleontological Society Papers, v. 4, p. 211-243.
99. Knoll, A. H., Hayes, J. M., Kaufman, A. J., Swett, K., and Lambert, I. B., 1986, Secular variation in carbon isotope ratios from upper Proterozoic successions of Svalbard and East Greenland: Nature, v. 321, p. 832-838.
100. Korbel, J. O., Snel, B., Huynen, M. A., and Bork, P., 2002, SHOT: a web server for the construction of genome phylogenies: Trends in Genetics, v. 18, p. 158-162.
101. Krüger, M., Meyerdierks, A., Glockner, F. O., Amann, R., Widdel, F., Kube, M., Reinhardt, R., Kahnt, J., Bocher, R., Thauer, R. K., and Shima, S., 2003, A conspicuous nickel protein in microbial mats that oxidize methane anaerobically: Nature, v. 426, p. 878-881.
102. Landing, W. M., and Bruland, K. W., 1987, The contrasting biogeochemistry of iron and manganese in the Pacific Ocean: Geochimica et Cosmochimica Acta, v. 51, p. 29-43.
103. Lepland, A., van Zuilen, M. A., Arrhenius, G., Whitehouse, M. J., and Fedo, C. M., 2005, Questioning the evidence for Earth's earliest life - Akilia revisited: Geology, v. 33, p. 77-79.
104. Lewis, B. L., and Landing, W. M., 1991, The biogeochemistry of manganese and iron in the Black Sea: Deep-Sea Research, v. 38, p. 773-803.
105. Lewis, B. L., and Landing, W. M., 1992, The investigation of dissolved and suspended-particulate trace metal fractionation in the Black Sea, in Millero, F.J., editor, Marine Chemistry: Amsterdam, Elsevier, p. 105-141.
106. Li, W., Fang, W., Ling, L., Wang, J., Xuan, Z., and Chen, R., 2002, Phylogeny based on whole genome as inferred from complete informationset analysis: Journal of Biological Physics, v. 28, p. 439-447.
107. Liermann, L. J., Kalinowski, B. E., Brantley, S. L., and Ferry, J. G., 2000, Role of bacterial siderophores in dissolution of hornblende: Geochimica et Cosmochimica Acta, v. 64, p. 587-602.
108. Lin, J., and Gerstein, M., 2000, Whole genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels: Genome Research, v. 10, p. 808-818.
109. Lipscomb, W. N., and Sträter, N., 1996, Recent advances in zinc enzymology: Chemical Review, v. 96, p. 2375-2433.
110. Londry, K. L., and Des Marais, D. J., 2003, Stable carbon isotope fractionation by sulfate-reducing bacteria: Applied and Environmental Microbiology, v. 69, p. 2942-2949.
111. Londry, K. L., Jahnke, L. L., and Des Marais, D.J., 2004, Stable carbon isotope ratios of lipid biomarkers of sulfate-reducing bacteria: Applied and Environmental Microbiology, v. 70, p. 745-751.
112. L'vov, N. P., Nosikov, A. N., and Antipov, A. N., 2002, Tungsten-containing enzymes: Biochemistry (Moscow), v. 67, p. 196-200.
113. Macalady, J., and Banfield, J. F., 2003, Molecular geomicrobiology; genes and geochemical cycling: Earth and Planetary Science Letters, v. 209, p. 1-17.
114. Madigan, M. T., Takigiku, R., Lee, R. G., Gest, H., and Hayes, J. M., 1989, Carbon isotope fractionation by thermophilic phototrophic sulfur bacteria: Evidence for autotrophic growth in natural populations: Applied and Environmental Microbiology, v. 55, p. 639-644.
115. Marsh, E. N., 1999, Coenzyme B12-dependent enzymes: Essays in Biochemistry, v. 34, p. 139-154.
116. Martin, J. H., and Gordon, R. M., 1988, Northeast Pacific iron distributions in relation to phytoplankton productivity: Deep-Sea Research, v. 35, p. 177-196.
117. Martin, J. H., Gordon, R. M., Fitzwater, S., and Broenkow, W. W., 1989, Vertex - Phytoplankton Iron Studies in the Gulf of Alaska: Deep-Sea Research Part A-Oceanographic Research Papers, v. 36, p. 649-680.
118. Martin, W., and Russell, M. J., 2004, The rocky roots of the acetyl-CoA pathway: Trends in Biochemical Sciences, v. 29, p. 358-363.
119. Martinez-Argudo, I., Little, R., Shearer, N., Johnson, P., and Dixon, R., 2004, The NifI-NifA system: a multidomain transcriptional regulatory complex that integrates environmental signals: Journal of Bacteriology, v. 186, p. 601-610.
120. Matte-Tailliez, O., Brochier, C., Forterre, P., and Philippe, H., 2002, Archaeal phylogeny based on ribosomal proteins: Molecular Biology and Evolution, v. 19, p. 631-639.
121. Meijer, W. G., Arnberg, A. C., Enequist, H. G., Terpstra, P., Lidstrom, M. E., and Dijkhuizen, L., 1991, Identification and organization of carbon dioxide fixation genes in Xanthobacter flavus H4-14: Molecular and General Genetics, v. 225, p. 320-330.
122. Menendez, C., Bauer, Z., Huber, H., Gad'on, N., Stetter, K. O., and Fuchs, G., 1999, Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic crenarchacaota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation: Journal of Bacteriology, v. 181, p. 1088-1098.
123. Mirkin, E., and Ruby, E. G., 1991, Stable carbon isotope fractionation in cultured chemoautotrophic bacteria: General Meeting of the American Society for Microbiology, v. 91, 199 p.
124. 13C of algae: Origins of Life, v. 12, p. 377-390.
125. Mojzsis, S. J., Arrhenius, G., McKeegan, K. D., Harrison, T. M., Nutman, A. P., and Friend, C. R. L., 1996, Evidence for life on Earth before 3,800 million years ago: Nature, v. 384, p. 55-59.
126. Mojzsis, S.J., Harrison, T. M., and Pidgeon, R. T., 2001, Oxygen-isotope evidence from ancient zircons for liquid water at the Earth's surface 4,300 Myr ago: Nature, v. 409, p. 178-181.
127. Morel, F. M. M., and Price, N. M., 2003, The biogeochemical cycles of trace metals in the oceans: Science, v. 300, p. 944-947.
128. Morford, J. L., and Emerson, S., 1999, The geochemistry of redox sensitive trace metals in sediments: Geochimica et Cosmochimica Acta, v. 63, p. 1735-1750.
129. Morowitz, H. J., Kostelnik, J. D., Yang, J., and Cody, G. D., 2000, The origin of intermediary metabolism: Proceedings of the National Academy of Sciences, v. 97, p. 7704-7708.
130. Mukund, S., and Adams, M. W. W., 1991, The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase - evidence or its participation in a unique glycolytic pathway: Journal of Biological Chemistry, v. 266, p. 14208-14216.
131. Neilands, J. B., 1984, Methodology of siderophores, Structure and Bonding: Berlin, Springer-Verlag, p. 1-24.
132. Normand, P., and Bousquet, J., 1989, Phylogeny of the nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms: Journal of Molecular Evolution, v. 29, p. 436-447.
133. Oremland, R. S., Whiticar, M. J., Strohmaier, F. E., and Keine, R. P., 1988, Bacterial ethane formation from reduced ethylated compounds in anoxic sediments: Geochemica et Cosmochimica Acta, v. 52, p. 1895-1904.
134. Orphan, V.J., Hinrichs, K. U., Ussler, W., III., Paull, C. K, Taylor, L. T., Sylva, S. P., Hayes, J. M., and DeLong, E. F., 2001a, Comparitive analysis of methane-oxidizing Archaea and sulfate-reducing bacteria in anoxic marine sediments: Applied and Environmental Microbiology, v. 67, p. 1922-1934.
135. Orphan, V.J., House, C. H., Hinrichs, K. U., McKeegan, K. D., and DeLong, E. F., 2001b, Coupled isotopic and phylogenetic characterization of single cells: direct evidence for a inethane-consuming archaeal/ bacterial consortium: Science, v. 293, p. 484-487.
136. Orphan, V.J., House, C. H., Hinrichs, K. U., McKeegan, K. D., and DeLong, E. F., 2002, Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments: Proceedings of the National Academy of Sciences of the United States of America, v. 99, p. 7663-7668.
137. Orphan, V. J., Ussler, W. I., Naehr, T. H., House, C. H., Hinrichs, K. U., and Paull, C. K., 2004, Geological, geochemical, and microbiological heterogeneity of the seafloor around methane vents in the Eel River Basin, offshore California: Chemical Geology, v. 205, p. 265-289.
138. Outten, C. E., and O'Halloran, T. V., 2001, Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis: Science, v. 292, p. 2488-2492.
139. Pardue, J. W., Scalan, R. S., Van Baalen, C., and Parker, P. L., 1976, Maximum carbon isotope fractionation in photosynthesis by blue-green algae and a green alga: Geochimica et Cosmochimica Acta, v. 40, p. 309-312.
140. 2 species, and sedimentary organic matter within samples from the Blake Ridge: gas source implications, in Paull, C. K., Matsumoto, R., Wallace, P.J., Dillon, W. P., and others, editors, Proceedings of the Ocean Drilling Program, Scientific Results 164: College Station, Texas, Ocean Drilling Program, p. 67-78.
141. Popp, B. N., Laws, E. A., Bidigare, R. P., Dore, J. E., Hanson, K. L., and Wakeham, S. G., 1998, Effect of phytoplankton cell geometry on carbon isotopic fractionation: Geochimica et Cosmochimica Acta, v. 62, p. 69-77.
142. Poulton, S. W., Fralick, P. W., and Canfield, D. E., 2004, The transition to a sulphidic ocean ∼1.84 billion years ago: Nature, v. 431, p. 173-177.
143. 2 fixation pathways: Zeitschrift fur Naturforschung, v. 44c, p. 397-402.
144. Quandt, L., Gottschalk, H., Ziegler, H., and Stichler, W., 1977, Isotope discrimination by photosynthetic bacteria: FEMS Microbiology Letters, v. 1, p. 125-129.
145. Ragsdale, S. W., and Kumar, M., 1996, Nickel-containing carbon monoxide dehydrogenase/Acetyl-CoA synthase: Chemical Review, v. 96, p. 2515-1539.
146. Raven, J. A., 1988, The iron and molybdenum use efficiencies of plant growth with different energy, carbon and nitrogen sources: New Phytologist, v. 109, p. 279-287.
147. Raven, J. A., 1990, Predictions of Mn and Fe use efficiencies of phototrophic growth as a function of light availability for growth and of C assimilation pathway: New Phytologist, v. 116, p. 18-18.
148. Raven, J. A., 1995, The early evolution of land plants: Aquatic ancestors and atmospheric interactions: Botanical Journal of Scotland, v. 47, p. 151-175.
149. 2 fixation in the halophilic archaebacterium, Halobacterium mediterranei: Biochemical and biophysical research communications, v. 156, p. 451-456.
150. Roberts, S., Lane, T., and Morel, F. M. M., 1997, Carbonic anhydrase in the marine diatom Thalassiosira weissflogii (Bacillariophyceae): Journal of Phycology, v. 33, p. 845-850.
151. Robinson, J.J., and Cavanaugh, C. M., 1995, Expression of form I and form II Rubisco in chemoautotrophic symbioses: implications for the interpretation of stable carbon isotope values: Limnology and Oceanography,, v. 40, p. 1496-1502.
152. Roeske, G. A., and O'Leary, M. H., 1984, Carbon isotope effects on the enzyme-catalyzed carboxylation of ribulose biphosphate: Biochemistry, v. 23, p. 6275-6284.
153. Roeske, G. A., and O'Leary, M. H., 1985, Carbon isotope effects on carboxylation of ribulose biphosphate catalyzed by ribulosebiphosphate carboxylase from Rhodospirillum rubrum: Biochemistry, v. 24, p. 1603-1607.
154. Romano, A. H., and Conway, T., 1996, Evolution of carbohydrate metabolic pathways: Research in Microbiology, v. 147, p. 448-455.
155. Rosing, M. T., 1999, C-13-depeleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from west Greenland: Science, v. 283, p. 674-676.
156. Ruby, E. G., Jannasch, H. W., and Deuser, W. G., 1987, Fractionation of stable carbon isotopes during chemoautotrophic growth of sulfur-oxidizing bacteria: Applied and Environmental Microbiology, v. 53, p. 1940-1943.
157. Rue, E. L., and Bruland, K. W., 1995, Complexation of Iron (Iii) by Natural Organic-Ligands in the Central North Pacific as Determined by a New Competitive Ligand Equilibration Adsorptive Cathodic Stripping Voltammetric Method: Marine Chemistry, v. 50, p. 117-138.
158. Ryder, G., 2003, Bombardment of the Hadean earth: Wholesome or deleterious: Astrobiology, v. 3, p. 3-6.
159. Rye, R., and Holland, H. D., 1998, Paleosols and the evolution of atmospheric oxygen: a critical review: American Journal of Science, v. 298, p. 621-672.
160. Saito, M. A., Sigman, D. M., and Morel, F. M. M., 2003, The bioinorganic chemistry of the ancient ocean: the co-evolution of cyanobacterial metal requirements and biogeochemical cycles at the Archean-Proterozoic boundary?: Inorganica Chimica Acta, v. 356, p. 308-318.
161. Schauder, R., Widdel, F., and Fuchs, G., 1987, Carbon assimilation pathways in sulfate-reducing bacteria. II. Enzymes of a reductive citric acid cycle in the autotrophic Desulfurobacter hydrogenophilus. Archives of Microbiology, v. 148, p. 218-225.
162. Schauder, R., Preuß, A., Jetten, M., and Fuchs, G., 1989, Oxidative and reductive acetyl-CoA/carbon monoxide dehydrogenase pathway in Desulfobacterium autotraphicum 2. Demonstration of the enzymes of the pathway and comparison of CO dehydrogenase: Archives of Microbiology, v. 151, p. 84-89.
163. Schidlowski, M., 2001, Carbon isotopes as biogeochemical recorders of life over 3.8 Ga of Earth history: evolution of a concept: Precambrian Research, v. 106, p. 117-134.
164. Schidlowski, M., Hayes,J. M., and Kaplan, I. R., 1983, Isotopic Inferences of Ancient Biochemistries: Carbon, Sulfur, Hydrogen, and Nitrogen, in Schopf, J. W., editor, The Earth's Earliest Biosphere: Princeton, Princeton University Press, p. 149-185.
165. Schopf, J. W., 1993, Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life: Science, v. 260, p. 640-646.
166. Schopf, J. W., and Packer, B. M., 1987, Early Archean (3.3-billion to 3.5-billion-year-old) microfossils from Warrawoona Group, Australia: Science, v. 237, p. 70-73.
167. Schopf, J. W., Kudryavtsev, A. B., Agresti, D. G., Wdowiak, T.J., and Czaja, A. D., 2002, Laser-Raman imagery of Earth's earliest fossils: Nature, v. 416, p. 73-76.
168. Schouten, S., Strous, M., Kuypers, M. M. M., Rijpstra, W. I. C., Baas, M., Schubert, C.J.,Jetten, M. S. M., and Sinninghe Damste, J. S., 2004, Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria: Applied and Environmental Microbiology, v. 70, p. 3785-3788.
169. Scott, A. I., 1998, How nature synthesizes B-12 without oxygen. Discoveries along the ancient, anaerobic pathway: Heterocycles, v. 47, p. 1051-1066.
170. Scott, A. I., 2001, Reflections on the discovery of nature's pathways to vitamin B12: Chemical Record, v. 1, p. 212-227.
171. Scott, A. I., 2003, Discovering nature's diverse pathways to vitamin B-12: A 35-year odyssey: Journal of Organic Chemistry, v. 68, p. 2529-2539.
172. Shen, Y., Buick, R., and Canfield, D. E., 2001, Isotopic evidence for microbial sulphate reduction in the early Archaean era: Nature, v. 410, p. 77-81.
173. Shen, Y., Canfield, D. E., and Knoll, A. H., 2002, Middle Proterozoic ocean chemistry: Evidence from the McArthur Basin, Northern Australia: American Journal of Science, v. 302, p. 81-109.
174. Shen, Y., Knoll, A. H., and Walter, M. R., 2003, Evidence for low sulphate and anoxia in a mid-Proterozoic marine basin: Nature, v. 423, p. 632-635.
175. Shively, J. M., Keulen, G., and Meijer, W. G., 1998, Something from almost nothing: Carbon dioxide fixation in chemoautotrophs: Annual Review in Microbiology, v. 52, p. 191-230.
176. Silver, V. S., and Postgate, J. R., 1973, Evolution of asymbiotic nitrogen fixation: Journal of Theoretical Biology, v. 40, p. 1-10.
177. Sirevag, R., 1974, Further studies on carbon doixide fixation in Chlorobium: Archives of Microbiology, v. 98, p. 3-18.
178. 2 fixation in bacterial photosynthesis studied by carbon isotope fractionation technique: Archives of Microbiology, v. 112, p. 35-38.
179. Slesarev, A. I., Mezhevaya, K. V., Makarova, K. S., Polushin, N. N., Shcherbinina, O. V., Shakbova, V. V., Belova, G. I., Aravind, L., Natale, D. A., Rogozin, I. B., Tatusov, R. L., Wolf, Y. I., Stetter, K. O., Malykh, A. G., Koonin, E. V., and Kozyavkin, S. A., 2002, The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens: Proceedings of the National Academy of Sciences, v. 99, p. 4644-4649.
180. Smith, K. S., Jakubzick, C., Whittam, T. S., and Ferry, J. G., 1999, Carbonic anhydrase is an ancient enzyme widespread in prokaryotes: Proceedings of the National Academy of Sciences, v. 96, p. 15184-15189.
181. Snel, B., Bork, P., and Huynen, M. A., 1999, Genome phylogeny based on gene content: Nature Genetics, v. 21, p. 108-110.
182. Solomen, E. I., Sundaran, V. M., and Machonkin, T. E., 1996, Multi copper oxidases and oxygenases: Chemical Reviews, v. 96, p. 2563-2603.
183. 2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle: European Journal of Biochemistry, v. 215, p. 633-643.
184. Stumm, W., and Morgan, J.J., 1996, Aquatic Chemistry: New York, John Wiley and Sons, Inc., 1022 p.
185. Summons, R. E., Jahnke, L. L., and Roksandic, Z., 1994, Carbon isotopic fractionation in lipids from methanotrophic bacteria - relevance for interpretation of the geochemical record of biomarkers: Geochimica et Cosmochimica Acta, v. 58, p. 2853-2863.
186. Summons, R. E., Jahnke, L. L., Hope, J. M., and Logan, G. A., 1999, 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis: Nature, v. 400, p. 554-557.
187. Swofford, D. L., 2002, PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods): Sunderland, MA, Sinauer Associates.
188. Taha, T. S. M., Brayman, T. G., Karplus, P. A., and Hausinger, R. P., 1997, Urease nickel metallocenter: Structure and assembly, in Winkelmann, G., and Carrano, C. J., editors, Transition Metals in Microbial Metabolism: Amsterdam, Harwood Academic Publishers, p. 391-414.
189. Tatusov, R. L., Koonin, E. V., and Lipman, D. J., 1997, A genomic perspective on protein families: Science, v. 278, p. 631-637.
190. Tekaia, F., Lazcano, A., and Dujon, B., 1999, The genomic tree as revealed from whole proteome comparisons: Genome Research, v. 9, p. 550-557.
191. Tice, M. M., and Lowe, D. R., 2004, Photosynthetic microbial mats in the 3,416-Myr-old ocean: Nature, v. 431, p. 549-552.
192. Turner, D., Whitfield, M., and Dickson, A. G., 1981, Inorganic speciation of trace metals: Geochimica et Cosmochimica Acta, v. 45, p. 855.
193. Ueno, Y., Isozaki, Y., Yurimoto, H., and Maruyama, S., 2001, Carbon isotopic signatures of individual Archean microfossils(?) from Western Australia: International Geology Review, v. 43, p. 196-212.
194. Ueno, Y., Yurimoto, H., Yoshioka, H., Komiya, T., and Maruyama, S., 2002, Ion microprobe analysis of graphite from ca. 3.8 Ga metasediments, Isua supracrustal belt, West Greenland: Relationship between metamorphism and carbon isotopic composition: Geochimica et Cosmochimica Acta, v. 66, p. 1257-1268.
195. Valentine, D. L., Chidthaisong, A., Rice, A., Reeburgh, W. S., and Tyler, S. C., 2004 Carbon and hydrogen isotope fractionation by moderately thermophilic methanogens: Geochimica et Cosmochimica Acta, v. 68, p. 1571-1590.
196. van der Meer, M. T., Schouten, S., de Leeuw, J. W., and Ward, D. M., 2000, Autotrophy of green non-sulphur bacteria in hot spring microbial mats: biological explanations for isotopically heavy organic carbon in the geological record: Environmental Microbiology, v. 2 p. 428-435.
197. van der Meer, M. T. J., Schouten, S., Rijpstra, W. I. C., Fuchs, G., and Damste, J. S. S., 2001a, Stable carbon isotope fractionations of hyperthermophilic crenarcheon Metallosphaera sedula: FEMS Microbiology Letter, v. 196, p. 67-70.
198. van der Meer, M. T. J., Schouten, S., van Dongen, D. E., Rijpstra, W. I. C., Fuchs. G., Damste, J. S. S. de Leeuw, J. W. and Ward, D. M., 2001b, Biosynthetic controls on the C-13 contents of organic components in the photoautotrophic Chloroflexus aurantiacus: Journal of Biological Chemistry, v. 276, p. 10971-10976.
199. 2 fixation in Archaeglobus lithotrophicus and the lack of carbon monoxide in the heterotrophic A. profundus: Archives of Microbiology, v. 163, p. 112-118.
200. Wachtershauser, G., 1990, Evolution of the first metabolic cycles: Proceedings of the National Academy of Sciences, v. 87, p. 200-204.
201. Wahlund, T. M., and Tabita, F. R., 1997, The reductive tricarboxylic acid cycle of carbon dioxide assimilation: Initial studies and purification of ATP-citrate lyase from the green sulfur bacterium Chlorobium tepidum: Journal of Bacteriology, v. 179, p. 4859-4867.
202. Waseda A., and Didyk, B. M., 1995, Isotopic compositions of gases in sediments from the Chile continental margin, in Lewis, S. D., Behrmann, J. H., Musgrave, R. J., Candy, S. C., and others, editors, Proceedings of the Ocean Drilling Program, Scientific Results 141: College Station, Texas, Ocean Drilling Program, p. 307-312.
203. Watson, G. M. F., Yu, J. P., and Tabita, F. R., 1999, Unusual ribulose 1,5-biphosphate carboxylase/oxygenase of anoxic Archaea: Journal of Bacteriology, y. 181, p. 1569-1575.
204. Whiticar, M. J., 1999, Carbon and hydrogen isotopic systematics of bacterial formation and oxidation of methane: Chemical Geology, V. 161, p. 291-314.
205. Wilde, S. A., Valley, J. W., Peck, W. H., and Graham, C. M, 2001, Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago: Nature, v. 409, p. 175-178.
206. Windhovel, U., and Bowien, B., 1990, On the operon structure of the cfx gene clusters in Alcaligenes eutrophus: Archives of Microbiology, v. 154, p. 85-91.
207. Winkelmann, G., 1991, Specificity of iron transport in bacteria and fungi, in Winkelmann, editor, Handbook of Microbial Iron Chelates: Boca Raton, Florida, CRIC Press, p. 366.
208. Wirsen, C. O., Sievert, S. M., Cavanaugh, C. M., Molyneaux, S.J., Ahmad, A., Taylor, L. T., DeLong, E. F., and Taylor, C. D., 2002, Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur: Applied and Environmental Microbiology, v. 68, p. 316-325.
209. Woese, C. R., 1987, Bacterial evolution: Microbiological Reviews, v. 51, p. 221-271.
210. Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L., and Koonin, E. V., 2001, Genome trees constructed using five different approaches suggest new bacterial clades: BMC Evolutionary Biology, v. 1, p. 8.
211. Wong, W., Sackett, W. M., and Benedict, C. R., 1975, Isotope fractionation in photosynthetic bacteria during carbon dioxide assimilation: Plant Physiology, v. 55, p. 475-479.
212. Yachandra, V. K., Sauer, K., and Klein, M. P., 1996, Manganese cluster in photosynthesis: Where plants oxidize water to dioxygen: Chemical Review, v. 96, p. 2927-2950.
213. Yang, S., Doolittle, R. F., and Bourne, P. E., 2005, Phylogeny determined by protein domain content: Proceedings of the National Academy of Sciences, v. 102, p. 373-378.
214. Young, J. P. W., 1992, Phylogenetic classification of nitrogen-fixing organism, in Stacey, G., Burris, R. H., and Evans, H.J., editors, Biological Nitrogen Fixation: Routledge, Chapman and Hall, p. 43-86.