Molecular geomicrobiology: Genes and geochemical cycling

Earth and Planetary Science Letters

Volumn 209, Issue 1-2, 2003, Pages 1-17

  Macalady, Jennifer ^a   Banfield, Jillian F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Ecology; Evolution; Genes; Genomes; Geochemistry; Geomicrobiology

Indexed keywords

BIOGEOCHEMISTRY; ECOLOGY; GENETICS; GEOMICROBIOLOGY;

EID: 0037446490     PISSN: 0012821X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0012-821X(02)01010-5     Document Type: Article

References (86)

1. B.L. Phillips, W.H. Casey, M. Karlsson, Bonding and reactivity at oxide mineral surfaces from model aqueous complexes, Nature 404 (2000) 379-382.
2. W.B. Whitman, D.C. Coleman, W.J. Wiebe, Prokaryotes: the unseen majority, Proc. Natl. Acad. Sci. USA 95 (1998) 6578-6583.
3. J.R. Brown, C.J. Douady, M.J. Italia, W.E. Marshall, M.J. Stanhope, Universal trees based on large combined protein sequence data sets, Nat. Genet. 28 (2001) 281-285.
4. C. Brochier, H. Philippe, A non-hyperthermophilic ancestor for Bacteria, Nature 417 (2002) 244.
5. E. Pennisi, Genome data shake tree of life, Science 280 (1998) 672-674.
6. G. Deckert, P.V. Warren, T. Gaasterland, W.G. Young, A.L. Lenox, D.E. Graham, R. Overbeek, M.A. Snead, M.Keller, M. Aujay, R. Huber, R.A. Feldman, J.M. Short, G.J. Olsen, R.V. Swanson, The complete genome of the hyperthermophilic bacterium Aquifex aeolicus, Nature 392 (1998) 353-358.
7. C. Woese, The universal ancestor, Proc. Natl. Acad. Sci. USA 95 (1998) 6854-6859.
8. C.R. Woese, G.J. Olsen, M. Ibba, D. Soll, Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process, Microbiol. Mol. Biol. Rev. 64 (2000) 202-236.
9. K.E. Nelson, R.A. Clayton, S.R. Gill, M.L. Gwinn, R.J. Dodson, D.H. Haft, E.K. Hickey, J.D. Peterson, W.C. Nelson, K.A. Ketchum, L. McDonald, T.R. Utterback, J.A. Malek, K.D. Linher, M.M. Garrett, A.M. Stewart, M.D. Cotton, M.S. Pratt, C.A. Phillips, D. Richardson, J. Heidelberg, G.G. Sutton, R.D. Fleischmann, J.A. Eisen, O. White, S.L. Salzberg, H.O. Smith, J.C. Venter, C.M. Fraser, Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima, Nature 399 (1999) 323-329.
10. K.S. Makarova, L. Aravind, Y.I. Wolf, R.L. Tatusov, K.W. Minton, E.V. Koonin, M.J. Daly, Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics, Microbiol. Mol. Biol. Rev. 65 (2001) 44-79.
11. H. Ochman, J.G. Lawrence, E.A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature 405 (2000) 299-304.
12. W.F. Doolittle, Phylogenetic classification and the universal tree, Science 284 (1999) 2124-2128.
13. A.K. Bansal, T.E. Meyer, Evolutionary analysis by whole-genome comparisons, J. Bacteriol. 184 (2002) 2260-2272.
14. S.T. Fitz-Gibbon, C.H. House, Whole genome-based phylogenetic analysis of free-living microorganisms, Nucleic Acids Res. 27 (1999) 4218-4222.
15. B. Snel, P. Bork, M.A. Huynen, Genome phylogeny based on gene content, Nat. Genet. 21 (1999) 108-110.
16. F. Tekaia, A. Lazcano, B. Dujon, The genomic tree as revealed from whole proteome comparisons, Genome Res. 9 (1999) 550-557.
17. G.D.P. Clarke, R.G. Beiko, M.A. Ragan, R.L. Charlebois, Inferring genome trees by using a filter to eliminate phylogenetically discordan sequences and a distrance matrix based on mean normalized BLASTP scores, J. Bacteriol.184 (2002) 2072-2080.
18. C.R. Woese, O. Kandler, M.L. Wheelis, Towards a natural system of organisms : proposal for the domains Archaea, Bacteria, and Eucarya, Proc. Natl. Acad. Sci. USA87 (1990) 4576-4579.
19. Y. Shen, R. Buick, D.E. Can field, Isotopic evidence for microbial sulphate reduction in the early Archaeanera, Nature 410 (2001) 77-81.
20. M. Klein, M. Friedrich, A.J. Roger, P. Hugenholtz, S. Fishbain, H. Abicht, L.L. Blackall, D.A. Stahl, M. Wagner, Multiple lateral transfers of dissimilatory sulfate reductase genes between major line ages of sulfate-reducing prokaryotes, J. Bacteriol. 183 (2001) 6028-6035.
21. J. Xiong, W.M. Fischer, K. Inoue, M. Nakahara, C.E. Bauer, Molecular evidence for the early evolution of photosynthesis, Science 289 (2000) 1724-1730.
22. D.J. Lessner, G.R. Johnson, R.E. Parales, J.C. Spain, D.T. Gibson, Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonassp. strain JS765, Appl. Environ. Microbiol. 68 (2002) 634-641.
23. B.P. Rosen, Families of arsenic transporters, Trends Microbiol. 7 (1999) 207-212.
24. T.M. Gihring, P.L. Bond, S. Peters, J.F. Banfield (2002) Arsenic resistance in the archaeon Ferroplasma acidarmanus: new insights into the structure and evolution of arsenic genes, Extremophiles (in press).
25. J.F. Banfield, C.R. Marshall, Earth science and evolution: genomics and the geosciences, Science 287 (2000) 605-606.
26. R.E. Summons, L.L. Jahnke, J.M. Hope, G.A. Logan, 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis, Nature 400 (1999) 554-557.
27. J.J. Brocks, G.A. Logan, R. Buick, R.E. Summons, Archean molecular fossils and the early rise of eukaryotes, Science 285 (1999) 1033-1036.
28. J.M. Moldowan, N.M. Talyzina, Biogeochemical evidence for the dinoflagellate ancestors in the Early Cambrian, Science 281 (1998) 1168-1170.
29. M.M.M. Kuypers, P. Blokker, J. Erbacher, H. Kinkel, R.D. Pancost, S. Schouten, J.S. SinningheDamste, Massive expansion of marine Archaea during a mid-Cretaceous oceanic anoxic event, Science 293 (2001) 92-94.
30. S. Schouten, E.C. Hopmans, R.D. Pancost, J.S. SinningheDamste, Widespread occurrence of structurally diverse tetraether membrane lipids: evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles, Proc. Natl. Acad. Sci. USA 97 (2000) 14421-14426.
31. J.M. Hayes, Lipids as a common interest of microorganisms and geochemists, Proc. Natl. Acad. Sci. USA 97 (2000) 14033-14034.
32. F. Widdel, R. Rabus, Anaerobic biodegradation of saturated and aromatic hydrocarbons, Curr. Opin. Biotechnol. 12 (2001) 259-276.
33. T.P.-A. Bregnard, A. Haner, P. Hohener, J. Zeyer, Anaerobic degradation of pristane in nitrate-reducing microcosms microcosms and enrichment cultures, Appl. Environ. Microbiol. 63 (1997) 2077-2081.
34. J.M. Hayes, Factors controlling C-13 contents of sedimentary organic compounds: principles and evidence, Mar. Geol. 113 (1993) 111-125.
35. L.L. Jahnke, R.E. Summons, J.M. Hope, D.J. DesMarais, Carbon isotopic fractionation in lipids from methanotrophic bacteria. II. The effects of physiology and environmental parameters on the biosynthesis and isotopic signatures of biomarkers, Geochim. Cosmochim. Acta 63(1999) 79-93.
36. T. Shigematsu, S. Hanada, M. Eguchi, Y. Kamagata, T. Kanagawa, R. Kurane, Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs duringin situ bioremediation, Appl. Environ. Microbiol. 65 (1999) 5198-5206.
37. S.C. Koh, J.P. Bowman, G.S. Sayler, Soluble methanemono oxygenase production and trichloroethylene degradation by a Type I methanotroph methylomonas-methanica 68-1, Appl. Environ. Microbiol. 59 (1993) 960-967.
38. T. Iwamoto, K. Tani, K. Nakamura, Y. Suzuki, M. Kitagawa, M. Eguchi, M. Nasu, Monitoring impact of insitu biostimulation treatment on groundwater bacterial community by DGGE, FEMS Microbiol. Ecol. 32 (2000) 129-141.
39. H. Fuse, M. Ohta, O. Takimura, K. Murakami, H. Inoue, Y. Yamaoka, J.M. Oclarit, T. Omori, Oxidation of trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing soluble methane monooxygenase, Biosci. Biotechnol. Biochem. 62 (1998) 1925-1931.
40. G.M.F. Watson, J.-P. Yu, F.R. Tabita, Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea, J. Bacteriol. 181 (1999) 1569-1575.
41. K.M. Scott, J.J. Robinson, D.T. Nguyen, C.M. Cavanaugh, Form I and Form II Rubisco in chemoautotrophic bacteria: influence on stable carbon isotope values, Abstr. Gen. Meet. Am. Soc. Microbiol. 99 (1999) 383.
42. M.T. van der Meer, S. Schouten, W.I. Rijpstra, G. Fuchs, J.S. Sinninghe Damste, Stable carbon isotope fractionations of the hyperthermophilic crenarchaeon Metallosphaera sedula, FEMS Microbiol. Lett. 196 (2001) 67-70.
43. R.K. Thauer, Enzymology nickel to the fore, Science 293(2001) 1264-1265.
44. C. Menendez, Z. Bauer, H. Huber, N. Gad'on, K.-O.Stetter, G. Fuchs, Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carbon fixylase in autotrophic Crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbonxation, J. Bacteriol. 181 (1999) 1088-1098.
45. N.R. Pace, A molecular view of microbial diversity and the biosphere, Science 276 (1997) 734-740.
46. D. Moreira, P. Lopez-Garcia, The molecular ecology of microbial eukaryotes unveils a hidden world, Trends Microbiol. 10 (2002) 31-38.
47. E.F. De Long, N.R. Pace, Environmental diversity of bacteria and archaea, Syst. Biol. 50 (2001) 470-478.
48. M. Strous, J.A. Fuerst, E.H.M. Kramer, S. Logemann, G. Muyzer, K.T. van de Pas-Schoonen, R. Webb, J.G. Kuenen, M.S.M. Jetten, Missing lithotroph identified as new planctomycete, Nature 400 (1999) 446-449.
49. F. Widdel, S. Schnell, S. Heising, A. Ehrenreich, B. Assmus, B. Schink, Ferrous iron oxidation by anoxygenic phototrophic bacteria, Nature 362 (1993) 834-836.
50. S. Heising, L. Richter, W. Ludwig, B. Schink, Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with 'Geospirillum' sp. strain, Arch. Microbiol. 172 (1999) 116-124.
51. B.B. Jorgensen, V.A. Gallardo, Thioploca spp. Filamentous sulfur bacteria with nitrate vacuoles, FEMS Microbiol. Ecol. 28 (1999) 301-313.
52. K.J. Edwards, P.L. Bond, T.M. Gihring, J.F. Banfield, An archaeal iron-oxidizing extreme acidophile importantin acid mine drainage, Science 287 (2000) 1796-1799.
53. D. Emerson, C. Moyer, Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition, Appl. Environ. Microbiol. 68 (2002) 3085-3093.
54. D.K. Newman, J.F. Banfield, Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems, Science 296 (2002) 1071-1077.
55. E.G. Nisbet, N.H. Sleep, The habitat and nature of early life, Nature 409 (2001) 1083-1091
56. A.-L. Reysenbach, E. Shock, Merging genomes with geochemistry in hydrothermal ecosystems, Science 296 (2002) 1077-1082.
57. M.A. Dojka, J.K. Harris, N.R. Pace, Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria, Appl. Environ. Microbiol. 66 (2000) 1617-1621.
58. M.B. Karner, E.F. De Long, D.M. Karl, Archaeal dominance in the mesopelagic zone of the Pacific Ocean, Nature 409 (2001) 507-510.
59. A. Felske, A.D.L. Akkermans, Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils, Lett. Appl. Microbiol. 26 (1998) 219-223.
60. D.H. Buckley, T.M. Schmidt, Environmental factors in-fluencing the distribution of rRNA from Verrucomicrobiain soil, FEMS Microbiol. Ecol. 35 (2001) 105-112.
61. S.M. Barns, S.L. Takala, C.R. Kuske, Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment, Appl. Environ. Microbiol. 65 (1999) 1731-1737.
62. S. Radajewski, P. Ineson, N.R. Parekh, J.C. Murrell, Stable-isotope probing as a tool in microbial ecology, Nature 403 (2000) 646-649.
63. V.J. Orphan, C.H. House, K.-U. Hinrichs, K.D. McKeegan, E.F. De Long, Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis, Science 293 (2001) 484-487.
64. O. Beja, E.V. Koonin, L. Aravind, L.T. Taylor, H. Seitz, J.L. Stein, D.C. Bensen, R.A. Feldman, R.V. Swanson, E.F. De Long, Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces, Appl. Environ. Microbiol. 68 (2002) 335-345.
65. M.R. Rondon, P.R. August, A.D. Bettermann, S.F.Brady, T.H. Grossman, M.R. Liles, K.A. Loiacono, B.A. Lynch, I.A. MacNeil, C. Minor, C.L. Tiong, M. Gilman, M.S. Osburne, J. Clardy, J. Handelsman, R.M. Goodman, Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms, Appl. Environ. Microbiol. 66 (2000) 2541-2547.
66. O. Beja, L. Aravind, E.V. Koonin, M.T. Suzuki, A. Hadd, L.P. Nguyen, S.B. Jovanovich, C.M. Gates, R.A. Feldman, J.L. Spudich, E.N. Spudich, E.F. De Long, Bacterial rhodopsin: evidence for a new type of phototrophyin the sea, Science 289 (2000) 1902-1906.
67. O. Beja, M.T. Suzuki, J.F. Heidelberg, W.C. Nelson, C.M. Preston, T. Hamada, J.A. Eisen, C.M. Fraser, E.F. De Long, Unsuspected diversity among marine aerobicanoxy genic phototrophs, Nature 415 (2002) 630-633.
68. Z.S. Kolber, C.L. Van Dover, R.A. Niederman, P.G. Falkowski, Bacterial photosynthesis in surface waters of the open ocean, Nature 407 (2000) 177-179.
69. S. Naeem, S. Li, Biodiversity enhances ecosystem reliability, Nature 390 (1997) 507-509.
70. J. McGrady-Steed, P.M. Harris, P.J. Morin, Biodiversity regulates ecosystem predictability, Nature 390 (1997) 162-165.
71. B.J.M. Bohannan, R.E. Lenski, The relative importance of competition and predation varies with productivity in a model community, Am. Nat. 156 (2000) 329-340.
72. P. Capy, G. Gasperi, C. Biemont, C. Bazin, Stress and transposable elements: co-evolution or useful parasites?, Heredity 85 (2000) 101-106.
73. H. Ilves, R. Horak, M. Kivisaar, Involvement of sigmas in starvation-induced transposition of Pseudomonas putida transposon Tn4652, J. Bacteriol. 183 (2001) 5445-5448.
74. D. Mazel, B. Dychinco, V.A. Webb, J. Davies, A distinctive class of integron in the Vibrio cholerae genome, Science 280 (1998) 605-608.
75. A. Campbell, J. Mrazek, S. Karlin, Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA, Proc. Natl. Acad. Sci. USA 96 (1999) 9184-9189.
76. D. Dubnau, DNA uptake in bacteria, Annu. Rev. Microbiol. 53 (1999) 217-244.
77. C.Y. He, B. Striepen, C.H. Pletcher, J.M. Murray, D.S. Roos, Targeting and processing of nuclear-encoded apicoplast proteins in plastid segregation mutants of Toxoplasma gondii, J. Biol. Chem. 276 (2001) 28436-28442.
78. W. Martin, M. Mueller, The hydrogen hypothesis for the first eukaryote, Nature 392 (1998) 37-41.
79. A. Boetius, K. Ravenschlag, C.J. Schubert, D. Rickert, F. Widdel, A. Gieseke, R. Amann, B.B. Jorgensen, U. Witte, O. Pfannkuche, A marine microbial consortium apparently mediating anaerobic oxidation of methane, Nature 407 (2000) 623-626.
80. J. Overmann, H. van Gemerden, Microbial interactions involving sulfur bacteria implications for the ecology and evolution of bacterial communities, FEMS Microbiol. Rev. 24 (2000) 591-599.
81. C. Rudolph, G. Wanner, R. Huber, Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology, Appl. Environ. Microbiol. 67 (2001) 2336-2344.
82. C. Moissl, C. Rudolph, R. Huber, Natural communities of novel archaea and bacteria with a string-of-pearls-like morphology: molecular analysis of the bacterial partners, Appl. Environ. Microbiol. 68 (2002) 933-937.
83. J.M. Bernhard, K.R. Buck, M.A. Farmer, S.S. Bowser, The Santa Barbara Basin is a symbiosis oasis, Nature 403 (2000) 77-80.
84. H. Huber, M.J. Hohn, R. Rachel, T. Fuchs, V.C. Wimmer, K.O. Stetter, A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont, Nature 417 (2002) 63-67.
85. P. Hugenholtz, Exploring prokaryotic diversity in the genomicera, Genome Biology 3 (2002) 3.1-3.8.
86. M. Meselson, F. Stahl, The replication of DNA in Escherichia coli, Proc. Nat. Acad. Sci. USA 44 (1958) 671-682.