Community structure and metabolism through reconstruction of microbial genomes from the environment (original) (raw)

• Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221–271 (1987)
  CAS PubMed PubMed Central Google Scholar
• Makarova, K. S. & Koonin, E. V. Comparative genomics of archaea: how much have we learned in six years, and what's next? Genome Biol. 4, 115.1–115.16 (2003)
  Article Google Scholar
• Koonin, E. V. & Mushegian, A. R. Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. Curr. Opin. Genet. Dev. 6, 757–762 (1996)
  Article CAS PubMed Google Scholar
• Amann, R. I., Ludwig, W. & Schleifer, K. H. Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol. Rev. 59, 143–169 (1995)
  CAS PubMed PubMed Central Google Scholar
• Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997)
  Article CAS PubMed Google Scholar
• Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, reviews0003.1–0003.8. (2002)
  Google Scholar
• Beja, O. et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2, 516–529 (2000)
  Article CAS PubMed Google Scholar
• Beja, O. et al. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68, 335–345 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• Rondon, M. R. et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66, 2541–2547 (2000)
  Article CAS PubMed PubMed Central Google Scholar
• Torsvik, V., Ovreas, L. & Thingstad, T. F. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296, 1064–1066 (2002)
  Article ADS CAS PubMed Google Scholar
• Singer, P. C. & Stumm, W. Acidic mine drainage rate-determining step. Science 167, 1121–1127 (1970)
  Article ADS CAS PubMed Google Scholar
• Edwards, K. J., Gihring, T. M. & Banfield, J. F. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl. Environ. Microbiol. 65, 3627–3632 (1999)
  CAS PubMed PubMed Central Google Scholar
• Bond, P. L., Smriga, S. P. & Banfield, J. F. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66, 3842–3849 (2000)
  Article CAS PubMed PubMed Central Google Scholar
• Bond, P. L., Druschel, G. K. & Banfield, J. F. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl. Environ. Microbiol. 66, 4962–4971 (2000)
  Article CAS PubMed PubMed Central Google Scholar
• Baker, B. J. & Banfield, J. F. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44, 139–152 (2003)
  Article CAS PubMed Google Scholar
• Edwards, K. J. et al. Geochemical and biological aspects of sulfide mineral dissolution: lessons from Iron Mountain, California. Chem. Geol. 169, 383–397 (2000)
  Article ADS CAS Google Scholar
• Silverman, M. P. & Ehrlich, H. L. Microbial formation and degradation of minerals. Adv. Appl. Microbiol. 6, 153–206 (1964)
  Article CAS Google Scholar
• Bond, P. L. & Banfield, J. F. Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. Microb. Ecol. 41, 149–161 (2001)
  CAS PubMed Google Scholar
• Coram, N. J. & Rawlings, D. E. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp nov dominates South African commercial biooxidation tanks that operate at 40 °C. Appl. Environ. Microbiol. 68, 838–845 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• Fraser, C. M., Eisen, J. A., Nelson, K. E., Paulsen, I. T. & Salzberg, S. L. The value of complete microbial genome sequencing (you get what you pay for). J. Bacteriol. 184, 6403–6405 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• Branscomb, E. & Predki, P. On the high value of low standards. J. Bacteriol. 184, 6406–6409 (2002)
  Article CAS PubMed PubMed Central Google Scholar
• Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002)
  Article ADS CAS PubMed Google Scholar
• Amils, R., Irazabal, N., Moreira, D., Abad, J. P. & Marin, I. Genomic organization analysis of acidophilic chemolithotropic bacteria using pulse field gel electrophoretic techniques. Biochimie 80, 911–921 (1998)
  Article CAS PubMed Google Scholar
• Sandberg, R. et al. Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res. 11, 1404–1409 (2001)
  Article CAS PubMed PubMed Central Google Scholar
• Abe, T. et al. Informatics for unveiling hidden genome signatures. Genome Res. 13, 693–702 (2003)
  Article CAS PubMed PubMed Central Google Scholar
• Spratt, B. G., Hanage, W. P. & Feil, E. J. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 4, 602–606 (2001)
  Article CAS PubMed Google Scholar
• Vulic, M., Dionisio, F., Taddei, F. & Radman, M. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl Acad. Sci. USA 94, 9763–9767 (1997)
  Article ADS CAS PubMed PubMed Central Google Scholar
• Magurran, A. E. & Henderson, P. A. Explaining the excess of rare species in natural species abundance distributions. Nature 422, 714–716 (2003)
  Article ADS CAS PubMed Google Scholar
• McGill, B. J. A test of the unified neutral theory of biodiversity. Nature 422, 881–885 (2003)
  Article ADS CAS PubMed Google Scholar
• Dewdney, A. K. A dynamical model of communities and a new species-abundance distribution. Biol. Bull. 198, 152–165 (2000)
  Article CAS PubMed Google Scholar
• Ruepp, A. et al. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508–513 (2000)
  Article ADS CAS PubMed Google Scholar
• Parro, V. & Moreno-Paz, M. Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc. Natl Acad. Sci. USA 100, 7883–7888 (2003)
  Article ADS CAS PubMed PubMed Central Google Scholar
• Blake, R., Shute, E. A., Waskovsky, J. & Harrison, A. P. Respiratory components in acidophilic bacteria that respire on iron. Geomicrobiol. J. 10, 173–192 (1992)
  Article CAS Google Scholar
• Blake, R. & Shute, E. A. Respiratory enzymes of _Thiobacillus ferrooxidans_—kinetic-properties of an acid-stable irron-rusticyanin oxidoreductase. Biochemistry 33, 9220–9228 (1994)
  Article CAS PubMed Google Scholar
• Yamanaka, T. & Fukumori, Y. Molecular aspects of the electron transfer system which participates in the oxidation of ferrous ion by Thiobacillus ferrooxidans. FEMS Microbiol. Rev. 17, 401–413 (1995)
  Article CAS PubMed Google Scholar
• Appia-Ayme, C., Guiliani, N., Ratouchniak, J. & Bonnefoy, V. Characterization of an operon encoding two c-type cytochromes, an aa(3)-type cytochrome oxidase, and rusticyanin in Thiobacillus ferrooxidans ATCC 33020. Appl. Environ. Microbiol. 65, 4781–4787 (1999)
  CAS PubMed PubMed Central Google Scholar
• Preisig, O., Zufferey, R. & Hennecke, H. The Bradyrhizobium japonicum fixGHIS genes are required for the formation of the high-affinity cbb(3)-type cytochrome oxidase. Arch. Microbiol. 165, 297–305 (1996)
  Article CAS PubMed Google Scholar
• Pitcher, R. S., Brittain, T. & Watmough, N. J. Cytochrome cbb(3) oxidase and bacterial microaerobic metabolism. Biochem. Soc. Trans. 30, 653–658 (2002)
  Article CAS PubMed Google Scholar
• Poole, R. K. & Hill, S. Respiratory protection of nitrogenase activity in _Azotobacter vinelandii_—roles of the terminal oxidases. Biosci. Rep. 17, 303–317 (1997)
  Article CAS PubMed Google Scholar
• Komorowski, L., Verheyen, W. & Schafer, G. The archaeal respiratory supercomplex SoxM from S. acidocaldarius combines features of quinole and cytochrome c oxidases. Biol. Chem. 383, 1791–1799 (2002)
  Article CAS PubMed Google Scholar
• Acuna, J., Rojas, J., Amaro, A. M., Toledo, H. & Jerez, C. A. Chemotaxis of Leptospirillum ferrooxidans and other acidophilic chemolithotrophs—comparison with the Escherichia coli chemosensory system. FEMS Microbiol. Lett. 96, 37–42 (1992)
  Article CAS Google Scholar
• Macalady, J. L. et al. Tetraether-linked membrane monolayers in Ferroplasma spp.: a key to survival in acid. Extremophiles (submitted)