2 Metagenome Analysis
63
Biddle JF, Fitz-Gibbon S, Schuster SC et al (2008) Metagenomic signatures of the Peru Margin
subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A
105:10583–10588
Binga EK, Lasken RS, Neufeld JD (2008) Something from (almost) nothing: the impact of multiple
displacement amplification on microbial ecology. ISME J 2:233–241
Blanco L, Bernad A, Lazaro JM et al (1989) Highly efficient DNA-synthesis by the phage
phi-29 DNA-Polymerase – symmetrical mode of DNA-replication. J Biol Chem 264:
8935–8940
Blanco L, Salas M (1984) Characterization and purification of a phage phi-29–encoded DNApolymerase required for the initiation of replication. Proc Natl Acad Sci USA-Biol Sci
81:5325–5329
Blanco L, Salas M (1985a) Characterization of a 3 -5 exonuclease activity in the phage phi-29encoded DNA-polymerase. Nucleic Acids Res 13:1239–1249
Blanco L, Salas M (1985b) Replication of phage phi-29 DNA with purified terminal protein
and DNA-polymerase – synthesis of full-length phi-29 DNA. Proc Natl Acad Sci U S A 82:
6404–6408
Boeckmann B, Bairoch A, Apweiler R et al (2003) The SWISS-PROT protein knowledgebase and
its supplement TrEMBL in 2003. Nucleic Acids Res 31:365–370
Borneman J (1999) Culture-independent identification of microorganisms that respond to specified
stimuli. Appl Environ Microbiol 65:3398–3400
Breitbart M, Rohwer F (2005) Method for discovering novel DNA viruses in blood using viral
particle selection and shotgun sequencing. Biotechniques 39:729–736
Breitbart M, Salamon P, Andresen B et al (2002) Genomic analysis of uncultured marine viral
communities. Proc Natl Acad Sci U S A 99:14250–14255
Bryant DA, Costas AMG, Maresca JA et al (2007) Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 317:523–526
Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends
Microbiol 14:488–496
Chung KT, Ferris DH (1996) Martinus Willem Beijerinck (1851–1931) – Pioneer of general
microbiology. ASM News 62:539–543
Ciccarelli FD, Doerks T, von Mering C et al (2006) Toward automatic reconstruction of a highly
resolved tree of life. Science 311:1283–1287
Cole JR, Chai B, Farris RJ et al (2007) The ribosomal database project (RDP-II): introducing
myRDP space and quality controlled public data. Nucleic Acids Res 35:D169–D172
Collins J, Hohn B (1978) Cosmids – type of plasmid gene-cloning vector that is packageable in
vitro in bacteriophage lambda-heads. Proc Natl Acad Sci U S A 75:4242–4246
Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in
very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:
3878–3885
Cottrell MT, Moore JA, Kirchman DL (1999) Chitinases from uncultured marine microorganisms.
Appl Environ Microbiol 65:2553–2557
Courtois S, Cappellano CM, Ball M et al (2003) Recombinant environmental libraries provide
access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol
69:49–55
Culley AI, Lang AS, Suttle CA (2006) Metagenomic analysis of coastal RNA virus communities.
Science 312:1795–1798
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl
Acad Sci U S A 99:10494–10499
de la Torre JR, Christianson LM, Beja O et al (2003) Proteorhodopsin genes are distributed among
divergent marine bacterial taxa. Proc Natl Acad Sci U S A 100:12830–12835
DeLong EE (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469
DeLong EF, Karl DM (2005) Genomic perspectives in microbial oceanography. Nature 437:
336–342
63
Biddle JF, Fitz-Gibbon S, Schuster SC et al (2008) Metagenomic signatures of the Peru Margin
subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A
105:10583–10588
Binga EK, Lasken RS, Neufeld JD (2008) Something from (almost) nothing: the impact of multiple
displacement amplification on microbial ecology. ISME J 2:233–241
Blanco L, Bernad A, Lazaro JM et al (1989) Highly efficient DNA-synthesis by the phage
phi-29 DNA-Polymerase – symmetrical mode of DNA-replication. J Biol Chem 264:
8935–8940
Blanco L, Salas M (1984) Characterization and purification of a phage phi-29–encoded DNApolymerase required for the initiation of replication. Proc Natl Acad Sci USA-Biol Sci
81:5325–5329
Blanco L, Salas M (1985a) Characterization of a 3 -5 exonuclease activity in the phage phi-29encoded DNA-polymerase. Nucleic Acids Res 13:1239–1249
Blanco L, Salas M (1985b) Replication of phage phi-29 DNA with purified terminal protein
and DNA-polymerase – synthesis of full-length phi-29 DNA. Proc Natl Acad Sci U S A 82:
6404–6408
Boeckmann B, Bairoch A, Apweiler R et al (2003) The SWISS-PROT protein knowledgebase and
its supplement TrEMBL in 2003. Nucleic Acids Res 31:365–370
Borneman J (1999) Culture-independent identification of microorganisms that respond to specified
stimuli. Appl Environ Microbiol 65:3398–3400
Breitbart M, Rohwer F (2005) Method for discovering novel DNA viruses in blood using viral
particle selection and shotgun sequencing. Biotechniques 39:729–736
Breitbart M, Salamon P, Andresen B et al (2002) Genomic analysis of uncultured marine viral
communities. Proc Natl Acad Sci U S A 99:14250–14255
Bryant DA, Costas AMG, Maresca JA et al (2007) Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 317:523–526
Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends
Microbiol 14:488–496
Chung KT, Ferris DH (1996) Martinus Willem Beijerinck (1851–1931) – Pioneer of general
microbiology. ASM News 62:539–543
Ciccarelli FD, Doerks T, von Mering C et al (2006) Toward automatic reconstruction of a highly
resolved tree of life. Science 311:1283–1287
Cole JR, Chai B, Farris RJ et al (2007) The ribosomal database project (RDP-II): introducing
myRDP space and quality controlled public data. Nucleic Acids Res 35:D169–D172
Collins J, Hohn B (1978) Cosmids – type of plasmid gene-cloning vector that is packageable in
vitro in bacteriophage lambda-heads. Proc Natl Acad Sci U S A 75:4242–4246
Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in
very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:
3878–3885
Cottrell MT, Moore JA, Kirchman DL (1999) Chitinases from uncultured marine microorganisms.
Appl Environ Microbiol 65:2553–2557
Courtois S, Cappellano CM, Ball M et al (2003) Recombinant environmental libraries provide
access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol
69:49–55
Culley AI, Lang AS, Suttle CA (2006) Metagenomic analysis of coastal RNA virus communities.
Science 312:1795–1798
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl
Acad Sci U S A 99:10494–10499
de la Torre JR, Christianson LM, Beja O et al (2003) Proteorhodopsin genes are distributed among
divergent marine bacterial taxa. Proc Natl Acad Sci U S A 100:12830–12835
DeLong EE (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469
DeLong EF, Karl DM (2005) Genomic perspectives in microbial oceanography. Nature 437:
336–342