62
A. Meyerdierks and F.O. Glöckner
understanding of how marine ecosystems function. In the long run these data could
represent the starting point for modelling the complex interplay and networks found
in the environment, leading to a new science of ecosystems biology.
Acknowledgments We cordially thank R. Amann, L. Raggi, I. Pizzetti for reading the manuscript
and valuable comments. The work was funded by the Max Planck Society.
References
Abe T, Sugawara H, Kanaya S et al (2006) A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental
microbes. Polar Biosci 20:103–112
Abe T, Sugawara H, Kinouchi M et al (2005) Novel phylogenetic studies of genomic sequence
fragments derived from uncultured microbe mixtures in environmental and clinical samples.
DNA Res 12:281–290
Abulencia CB, Wyborski DL, Garcia JA et al (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:
3291–3301
Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved
fluorescence in situ hybridization techniques. Nat Rev Microbiol 6:339–348
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of
individual microbial cells without cultivation. Microbiol Rev 59:143–169
Angly FE, Felts B, Breitbart M et al (2006) The marine viromes of four oceanic regions. PLoS
Biol 4:2121–2131
Aparicio S, Chapman J, Stupka E et al (2002) Whole-genome shotgun assembly and analysis of
the genome of Fugu rubripes. Science 297:1301–1310
Apweiler R, Bairoch A, Wu CH et al (2004) UniProt: the Universal Protein knowledgebase.
Nucleic Acids Res 32:D115–D119
Asakawa S, Abe I, Kudoh Y et al (1997) Human BAC library: construction and rapid screening.
Gene 191:69–79
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems
technology. BMC Genomics 9:75
Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative
analysis. Mol Biol Evol 16:512–524
Bailly J, Fraissinet-Tachet L, Verner MC et al (2007) Soil eukaryotic functional diversity, a
metatranscriptomic approach. ISME J 1:632–642
Bateman A, Coin L, Durbin R et al (2004) The PFAM protein families database. Nucleic Acids
Res 32:D138–D141
Bauer M, Kube M, Teeling H et al (2006) Whole genome analysis of the marine Bacteroidetes
‘Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter. Environ
Microbiol 8:2201–2213
Beja O, Aravind L, Koonin EV et al (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289:1902–1906
Beja O, Koonin EV, Aravind L et al (2002) Comparative genomic analysis of archaeal genotypic
variants in a single population and in two different oceanic provinces. Appl Environ Microbiol
68:335–345
Beja O, Spudich EN, Spudich JL et al (2001) Proteorhodopsin phototrophy in the ocean. Nature
411:786–789
Bench SR, Hanson TE, Williamson KE et al (2007) Metagenomic characterization of Chesapeake
bay virioplankton. Appl Environ Microbiol 73:7629–7641
Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP
3.0. J Mol Biol 340:783–795
A. Meyerdierks and F.O. Glöckner
understanding of how marine ecosystems function. In the long run these data could
represent the starting point for modelling the complex interplay and networks found
in the environment, leading to a new science of ecosystems biology.
Acknowledgments We cordially thank R. Amann, L. Raggi, I. Pizzetti for reading the manuscript
and valuable comments. The work was funded by the Max Planck Society.
References
Abe T, Sugawara H, Kanaya S et al (2006) A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental
microbes. Polar Biosci 20:103–112
Abe T, Sugawara H, Kinouchi M et al (2005) Novel phylogenetic studies of genomic sequence
fragments derived from uncultured microbe mixtures in environmental and clinical samples.
DNA Res 12:281–290
Abulencia CB, Wyborski DL, Garcia JA et al (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:
3291–3301
Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved
fluorescence in situ hybridization techniques. Nat Rev Microbiol 6:339–348
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of
individual microbial cells without cultivation. Microbiol Rev 59:143–169
Angly FE, Felts B, Breitbart M et al (2006) The marine viromes of four oceanic regions. PLoS
Biol 4:2121–2131
Aparicio S, Chapman J, Stupka E et al (2002) Whole-genome shotgun assembly and analysis of
the genome of Fugu rubripes. Science 297:1301–1310
Apweiler R, Bairoch A, Wu CH et al (2004) UniProt: the Universal Protein knowledgebase.
Nucleic Acids Res 32:D115–D119
Asakawa S, Abe I, Kudoh Y et al (1997) Human BAC library: construction and rapid screening.
Gene 191:69–79
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems
technology. BMC Genomics 9:75
Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative
analysis. Mol Biol Evol 16:512–524
Bailly J, Fraissinet-Tachet L, Verner MC et al (2007) Soil eukaryotic functional diversity, a
metatranscriptomic approach. ISME J 1:632–642
Bateman A, Coin L, Durbin R et al (2004) The PFAM protein families database. Nucleic Acids
Res 32:D138–D141
Bauer M, Kube M, Teeling H et al (2006) Whole genome analysis of the marine Bacteroidetes
‘Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter. Environ
Microbiol 8:2201–2213
Beja O, Aravind L, Koonin EV et al (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289:1902–1906
Beja O, Koonin EV, Aravind L et al (2002) Comparative genomic analysis of archaeal genotypic
variants in a single population and in two different oceanic provinces. Appl Environ Microbiol
68:335–345
Beja O, Spudich EN, Spudich JL et al (2001) Proteorhodopsin phototrophy in the ocean. Nature
411:786–789
Bench SR, Hanson TE, Williamson KE et al (2007) Metagenomic characterization of Chesapeake
bay virioplankton. Appl Environ Microbiol 73:7629–7641
Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP
3.0. J Mol Biol 340:783–795