Specific single-cell isolation and genomic amplification of uncultured microorganisms (original) (raw)
References
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169 CASPubMedPubMed Central Google Scholar
Amann R, Snaidr J, Wagner M, Ludwig W, Schleifer KH (1996) In situ visualization of high genetic diversity in a natural microbial community. J Bacteriol 178:3496–3500 CASPubMedPubMed Central Google Scholar
Angelidaki I, Petersen SP, Ahring BK (1990) Effects of lipids on thermophilic anaerobic digestion and reduction of lipid inhibition upon addition of bentonite. Appl Microbiol Biotechnol 33:469–472 CASPubMed Google Scholar
Ashelford KE, Weightman AJ, Fry JC (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30:3481–3489 CASPubMedPubMed Central Google Scholar
Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA 94:277–282 CASPubMedPubMed Central Google Scholar
Burmolle M, Hansen LH, Oregaard G, Sorensen SJ (2003) Presence of N-acyl homoserine lactones in soil detected by a whole-cell biosensor and flow cytometry. Microb Ecol 45:226–236 CASPubMed Google Scholar
Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499 CASPubMedPubMed Central Google Scholar
Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11:1095–1099 CASPubMedPubMed Central Google Scholar
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99:5261–5266 CASPubMedPubMed Central Google Scholar
Delong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469 CASPubMed Google Scholar
Delong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50:470–478 CASPubMed Google Scholar
Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390 CASPubMed Google Scholar
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98 CAS Google Scholar
Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, Du J, Kingsmore SF, Egholm M, Lasken RS (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res 13:954–964 CASPubMedPubMed Central Google Scholar
Huber R, Burggraf S, Mayer T, Barns SM, Rossnagel P, Stetter KO (1995) Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis. Nature 376:57–58 CASPubMed Google Scholar
Ishoy T, Kvist T, Westermann P, Ahring BK (2006) An improved method for single cell isolation of prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69:510–514 CASPubMed Google Scholar
Jürgens G, Lindstrom K, Saano A (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Appl Environ Microbiol 63:803–805 PubMedPubMed Central Google Scholar
Jürgens G, Glockner F, Amann R, Saano A, Montonen L, Likolammi M, Munster U (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34:45–56 PubMed Google Scholar
Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129 CASPubMed Google Scholar
Kvist T, Mengewein A, Manzei S, Ahring BK, Westermann P (2005) Diversity of thermophilic and non-thermophilic Crenarchaeota at 80 degrees C. FEMS Microbiol Lett 244:61–68 CASPubMed Google Scholar
Leininger S, Ulrich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soil. Nature 442:806–809 CASPubMed Google Scholar
Lopez-Garcia P, Brochier C, Moreira D, Rodriguez-Valera F (2004) Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol 6:19–34 CASPubMed Google Scholar
Maidak BL, Cole JR, Parker CT Jr, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese C R (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27:171–173 CASPubMedPubMed Central Google Scholar
McInerney JO, Wilkinson M, Patching JW, Embley TM, Powell R (1995) Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl Environ Microbiol 61:1646–1648 CASPubMedPubMed Central Google Scholar
Nelson JR, Cai YC, Giesler TL, Farchaus JW, Sundaram ST, Ortiz-Rivera M, Hosta LP, Hewitt PL, Mamone JA, Palaniappan C, Fuller CW (2002) TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques Suppl:44–47 PubMed Google Scholar
Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5:787–797 CASPubMed Google Scholar
Quaiser A, Ochsenreiter T, Klenk HP, Kletzin A, Treusch AH, Meurer G, Eck J, Sensen CW, Schleper C (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4:603–611 CASPubMed Google Scholar
Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71:3342–3347 CASPubMedPubMed Central Google Scholar
Schleper C, Jürgens G, Jonuscheit M (2005) Genomic studies of uncultivated Archaea. Nat Rev Microbiol 3:479–488 CASPubMed Google Scholar
Schloss PD, Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 6:229 PubMedPubMed Central Google Scholar
Simon HM, Jahn CE, Bergerud LT, Sliwinski MK, Weimer PJ, Willis DK, Goodman RM (2005) Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. Appl Environ Microbiol 71:4751–4760 CASPubMedPubMed Central Google Scholar
Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol 179:7135–7155 CASPubMedPubMed Central Google Scholar
Stahl DA, Amann R (1991) Development and application of nucleic acid probes. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, United Kingdom, pp 205–248 Google Scholar
Treusch AH, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A, Meurer G, Schuster SC, Schleper C (2004) Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol 6:970–980 CASPubMed Google Scholar
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk, HP, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995 CASPubMed Google Scholar
Van de Peer Y, De Wachter R (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13:227–230 PubMed Google Scholar
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74 CASPubMed Google Scholar
Yu W, Dodds WK, Banks MK, Skalsky J, Strauss EA (1995) Optimal staining and sample storage time for direct microscopic enumeration of total and active bacteria in soil with two fluorescent dyes. Appl Environ Microbiol 61:3367–3372 CASPubMedPubMed Central Google Scholar