Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

de Caralt S, Agell G, Uriz MJ (2003) Long-term culture of sponge explants: conditions enhancing survival and growth, and assessment of bioactivity. Biomol Eng 20:339–347

Everett KD, Bush RM, Andersen AA (1999) Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int J Syst Bacteriol 49:415–440

Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

Gest H, Favinger J (2001) Taxonomic ambiguities: a case history. Int J Syst Evol Microbiol 51:707–710

Gordon RE, Haynes WC, Pang CH (1973) The genus Bacillus. USDA, Washington

Henckel T, Friedrich M, Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65:1980–1990

Hoffmeister M, Martin W (2003) Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer. Environ Microbiol 5:641–649

Huang CY, Patel BK, Mah RA, Baresi L (1998) Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium. Int J Syst Bacteriol 48:91–97

Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67

Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774 (Erratum, 4180:6793)

Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3:1-8

Janssen PH, Schuhmann A, Morschel E, Rainey FA (1997) Novel anaerobic ultramicrobacteria belonging to the verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl Environ Microbiol 63:1382–1388

Kaeberlein T, Lewis K, Epstein SS (2002) Isolating uncultivable microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129

Kristjansson JK, Stetter K (1992) Thermophilic bacteria. CRC Press, Boca Raton, FL

Mathrani IM, Ahring BK (1991) Isolation and characterization of a strictly xylan-degrading Dictyoglomus from a man-made, thermophilic anaerobic environment. Arch Microbiol 157:13–17

Maymo-Gatell X, Chien Y, Gossett JM, Zinder SH (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568–1571

Ohno M et al (2000) Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth. Int J Syst Evol Microbiol 50:1829–1832

Parker MA (2003) Genetic markers for analysing symbiotic relationships and lateral gene transfer in Neotropical bradyrhizobia. Mol Ecol 12:2447–2455

Powers EM (1995) Efficacy of the ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758

Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

Rhee S-K et al (2002) Characterization of symbiobacterium toebii, an obligate commensal thermophile isolated from compost. Extremophiles 6:57–64

Rondon MR, Goodman RM, Handelsman J (1999) The Earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17:403–409

Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666

Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236

Sung M-H et al (2002) Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost. Int J Syst Evol Microbiol 52:2251–2255

Sung M-H et al (2003) Symbiobacterium toebii sp. nov., commensal thermophile isolated from Korean compost. J Microbiol Biotechnol 13:1013–1017

Tamaoka J, Komagata K (1984) Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science 296:1064–1066

Wais AC (1988) Recovery of halophilic archaebacteria from natural environments. FEMS Microbiol Lett 53:211–216

Wayne LG et al (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

Widdel F, Bak F (1992) The prokaryotes. Springer-Verlag, New York

Xu J, Gordon JI (2003) Inaugural article: honor thy symbionts. Proc Natl Acad Sci USA 100:10452–10459

Yeates C, Gillings MR, Davison AD, Altavilla N, Veal DA (1998) Methods for microbial DNA extraction from soil for PCR amplification. Biol Proced Online 1:40–47

Yoon J-H et al (1996) Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46:502–505

Zeikus JG (1979) Thermophilic bacteria: ecology, physiology and technology. Enzyme Microb Technol 1:243–252

Zengler K et al (2002) Cultivating the uncultured. Proc Natl Acad Sci USA 99:15681–15686

Zinder SH, Salyers AA (2001) Microbial ecology-new directions, new importance. Springer-Verlag, New York