Phylogenetic relationships ofThiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments

Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organisation and primary structure of a ribosomal RNA operon fromEscherichia coli. J Mol Biol 148:107–127

Cavanaugh CM, Gardiner SL, Jones ML, Jannasch HW, Waterbury JB (1981) Prokaryotic cells in the hydrothermal vent tube wormRiftia pachyptila Jones: possible chemoautotrophic symbionts. Science 213:340–342

Distel DL, Wood AP (1992) Characterization of the gill symbiont ofThyasira flexuosa (Thyasiridae: Bivalvia) by use of polymerase chain reaction and 16S rRNA sequence analysis. J Bacteriol 174:6317–6320

Distel DL, Felbeck H, Cavanaugh CM (1994) Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalve hosts. J Mol Evol 38:533–542

Don RH, Cox PT, Wainwright B, Baker K, Mattick JS (1991) “Touchdown” PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008

Elsgaard L, Guezennec J, Benbouzid-Rollet N, Prieur D (1991) Fatty acid composition of sulfate-reducing bacteria isolated from deep-sea hydrothermal vents (13°N, East Pacific Rise). Kiel Meeresforsch Sonderh 8:182–187

Evers S, Weizenegger M, Ludwig W, Schink B, Schleifer KH (1993) The phylogenetic positions ofPelobacter acetylenicus andPelobacter propionicus. Syst Appl Microbiol 16:216–218

Felbeck H, Childress JJ, Somero GN (1981) Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats. Nature 293:291–293

Felsenstein J (1989) Phylip—Phylogeny inference package. Cladistics 5:164–166

Fitch WM, Margoliash E (1967) Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochromec sequences is of general applicability. Science 155:279–284

Garcia-Pichel F (1989) Rapid bacterial swimming measured in swarming cells ofThiovulum majus. J Bacteriol 171:3560–3563

Gilbert DG (1992) SeqApp—a bio-sequence analysis application. Indiana University, Bloomington

Jannasch HW (1985) The chemosynthetic support of life and the microbial diversity at deep-sea hydrothermal vents. Proc R Soc Lond [Biol] 225:277–297

Jannasch HW, Wirsen CO, Nelson DC, Robertson LA (1985)Thiomicrospira crunogena sp. nov., a colorless, sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J System Bacteriol 35:422–424

Jukes TH, Cantor RR (1969) Evolution of protein molecules, In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132

Kuenen JG, Veldkamp H (1972)Thiomicrospira pelophila nov. gen., nov. sp., a new obligately chemolithotrophic colorless sulfur bacterium. Antonie Van Leeuwenhoek 38:241–25

Kuenen JG, Robertson LA, Tuovinen OH (1991) The generaThiobacillus, Thiomicrospira, andThiosphaera. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, Berlin Heidelberg New York, pp 2638–2657

Lane DJ, Stahl DA, Olsen GJ, Heller DJ, Pace NR (1985) Phylogenetic analysis of the generaThiobacillus andThiomicrospira by 5S rRNA sequences. J Bacteriol 163:75–81

Lane DJ, Harrison AP, Stahl DA, Pace B, Giovannoni SJ, Olsen GJ, Pace NR (1992) Evolutionary relationships among sulfur-and iron-oxidizing eubacteria. J Bacteriol 174:269–278

La Riviere JWM, Schmidt K (1991) Morphologically conspicuous sulfur-oxidizing eubacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn., Springer, Berlin Heidelberg New York, pp 3934–3947

Larsen N, Olsen GJ, Maidanek BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR (1993) The Ribosomal Data-base Project. Nucleic Acids Res 21:3021–3023

Lessa EP, Applebaum G (1993) Screening techniques for detecting allelic variation in DNA sequences. Mol Ecol 2:119–129

Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078

Medlin L, Ellwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71:491–499

Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 60:871–879

Moyer Cl, Dobbs FC, Karl DM (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 61:1555–1562

Muyzer G, De Waal EC (1994) Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rDNA. In: Stal LJ, Caumette P (eds) Microbial mats, structure, development and environmental significance. NATO ASI Series G35, pp 207–214

Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695–700

Muyzer G, Hottenträger S, Teske A, Wawer C (1995) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA. A new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans ADL, Van Elsas JD, De Bruijn FJ (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, Dordrecht (in press)

Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6

Paster BJ, Dewhirst FE (1988) Phylogeny ofCampylobacter, Wolinella, Bacteroides gracilis, andBacteroides ureolyticus by 16S ribosomal nucleic acid sequencing. Int J Syst Bacteriol. 38:56–62

Rochelle PA, Fry JC, Parkes RJ, Weightman AJ (1992) DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediments communities. FEMS Microbiol Lett 100:59–66

Ruby EG, Jannasch HW (1982) Physiological characteristics ofThiomicrospira sp. strain L-12 isolated from deep-sea hydrothermal vents. J Bacteriol 149:161–165

Ruby EG, Wirsen CO, Jannasch HW (1981) Chemolithothrophic sulfur-oxidizing bacteria from the Galapagos Rift hydrothermal vents. Appl Environ Microbiol 42:317–324

Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

Timmer-ten Hoor A (1975) A new type of thiosulphate oxidizing, nitrate-reducing microorganism:Thiomicrospira denitrificans sp. nov. Netherlands. J Sea Res 9:343–351

Vandamme P, Falsen E, Rossau R, Hoste B, Segers P, Tytgat R, De Ley J (1991) Revision ofCampylobacter, Heliocobacter, andWolinella taxonomy: emendation of generic descriptions and proposal ofArcobacter gen. nov. Int J Syst Bacteriol 41:88–103

Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. In: Marschall KC (ed) Advances in microbial ecology, vol 12. Plenum Press, New York, pp 219–286

Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

Wood AP, Kelly DP (1989) Isolation and physiological characterisation ofThiobacillus thyasiris sp. nov., a novel marine facultative autotroph and the putative symbiont ofThyasira flexuosa. Arch Microbiol 152:160–166

Wood AP, Kelly DP (1993) Reclassification ofThiobacillus thyasiris asThiomicrospira thyasirae comb. nov., an organism exhibiting pleomorphism in response to environmental conditions. Arch Microbiol 159:45–47