Reviewing the DA001-files: A 16S rRNA chase on suspect #X99967, a Bacillus and Dutch underground activist

Journal of Microbiological Methods

Volumn 36, Issue 1-2, 1999, Pages 77-93

  Felske, Andreas ^a  

^a INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SEVILLA   (Spain)

Author keywords

16S rDNA clone libraries; 16S rRNA targeted oligonucleotide probes; Bacillus; Grassland soil; TGGE

Indexed keywords

RIBOSOME RNA;

BACILLUS; BACTERIUM IDENTIFICATION; CONFERENCE PAPER; DOT HYBRIDIZATION; ECOLOGY; GRASS; PHYLOGENY; PRIORITY JOURNAL; RNA ANALYSIS; SOIL MICROFLORA; SOUTHERN BLOTTING; TECHNIQUE;

BACILLUS; BLOTTING, SOUTHERN; CLONING, MOLECULAR; DNA, BACTERIAL; ECOSYSTEM; IMMUNOBLOTTING; IN SITU HYBRIDIZATION; MOLECULAR SEQUENCE DATA; NETHERLANDS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); UNCULTURED BACTERIUM;

EID: 0033135928     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(99)00013-5     Document Type: Conference Paper

References (104)

1. Amann R.I., Ludwig W., Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
2. Amann R.I., Krumholz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:1990;762-770.
3. Bakker J.P. Geobotany 14: Nature Management By Grazing and Cutting. 1989;Kluwer Academic, Dordrecht.
4. Begon M., Harper J.L., Townsend C.R. The description of community composition. Ecology. 1990;615-617 Blackwell Scientific, Oxford.
5. Bintrim S.B., Donohue T.J., Handelsman J., Roberts G.P., Goodman R.M. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA. 94:1997;277-282.
6. Borneman J., Skroch P.W., O'Sullivan K.M., Palus J.A., Rumjanek N.G., Jansen J.L., Nienhuis J., Triplett E.W. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1996;1935-1943.
7. Borneman J., Triplett E.W. Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:1997;2647-2653.
8. Britschgi T.B., Giovannoni S.J. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1991;1707-1713.
9. Cairns M.J., Murray V. Rapid silver staining and recovery of PCR products separate on polyacrylamide gels. BioTechniques. 17:1994;915-919.
10. Chandler D.P., Fredrickson J.K., Brockman F.J. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:1997;475-482.
11. Cole S.T., Girons I.S. Bacterial genomics. FEMS Microbiol. Rev. 14:1994;139-160.
12. Donner G., Schwarz K., Hoppe H.-G., Muyzer G. Profiling the succession of bacterial populations in pelagic chemoclines. Arch. Hydrobiol. Spec. Issues Adv. Limnol. 48:1996;7-14.
13. Farrelly V., Rainey F.A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:1995;2798-2801.
14. Felske A., Engelen B., Nübel U., Backhaus H. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62:1996;4162-4167.
15. Felske A., Rheims H., Wolterink A., Stackebrandt E., Akkermans A.D.L. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology. 143:1997;2983-2989.
16. Felske A., Akkermans A.D.L. Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales-cluster in grassland soils. Lett. Appl. Microbiol. 26:1998;219-223.
17. Felske A., Akkermans A.D.L. Spatial homogeneity of the most abundant bacterial 16S rRNA molecules in grassland soils. Microb. Ecol. 36:1998;31-36.
18. Felske A., Wolterink A., van Lis R., Akkermans A.D.L. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64:1998;871-879.
19. Felske A., Akkermans A.D.L., De Vos W.M. In situ detection of an uncultured predominant Bacillus in Dutch grassland soils. Appl. Environ. Microbiol. 64:1998;4588-4590.
20. Felske, A., Akkermans, A.D.L., De Vos, W.M., 1998c. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive RT-PCR in TGGE fingerprints. Appl. Environ. Microbiol. 64, in press.
21. Felske A., Backhaus H., Akkermans A.D.L. Direct ribosome isolation from soil. Akkermans A.D.L., van Elsas J.D., de Bruijn F.J. Molecular Microbial Ecology Manual, Supplement 3. 1998;1.2.4/1-1.2.4/10 Kluwer Academic, Dordrecht.
22. Felske A., Vancanneyt M., Kersters K., Akkermans A.D.L. Application of temperature gradient gel electrophoresis in taxonomy of coryneform bacteria. Int. J. Syst. Microbiol. 49:1999;113-121.
23. Ferris M.J., Muyzer G., Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:1996;340-346.
24. Ferris M.J., Ward D.M. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1997;1375-1381.
25. Fischer S.G., Lerman L.S. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell. 16:1979;191-200.
26. Flaerdh K., Cohen P.S., Kjelleberg S. Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain CCUG 15956. J. Bacteriol. 174:1992;6780-6788.
27. Giovannoni S.J., Britschgi T.B., Moyer C.L., Field K.G. Genetic diversity in Sargasso Sea bacterioplancton. Nature. 345:1990;60-63.
28. Giovannoni S.J., DeLong E.F., Olsen G.J., Pace N.R. Phylogenetic group-specific oligonucleotide probes for identification of single microbial cells. J. Bacteriol. 170:1988;720-726.
29. Großkopf R., Janssen P.H., Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64:1998;960-969.
30. Hahn D., Kester R., Starrenburg M.J.C., Akkermans A.D.L. Extraction of ribosomal RNA from soil for detection of Frankia with oligonucleotide probes. Arch. Microbiol. 154:1990;329-335.
31. Hahn D., Amann R.I., Zeyer J. Detection of mRNA in Streptomyces cells by in situ hybridization with digoxigenin-labelled probes. Appl. Environ. Microbiol. 59:1993;2753-2757.
32. Hartung, K., 1996. Diploma thesis. Fachhochschule Lippe, Germany.
33. Heuer H., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. van Elsas J.D., Wellington E.M.H., Trevors J.T. Modern Soil Microbiology. 1997;353-373 Marcel Dekker, New York.
34. Josephson K.L., Gerba C.P., Pepper T.L. Polymerase chain reaction of nonviable bacterial pathogens. Appl. Environ. Microbiol. 59:1993;3513-3515.
35. Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J.I., Embley T.M., Woldendorp J.W. Analysis of ammonia-oxidizing bacteria of the β-subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1997;1489-1497.
36. Kuske C.R., Barns S.M., Busch J.D. Diverse uncultivated bacterial groups from soil of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63:1997;3614-3621.
37. 2′-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bond in proteins. Biochimie. 77:1995;7-15.
38. Lee S.-Y., Bollinger J., Bezdicek D., Ogram A. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62:1996;3787-3793.
39. Leff L.G., Dana J.R., McArthur J.V., Shimkets L.J. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1995;1141-1143.
40. Liesack W., Stackebrandt E. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:1992;5072-5078.
41. Liesack W., Stackebrandt E. Unculturable microbes detected by molecular sequences and probes. Biodivers. Conserv. 1:1992;250-262.
42. Liesack W., Janssen P.H., Rainey F.A., Ward-Rainey N.L., Stackebrandt E. Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. van Elsas J.D., Wellington E.M.H., Trevors J.T. Modern Soil Microbiology. 1997;375-439 Marcel Dekker, New York.
43. Lin C., Stahl D.A. Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations. Appl. Environ. Microbiol. 61:1995;1348-1351.
44. Lloyd D., Thomas K.L., Hayes A., Hill B., Hales B.A., Edwards C., Saunders J.R., Ritchie D.A., Upton M. Micro-ecology of peat: minimally invasive analysis using confocal laser scanning microscopy, membrane inlet mass spectrometry and PCR amplification of methanogen-specific gene sequences. FEMS Microbiol. Ecol. 25:1998;179-188.
45. Lorenz M.G., Wackernagel W. Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53:1987;2948-2952.
46. Ludwig W., Bauer S.H., Bauer M., Held I., Kirchhof G., Schulze R., Huber I., Spring S., Hartmann A., Schleifer K.-H. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:1997;181-190.
47. Maden B.E.H. The numerous modified nucleosides in eukaryotic ribosomal RNA. Prog. Nucl. Acids Res. Mol. Biol. 39:1990;241-303.
48. Maidak B.L., Larsen N., McCaughey M.J., Overbeck R., Olsen G.J., Fogel K., Blandy J., Woese C.R. The ribosomal database project. Nucl. Acids Res. 22:1994;3483-3487.
49. Manz W., Amann R., Ludwig W., Wagner M., Schleifer K.-H. Phylogenetic oligonucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:1992;593-600.
50. Moran M.A., Torsvik V.L., Torsvik T., Hodson R.E. Direct extraction and purification of rRNA for ecological studies. Appl. Environ. Microbiol. 59:1993;915-918.
51. Munson M.A., Nedwell D.B., Embley T.M. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63:1997;4729-4733.
52. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek. 73:1998;127-141.
53. Muyzer G., Ramsing N.B. Molecular methods to study the organization of microbial communities. Water Sci. Tech. 32:1995;1-9.
54. Muyzer G., De Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:1993;695-700.
55. Myers R.M., Fischer S.G., Lerman L.S., Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucl. Acids Res. 13:1985;3131-3145.
56. Mylvaganam S., Dennis P.P. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics. 130:1992;399-410.
57. Nold S.C., Ward D.M. Photosynthate partitioning and fermentation in hot spring microbial mat communities. Appl. Environ. Microbiol. 62:1997;4598-4607.
58. Noon K.R., Bruenger E., McCloskey J.A. Post-transcriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J. Bacteriol. 180:1998;2883-2888.
59. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:1996;5636-5643.
60. Nüsslein K., Tiedje J.M. Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl. Environ. Microbiol. 64:1998;1283-1289.
61. Ofengand J., Bakin A., Wrzesinski J., Nurse K., Lane B.G. The pseudouridine residues of ribosomal RNA. Biochem. Cell Biol. 73:1995;915-924.
62. Olff, H., 1992. On the mechanisms of vegetation succession. Ph.D. thesis, State University of Groningen.
63. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:1986;337-365.
64. dØvreås L., Jensen S., Daae F.L., Torsvik V. Microbial community changes in a perturbed agricultural soil investigated by molecular and physiological approaches. Appl. Environ. Microbiol. 64:1998;2739-2742.
65. Pace N.R., Stahl D.A., Lane D.J., Olsen G.J. The analysis of natural microbial communities by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1986;1-55.
66. Polz M.F., Cavanaugh C.M. A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl. Environ. Microbiol. 63:1997;1028-1033.
67. Poulsen L.K., Dalton H.M., Angles M.L., Marshall K.C., Molin S., Goodman A.E. Simultaneous determination of gene expression and bacterial identity in single cells in defined mixtures of pure cultures. Appl. Environ. Microbiol. 63:1997;3698-3702.
68. Purdy K.J., Embley T.M., Takii S., Nedwell D.B. Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Appl. Environ. Microbiol. 62:1996;3905-3907.
69. Rainey, F.A., Ward, N.L., Stackebrandt, E., 1993. Molecular ecology study of a New Zealand acidothermal soil. In: Thermophiles '93, Hamilton, New Zealand. University of Waikato, Hamilton, Abstract
70. Raskin L., Poulsen L.K., Noguera D.R., Rittmann B.E., Stahl D.A. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60:1994;1241-1248.
71. Rheims H., Spröer C., Rainey F.A., Stackebrandt E. Molecular biological evidence for the occurrence of uncultured members of the Actinomycete line of descent in different environments and geographic locations. Microbiology. 142:1996;2863-2870.
72. Rosenbaum V., Riesner D. Temperature-gradient gel electrophoresis - thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys. Chem. 26:1987;235-246.
73. Saano, A., Lindström, K., van Elsas, J.D., 1995. Eubacterial diversity in Finnish forest soil. In: 7th International Symposium on Microbial Ecology, Santos, Brazil. Brazilian Society for Microbiology, Santos, Abstract P1-3.9.
74. Saitou N., Nei M. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
75. Schmidt T.M., DeLong E.F., Pace N.R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:1991;4371-4378.
76. Selenska S., Klingmüller W. Direct recovery and molecular analysis of DNA and RNA from soil. Microb. Releases. 1:1992;41-46.
77. Selenska-Pobell S., Evguenieva-Hackenberg E. Fragmentations of the large-subunit rRNA in the family Rhizobiaceae. J. Bacteriol. 177:1995;6993-6998.
78. Stackebrandt E., Liesack W., Goebel B.M. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:1993;232-236.
79. Stahl D.A., Flesher B., Mansfield H.R., Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1988;1079-1084.
80. Staley J.T., Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:1985;321-346.
81. Stephen J.R., Kowalchuk G.A., Bruns M.-A.v., McCaig A.E., Phillips C.J., Embley T.M., Prosser J.I. Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:1998;2958-2965.
82. Stienstra A.W., Klein Gunnewiek P., Laanbroek H.J. Repression of nitrification in soils under climax grassland vegetation. FEMS Microbiol. Ecol. 14:1994;45-52.
83. Strunk, O., Ludwig, W., 1995. ARB - a software environment for sequence data. In: http://www.mikro.biologie.tu-muenchen.de/pub/ARB/(Internet). Department of Microbiology, Technical University of Munich, München, Germany.
84. Teske A., Wawer C., Muyzer G., Ramsing N.B. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and DGGE of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1996;1405-1415.
85. Tolker-Nielsen T., Holmstrom K., Boe L., Molin S.N. Non-genetic population heterogeneity studied by in situ polymerase chain reaction. Mol. Microbiol. 27:1998;1099-1105.
86. Torsvik V., Goksøyr J., Daae F.L. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:1990;782-787.
87. Tsai Y.L., Park M.J., Olson B.H. Rapid method for direct extraction of mRNA from seeded soils. Appl. Environ. Microbiol. 57:1991;765-768.
88. Ueda T., Suga Y., Matsuguchi T. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil. Sci. 46:1995;415-421.
89. Vallaeys T., Topp E., Muyzer G., Macheret V., Laguerre G., Soulas G. Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24:1997;279-285.
90. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:1996;407-438.
91. Wagner M., Erhart R., Manz W., Amann R., Lemmer H., Wede D., Schleifer K.-H. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:1994;792-800.
92. Wagner R. The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch. Microbiol. 161:1994;100-106.
93. Ward D.M., Weller R., Bateson M.M. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 345:1990;63-65.
94. Ward D.M., Bateson M.M., Weller R., Ruff-Roberts A.L. Ribosomal RNA analysis of microorganisms as they occur in nature. Marshall K.C. Advances in Microbial Ecology, vol. 12. 1992;219-286 Plenum Press, New York.
95. Ward-Rainey N., Rainey F.A., Schlesner H., Stackebrandt E. Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria. Microbiology. 141:1995;3247-3250.
96. Wawer C., Muyzer G. Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments. Appl. Environ. Microbiol. 61:1995;2203-2210.
97. Weller R., Weller J.W., Ward D.M. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed complementary DNA. Appl. Environ. Microbiol. 57:1991;1146-1151.
98. Wilson K.H., Blitchington R.B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:1996;2273-2278.
99. Wintzlingerode F.V., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:1997;213-229.
100. Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA. 74:1977;5088-5090.
101. Young C.C., Burghoff R.L., Keim L.G., Minak-Bernero V., Lute J.R., Hinton S.M. Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils. Appl. Environ. Microbiol. 59:1993;1972-1974.
102. Young M., Cole S.T. Clostridium . Sonenshein A.L., Hoch J.A., Losick R. Bacillus subtilis and Other Gram-positive Organisms. 1993;35-52 American Society for Microbiology, Washington, DC.
103. Zarda B., Hahn D., Chazinotas A., Schönhuber W., Neef A., Amann R.I., Zeyer J. Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch. Microbiol. 168:1997;185-192.
104. Zwart G., Huismans R., van Agterveld M.P., Van de Peer Y., De Rijk P., Eenhorn H., Muyzer G., van Hannen E.J., Gons H.J., Laanbroek H.J. Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol. Ecol. 25:1998;159-169.