The double helix meets the crystal lattice: The power and pitfalls of nucleic acid approaches for biomineralogical investigations

American Mineralogist

Volumn 83, Issue 11-12 PART 2, 1998, Pages 1593-1607

  Siering, Patricia Lynne ^a,b  

^a Lockheed Martin Idaho Technology Company   (United States)

^b HUMBOLDT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOCHEMISTRY; BIOMINERALIZATION; ECOLOGY; GENE EXPRESSION; NUCLEIC ACIDS;

CHEMICAL MICROENVIRONMENT; DEVELOPMENT AND APPLICATIONS; DISSOLUTION PROCESS; ENVIRONMENTAL SAMPLE; MICROBIAL ACTIVITIES; MICROBIAL COMMUNITIES; MOLECULAR TECHNIQUES; QUANTITATIVE INFORMATION;

MICROORGANISMS;

BIOMINERALIZATION;

EID: 0032444305     PISSN: 0003004X     EISSN: None     Source Type: Journal    
DOI: 10.2138/am-1998-11-1247     Document Type: Article

References (153)

1. Alfreider, A., Pernthaler, J., Amann, R., Sattler, B., Glöckner, F.-O., Wille, APsenner, R. (1996) Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Applied and Environmental Microbiology, 62, 2138- 2144.
2. Aim, E.W., Oerther, D.B., Larsen, N., Stahl, D.ARaskin, L. (1996) The oligonucleotide probe database. Applied and Environmental Microbiology, 62, 3557-3559. (http://www.cme.msu.edu/OPD/)
3. Amann, R., Glöckner, F.-ONeef, A. (1997) Modern methods in subsurface microbiology, in situ identification of microorganisms with nucleic acid probes. FEMS Microbiology Reviews, 20, 191-200.
4. Amann, R., Springer, N., Ludwig, W., Görtz, H.-DSchleifer, K.-H. (1991) Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature, 351, 161-164.
5. Amann, R.I., Krumholz, LStahl, D.A. (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. Journal of Bacteriology, 172, 762-770.
6. Amann, R.I., Ludwig, WSchleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59, 143-169.
7. Amann, R.I., Stromley, J., Devereux, R., Key, RStahl, D.A. (1992) Molecular and microscopic identification of sulfate-reducing bacteria in " multispecies biofilms. Applied and Environmental Microbiology, 58, 614-623.
8. Andreasen, K. and Nielsen, P.H. (1997) Application of microautoradiography to the study of substrate uptake by filamentous microorganisms in activated sludge. Applied and Environmental Microbiology, 63, 3662-3668.
9. Balkwill, D.L., Maratea, DBlakemore, R.P. (1980) Ultrastructure of a magnetic spirillum. Journal of Bacteriology, 141, 1399-1408.
10. Barns, S.M. and Nierzwicki-Bauer, S.A. (1997) Microbial diversity in ocean, surface, and subsurface environments. In Mineralogical Society of America Reviews in Mineralogy, 35, 35-79.
11. Bams, S.M., Funyga, R.E., Jeffries, M.WPace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proceedings of the National Academy of Sciences USA, 91, 1609-1613.
12. Bazylinski, D.A. and Moskowitz, B.M. (1997) Microbial biomineralization of magnetic iron minerals, microbiology, magnelism, and environmental significance. In Mineralogical Society of America Reviews in Mineralogy, 35, 181-223.
13. Bazylinski, D.A., Garratt-Reed, A.JFrankel, R.B. (1994) Electron microscopic studies of magnetosomes in magnetotactic bacteria. Microscopy Research Techniques, 27, 389-401.
14. Bazylinski, D.A., Frankel, R.B., Heywood, B.R., Mann, S., King, J.W., Donaghay, P.LHanson, A.K. (1995) Controlled biomineralization of magnetite (FejOJ and greigite (Fe3S;) in a magnetotactic bacterium. Applied and Environmental Microbiology, 61, 3232-3239.
15. Beveridge, T.J., Hughes, M.N., Lee, H., Leung, K.T., Poole, R.K., Savvaidis, I., Silver, STrevors, J.T. (1997) Metal-microbe interactions, contemporary approaches. Advances in Microbial Physiology, 38, 178243.
16. Bier, F.F. and Fiirste, J.P. (1997) Nucleic acid based biosensors. Experientia Supplementum, 80, 97-120.
17. Bogan, B.W., Schoenike, B., Lamar, R.TCullen, D. (1996) Manganese peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic aromatic hydrocarbon-contaminated soil with Plianerocliaete clirysporium. Applied and Environmental Microbiology, 62, 2381- 2386.
18. Borneman, J., Skroch, P.W., O'Sullivan, K.M., Palus, J.A., Rumjanek, N.G., Jansen, J.L., Nienhuis, JTriplett, E.W. (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Applied and Environmental Microbiology, 62, 1935-1943.
19. Bremer, H. and Dennis, P.P. (1987) Modulation of chemical composition and other parameters of the cell by growth rate. In EC. Neidhardt, J.L. Ingraham, K.B. Low, B. Magasanik, M. Schaecter, and H.E. Umbarger, Eds., Escherichia coli and Salmonella typhimuriitm: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
20. Brock, T.D. (1987) The study of microorganisms in situ: progress and problems. Symposia of the Society for General Microbiology, 41, 117.
21. Brock, J.D. and Brock, M.L. (1966) Autoradiography as a tool in microbial ecology. Nature, 209, 734-736.
22. Brockman, FJ. (1995) Nucleic-acid-based methods for monitoring the performance of in siiu bioremediation. Molecular Ecology, 4, 567-578.
23. Brockman, EJ. and Murray, C.J. (1997) Subsurface microbiological heterogeneity: current knowledge, descriptive approach and applications. FEMS Microbiology Reviews, 20, 231-247.
24. Brace, K.D., Osborn, A.M., Pearson, A.J., Strike, PRitchie, D.A. (1995) Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria. Molecular Ecology, 4, 605-612.
25. Burggraf, S., Heyder, PEis, N. (I997) A pivotal Archae group. Nature, 385, 780.
26. Burlage, R.S. (1997) Emerging technologies: bioreporters, biosensors, and microprobes. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 115-123. American Society for Microbiology Press, Washington, D.C.
27. Capone, D.G. (1997) Microbial nitrogen cycling. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 334-342. ASM Press, Washington, D.C.
28. Chen, F., Gonzalez, J.M., Dustman, W.A., Moran, M.AHodson, R.E. (1997) In situ reverse transcription, an approach to characterize genetic diversity and activity of prokaryotes. Applied and Environmental Microbiology, 63, 4907-4913.
29. Christensen, H., Bakken, L.ROlsen, R.A. (1993) Soil bacterial DNA and biovolume profiles measured by flow cytometry. FEMS Microbiology Ecology, 102, 129-140.
30. Colwell, R.R., Clayton, R.A., Ortiz-Conde, B.A., Jacobs, DRussekCohen, E. (1995) The microbial species concept and biodiversity. In D. Allsopp, R.R. Colwell, and D.L. Hawksworth, Eds., Microbial Diversity and Ecosystem Function, p. 3-15. Center for Agriculture and Biosciences International, New York.
31. Damgaard, L.R., Larsen, L.HRevsbach, N.P. (1995) Microscale bios-ensors for environmental monitoring. Trends in Analytical Chemistry, 14, 300-303.
32. Davey, H.M. and Kell, D.B. (1996) Row cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiological Reviews, 60, 641-696.
33. de Beer, D., Schramm, A., Santegoeds, CMKühl, M. (1997) A nitrite microsensor for profiling environmental biofilms. Applied and Environmental Microbiology, 63, 973-977.
34. DeLeo, P.C. and Baveye, P. (1996) Enumeration and biomass estimation of bacteria in aquifer microcosm studies by flow cytometry. Applied and Environmental Microbiology, 62, 4580-4586.
35. Delong, E.F. (1993) Single-cell identification using fluorescently labeled ribosomal RNA-specific probes. In P.P. Kemp, B.F. Sherr, E.B. Sherr, and J.J. Cole, Eds., Handbook of Methods in Aquatic Microbial Ecology, p. 285-294. Lewis Publishers, Boca Raton, Florida.
36. Delong, E.E, Wickham, G.SPace, N.R. (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science, 243, 1360-1363.
37. de Vrind-de Jong, E.W. and de Vrind, J.P.M. (1997) Algal deposition of carbonates and silicates. In Mineralogical Society of America Reviews in Mineralogy, 35, 267-307.
38. Diaper, J.P. and Edwards, C. (1994) Flow cytometric detection of viable bacteria in compost. FEMS Microbiology Ecology, 14, 213-220.
39. DiChristina, T.J. and DeLong, E.F. (1993) Design and application of rRNA-targeted oligonucleotide probes for the dissimilatory iron- and manganese-reducing bacterium SheH-anella pulrefaciens. Applied and Environmental Microbiology, 59, 4152-4160.
40. Dieffenbach, C.W. and Dveksler, G.S. (1995) PCR Primer-A Laboratory Manual. Cold Spring Harbor Press, New York.
41. Ehrlich, H.J. (1995) Geomicrobiology. Marcel Dekker, Inc., New York.
42. Elus, R.J. (1979) The most abundant protein in the world. Trends in Biochemical Sciences, 4, 241- 244.
43. Farrelly, V., Rainey, EAStackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Applied and Environmental Microbiology, 61, 2798-2801.
44. Ferns, EG., Wiese, R.GFyfe, W.S. (1994) Precipitation of carbonate minerals by microorganisms: Implications for silicate weathering and the global carbon dioxide budget. Geomicrobiology Journal, 12, 1-13.
45. Fink, T., Buescher, S., Gaebler, R., Yu, Q., Dax, AUrban, W. (1996) An improved CO; laser intracavity photoacoustic spectrometer for trace gas analysis. Review of Scientific Instruments, 67, 4000-4004.
46. Fleming, J.T., Sanseverino, JSayler, G.S. (1993) Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environmental Science and Technology, 27, 1068-1074.
47. Fuhrman, J.A., Comeau, D.E., Hagström, AChan, A.M. (1988) Extraction from natural planktonic microorganism of DNA suitable for molecular biological studies. Applied and Environmental Microbiology, 54, 1426-1429.
48. Ghiorse, W.C. and Ehrlich, H.L. (1992) Microbial biomineralization of iron and manganese. In R.W. Fitzpatrick and H.C.W. Skinner, Eds., Biomineralization Processes of Iron and Manganese: Modern and Ancient Environments, p. 75-101. Catena Verlag, Cremlingen-Destedt, Germany.
49. Ghiorse, W.C., Miller, D.N., Sandoli, R.LSiering, P.L. (1996) Applications of laser scanning microscopy for analysis of aquatic microhabitats. Microscopy Research Technique, 33, 73-86.
50. Giovannoni, S.J., DeLong, E.F., Olsen, G.JPace, N.R. (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. Journal of Bacteriology, 170, 720-726.
51. Giovannoni, S.J., Rappé, M.S., Vergin, K.LAdair, N.L. (1996) 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to green non-sulfur bacteria. Proceedings of the National Academy of Sciences USA, 93, 7979-7984.
52. Glöckner, EO., Amann, R., Alfreider, A., Pernthaler, J., Psenner, R., Trebesius, KSchleifer, K.-H. (1996) An in situ hybridization protocol for detection and identification of planktonic bacteria. Systematic and Applied Microbiology, 19, 403-406.
53. Grossman, E.L. (1997) Stable carbon isotopes as indicators of microbial activity in aquifers. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 565-576. American Society for Microbiology Press, Washington, D.C.
54. Guschin, D.Y., Mobarry, B.K., Proudnikov, D., Stahl, D.A., Rittmann, B.EMirzabekov, A.D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Applied and Environmental Microbiology, 63, 2397-2402.
55. Hanson, P.D. and von Usedon, A. (1997) New biosensors for environmental analysis. Experientia Supplementum, 81, 109-120.
56. Harmsen, H.J.M., Prieur, DJeamhon, C. (1997) Group-specific 16S rRNA targeted oligonucleotide probes to identify thermophilic bacteria in marine hydrothermal vents. Applied and Environmental Microbiology, 63, 4061-4068.
57. Herrick, J.B., Madsen, E.L., Bau, C.AGhiorse, W.C. (1993) Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Applied and Environmental Microbiology, 59, 687-694.
58. Hincs, M.E., Visscher, P.TDevereux, R. (1997) Sulfur cycling. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 324-333. American Society for Microbiology Press, Washington, D.C.
59. Hodson, R.E., Dustman, W.A., Garg, R.PMoran, M.A. (1995) In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities. Applied and Environmental Microbiology, 61, 4074-4082.
60. Hsieh, Y.P. and Yang, C.H. (1989) Diffusion methods for the determination of reduced inorganic sulfur species in sediments. Limnology and Oceanography, 34. 1126-1130.
61. Jacobs, D., Angles, M.L., Goodman, A.ENeilan, B.A. (1997) Improved methods for in situ amplification and detection of low copy number genes in bacteria. FEMS Microbiology Letters, 152, 65-73.
62. Jeffrey, W.H., Nazaret, SBarkay, T. (I996) Detection of the merA gene and its expression in the environment. Microbial Ecology, 32, 293-303.
63. Jeffrey, W.H., Nazaret, SVon Haven, R. (1994) Improved method for recovery of mRNA from aquatic samples and its application to detection of mer expression. Applied and Environmental Microbiology, 60, 1814-1821.
64. Jones, R.D. (1997) Phosphorous cycling. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 343-348. American Society for Microbiology Press, Washington, D.C.
65. Juniper, S.K. and Tebo, B.M. (1995) Microbe-metal interactions and mineral deposition at hydrothermal vents. In D.M. Karl, Ed., The Microbiology of Deep Sea Hydrothermal Vents, p. 219-253. CRC Press, Boca Raton, Florida.
66. Kemp, P.p., Lee, SLaRoche, J. (1993) Estimating the growth rate of slowly growing marine bacteria from RNA content. Applied and Environmental Microbiology, 59, 2594-2601.
67. Klein, P.O. and Juneja, V.K. (1997) Sensitive detection of viable Listeria monocytogenes by reverse transcription-PCR. Applied and Environmental Microbiology, 63, 4441-4448.
68. Komatsoulis, G.A. and Waterman, M.S. (1997) A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Applied and Environmental Microbiology, 63, 2338-2346.
69. Kopczynski, E.D., Bateson, M.MWard, D.M. (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultured organisms. Applied and Environmental Microbiology, 60,746748.
70. Kuske, C.R., Bams, S.MBusch, J.D. (1997) Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Applied and Environmental Microbiology, 63, 3614-3621.
71. Larsen, L.H. and Revsbach, N.P. (1996) A microsensor for nitrate based on immobilized denitrifying bacteria. Applied and Environmental Microbiology, 62, 1248-1251.
72. Lebaron, P., Catala, P., Fajon, C., Joux, E, Baudart, JBernard, L. (1997) A new sensitive, whole-cell hybridization technique for detec-lion of bacteria involving a biotinylated oligonucleotide probe targeting rRNA and tyramide signal amplification. Applied and Environmental Microbiology, 63, 3274-3278.
73. Liesack, W. and Stackebrandt, E. (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. Journal of Bacteriology, 174, 5072-5078.
74. Liesack, W.H., Weyland, HStackenbrandt, E. (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microbial Ecology, 21, 192-198.
75. Lim, E.L., Amaral, L.A., Caron, D.ADeLong, E.F. (1995) Application of rRNA-based probes for observing marine nanoplankton prolists. Applied and Environmental Microbiology, 59, 1647- 1655.
76. Lowenstam, H.A. (1981) Minerals formed by organisms. Science, 211, 1126-1131.
77. Madan, A.P. and Nierzwicki-Bauer, S.A. (1993) In situ detection of transcripts for ribulose-l,5-bisphosphate carboxylase in cyanobacterial heterocysts. Journal of Bacteriology, 175, 7301-7306.
78. Madsen, E.L.M. (1996) A critical analysis of methods determining the composition and biogeochemical activities of soil microbial communities in situ. In G. Stotsky and J.-M. Bollag, Eds., Soil Biochemistry, p. 287-370. Marcel Dekker, New York.
79. Maidak, B.L., Olsen, G.J., Larsen, N., Overbook, R., McCaughey, M.JWoese, C.R. (1997) The ribosomal database project. Nucleic Acids Research, 25, 109-111. (http://rdp.life.uiuc.edu/)
80. Mann, S., Sparks, N.H.CBlakemore, R.P. (1987a) Ultrastructure and characterization of anisotropic magnetite crystals in magnetotactic bacteria. Proceedings of the Royal Society of London Series B 231, 469476.
81. (1987b) Structure, morphology, and crystal growth of anisotropic magnetite crystals in magnetotactic bacteria. Proceedings of the Royal Society of London Series B 231, 477-487.
82. Manz, W., Amann, R., Ludwig, W., Wagner, MSchleifer, K.H. (1992) Phylogenetic oligonucleotide probes for major subclasses of proteobacteria, problems and solutions. Systematic and Applied Microbiology, 15, 593-600.
83. McCulloch, R.K., Choong, C.SHurley, D.M. (1995) An evaluation of competitor type and size for use in the determination of mRNA by competitive PCR. PCR Methods and Applications, 4, 219- 226.
84. Mobarry, B.K., Wagner, M., Urbain, V., Rittmann, B.EStahl, D.A. (1996) Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Applied and Environmental Microbiology, 62, 2156-2162.
85. Moller, S Pedersen, A.R., Poulsen, L.K., Arvin, EMolin, S. (1996) Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Applied and Environmental Microbiology, 62, 4632-4640.
86. Moran, M.A., Torsvik, V.L., Torsvik, THodson, R.E. (1993) Direct extraction and purification of rRNA for ecological studies. Applied and Environmental Microbiology, 59, 915-918.
87. More, M., Herrick, J.B., Suva, M., Ghiorse, W.CMadsen, E.L. (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Applied and Environmental Microbiology, 60, 1572-1580.
88. Morrison, C. and Cannon, E (I995) The impact of PCR plateau on the quantitative PCR. Biochimica et Biophysica Acta, 1219, 493-498.
89. Nealson, K.H., Rosson, R.AMyers, C.R. (1989) Mechanisms of oxidation and reduction of manganese. In T.J. Beveridge and R.J. Doyle, Eds., Metal Ions and Bacteria, p. 383-413. Wiley, New York.
90. Nealson, K.H., Tebo, B.MRosson, R.A. (1988) Occurrence and mechanisms of microbial oxidation of manganese. Advances in Applied Microbiology, 33, 279-319.
91. Ogram, A., Sun, W., Brockman, F.JFredrickson, J.K. (1995) Isolation and characterization of RNA from low-biomass deep subsurface sediments. Applied and Environmental Microbiology, 61, 763-768.
92. Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.RStahl, D.A. (1986) Microbial ecology and evolution, A ribosomal RNA approach. Annual Review of Microbiology, 40, 337-365.
93. Ouverney, C.C. and Fuhrman, J.A. (1997) Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol. Applied and Environmental Microbiology, 63, 2735-2740.
94. Pace, N.R., Stahl, D.A., Lane, D.JOlsen, G.J. (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology, 9, 1-55.
95. Paul, J.H., Cesares, LThurmond, J. (1990) Amplification of the rbcL gene from dissolved and paniculate DNA from aquatic environments. Applied and Environmental Microbiology, 56, 1963-1966.
96. Pepper, I.L. (1997) PCR: applications for plant and soil microbes. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L.D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 437-443. American Society for Microbiology Press, Washington, D.C.
97. Pichard, S.L. and Paul, J.H. (1991) Detection of gene expression in genetically engineered microorganisms and natural phytoplankton populations in the marine environment. Applied and Environmental Microbiology, 57, 1721-1727.
98. (1993) Gene expression per gene dose-a specific measure of gene expression in aquatic microorganisms. Applied and Environmental Microbiology, 59, 451-457.
99. Pichard, S.L., Campbell, LPaul, J.H. (1997) Diversity of the ribulose carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities. Applied and Environmental Microbiology, 63, 36003606.
100. Porter, J., Pickup, REdwards, C. (1995) Flow cytometric detection of specific genes in genetically modified bacteria using in situ polymerase chain reaction. FEMS Microbiology Letters, 134, 51-56.
101. Raeymaekers, L. (1995) A commentary on the practical applications of quantitative PCR. Genome Research, 5, 91-94.
102. Ramsing, N.B., Kühl, MJorgensen, B.B. (1993) Distribution of sulfate-reducing bacteria, O2, and H,S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Applied and Environmental Microbiology, 59, 3840-3849.
103. Ramsing, N.B., Fossing, H., Ferdelman, T.G., Andersen, E, andThamdrup, B. (1996) Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Applied and Environmental Microbiology, 62, 1391-1404
104. Rapp, A.K., van de Corput, M.P.C., Vernenne, A.W., van Gijlswijk, R.P.M., Tanke, HJWiegant, J. (1995) Ultra-sensitive FISH using pcroxidase-mediated deposition of biotin- or (luorochrome tyramides. Human Molecular Genetics, 4, 529-534.
105. Raskin, L., Poulsen, L.K., Noguera, D.R., Rittmann, B.EStahl, D.A. (1994) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Applied and Environmental Microbiology, 60, 1241-1248.
106. Reysenbach, A.-L., Giver, L.J., Wickham, G.SPace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Applied and Environmental Microbiology, 58, 3417- 3418.
107. Robison-Cox, J.F, Bateson. M.MWard, D.M. (1995) Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Applied and Environmental Microbiology, 61, 1240-1245.
108. Rotthauwe, J.-H., Witzel, K.-PLiesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker, molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology, 63, 4704-4712.
109. Schmidt, T.M., DeLong, E.FPace, N.R. (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Applied and Environmental Microbiology, 173, 4371-4378.
110. Schönhuber, W., Fuchs, BJuretschko, S. (1997) Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Applied and Environmental Microbiology, 63, 3268-3273.
111. Schramm, A., Larsen, L.H., Revsbach, N.R, Ramsing, N.B., Amann, RSchleifer, K.-H. (1996) Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Applied and Environmental Microbiology, 62, 4641-4647.
112. Schrenk, M.O., Edwards, K.J., Goodman, R.M., Hamers, R.JBanfield, J.F. (1998) Distribution of Tliiobacillus ferroo.ridans and Lepios-
113. pirilliim ferrooxidans: implications for generation of acid mine drainage. Science, 279, 1519-1522.
114. Schultze-Lam, S. and Beveridge, T.J. (1994) Nucleation of celesite and strontianite on a cyanobacterial S-layer. Applied and Environmental Microbiology, 60, 447-453.
115. Selvaratnam, S., Schoedel, B.A., McFarland, B.LKulpa, C.F. (1995) Application of reverse transcriptase PCR for monitoring expression of the catabolic dmpN gene in a phenol-degrading sequencing batch reactor. Applied and Environmental Microbiology, 61, 3981-3985.
116. Shapiro, H.M. (1995) Practical Flow Cytometry. Alan R. Liss, Inc., New York.
117. Sisring, P.L. (1996) Application of molecular approaches to investigate the role of microorganisms in manganese cycling in wetland environments. Ph.D. dissertation. Cornell University, Ithaca, New York.
118. Siering, P.L. and Ghiorse, W.C. (1997) Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples. Applied and Environmental Microbiology, 63, 644-651.
119. 1997) PCR detection of a putative manganese oxidation gene (mofA) in environmental samples and assessment of mofA gene homology among diverse manganese oxidizing bacteria. Geomicrobiology Journal, 14, 109-125.
120. Simon, N., LeBot, N., Marie, D., Partensky, E, and Vaulot, D. (1995) Fluorescent in situ hybridization with rRNA-targeted probes to identify small phytoplankton by flow cytometry. Applied and Environmental Microbiology, 61, 2506-2513.
121. Sinigalliano, C.D., Kühn, D.NJones R.D. (1995) Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Applied and Environmental Microbiology, 61, 2702-2706.
122. Sprenson, A.H., Torsvik, V., Torsvik, T., Poulsen, L.KAhring, B.K. (1997) Whole-cell hybridization of htethanosarcina cells with two new oligonucleotide probes. Applied and Environmental Microbiology, 63, 3043-3050.
123. Sparks, N.H.C., Mann, S., Bazylinski, D.A., Lovley, D.R., Jannasch, H.WFrankel, R.B. (1990) Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium. Earth and Planetary Science Letters, 98, 14-22.
124. Stahl, D.A. (1997) Molecular approaches for the measurement of density, diversity, and phylogeny. In C.J. Hurst, G.R. Knudsen, M.J. Mclnerney, L D. Stetzenbach, and M.V. Walter, Eds., Manual of Environmental Microbiology, p. 102-114. American Society for Microbiology Press, Washington, D.C.
125. Stahl, D.A. and Amann, R. (1991) Development and application of nucleic acid probes. In E. Stackebrandt and M. Goodfellow, Eds., Nucleic acid techniques in bacterial systematics, p. 205-248. Wiley, New York.
126. Sunda, W.O. and Huntsman, S.A. (1987) Microbial oxidation of manganese in a North Carolina estuary. Limnology and Oceanography, 32, 552-564.
127. (1988) Effect of sunlight on redox cycles of manganese in the southwestern Sargasso sea. Deep-Sea Research, 35, 1297-1317.
128. Suzuki, M.T. and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology, 62, 625-630.
129. Suzuki, M.T., Rappé, M.S., Haimberger, Z.W., Winfield, H., Adair, N., Ströbel, JGiovannoni, S.J. (1997) Bacterial diversity among small subunit rRNA gene clones and cellular isolates from the same seawater sample. Applied and Environmental Microbiology, 63, 983-989.
130. Tebo, B.M. and Emerson, S. (1985) The effect of oxygen tension, Mn(II) concentration and temperature on the microbially catalyzed Mn(II) oxidation rate in a marine fjord. Applied and Environmental Microbiology, 50, 1268-1273.
131. (1986) Microbial Mn(II) oxidation in the marine environment: a
132. quantitative study. Biogeochemistry, 2, 149-161. Tebo, B.M., Ghiorse, W.C., vanWaasbergen, L.G., Siering, P.LCaspi,
133. R. (1997) Bacterially mediated mineral formation: insights into man-
134. ganese(II) oxidation from molecular genetic and biochemical studies.
135. In Mineralogical Society of America Reviews in Mineralogy, 35, 225-266.
136. Thompson, J.B. and Ferris, EG. (1990) Cyanobacterial precipitation of gypsum, calcite, and magnesite from natural alkaline lake water. Geology, 18, 995-998.
137. Tiedje, J.M. (1995) Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat. In D. Allsopp, R.R. Cohvell, and D L. Hawksworth, Eds., Microbial Diversity and Ecosystem Function, p. 7388. Center for Agriculture and Biosciences International, New York.
138. Towe, K.M. and Moench, T.T. (1981) Electron-optical characterization of bacterial magnetite. Earth and Planetary Science Letters, 52, 213-220.
139. Ulrich, G.A., Krumholz, L.RSuflita, J.M. (1997) A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides. Applied and Environmental Microbiology, 63, 16271630.
140. Wagner, M., Amann, R., Kämpfer, R, Assmus, B., Hartmann, A., Hutzier, P., Springer, NSchleifer, K.-H. (1994) Identification and in-situ detection of gram-negative filamentous bacteria in activated sludge. Systematic and Applied Microbiology, 17, 405-417.
141. Wagner, M., Assmus, B., Hartmann, A., Hutzier, PAmann, R.I. (1994) In situ analysis of microbial consortia in activated sludge using (luorescently labelled, rRNA targeted probes and confocal scanning laser microscopy. Journal of Microscopy, 176, 181-187.
142. Wallner, G., Erhart, RAmann, R. (1995) Flow cytometric analysis of activated sludge with rRNA-targeted probes. Applied and Environmental Microbiology, 61, 1859-1866.
143. Wallner, G., Fuchs, B., Spring, S., Beisker, W, and Amann, R. (1997) Flow sorting of microorganisms for molecular analysis. Applied and Environmental Microbiology, 63, 4223-4231.
144. Wang, G.C.-Y. and Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Applied and Environmental Microbiology, 63, 4645-4650.
145. Ward, B.B. (1984) Combined autoradiography and immunofluorescence for estimation of single cell activity of ammonium-oxidizing bacteria. Limnology and Oceanography, 29,'402-410.
146. Ward, D.M., Bateson, M.M., Weller, RRuff-Roberts, A.L. (1992) Ribosomal RNA anJysis of microorganisms as they occur in nature. In K.C. Marshall, Ed., Advances in Microbial Ecology, p. 219-286. Plenum Press, New York.
147. Wilson, M.S. (1998) Transient molecular markers of in situ napthalene biodégradation at a coal tar-contaminated field site. Ph.D. dissertation. Cornell University. Ithaca, New York.
148. Wise, M.G., McArthur, J.VShimkets, L.J. (1997) Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Applied and Environmental Microbiology, 63, 1505-1514.
149. Woese, C.R. (1987) Bacterial evolution. Microbiological Reviews, 51, 221-271.
150. Xu, H.H. and Tabita, ER. (1996) Ribulose-l,5-bisphosphate carboxylase/ oxygenase gene expression and diversity of Lake Erie planktonic microorganisms. Applied and Environmental Microbiology, 62, 19131921.
151. Zheng, D., Alm, E.W., Stahl, D.ARaskin, L. (1996) Characterization of universal small subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Applied and Environmental Microbiology, 62, 4504-4513.
152. Zhou, J., Bruns, M.ATiedje, J.M. (1996) DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 62, 316-322.
153. Zuckermann, H., Staal, M., Stal, L.J., Reuss, J., Hekkert, S.L., Harren, FParker, D. (1997) On-line monitoring of nitrogenase activity in cyanobacteria by sensitive laser photoacoustic detection of ethylene. Applied and Environmental Microbiology, 63, 4243-4251.