1887

Chapter 61 : Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap61-1.gif /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap61-2.gif

Abstract:

This chapter examines experimental design considerations for a population-based approach for identifying microorganisms involved in specific in situ functions. Although this chapter focuses on a particular population-based approach, many of the experimental design considerations discussed here apply to a wide range of rRNA gene-based population studies and sequence selective PCR assays. This chapter examines an experimental approach that uses the population-based strategy. The approach has the following three phases: (i) identifying populations of rRNA genes whose abundances correlate with the functional parameter, (ii) validating the rRNA gene correlates identified in phase I by using an independent quantitative assay, and (iii) isolating the microorganisms identified by the rRNA gene correlates and reintroducing them into the environment to assess their functions in situ. This approach was recently used to identify microorganisms that suppress the population development of the plant parasitic nematode in southern California soil. Functional gradients are created by manipulating the microbial community with methods such as differential heat treatments, targeted antimicrobial agents, and nutritional amendments. Microbial community composition is examined by rRNA gene analysis. Nucleotide sequence analysis of rRNA gene clone libraries can be used to generate detailed depictions of microbial community composition. PCR assays can be validated by using them to amplify DNAs extracted from different environmental samples and then cloning and sequencing several randomly selected clones from each sample. The assays can be considered selective if they exclusively amplify the target sequence.

Citation: Borneman J, Becker J, Bent E, Lanoil B, McSpadden Gardener B, Olatinwo R, Presley L, Scupham A, Valinsky L, Yin B. 2007. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, p 748-757. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch61

Key Concept Ranking

Quantitative PCR
0.64533144
Real-Time PCR
0.63962054
Microbial Ecology
0.6182047
Culture Methods
0.5425447
DNA Synthesis
0.532832
0.64533144
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Experimental strategy for OFRG.

Citation: Borneman J, Becker J, Bent E, Lanoil B, McSpadden Gardener B, Olatinwo R, Presley L, Scupham A, Valinsky L, Yin B. 2007. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, p 748-757. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch61
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

rRNA operon and positions of PCR primers.

Citation: Borneman J, Becker J, Bent E, Lanoil B, McSpadden Gardener B, Olatinwo R, Presley L, Scupham A, Valinsky L, Yin B. 2007. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, p 748-757. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch61
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Effect of annealing temperature on a PCR assay.

Citation: Borneman J, Becker J, Bent E, Lanoil B, McSpadden Gardener B, Olatinwo R, Presley L, Scupham A, Valinsky L, Yin B. 2007. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, p 748-757. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch61
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Effect of template concentration on mismatch discrimination of a PCR assay.

Citation: Borneman J, Becker J, Bent E, Lanoil B, McSpadden Gardener B, Olatinwo R, Presley L, Scupham A, Valinsky L, Yin B. 2007. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, p 748-757. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch61
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815882.ch61
1. Adamczyk, J.,, M. Hesselsoe,, N. Iversen,, M. Horn,, A. Lehner,, P. H. Nielsen,, M. Schloter,, P. Roslev, and, M. Wagner. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69:68756887.
2. Alabouvette, C.,, F. Rouxel, and, J. Louvet. 1979. Characteristics of fusarium wilt-suppressive soils and prospects for their utilization in biological control, p. 165–182. In B. Schippers and, W. Gams (ed.), Soil-Borne Plant Pathogens. Academic Press, London, United Kingdom.
3. Altschul, S. F.,, T. L. Madden,, A. A. Schaffer,, J. Zhang,, Z. Zhang,, W. Miller, and, D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:33893402.
4. Ashelford, K. E.,, A. J. Weightman, and, J. C. Fry. 2002. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDPII database. Nucleic Acids Res. 30:34813489.
5. Atlas, R. M. 2004. Handbook of Microbiological Media, 3rd ed. CRC Press, Boca Raton, Fla.
6. Avrahami, S.,, W. Liesack, and, R. Conrad. 2003. Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environ. Microbiol. 5:691705.
7. Barns, S. M.,, R. E. Fundyga,, M. W. Jeffries, and, N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:16091613.
8. Beja, O.,, M. T. Suzuki,, E. V. Koonin,, L. Aravind,, A. Hadd,, L. P. Nguyen,, R. Villacorta,, M. Amjadi,, C. Garrigues,, S. B. Jovanovich,, R. A. Feldman, and, E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516529.
9. Bergersen, F. J. 1961. The growth of rhizobium in synthetic media. Aust. J. Biol. 14:349360.
10. Bock, M.,, M. Maiwald,, R. Kappe,, P. Nickel, and, H. Naeher. 1994. Polymerase chain reaction-based detection of dermatophyte DNA with a fungus-specific primer system. Mycoses 37:7984.
11. Bonnet, R.,, A. Suau,, J. Dore,, G. R. Gibson, and, M. D. Collins. 2002. Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int. J. Syst. Evol. Microbiol. 52:757763.
12. Borneman, J. 1999. Culture-independent identification of microorganisms that respond to specified stimuli. Appl. Environ. Microbiol. 65:33983400.
13. Borneman, J.,, M. Chrobak,, G. D. Vedova,, A. Figueroa, and, T. Jiang. 2001. Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17:S39S48.
14. Borneman, J.,, and R. J. Hartin. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66:43564360.
15. Borneman, J.,, and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:26472653.
16. Boschker, H. T. S.,, S. C. Nold,, P. Wellsbury,, D. Bos,, W. De Graaf,, R. Pel,, R. J. Parkees, and, T. E. Cappenberg. 1998. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392:801805.
17. Broadbent, P.,, and K. F. Baker. 1975. Presented at the Biology and Control of Soil-Borne Plant Pathogens, Minneapolis, Minn.
18. Brockhurst, M. A.,, P. B. Rainey, and, A. Buckling. 2004. The effect of spatial heterogeneity and parasites on the evolution of host diversity. Proc. R. Soc. Lond. B. 271:107111.
19. Cardinale, M.,, L. Brusetti,, P. Quatrini,, S. Borin,, A. M. Puglia,, A. Rizzi,, E. Zanardini,, C. Sorlini,, C. Corselli, and, D. Daffonchio. 2004. Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl. Environ. Microbiol. 70:61476156.
20. Chandler, D. P.,, J. K. Fredrickson, and, F. J. Brockman. 1997. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:475482.
21. Cole, J. R.,, B. Chai,, R. J. Farris,, Q. Wang,, S. A. Kulam,, D. M. McGarrell,, G. M. Garrity, and, J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294D296.
22. Connon, S. A.,, and S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:38783885.
23. Cook, R. J. 1973. Influence of low plant and soil water potentials on diseases caused by soil-borne fungi. Phytopathology 63:451458.
24. Cook, R. J.,, and K. F. Baker. 1983. The nature and practice of biological control of plant pathogens. APS Press, St. Paul, Minn.
25. Corless, C. E.,, M. Guiver,, R. Borrow,, V. Edwards-Jones,, E. B. Kaczmarski, and, A. J. Fox. 2000. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol. 38:17471752.
26. Crump, D. H.,, and B. R. Kerry. 1987. Studies on the population dynamics and fungal parasitism of Heterodera schachtii in soil from a sugar beet monoculture. Crop Prot. 6:4955.
27. Dawson, S. C.,, and N. R. Pace. 2002. Novel kingdomlevel eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99:83248329.
28. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:56855689.
29. DeLong, E. F.,, L. T. Taylor,, T. L. Marsh, and, C. M. Preston. 1999. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65:55545563.
30. DeLong, E. F.,, G. S. Wickham, and, N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:13601363.
31. Dieffenbach, C. W.,, and G. S. Dveksler. 2003. PCR Primer: a Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
32. Edgcomb, V. P.,, D. T. Kysela,, A. Teske,, A. D. Gomez, and, M. L. Sogin. 2002. Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad. Sci. USA 99:76587662.
33. Egert, M.,, and M. W. Friedrich. 2005. Post-amplification Klenow fragment treatment alleviates PCR bias caused by partially single-stranded amplicons. J. Microbiol. Methods 61:6975.
34. Ehlen, T.,, and L. Dubeau. 1989. Detection of ras point mutations by polymerase chain-reaction using mutation-specific, inosine-containing oligonucleotide primers. Biochem. Biophys. Res. Commun. 160:441447.
35. Eijsackers, H. 2001. A future for soil ecology? Connecting the system levels: moving from genomes to ecosystems. Opening lecture to the XIII ICSZ, “Biodiversity of soil organisms and ecosystem functioning.” Eur. J. Soil Biol. 37:213220.
36. Erlich, H. A. 1989. PCR Technology: Principles and Applications for DNA Amplification. Stockton Press, New York, N.Y.
37. Farrelly, V.,, F. A. Rainey, and, E. Stackebrandt. 1995. 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. 61:27982801.
38. Franklin, R. B.,, and A. L. Mills. 2003. Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol. Ecol. 44:335346.
39. Garcia-Pichel, F.,, S. L. Johnson,, D. Youngkin, and, J. Belnap. 2003. Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado Plateau. Microb. Ecol. 46:312321.
40. Gardes, M.,, and T. D. Bruns. 1993. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol. Ecol. 2:113118.
41. Giovannoni, S. J.,, E. F. DeLong,, G. J. Olsen, and, N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720726.
42. Gray, N. D.,, R. C. Hastings,, S. K. Sheppard,, P. Loughnane,, D. Lloyd,, A. J. McCarthy, and, I. M. Head. 2003. Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soil. FEMS Microbiol. Ecol. 46:1122.
43. Horz, H.-P.,, M. T. Yimga, and, W. Liesack. 2001. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 67:41774185.
44. Hutchinson, C. M.,, M. E. McGiffen, Jr.,, H. D. Ohr,, J. J. Sims, and, J. O. Becker. 2000. Efficacy of methyl iodide and synergy with chloropicrin for control of fungi. Pest Manag. Sci. 56:413418.
45. Innis, M. A. 1990. PCR Protocols: a Guide to Methods and Applications. Academic Press, San Diego, Calif.
46. Jaspers, E.,, and J. Overmann. 2004. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl. Environ. Microbiol. 70:48314839.
47. Jensen, M. A.,, and N. Straus. 1993. Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl. 3:186194.
48. Jiang, L.,, and P. J. Morin. 2004. Productivity gradients cause positive diversity-invasibility relationships in microbial communities. Ecol. Lett. 7:10471057.
49. Johnsen, K.,, C. S. Jacobsen,, V. Torsvik, and, J. Sorensen. 2001. Pesticide effects on bacterial diversity in agricultural soils—a review. Biol. Fert. Soils 33:443453.
50. Joseph, S. J.,, P. Hugenholtz,, P. Sangwan,, C. A. Osborne, and, P. H. Janssen. 2003. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69:72107215.
51. Kaeberlein, T.,, K. Lewis, and, S. S. Epstein. 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:11271129.
52. Kao, C. W.,, and W. H. Ko. 1983. Nature of suppression of Pythium splendens in a pasture soil in south Kohala Hawaii USA. Phytopathology 73:12841289.
53. Kappe, R.,, C. Fauser,, C. N. Okeke, and, M. Maiwald. 1996. Universal fungus-specific primer systems and group-specific hybridization oligonucleotides for 18S rDNA. Mycoses 39:2530.
54. Kerry, B. R.,, D. H. Crump, and, L. A. Mullen. 1980. Parasitic fungi soil moisture and multiplication of the cereal cyst nematode, Heterodera avenae. Nematologica 26:5768.
55. Kirk, J. L.,, L. A. Beaudette,, M. Hart,, P. Moutoglis,, J. N. Klironomos,, H. Lee, and, J. T. Trevors. 2004. Methods of studying soil microbial diversity. J. Microbiol. Methods 58:169188.
56. Kowalchuk, G. A.,, F. J. de Bruijn,, I. M. Head,, A. D. L. Akkermans, and, J. D. van Elsas. 2004. Molecular Microbial Ecology Manual, 2nd ed. Kluwer Academic, Dordrecht, The Netherlands.
57. Kwok, S.,, D. E. Kellogg,, N. McKinney,, D. Spasic,, L. Goda,, C. Levenson, and, J. J. Sninsky. 1990. Effects of primer template mismatches on the polymerase chain-reaction—human-immunodeficiency-virus type-1 model studies. Nucleic Acids Res. 18:9991005.
58. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115–175. In E. Stackebrandt and, M. Goodfellow (ed.), Nucleic Acid Techniques in Bacterial Systematics. Wiley, New York, N.Y.
59. Lane, D. J.,, B. Pace,, G. J. Olsen,, D. A. Stahl,, M. L. Sogin, and, N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82:69556959.
60. Lee, N.,, P. H. Nielsen,, K. H. Andreasen,, S. Juretschko,, J. L. Nielsen,, K.-H. Schleifer, and, M. Wagner. 1999. Combination of fluorescent in situ hybridization and microautoradiography—a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 65:12891297.
61. Lepp, P. W.,, M. M. Brinig,, C. C. Ouverney,, K. Palm,, G. C. Armitage, and, D. A. Relman. 2004. Methanogenic Archaea and human periodontal disease. Proc. Natl. Acad. Sci. USA 101:61766181.
62. Liesack, W.,, H. Weyland, and, E. Stackebrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21:191198.
63. Livak, K. J.,, S. J. A. Flood,, J. Marmaro,, W. Giusti, and, K. Deetz. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic-acid hybridization. PCR Methods Appl. 4:357362.
64. Lowell, J. L.,, and D. A. Klein. 2000. Heteroduplex resolution using T7 endonuclease I in microbial community analyses. BioTechniques 28:676681.
65. Ludwig, W.,, O. Strunk,, R. Westram,, L. Richter,, H. Meier,, Yadhukumar,, A. Buchner,, T. Lai,, S. Steppi,, G. Jobb,, W. Forster,, I. Brettske,, S. Gerber,, A. W. Ginhart,, O. Gross,, S. Grumann,, S. Hermann,, R. Jost,, A. Konig,, T. Liss,, R. Lussmann,, M. May,, B. Nonhoff,, B. Reichel,, R. Strehlow,, A. Stamatakis,, N. Stuckmann,, A. Vilbig,, M. Lenke,, T. Ludwig,, A. Bode, and, K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:13631371.
66. Lukow, T.,, P. F. Dunfield, and, W. Liesack. 2000. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol. Ecol. 32:241247.
67. Makimura, K.,, S. Y. Murayama, and, H. Yamaguchi. 1994. Detection of a wide range of medically important fungi by the polymerase chain reaction. J. Med. Microbiol. 40:358364.
68. Marchesi, J. R.,, T. Sato,, A. J. Weightman,, T. A. Martin,, J. C. Fry,, S. J. Hiom, and, W. G. Wade. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64:795799.
69. McSpadden Gardener, B. B.,, D. V. Mavrodi,, L. S. Thomashow, and, D. M. Weller. 2001. A rapid polymerase chain reaction-based assay characterizing rhizosphere populations of 2,4-diacetylphloroglucinol-producing bacteria. Phytopathology 91:4454.
70. McSpadden-Gardener, B. B.,, and D. M. Weller. 2001. Changes in populations of rhizosphere bacteria associated with take-all disease of wheat. Appl. Environ. Microbiol. 67:44144425.
71. Murray, R. E.,, Y. S. Feig, and, J. M. Tiedje. 1995. Spatial heterogeneity in the distribution of denitrifying bacteria associated with denitrification activity zones. Appl. Environ. Microbiol. 61:27912793.
72. Nichols, W. C.,, J. J. Liepnieks,, V. A. McKusick, and, M. D. Benson. 1989. Direct sequencing of the gene for Maryland German familial amyloidotic polyneuropathy type-Ii and genotyping by allele-specific enzymatic amplification. Genomics 5:535540.
73. Nicol, G. W.,, L. A. Glover, and, J. I. Prosser. 2003. Spatial analysis of archaeal community structure in grassland soil. Appl. Environ. Microbiol. 69:74207429.
74. Nunan, N.,, K. Wu,, I. M. Young,, J. W. Crawford, and, K. Ritz. 2002. In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microb. Ecol. 44:296305.
75. Okayama, H.,, D. T. Curiel,, M. L. Brantly,, M. D. Holmes, and, R. G. Crystal. 1989. Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. J. Lab. Clin. Med. 114:105113.
76. Olatinwo, R.,, B. Yin,, J. O. Becker, and, J. Borneman. 2006. Suppression of the plant-parasitic nematode Heterodera schachtii by the fungus Dactylella oviparasitica. Phytopathology 96:111114.
77. Ouverney, C. C.,, and J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65:17461752.
78. Qiu, X.,, L. Wu,, H. Huang,, P. Mcdonel,, A. Palumbo,, J. Tiedje, and, J. Zhou. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rDNA gene-based cloning. Appl. Environ. Microbiol. 67:880887.
79. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403:646649.
80. Rainey, F. A.,, N. Ward,, L. I. Sly, and, E. Stackebrandt. 1994. Dependence on the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used. Experientia 50:796797.
81. Reysenbach, A.-L.,, L. J. Giver,, G. S. Wickham, and, N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:34173418.
82. Rice, J.,, M. A. Sleigh,, P. H. Burkill,, G. A. Tarran,, C. D. O’Connor, and, M. V. Zubkov. 1997. Flow cytometric analysis of characteristics of hybridization of species-specific fluorescent oligonucleotide probes to rRNA of marine nanoflagellates. Appl. Environ. Microbiol. 63:938944.
83. Rigottier-Gois, L.,, V. Rochet,, N. Garrec,, A. Suau, and, J. Dore. 2003. Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes. Syst. Appl. Microbiol. 26:110118.
84. Roslev, P.,, N. Iversen, and, K. Henriksen. 1998. Direct fingerprinting of metabolically active bacteria in environmental samples by substrate specific radiolabelling and lipid analysis. J. Microbiol. Methods 31:99111.
85. Sait, M.,, P. Hugenholtz, and, P. H. Janssen. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:654666.
86. Scher, F. M.,, and R. Baker. 1980. Mechanism of biological control in a fusarium suppressive soil. Phytopathology 70:412417.
87. Schmidt, T. M.,, B. Pace, and, N. R. Pace. 1991. Detection of DNA contamination in Taq polymerase. BioTechniques 11:176177.
88. Seymour, J. R.,, J. G. Mitchell,, L. Pearson, and, R. L. Waters. 2000. Heterogeneity in bacterioplankton abundance from 4.5 millimetre resolution sampling. Aquat. Microb. Ecol. 22:143153.
89. Shipton, P. J.,, R. J. Cook, and, J. W. Sitton. 1973. Occurrence and transfer of a biological factor in soil that suppresses take-all of wheat in eastern Washington. Phytopathology 63:511517.
90. Sievert, S. M.,, T. Brinkhoff,, G. Muyzer,, W. Ziebis, and, J. Kuever. 1999. Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl. Environ. Microbiol. 65:38343842.
91. Simon, L.,, M. Lalonde, and, T. D. Bruns. 1992. Specific amplification of 18S fungal ribosomal genes from vesiculararbuscular endomycorrhizal fungi colonizing roots. Appl. Environ. Microbiol. 58:291295.
92. Sliwinski, M. K.,, and R. M. Goodman. 2004. Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling. Appl. Environ. Microbiol. 70:18111820.
93. Smiley, R. W.,, and R. J. Cook. 1973. Relationship between take-all of wheat and rhizosphere pH in soils fertilized with ammonium vs nitrate nitrogen. Phytopathology 63:882890.
94. Smit, E.,, P. Leeflang,, B. Glandorf,, J. D. van Elsas, and, K. Wernars. 1999. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 65:26142621.
95. Speksnijder, A.,, G. A. Kowalchuk,, S. De Jong,, E. Kline,, J. R. Stephen, and, H. J. Laanbroek. 2001. Micro-variation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl. Environ. Microbiol. 67:469472.
96. Stahl, D. A.,, B. Flesher,, H. R. Mansfield, and, L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:10791084.
97. Sutherland, J. B.,, and R. J. Cook. 1980. Effects of chemical and heat treatments on ethylene production in soil. Soil Biol. Biochem. 12:357362.
98. Suzuki, M.,, M. S. Rappe, and, S. J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:45224529.
99. Suzuki, M. T.,, and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625630.
100. Swidsinski, A.,, V. Loening-Baucke,, H. Lochs, and, L. P. Hale. 2005. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J. Gastroenterol. 11:11311140.
101. Teng, F.,, F. Hsu,, I. Peterson,, K. E. Cardon,, G. Caponigro, and, A. Kamb. 2001. Template selection during manipulation of complex mixtures by PCR. BioTechniques 30:868877.
102. Thompson, J. R.,, L. A. Marcelino, and, M. F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ‘reconditioning PCR.’ Nucleic Acids Res. 30:20832088.
103. Thompson, J. R.,, S. Pacocha,, C. Pharino,, V. Klepac-Ceraj,, D. E. Hunt,, J. Benoit,, R. Sarma-Rupavtarm,, D. L. Distel, and, M. F. Polz. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:13111313.
104. Urbach, E.,, K. L. Vergin, and, S. J. Giovannoni. 1999. Immunochemical detection and isolation of DNA from metabolically active bacteria. Appl. Environ. Microbiol. 65:12071213.
105. Valinsky, L.,, G. Della Vedova,, T. Jiang, and, J. Borneman. 2002. Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl. Environ. Microbiol. 68:59996004.
106. Valinsky, L.,, G. Della Vedova,, A. J. Scupham,, S. Alvey,, A. Figueroa,, B. Yin,, J. Hartin,, M. Chrobak,, D. E. Crowley,, T. Jiang, and, J. Borneman. 2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68:32433250.
107. Valinsky, L.,, A. J. Scupham,, G. D. Vedova,, Z. Liu,, A. Figueroa,, K. Jampachaisri,, B. Yin,, E. Bent,, R. Mancini-Jones,, J. Press,, T. Jiang, and, J. Borneman. 2004. Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG), p. 569–585. In G. A. Kowalchuk,, F. J. de Bruijn,, I. M. Head,, A. D. L. Akkermans, and, J. D. van Elsas (ed.), Molecular Microbial Ecology Manual, 2nd ed. Kluwer Academic Publishers, Dordrecht, The Netherlands.
108. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y. H. Rogers, and, H. O. Smith. 2004. Environ-mental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
109. Viaud, M.,, A. Pasquier, and, Y. Brygoo. 2000. Diversity of soil fungi studied by PCR-RFLP of ITS. Mycol. Res. 104:10271032.
110. Wang, G. C.-Y.,, and Y. Wang. 1996. The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142:11071114.
111. Watanabe, K.,, Y. Kodama, and, S. Harayama. 2001. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J. Microbiol. Methods 44:253262.
112. Weller, D. M.,, J. M. Raaijmakers,, B. B. McSpadden-Gardener, and, L. S. Thomashow. 2002. Microbial population responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 40:309348.
113. Westphal, A.,, and J. O. Becker. 1999. Biological suppression and natural population decline of Heterodera schachtii in a California field. Phytopathology 89:434440.
114. Westphal, A.,, and J. O. Becker. 2001. Components of soil suppressiveness against Heterodera schachtii. Soil Biol. Biochem. 33:916.
115. Westphal, A.,, and J. O. Becker. 2000. Transfer of biological soil suppressiveness against Heterodera schachtii. Phytopathology 90:401406.
116. White, T. J.,, T. Bruns,, S. Lee, and, J. W. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315–322. In M. A. Innis,, D. H. Gelfand,, J. J. Sninsky, and, T. J. White (ed.), PCR Protocols: a Guide to Methods and Applications. Academic Press, Inc., New York, N.Y.
117. Wintzingerode, F. V.,, U. B. Goebel, and, E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213229.
118. Wu, D. Y.,, L. Ugozzoli,, B. K. Pal, and, R. B. Wallace. 1989. Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle-cell anemia. Proc. Natl. Acad. Sci. USA 86:27572760.
119. Yin, B.,, L. Valinsky,, X. Gao,, J. O. Becker, and, J. Borneman. 2003. Bacterial rRNA genes associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Appl. Environ. Microbiol. 69:15731580.
120. Yin, B.,, L. Valinsky,, X. Gao,, J. O. Becker, and, J. Borneman. 2003. Identification of fungal rDNA associated with soil suppressiveness against Heterodera schachtii using oligonucleotide fingerprinting. Phytopathology 93:10061013.
121. Zengler, K.,, G. Toledo,, M. Rappe,, J. Elkins,, E. J. Mathur,, J. M. Short, and, M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:1568115686.
122. Zheng, D.,, E. W. Alm,, D. A. Stahl, and, L. Raskin. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62:45044513.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error