Molecular microbial diversity of an agricultural soil in Wisconsin

Applied and Environmental Microbiology

Volumn 62, Issue 6, 1996, Pages 1935-1943

  Borneman, James ^a   Skroch, Paul W ^a   O'Sullivan, Katherine M ^a   Palus, James A ^a   Rumjanek, Norma G ^a   Jansen, Jennifer L ^a   Nienhuis, James ^a   Triplett, Eric W ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURE; ARTICLE; BACTEROIDES; DNA PURIFICATION; DNA SEQUENCE; DNA TEMPLATE; FUSOBACTERIUM; GENE DELETION; MICROBIAL GROWTH; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPIROCHETE;

EID: 0030011823     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.62.6.1935-1943.1996     Document Type: Article

References (55)

1. Alexander, M. 1977. Introduction to soil microbiology, p. 472. John Wiley & Sons, New York.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Atlas, R. M. 1984. Diversity of microbial communities. Adv. Microb. Ecol. 7:1-47.
4. Atlas, R. M., A. Horowitz, M. Krichevsky, and A. K. Bej. 1991. Response of microbial populations to environmental disturbance. Microb. Ecol. 22:249-256.
5. Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace. 1994. Remark able archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.
6. Biovin-Jahns, V., A. Bianchi, R. Ruimy, J. Garcin, S. Daumas, and R. Christen. 1995. Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl. Environ. Microbiol. 61:3400-3406.
7. Brock, T. D., D. W. Smith, and M. T. Madigan. 1984. Biology of microorganisms, 4th ed. Prentice-Hall, Inc., Englewood Cliffs, N.J.
8. Choi, B. K., B. J. Paster, F. E. Dewhirst, and U. B. Gobel. 1994. Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontis. Infect. Immun. 62:1889-1895.
9. DeLong, E. F., K. Y. Wu, B. B. Prezelin, and R. V. Jovine. 1994. High abundance of Archaea in Antarctic marine picoplankton. Nature (London) 371:695-697.
10. Embley, T. M., R. P. Hirt, and D. M. Williams. 1994. Biodiversity at the molecular level: the domains, kingdoms, and phyla of life. Phil. Trans. R. Soc. Lord. Ser. B 345:21-33.
11. 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. 61:2798-2801.
12. Fredrickson, J. K., and C. Hagedorn. 1992. Overview: identifying ecological effects from the release of genetically engineered microorganisms and microbial pest control agents, p. 559-578. In M. A. Levin, R. J. Seidler, and M. Rogul (ed.), Microbial ecology: principles, methods and applications. McGraw-Hill, New York.
13. Harris, D. 1994. Analyses of DNA extracted from microbial communities, p. 111-118. In K. Ritz, J. Dighton, and K. E. Giller (ed.), Beyond the biomass. John Wiley & Sons, Chichester, United Kingdom.
14. Hassink, J., G. Lebbink, and J. A. van Veen. 1991. Microbial biomass and activity of a reclaimed polder soil under conventional or reduced-input farming system. Soil Biol. Biochem. 23:507-513.
15. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York.
16. Kennedy, A. C., and K. L. Smith. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75-86.
17. Klug, M. J., and J. M. Tiedje. 1994. Response of microbial communities to changing environmental conditions: chemical and physiological approaches, p. 371-378. In R. Guerrero and C. Pedros-Alio, Trends in microbial ecology. Spanish Society for Microbiology, Barcelona, Spain.
18. Kopczynski, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
19. Kumar, S., K. Tomura, and M. Nei. 1993. MEGA: Molecular Evolutionary Genetics Analysis, version 1.0. The Pennsylvania State University, University Park.
20. 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.
21. 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 82:6955-6959.
22. Leff, G. L., J. R. Dana, J. V. McArthur, and L. J. Shimkets. 1995. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1141-1143.
23. Leung, K., L. S. England, M. B. Cassidy, J. T. Trevors, and S. Weir. 1994. Microbial diversity in soil: effect of releasing genetically engineered microorganisms. Mol. Ecol. 3:413-422.
24. Liesack, W., and E. Stackebrandt. 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.
25. 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. 21:191-198.
26. MacArthur, R. 1960. On the relative abundance of species. Am. Nat. 94:25-35.
27. More, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
28. Neefs, J.-M., Y. Van de Peer, L. Hendricks, and R. de Wachter. 1990. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 18:2237-2317.
29. Ogram, A. V., G. S. Sayler, and T. J. Barkay. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
30. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
31. Peet, R. K. 1984. The measurement of species diversity. Annu. Rev. Ecol. Sys. 5:285-307.
32. 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. 58:3417-3418.
33. Richardson, M. W. 1938. Multidimensional psychophysics. Psychol. Bull. 35:659-660.
34. Robison-Cox, J. F., M. M. Bateson, and D. M. Ward. 1995. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61:1240-1245.
35. Rosswall, T., and E. Kvillner. 1978. Principal components and factor analysis for the description of microbial populations. Adv. Microb. Ecol. 2:1-48.
36. Roszak, D. B., and R. R. Colwell. 1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51:365-379.
37. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
38. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
39. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine phytoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
40. Schulte, E. E., J. B. Peters, and P. R. Hodgson. 1987. Wisconsin procedures for soil testing, plant analysis, and feed and forage analysis. Department of Soil Science, University of Wisconsin - Madison.
41. Shannon, C. E., and W. Weaver. 1949. The mathematical theory of communication, p. 117. University of Illinois Press, Urbana.
42. Simpson, E. H. 1949. Measurement of diversity. Nature (London) 163:688.
43. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
44. Stackebrandt, E., W. Liesack, and B. M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:232-236.
45. Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321-346.
46. Torgerson, W. S. 1952. Multidimensional scaling. I. Theory and method. Psychometrica 17:401-419.
47. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
48. Ueda, T., Y. Suga, and T. Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:415-421.
49. 2-fixing bacteria associated with rice roots by molecular evolutionary analysis of a nifD library. Can. J. Microbiol. 41:235-240.
50. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345:63-65.
51. Weinberg, S. R., and G. Stotzky. 1972. Conjugation and genetic recombination of Escherichia coli in soil. Soil Biol. Biochem. 4:171-180.
52. Wilkinson, L. 1992. SYSTAT: the system for statistics. Version 5.2. SYSTAT, Evanston, Ill.
53. Winter, K., J. Filser, and F. Beese. 1991. Mikrobielle Biomasse und Aktivität in Hopfengarten unterschiedlicher Bewirtschaftung. Verh. Ges. Okol. XX/1:49-54.
54. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
55. Young, F. W. 1987. Multidimensional scaling: history, theory, and applications, p. 317. Lawrence Erlbaum Publishers, Hillsdale, N.J.