Soil microbial diversity: Present and future considerations

Soil Science

Volumn 162, Issue 9, 1997, Pages 607-617

  Kennedy, Ann C ^a   Gewin, Virginia L ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LAND MANAGEMENT; MICROBIAL DIVERSITY; MICROBIAL POPULATION; POPULATION DIVERSITY; SOIL MICROORGANISM; SOIL ORGANISM; SOIL PROCESSES;

CELLULAR ORGANISMS;

EID: 0031415425     PISSN: 0038075X     EISSN: None     Source Type: Journal    
DOI: 10.1097/00010694-199709000-00002     Document Type: Article

References (77)

1. 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.
2. American Society for Microbiology. 1994. Microbial diversity research priorities. American Society for Microbiology, Washington DC.
3. Anderson, T.-H., and K. H. Domsch. 1989. Ratios of microbial biomass carbon to total organic carbon in arable soils. Soil Biol. Biochem. 21:417-479.
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. Baath, E., A. Frostegard, and H. Fritze. 1992. Soil bacterial biomass, activity, phospholipid fatty acid pattern, and pH tolerance in an area polluted with alkaline dust deposition. Appl. Environ. Microbiol. 58:4026-4031.
6. Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
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 91:1609-1613.
8. Beare, M. H., D. C. Coleman, D. A. Crossley Jr., P. F. Hendrix, and E. P. Odum. 1994. A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant Soi. 170:1-5.
9. Boddy, L., R. Watling, and A. J. E. Lyon. 1988. Fungi and ecological disturbance. Proc. R. Soc. Edinburgh, Section B, Vol. 94.
10. Bolton Jr., H., L. F. Elliott, R. I. Papendick, and D. F. Bezdicek. 1985. Soil microbial biomass and selected soil enzyme activities: Effect of fertilization and cropping practices. Soil. Biol. Biochem. 17:297-302.
11. Borneman, J., P. W. Skroch, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
12. Bossio D. A., and K. M. Scow. 1995. Impact of carbon and flooding on the metabolic diversity of microbial communities in soils. Appl. Environ. Microbiol. 61:4043-4050.
13. Cavigelli, M. A., G. P. Robertson, and M. J. Klug. 1995. Fatty acid methyl ester (FAME) profiles as measures of soil microbial community structure. In The significance and regulation of soil biodiversity. H. P. Collins, G. P. Robertson, M. J. Klug (eds.). Kluwer Academic Publishers, The Netherlands, pp. 99-113.
14. Christensen, M. 1989. A view of fungal ecology. Mycologia 81:1-19.
15. DeLeij, F. A. A. M., and J. M. Whipps. 1993. The use of colony development for the characterization of bacterial communities in soil and on roots. Microb. Ecol. 27:81-97.
16. Dodds, W., M. K. Banks, C. S. Clenan, C. W. Rice, D. Sotomayor, E. A. Strauss, and W. Yu. 1996. Biological properties of soil and subsurface sediments under abandoned pasture and cropland. Soil Biol. Biochem. 28:837-846.
17. Doran, J. W. 1996. Soil health and sustainability. Adv. Agron. 56:1-54.
18. Federle, T. W. 1986. Microbial distribution in soil. In Perspectives in microbial ecology. F. Megusar and M. Gantar (eds.). Slovene Society for Microbiology, Ljubljana, pp. 493-498.
19. Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. 62:340-346.
20. Fredrickson, J. K., D. L. Balkwill, J. M. Zachara, S. M. W. Li, F. J. Brockman, and M. A. Simmons. 1991. Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the Atlantic coastal plain. Appl. Environ. Microbiol. 57:402-411.
21. Frostegard, A., A. Tunlid, and E. Baath. 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl. Environ. Microbiol. 59:3605-3617.
22. Garland, J. L. 1996. Patterns of potential C source utilization by rhizosphere communities. Soil Biol. Biochem. 28:223-230.
23. Garland, J. L. and A. L. Mills. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole-carbon-source utilization. Appl. Environ. Microbiol. 57:2351-2359.
24. Gregorich, E. G., M. R. Carter, D. A. Angers, C. M. Monreal, and B. H. Ellert. 1994. Towards a minimum data set to assess soil organic matter quality in agricultural soils. Can. J. Soil Sci. 74:367-385.
25. Griffiths, B. S. and L. A. Glover. 1996. Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique. Microb. Ecol. 31:269-280.
26. Haack, S. K., H. Garchow, D. A. Odelson, L. J. Forney, and M. J. Klug. 1994. Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities. Appl. Environ. Microbiol. 60:2483-2483.
27. Haack, S. K., H. Garchow, M. J. Klug, and L. J. Forney. 1995. Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns. Appl. Environ. Microbiol. 61:1458-1468.
28. Halden, R. U., G. W. Mundfrom, E. G. Peters, and D. F. Dwyer. 1995. Monitoring the fate and activity of diaryl ether-degrading bacteria in soil. In 50th Purdue Industrial Waste Conference Proceedings, West Lafayette, IN., May 8-10, pp. 57-64.
29. Harris, P. J. 1994. Consequences of the spatial distribution of microbial communities in soil. In Beyond the biomass. K. Ritz, J. Dighton, and K. E. Giller (eds.). British Society of Soil Science, Sayce Publishing, West Sussex, UK, pp. 239-246.
30. Hassink, J., J. H. O. Voshaar, E. H. Nijhuis, and J. A. Van Veen. 1991. Dynamics of the microbial populations of a reclaimed-polder soil under a conventional and a reduced-input farming system. Soil Biol. Biochem. 23:515-524.
31. Hawksworth, D. L and L. A. Mound. 1991. Biodiversity databases: The crucial significance of collections. In The Biodiversity of microorganisms and invertebrates: Its role in sustainable agriculture. D. L. Hawksworth (ed.). CAB International, Redwood Press Ltd., Melksham, UK, pp. 17-29.
32. Johri, A. K., M. Dua, D. Tuteja, R. Saxena, D. M. Saxena, and R. Lal. 1996. Genetic manipulations of microorganisms for the degradation of hexachlorocyclohexane. FEMS Microbiol. Rev. 19:69-84.
33. Johnson, R. A. and D. W. Wichern. 1992. Applied multivariate statistical analysis. Prentice Hall, Englewood Cliffs, NJ.
34. Ka, J. O., W. E. Holben, and J. M. Tiedje. 1994. Genetic and phenotypic diversity of 2, 4-dichlorophenoxyacetic acid (2, 4-D)-degrading bacteria isolated from 2, 4-D-treated field soils. Appl. Environ. Microbiol. 60:1106-1115.
35. Kennedy, A. C. 1995. Carbon utilization and fatty acid profiles for characterization of bacteria. In Methods of soil analysis, part 2. Microbiological and biochemical properties. R. Weaver and J. S. Angle (eds.). SSSA, Madison, WI, pp. 543-554.
36. Kennedy, A. C. 1996. Soil microbial diversity in agricultural systems. In Exploring the role of diversity in sustainable agriculture. R. K. Olson, C. A. Francis, and S. Kaffka (eds.) ASA, Madison, WI, pp. 35-54.
37. Kennedy, A. C. and A. J. Busacca. 1995. Microbial analysis to identify source of PM-10 material. In Proceedings of the Air and Waste Management Association specialty conference on Particulate Matter: Health and Regulatory Issues. Pittsburgh, PA, April 5, 1994. pp. 670-675.
38. Kennedy, A. C., L. F. Elliott, F. L. Young, and C. L. Douglas. 1991. Rhizobacteria suppressive to the weed downy brome. Soil Sci. Soc. Am. J. 55:722-727.
39. Kennedy, A. C. and V. Gewin. 1997. Characterization of microbial communities in agroecosystems. SUBMECO Proceedings (in press).
40. Kennedy, A. C. and K. L. Smith. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75-86.
41. Killham, K. 1994. Soil ecology. Cambridge University Press, Cambridge, UK.
42. Klug, J. M., and J. Tiedje. 1993. Response of microbial communities to changing environmental conditions: chemical and physiological approaches. In Trends in microbial ecology. R. Guerrero and C. Pedros-Alio (eds.). Spanish Society for Microbiology, Barcelona, Spain, pp. 371-374.
43. Korner, J., and E. Laczko. 1992. A new method for assessing soil microorganisms diversity and evidence of vitamin deficiency in low diversity communities. Biol. Fertil. Soils. 13:58-60.
44. Kroppenstedt, R. M. 1985. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical methods in bacterial systematics. M. Goodfellow and D. E. Minnikin (eds.). Academic Press, London, pp. 173-179.
45. Kuritz, T., and C. P. Wolk. 1995. Use of filamentous cyanobacteria for biodegradation of organic pollutants. Appl. Environ. Microbiol. 61:234-238.
46. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. Mc-Caughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21:3021-3023.
47. Lee, D. H., Y. G. Zo, and S. J. Kim. 1996. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphisms. Appl. Environ. Microbiol. 62:3112-3120.
48. Lee, K. E. and R. C. Foster. 1991. Soil fauna and soil structure. Aust. J. Soil Res. 29:745-775.
49. Metting, B., F. 1993. Soil microbiology ecology. Marcel Dekker, Inc., New York.
50. Miller, H., J. G. Henken, and J. A. Van Veen. 1989. Variations and composition of bacterial populations in the rhizosphere of maize, wheat, and grass cultivars. Can. J. Microbiol. 35:656-660.
51. Muyzer, G., and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695-700.
52. Neal, J. L., R. I. Larson, and T. G. Atkinson. 1973. Changes in rhizosphere populations of selected physiological groups of bacteria related to substitution of specific pairs of chromosomes in spring wheat. Plant Soil 39:209-212.
53. Neef, J. M., Y. Vandepeer, P. DeRijk, S. Chapelle, and R. DeWachter. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21:3025-3049.
54. Odum, H. T. 1983. Systems ecology: An introduction. John Wiley & Sons, New York.
55. Pankhurst, C. E., K. Ophel-Keller, B. M. Doube, and V. V. S. R. Gupta. 1996. Biodiversity of soil microbial communities in agricultural systems. Biodivers. Conserv. 5:197-209.
56. Reganold, J. P., A. S. Palmer, J. C. Lockhart, and A. N. Macgregor. 1993. Soil quality and financial performance of biodynamic and conventional farms in New Zealand. Science. 260:344-349.
57. Richaume, A., C. Steinberg, L. Jocteur-Monrozier, and G. Faurie. 1993. Differences between direct and indirect enumeration of soil bacteria: The influence of soil structure and cell location. Soil Biol. Biochem. 25:641-643.
58. Ritz, K., and B. S. Griffiths. 1994. Potential application of a community hybridization technique for assessing changes in the population structure of soil microbial communities. Soil Biol. Biochem. 26:963-971.
59. Rovira, A. D. 1965. Plant root exudates and their influence upon soil microorganisms. In Ecology of soil borne pathogens - Prelude to biological control. K. F. Baker and W. C. Snyder (eds.). University of California Press, Berkely, pp. 170-186.
60. Rudd, L. E., J. J. Perry, V. S. Houk, R. W. Williams, and L. D. Claxton. 1996. Changes in mutagenicity during crude oil degradation by fungi. Biodegradation. 7:335-343.
61. Saiki, R. K., S. J. Scharf, F. Flaoona, K. B. Mullis, G. T. Horn, H. A. Erlich, and N. Arnheim. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350-1354.
62. Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
63. Turco, R. F., and D. F. Bezdicek. 1987. Diversity within two serogroups of Rhizobium leguminosarum native to soils in the Palouse of Eastern Washington. Ann. Appl. Biol. 111:103-114.
64. Turco, R. F., A. C. Kennedy, and M. D. Jawson. 1994. Microbial indicators of soil quality. In Defining soil quality for a sustainable environment. J. W. Doran, D. C. Coleman, D. F. Bezdicek, and B. A. Stewart (eds.). American Society of Agronomy Special Publication No. 35, Madison, WI, pp. 73-90.
65. Tunlid, A., and D. C. White. 1990. Use of lipid biomarkers in environmental samples. In: Analytical microbial methods. A. Fox, S. L. Morgan, L. Lennart, and G. Odham (eds.). Plenum Press, New York, pp. 259-274.
66. Veres, G., R. A. Gibbs, S. E. Scherer, and C. T. Caskey. 1987. The molecular basis of the sparse fur mouse mutation. Science 237:415-417.
67. Visser, S., and D. Parkinson. 1992. Soil biological criteria as indicators of soil quality: Soil microorganisms. Am. J. Altern. Agric. 7:33-37.
68. Walker, B. H. 1992. Biodiversity and ecological redundancy. Conserv. Biol. 6:63-65.
69. Wander, M. M., D. S. Hedrick, D. Kaufman, S. J. Traina, B R. Stinner, S. R. Kehrmeyer, and D. C. White. 1995. The functional significance of the microbial biomass in organic and conventionally managed soils. In The significance and regulation of soil biodiversity. H. P. Collins, G. P. Robertson, M. J. Klug (eds.). Kluwer Academic Publishers, The Netherlands, pp. 87-97.
70. Ward, D., M. Bateson, R. Weller, and A. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microbial Ecology. 12:219-286.
71. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-464.
72. Wunsche, L., L. Bruggemann, and W. Babel. 1995. Determination of substrate utlization patterns of soil microbial communities: An approach to assess population changes after hydrocarbon pollution. FEMS Microbiol. Ecol. 17:295-306.
73. Zak J. C., M. R. Willig, D. L. Morrehead, and H. G. Wildman. 1994. Functional diversity of microbial communities: A quantitative approach. Soil Biol. Biochem. 26:1101-1108.
74. Zak, J. C., and S. Visser. 1996. An appraisal of soil fungal biodiversity: The crossroads between taxonomic and functional biodiversity. Biodiversity Cons. 5:169-183.
75. Zelles, L., Q. Y. Bai, T. Beck, and F. Beese. 1992. Signature fatty acids in phospholipds and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol. Biochem. 24:317-323.
76. Zelles, L., Q. Y. Gai, R. X. Ma, R. Rackwitz, K. Winter, and F. Beese. 1994. Microbial biomass, metabolic activity and nutritional status determined from fatty acid patterns and poly-hydrozybutyrate in agriculturally-managed soils. Soil Biol. Biochem. 26:439-446.
77. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.