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Applied and Environmental Soil Science
Volume 2011, Article ID 537459, 10 pages
http://dx.doi.org/10.1155/2011/537459
Research Article

Relationships among Contrasting Measurements of Microbial Dynamics in Pasture and Organic Farm Soils

1Department of Biology, Chatham University, Pittsburgh, PA 15232, USA
2Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506-6108, USA

Received 1 March 2011; Revised 16 May 2011; Accepted 20 May 2011

Academic Editor: M. Miransari

Copyright © 2011 S. L. Edenborn et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. C. Kennedy and R. I. Papendick, “Microbial characteristics of soil quality,” Journal of Soil & Water Conservation, vol. 50, no. 3, pp. 243–248, 1995. View at Google Scholar · View at Scopus
  2. H. Y. Sun, S. P. Deng, and W. R. Raun, “Bacterial community structure and diversity in a century-old manure-treated agroecosystem,” Applied and Environmental Microbiology, vol. 70, no. 10, pp. 5868–5874, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. B. Stenberg, “Monitoring soil quality of arable land: microbiological indicators,” Acta Agriculturae Scandinavica, vol. 49, no. 1, pp. 1–24, 1999. View at Google Scholar · View at Scopus
  4. A. M. Ibekwe, A. C. Kennedy, P. S. Frohne, S. K. Papiernik, C. H. Yang, and D. E. Crowley, “Microbial diversity along a transect of agronomic zones,” FEMS Microbiology Ecology, vol. 39, no. 3, pp. 183–191, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. P. Templer, S. Findlay, and G. Lovett, “Soil microbial biomass and nitrogen transformations among five tree species of the Catskill Mountains, New York, USA,” Soil Biology and Biochemistry, vol. 35, no. 4, pp. 607–613, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. M. Schloter, O. Dilly, and J. C. Munch, “Indicators for evaluating soil quality,” Agriculture, Ecosystems and Environment, vol. 98, no. 1–3, pp. 255–262, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. K. Smalla, U. Wachtendorf, H. Heuer, W. T. Liu, and L. Forney, “Analysis of BIOLOG GN substrate utilization patterns by microbial communities,” Applied and Environmental Microbiology, vol. 64, no. 4, pp. 1220–1225, 1998. View at Google Scholar · View at Scopus
  8. J. L. Garland, “Potential and limitations of BIOLOG for microbial community analysis,” in Proceedings of the 8th International Symposium on Microbial Ecology Atlantic Canada Society for Microbial Ecology, C. R. Bell, M. Brylinsky, and P. Johnson-Green , Eds., pp. 1–7, Society for Microbial Ecology, Halifax, NS, Canada, 1999.
  9. A. Konopka, L. Oliver, and R. F. Turco, “The use of carbon substrate utilization patterns in environmental and ecological microbiology,” Microbial Ecology, vol. 35, no. 2, pp. 103–115, 1998. View at Publisher · View at Google Scholar · View at Scopus
  10. J. Preston-Mafham, L. Boddy, and P. F. Randerson, “Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles—a critique,” FEMS Microbiology Ecology, vol. 42, no. 1, pp. 1–14, 2002. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Sharma, A. Rangger, and H. Insam, “Effects of decomposing maize litter on community level physiological profiles of soil bacteria,” Microbial Ecology, vol. 35, no. 3, pp. 301–310, 1998. View at Publisher · View at Google Scholar · View at Scopus
  12. G. D. Bending, C. Putland, and F. Rayns, “Changes in microbial community metabolism and labile organic matter fractions as early indicators of the impact of management on soil biological quality,” Biology and Fertility of Soils, vol. 31, no. 1, pp. 78–84, 2000. View at Google Scholar · View at Scopus
  13. B. Williams, S. Grayston, and E. Reid, “Influence of synthetic sheep urine on the microbial biomass, activity and community structure in two pastures in the Scottish uplands,” Plant and Soil, vol. 225, no. 1-2, pp. 175–185, 2000. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Miethling, G. Wieland, H. Backhaus, and C. C. Tebbe, “Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33,” Microbial Ecology, vol. 40, no. 1, pp. 43–56, 2000. View at Google Scholar · View at Scopus
  15. F. Widmer, A. Fließbach, E. Laczkó, J. Schulze-Aurich, and J. Zeyer, “Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and biolog analyses,” Soil Biology and Biochemistry, vol. 33, no. 7-8, pp. 1029–1036, 2001. View at Publisher · View at Google Scholar · View at Scopus
  16. G. D. Bending, M. K. Turner, and J. E. Jones, “Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities,” Soil Biology and Biochemistry, vol. 34, no. 8, pp. 1073–1082, 2002. View at Publisher · View at Google Scholar · View at Scopus
  17. M. S. Girvan, J. Bullimore, J. N. Pretty, A. M. Osborn, and A. S. Ball, “Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils,” Applied and Environmental Microbiology, vol. 69, no. 3, pp. 1800–1809, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. E. Malosso, L. English, D. W. Hopkins, and A. G. O'Donnell, “Community level physiological profile response to plant residue additions in Antarctic soils,” Biology and Fertility of Soils, vol. 42, no. 1, pp. 60–65, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. C. H. Nakatsu, “Soil microbial community analysis using denaturing gradient gel electrophoresis,” Soil Science Society of America Journal, vol. 71, no. 2, pp. 562–571, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. J. E. Thies, “Soil microbial community analysis using terminal restriction fragment length polymorphisms,” Soil Science Society of America Journal, vol. 71, no. 2, pp. 579–591, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. G. Muyzer and K. Smalla, “Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology,” Antonie van Leeuwenhoek, vol. 73, no. 1, pp. 127–141, 1998. View at Publisher · View at Google Scholar · View at Scopus
  22. S. J. Bent, J. D. Pierson, L. J. Forney et al., “Measuring species richness based on microbial community fingerprints: the emperor has no clothes,” Applied and Environmental Microbiology, vol. 73, no. 7, pp. 2399–2401, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. R. I. Amann, “Fluorescently labeled, ribosomal RNA-targeted oligonucleotide probes in the study of microbial ecology,” Molecular Ecology, vol. 4, pp. 543–553, 1995. View at Google Scholar
  24. P. Hugenholtz, B. M. Goebel, and N. R. Pace, “Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity,” Journal of Bacteriology, vol. 180, no. 18, pp. 4765–4774, 1998. View at Google Scholar · View at Scopus
  25. L. Øvreås and V. Torsvik, “Microbial diversity and community structure in two different agricultural soil communities,” Microbial Ecology, vol. 36, no. 3, pp. 303–315, 1998. View at Publisher · View at Google Scholar · View at Scopus
  26. S. M. Barns, S. L. Takala, and C. R. Kuske, “Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment,” Applied and Environmental Microbiology, vol. 65, no. 4, pp. 1731–1737, 1999. View at Google Scholar · View at Scopus
  27. R. J. Ellis, P. Morgan, A. J. Weightman, and J. C. Fry, “Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3223–3230, 2003. View at Google Scholar · View at Scopus
  28. S. L. Edenborn and A. J. Sexstone, “DGGE fingerprinting of culturable soil bacterial communities complements culture-independent analyses,” Soil Biology and Biochemistry, vol. 39, no. 7, pp. 1570–1579, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. Soil Survey Staff, Soil Taxonomy, A Basic System of Soil Classification for Making and Interpreting Soil Surveys, Agricultural Handbook Number 436, Natural Resources Conservation Service, Washington, DC, USA, 2nd edition, 1999.
  30. T. B. Childers, The effects of low and high fertility treatments on soil quality, yields, pest incidence and labor requirements of a post-translational organic market garden system, M.S. thesis, West Virginia University, Morgantown, WVa, USA, 2005.
  31. Y. Sutanto, Manure from grazing cattle: effects on soil microbial communities and soil quality in northern West Virginia pastures, M.S. thesis, West Virginia University, Morgantown, WVa, USA, 2005.
  32. K. R. Islam and R. R. Weil, “Microwave irradiation of soil for routine measurement of microbial biomass carbon,” Biology and Fertility of Soils, vol. 27, no. 4, pp. 408–416, 1998. View at Publisher · View at Google Scholar · View at Scopus
  33. D. Keeney, “Nitrogen—availability indices,” in Methods of Soil Analysis, Part 2—Chemical and Microbiological Properties, A. L. Page, R. H. Miller, and D. R. Keeney, Eds., pp. 711–733, American Society of Agronomy, Madison, Wis, USA, 2nd edition, 1982. View at Google Scholar
  34. J. L. Garland and A. L. Mills, “Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization,” Applied and Environmental Microbiology, vol. 57, no. 8, pp. 2351–2359, 1991. View at Google Scholar · View at Scopus
  35. D. A. Zuberer, “Recovery and enumeration of viable bacteria,” in Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties, R.W. Weaver, Ed., pp. 119–144, Soil Science Society of America, Madison, Wis, USA, 1994. View at Google Scholar
  36. G. Caetano-Anolles and P. M. Gresshoff, “Staining nucleic acids with silver: an alternative to radioisotopic and fluorescent labeling,” Promega Notes Magazine, vol. 45, pp. 13–18, 1994. View at Google Scholar
  37. G. Rees, D. Baldwin, B. Watson, S. Perryman, and D. Nielsen, “Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics,” Antonie van Leeuwenhoek, vol. 86, no. 4, pp. 339–347, 2004. View at Publisher · View at Google Scholar · View at Scopus
  38. N. Fromin, J. Hamelin, S. Tarnawski et al., “Statistical analysis of denaturing gel electrophoresis (DGGE) fingerprinting patterns,” Environmental Microbiology, vol. 4, no. 11, pp. 634–643, 2002. View at Publisher · View at Google Scholar · View at Scopus
  39. J. D. Knoepp, D. C. Coleman, D. A. Crossley Jr., and J. S. Clark, “Biological indices of soil quality: an ecosystem case study of their use,” Forest Ecology and Management, vol. 138, no. 1–3, pp. 357–368, 2000. View at Publisher · View at Google Scholar
  40. J. Oksanen, R. Kindt, P. Legendre, and B. O'Hara, “Vegan: community ecology package,” R package version 1.8-5, 2007 http://cran.r-project.org/.
  41. F. B. Bryant and P. R. Yarnold, “Principal-components analysis and exploratory and confirmatory factor analysis,” in Reading and Understanding Multivariate Statistics, L. G. Grimm and P. R. Yarnold, Eds., pp. 99–136, American Psychological Association, Washington, DC, USA, 1995. View at Google Scholar
  42. J. W. Doran and T. B. Parkin, “Quantitative indicators of soil quality: a minimum data set,” in Methods for Assessing Soil Quality, J. W. Doran and A. J. Jones, Eds., pp. 25–37, Soil Science Society of America, Madison, Wis, USA, 1996. View at Google Scholar
  43. S. D. Allison and J. B. H. Martiny, “Resistance, resilience, and redundancy in microbial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 1, pp. 11512–11519, 2008. View at Publisher · View at Google Scholar · View at PubMed
  44. E. C. Prigge, W. B. Bryan, and E. S. Goldman-Innis, “Early- and late-season grazing of orchardgrass and fescue hayfields overseeded with red clover,” Agronomy Journal, vol. 91, no. 4, pp. 690–696, 1999. View at Google Scholar
  45. C. B. Zhang, L. N. Huang, W. S. Shu, J. W. Qiu, J. T. Zhang, and C. Y. Lan, “Structural and functional diversity of a culturable bacterial community during the early stages of revegetation near a Pb/Zn smelter in Guangdong, PR China,” Ecological Engineering, vol. 30, no. 1, pp. 16–26, 2007. View at Publisher · View at Google Scholar
  46. W. B. Bryan, T. A. Mills, and F. X. Rosica, “Effects of grazing management and soil amendments on hill land pasture botanical composition,” Applied Agricultural Research, vol. 1, pp. 279–302, 1987. View at Google Scholar
  47. N. Kennedy, E. Brodie, J. Connolly, and N. Clipson, “Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms,” Environmental Microbiology, vol. 6, no. 10, pp. 1070–1080, 2004. View at Publisher · View at Google Scholar · View at PubMed
  48. H. Chu, T. Fujii, T. Morimoto et al., “Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil,” Applied and Environmental Microbiology, vol. 73, no. 2, pp. 485–491, 2007. View at Publisher · View at Google Scholar · View at PubMed
  49. C. H. Orr, A. James, C. Leifert, J. M. Cooper, and S. P. Cummings, “Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils,” Applied and Environmental Microbiology, vol. 77, no. 3, pp. 911–919, 2011. View at Publisher · View at Google Scholar · View at PubMed
  50. W. R. Cookson, M. Osman, P. Marschner et al., “Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature,” Soil Biology and Biochemistry, vol. 39, no. 3, pp. 744–756, 2007. View at Publisher · View at Google Scholar
  51. L. Kerkhof, M. Santoro, and J. Garland, “Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis,” FEMS Microbiology Letters, vol. 184, no. 1, pp. 95–101, 2000. View at Publisher · View at Google Scholar
  52. E. Brodie, S. Edwards, and N. Clipson, “Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem,” Microbial Ecology, vol. 44, no. 3, pp. 260–270, 2002. View at Publisher · View at Google Scholar · View at PubMed
  53. S. J. Grayston, C. D. Campbell, R. D. Bardgett et al., “Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques,” Applied Soil Ecology, vol. 25, no. 1, pp. 63–84, 2004. View at Publisher · View at Google Scholar
  54. S. Langenheder, E. S. Lindstrom, and L. J. Tranvik, “Structure and function of bacterial communities emerging from different sources under identical conditions,” Applied and Environmental Microbiology, vol. 72, no. 1, pp. 212–220, 2006. View at Publisher · View at Google Scholar · View at PubMed
  55. K. Ritz, “The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology,” FEMS Microbiology Ecology, vol. 60, no. 3, pp. 358–362, 2007. View at Publisher · View at Google Scholar · View at PubMed
  56. D. Nichols, “Cultivation gives context to the microbial ecologist,” FEMS Microbiology Ecology, vol. 60, no. 3, pp. 351–357, 2007. View at Publisher · View at Google Scholar · View at PubMed