This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by McCaig, A. E.
Right arrow Articles by Prosser, J. I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by McCaig, A. E.
Right arrow Articles by Prosser, J. I.
Agricola
Right arrow Articles by McCaig, A. E.
Right arrow Articles by Prosser, J. I.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, October 2001, p. 4554-4559, Vol. 67, No. 10
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.10.4554-4559.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Numerical Analysis of Grassland Bacterial Community Structure under Different Land Management Regimens by Using 16S Ribosomal DNA Sequence Data and Denaturing Gradient Gel Electrophoresis Banding Patterns

Allison E. McCaig,* L. Anne Glover, and James I. Prosser

Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom

Received 20 February 2001/Accepted 11 July 2001

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ~45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721-1730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total amplification products. Semi-improved grassland soils were analyzed only by DGGE. No differences between communities were detected by calculation of diversity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of individual unimproved and improved grassland DGGE profiles, although considerable spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland samples and had much lower within-group variation. DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate analysis but not by principal-coordinate analysis, using unweighted data (considering only the presence and absence of bands) and weighted data (considering the relative intensity of each band), demonstrated that there were clear differences between grasslands, and the results were not affected by weighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differences between complex microbial communities.

* Corresponding author. Mailing address: Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom. Phone: (44) 1224 273149. Fax: (44) 1224 273144. E-mail: a.mccaig{at}abdn.ac.uk.

Applied and Environmental Microbiology, October 2001, p. 4554-4559, Vol. 67, No. 10
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.10.4554-4559.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Lauber, C. L., Hamady, M., Knight, R., Fierer, N. (2009). Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Appl. Environ. Microbiol. 75: 5111-5120 [Abstract] [Full Text]  
  • Huang, H., Shi, P., Wang, Y., Luo, H., Shao, N., Wang, G., Yang, P., Yao, B. (2009). Diversity of Beta-Propeller Phytase Genes in the Intestinal Contents of Grass Carp Provides Insight into the Release of Major Phosphorus from Phytate in Nature. Appl. Environ. Microbiol. 75: 1508-1516 [Abstract] [Full Text]  
  • Hartman, W. H., Richardson, C. J., Vilgalys, R., Bruland, G. L. (2008). Environmental and anthropogenic controls over bacterial communities in wetland soils. Proc. Natl. Acad. Sci. USA 105: 17842-17847 [Abstract] [Full Text]  
  • Zul, D., Denzel, S., Kotz, A., Overmann, J. (2007). Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity. Appl. Environ. Microbiol. 73: 6916-6929 [Abstract] [Full Text]  
  • Das, M., Royer, T. V., Leff, L. G. (2007). Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream. Appl. Environ. Microbiol. 73: 756-767 [Abstract] [Full Text]  
  • Li, Y., Ge, Y., Saxena, D., Caufield, P. W. (2007). Genetic Profiling of the Oral Microbiota Associated with Severe Early-Childhood Caries. J. Clin. Microbiol. 45: 81-87 [Abstract] [Full Text]  
  • Hartmann, M., Widmer, F. (2006). Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices. Appl. Environ. Microbiol. 72: 7804-7812 [Abstract] [Full Text]  
  • Freitag, T. E., Chang, L., Clegg, C. D., Prosser, J. I. (2005). Influence of Inorganic Nitrogen Management Regime on the Diversity of Nitrite-Oxidizing Bacteria in Agricultural Grassland Soils. Appl. Environ. Microbiol. 71: 8323-8334 [Abstract] [Full Text]  
  • Castaldini, M., Turrini, A., Sbrana, C., Benedetti, A., Marchionni, M., Mocali, S., Fabiani, A., Landi, S., Santomassimo, F., Pietrangeli, B., Nuti, M. P., Miclaus, N., Giovannetti, M. (2005). Impact of Bt Corn on Rhizospheric and Soil Eubacterial Communities and on Beneficial Mycorrhizal Symbiosis in Experimental Microcosms. Appl. Environ. Microbiol. 71: 6719-6729 [Abstract] [Full Text]  
  • Nunan, N., Daniell, T. J., Singh, B. K., Papert, A., McNicol, J. W., Prosser, J. I. (2005). Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques. Appl. Environ. Microbiol. 71: 6784-6792 [Abstract] [Full Text]  
  • Jasti, S., Sieracki, M. E., Poulton, N. J., Giewat, M. W., Rooney-Varga, J. N. (2005). Phylogenetic Diversity and Specificity of Bacteria Closely Associated with Alexandrium spp. and Other Phytoplankton. Appl. Environ. Microbiol. 71: 3483-3494 [Abstract] [Full Text]  
  • Siddique, T., Okeke, B. C., Zhang, Y., Arshad, M., Han, S. K., Frankenberger, W. T. Jr. (2005). Bacterial Diversity in Selenium Reduction of Agricultural Drainage Water Amended with Rice Straw. J. Environ. Qual. 34: 217-226 [Abstract] [Full Text]  
  • Holben, W. E., Feris, K. P., Kettunen, A., Apajalahti, J. H. A. (2004). GC Fractionation Enhances Microbial Community Diversity Assessment and Detection of Minority Populations of Bacteria by Denaturing Gradient Gel Electrophoresis. Appl. Environ. Microbiol. 70: 2263-2270 [Abstract] [Full Text]  
  • Nicol, G. W., Glover, L. A., Prosser, J. I. (2003). Spatial Analysis of Archaeal Community Structure in Grassland Soil. Appl. Environ. Microbiol. 69: 7420-7429 [Abstract] [Full Text]  
  • Girvan, M. S., Bullimore, J., Pretty, J. N., Osborn, A. M., Ball, A. S. (2003). Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils. Appl. Environ. Microbiol. 69: 1800-1809 [Abstract] [Full Text]  
  • Ronn, R., McCaig, A. E., Griffiths, B. S., Prosser, J. I. (2002). Impact of Protozoan Grazing on Bacterial Community Structure in Soil Microcosms. Appl. Environ. Microbiol. 68: 6094-6105 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»