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Applied and Environmental Microbiology, December 2006, p. 7804-7812, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01464-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices{triangledown}

Martin Hartmann and Franco Widmer*

Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, 8046 Zurich, Switzerland

Received 26 June 2006/ Accepted 2 October 2006

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.

* Corresponding author. Mailing address: Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zurich, Switzerland. Phone: 41 (0)44 377 73 76. Fax: 41 (0)44 377 72 01. E-mail: franco.widmer{at}art.admin.ch.

{triangledown} Published ahead of print on 13 October 2006.

Applied and Environmental Microbiology, December 2006, p. 7804-7812, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01464-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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