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Applied and Environmental Microbiology, June 2004, p. 3541-3551, Vol. 70, No. 6
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.6.3541-3551.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery

M. Filion,1,{dagger} R. C. Hamelin,2 L. Bernier,3 and M. St-Arnaud1*

Institut de Recherche en Biologie Végétale, Jardin Botanique de Montréal, Montréal, Québec, Canada H1X 2B2,1 Laurentian Forestry Centre, Natural Resources Canada, Sainte-Foy, Québec, Canada G1V 4C7,2 Centre de Recherche en Biologie Forestière, Université Laval, Sainte-Foy, Québec, Canada G1K 7P43

Received 14 October 2003/ Accepted 5 February 2004

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.

* Corresponding author. Mailing address: Institut de Recherche en Biologie Végétale, Jardin Botanique de Montréal, 4101 Sherbrooke St. East, Montréal, Québec, Canada H1X 2B2. Phone: (514) 872-1439. Fax: (514) 872-9406. E-mail: marc.st-arnaud{at}umontreal.ca.

{dagger} Present address: Department of Biology, University of Moncton, Moncton, New Brunswick, Canada E1A 3E9.

Applied and Environmental Microbiology, June 2004, p. 3541-3551, Vol. 70, No. 6
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.6.3541-3551.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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