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Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel... Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed K. Smalla 1 , * , G. Wieland 1 , † , A. Buchner 1 , A. Zock 1 , J. Parzy 1 , S. Kaiser 1 , N. Roskot 2 , H. Heuer 1 , ‡ , and G. Berg 2 Federal Biological Research Centre for Agriculture and Forestry, D-38104 Braunschweig, 1 and Department of Biological Sciences, Microbiology, University of Rostock, D-18051 Rostock, 2 Germany ABSTRACT The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae , field-grown strawberry ( Fragaria ananassa Duch.), oilseed rape ( Brassica napus L.), and potato ( Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Applied and Environmental Microbiology American Society For Microbiology

Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed

Applied and Environmental Microbiology , Volume 67 (10): 4742 – Oct 1, 2001

Abstract

Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed K. Smalla 1 , * , G. Wieland 1 , † , A. Buchner 1 , A. Zock 1 , J. Parzy 1 , S. Kaiser 1 , N. Roskot 2 , H. Heuer 1 , ‡ , and G. Berg 2 Federal Biological Research Centre for Agriculture and Forestry, D-38104 Braunschweig, 1 and Department of Biological Sciences, Microbiology, University of Rostock, D-18051 Rostock, 2 Germany ABSTRACT The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae , field-grown strawberry ( Fragaria ananassa Duch.), oilseed rape ( Brassica napus L.), and potato ( Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands.

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References (50)

Publisher
American Society For Microbiology
Copyright
Copyright © 2001 by the American society for Microbiology.
ISSN
0099-2240
eISSN
1098-5336
DOI
10.1128/AEM.67.10.4742-4751.2001
Publisher site
See Article on Publisher Site

Abstract

Bulk and Rhizosphere Soil Bacterial Communities Studied by Denaturing Gradient Gel Electrophoresis: Plant-Dependent Enrichment and Seasonal Shifts Revealed K. Smalla 1 , * , G. Wieland 1 , † , A. Buchner 1 , A. Zock 1 , J. Parzy 1 , S. Kaiser 1 , N. Roskot 2 , H. Heuer 1 , ‡ , and G. Berg 2 Federal Biological Research Centre for Agriculture and Forestry, D-38104 Braunschweig, 1 and Department of Biological Sciences, Microbiology, University of Rostock, D-18051 Rostock, 2 Germany ABSTRACT The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae , field-grown strawberry ( Fragaria ananassa Duch.), oilseed rape ( Brassica napus L.), and potato ( Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands.

Journal

Applied and Environmental MicrobiologyAmerican Society For Microbiology

Published: Oct 1, 2001

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