Phylogenetic Analysis Of Microbial Diversity In The Rhizoplane Of Oilseed Rape (Brassica Napus Cv. Westar) Employing Cultivation-Dependent And Cultivation-Independent Approaches
Olaf Kaiser, Alfred Pühler, Werner Selbitschka
Published 2001 · Biology, Medicine
Download PDFAnalyze on Scholarcy
The structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16S rDNA amplification. After isolation of the microbial community from the rhizoplane of oilseed rape (Brassica napus cv. Westar), the collected suspension was divided into two parts. One part was used for cultivation of bacteria onto three different growth media to establish a culture collection. From the other part of the rhizoplane suspension, genomic DNA was isolated and purified. Thereafter, 16S rDNA was amplified by PCR and cloned to obtain a library of 16S rDNA genes representative for the bacterial communities of this habitat. Phylogenetic 16S rDNA sequence analysis of 103 clones of this library revealed considerable differences from the corresponding nucleotide sequences of 111 cultured bacteria. Whereas the 16S rDNA clone library was dominated by a-Proteobacteria and bacteria of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum (51% and 30%, respectively), less than 17% of the cultured bacteria belonged to these two groups. More than 64% of the cultivated isolates were allocated to the b- and g-subclasses of the Proteobacteria, which were present in the clone library at about 14%. Most of the clones of the a-Proteobacteria of the library showed highest similarity to Bradyrhizobium sp. No such bacteria were found in the culture collection. Similarly, the second dominant group of the clone library comprising members of the CFB phylum was represented in the culture collection by a single isolate. The phylogenetic analysis of isolates of the culture collection clearly emphasized the need to use different growth media for recovery of rhizoplane bacteria. Whereas most of the a-Proteobacteria were recovered on complex medium, most of the b-Proteobacteria were isolated onto minimal media. Our results demonstrate that the combined approach pursued in this paper is necessary to explore the biodiversity of bacterial rhizoplane communities.
This paper references
Transfer of Pseudomonas maltophilia Hugh 1981 to the Genus Xanthomonas as Xanthomonas maltophilia (Hugh 1981) comb. nov.
Jean Swings (1983)
Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.
Juergen Brosius (1978)
A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria.
Thomas Eckhardt (1978)
Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing.
Theresa B. Britschgi (1991)
Comparison of aerobic heterotrophic taxa isolated from four root domains of mature sugar beet (Beta vulgaris)
Andrew K. Lilley (1996)
Genetic aspects of rhizosphere interactions
RW Hedges (1990)
Bacterial endophytes in agricultural crops
Johannes Hallmann (1997)
Nucleic acids classification. In: Goodfellow M, O’Donnell AG (eds) Handbook of New Bacterial Systematics
E Stackebrandt (1993)
XL1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection.
W O Bullock (1987)
A single rRNA gene region in Bradyrhizobium japonicum.
C Kündig (1995)
Anatomy and community structures of the rhizosphere. In: Lynch JM (ed) The Rhizosphere
R Campbell (1990)
Barley rhizobacterial population characterised by fatty acid profiling
Stig Olsson (1999)
Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.)
James J. Germida (1998)
ferential amplification of rRNA genes by polymerase chain reaction
Reysenbach A-L (1992)
Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots
Laurent Marilley (1999)
Rapid method for direct extraction of DNA from soil and sediments
YL Tsai (1991)
Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.
Marcelino T Suzuki (1997)
Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift
Andreas Wagner (1994)
Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes.
Stefan Weidner (1996)
Nucleic acids classification
E Stackebrandt (1993)
Humus bacteria of Norway spruce stands: plant growth promoting properties and birch, red fescue and alder colonizing capacity.
Anatomy and community structure of the rhizosphere.
Richard T Campbell (1990)
Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries.
Darrell P. Chandler (1997)
The dynamics of actinomycetes and fluorescent pseudomonads in wheat rhizoplane and rhizosphere.
Howard J. Miller (1990)
Practical Methods in Molecular Biology
Robert Schleif (1981)
Temporal Changes in the Bacterial Communities of Soil, Rhizosphere, and Endorhiza Associated with Field-Grown Cucumber (Cucumis sativus L.)
W.F. Mahaffee (1997)
tin - mediated changes in bacterial communities of the soil , rhizosphere and within roots of cotton in relation to nematode control
J Hallmann (1999)
Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum
Akihiro Saito (1998)
The history, biology, and taxonomy of the Cytophaga group.
P J Christensen (1977)
Identity and behavior of xylem-residing bacteria in rough lemon roots of Florida citrus trees.
John M. Gardner (1982)
Fundamental aspects of rhizobacterial plant growth promotion research
Bart Lambert (1989)
Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures
Allison E. McCaig (1999)
Molecular cloning: A laboratory manual 2nd ed. Edited by J. . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989 (in 3 volumes)
P. Deininger (1990)
Bacterial antagonists to Verticillium dahliae Kleb.
Gabriele Berg (1994)
Genetic diversity in Sargasso Sea bacterioplankton
S. Giovannoni (1990)
Introduction: some consequences of microbial rhizosphere competence for plant and soil.
James M. Lynch (1990)
Survey of indigenous bacterial endophytes from cotton and sweet corn
John A. McInroy (2004)
Differential amplification of rRNA genes by polymerase chain reaction.
A L Reysenbach (1992)
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
F von Wintzingerode (1997)
Evolutionary trees from DNA sequences: A maximum likelihood approach
Joseph Felsenstein (1981)
Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: Effect on radishes (Raphanus sativus L.)
Hani Antoun (1998)
A new version of the RDP (Ribosomal Database Project)
B. Maidak (1999)
The European Bioinformatics Institute (EBI) databases
Patricia Rodriguez-Tomé (1996)
Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium.
Mariko Takeuchi (1998)
Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment.
Margret Irmgard Moré (1994)
Taxonomic diversity of bacteria associated with the roots of field-grown transgenic Brassica napus cv. Quest, compared to the non-transgenic B. napus cv. Excel and B. rapa cv. Parkland
Steven Douglas Siciliano (1999)
16S/23S rRNA sequencing
David J. W. Lane (1991)
Identification of rhizobacteria from maize and determination of their plant-growth promoting potential
Roger Lalande (2005)
Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana.
Wafa Achouak (2000)
Soil microbial ecology: applications in agricultural and environmental management.
F. Blaine Metting (1992)
Phylogeny and Identification In Situ ofNevskia ramosa
Frank Oliver Glöckner (1998)
Catabolism of biphenyl by Pseudomonas sp. NCIB 10643 and Nocardia sp. NCIB 10503
Mark R. Smith (2004)
Transformation in Escherichia coli: cryogenic preservation of competent cells.
Donald A. Morrison (1977)
Analysis of bacterial populations in a grassland soil according to rates of development on solid media
Yasuhiro Kasahara (1991)
Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species.
V Farrelly (1995)
Enumeration, location, and characterization of endophytic bacteria within sugar beet roots
Mark J. Jacobs (1985)
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
Gary J. Olsen (1994)
Ratios of microbial biomass carbon to total organic carbon in arable soils
Timothy Nicholas Anderson (1989)
Stenotrophomonas maltophilia in the rhizosphere of oilseed rape — occurrence, characterization and interaction with phytopathogenic fungi
Gabriele Berg (1996)
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR.
Marcelino T Suzuki (1996)
Increasing the efficiency of the plate counting method for estimating bacterial diversity
G. M. Balestra (1997)
Suppression of summer patch by rhizosphere competent bacteria and their establishment on Kentucky bluegrass
David C. Thompson (1998)
The composition of bacterial populations in soil fractions differing in their degree of adherence to barley roots
Stig Olsson (1999)
Plant and bacterial mucilages of the maize rhizosphere: Comparison of their soil binding properties and histochemistry in a model system
Michelle Watt (2004)
Gram-negative bacterial flora on the root surface of wheat (Triticum aestivum) grown under different soil conditions
Kyō Sato (2004)
Genetic aspects of rhizosphere interactions. In: Lynch JM (ed) The Rhizosphere
RW Hedges (1990)
Rhizobacteria of maize and their antifungal activities.
Bernard Lambert (1987)
Chitin-mediated changes in bacterial communities of the soil, rhizosphere and within roots of cotton in relation to nematode control
Johannes Hallmann (1999)
This paper is referenced by
Screening of plant growth promoting Rhizobacteria isolated from sunflower (Helianthus annuus L.)
Adriana Ambrosini (2011)
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys.
Michelle Sait (2002)
Long-Term Rice and Green Manure Rotation Alters the Endophytic Bacterial Communities of the Rice Root
Xiao-Xia Zhang (2013)
Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10
Yasuhiro Tanaka (2012)
Genetic Diversity of Bacterial Communities of Serpentine Soil and of Rhizosphere of the Nickel-Hyperaccumulator Plant Alyssum bertolonii
Alessio Mengoni (2003)
Exploration of hitherto‐uncultured bacteria from the rhizosphere
Ulisses Nunes da Rocha (2009)
Effects of Root Isoflavonoids and Hairy Root Transformation on the Soybean Rhizosphere Bacterial Community Structure
Laura White (2017)
Ecology of Acidobabacteria and Verrucomicrobia in the plant-soil system
Ulisses Nunes da Rocha (2010)
Structural and functional characterization of bacterial diversity in the rhizospheres of three grain legumes
Shilpi Sharma (2004)
The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors
Marc Buée (2009)
Variability of soil microbial respiration under different vegetation succession stages in Jiuduansha wetland
Yushu Tang (2011)
Characterization of bacterial diversity at different depths in the Moravia Hill landfill site at Medellín, Colombia
Andrés F Lozada Gómez (2011)
Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)
R. Rathore (2017)
Ecological and phenotypic differentiation in sympatric 1 populations of aquatic Stenotrophomonas uncovered by 2 evolutionary species delimitation 3 4 5
Luz Edith Ochoa-Sánchez (2017)
Pseudomonas Inoculants as Agents for Plant Disease Management
Nobutaka Someya (2013)
Microbial Life in Volcanic Lakes
Francesca Joyce Mapelli (2015)
Analysis of the Cultivable Endophytic Bacterial Diversity in the Date Palm (Phoenix dactylifera L.) and Evaluation of Its Antagonistic Potential against Pathogenic Fusarium Species that Cause Date Palm Bayound Disease
Rayda Siala (2016)
Culture clash: challenging the dogma of microbial diversity
Stuart P. Donachie (2007)
Physiko-Chemie und Mikrobiologie der Rhizosphäre
Johannes C. G. Ottow (2011)
Culture-dependent and culture-independent microbial investigation of pine litters and soil in subtropical Australia
Li Cui Zhang (2009)
Opening the Black Box: Understanding the Influence of Cropping Systems and Plant Communities on Bacterial and Fungal Population Dynamics
W. G. Dilantha Fernando (2013)
A comparative study of bacterial diversity based on culturable and culture-independent techniques in the rhizosphere of maize (Zea mays L.)
Muther Mansoor Qaisrani (2019)
Multifaceted Plant-Associated Microbes and Their Mechanisms Diminish the Concept of Direct and Indirect PGPRs
Naveen Kumar Arora (2013)
Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling
Yuxuan Qin (2017)
Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis
L. Sun (2007)
Evaluation of Microbial Inocula for Initiation of Biological Life Support Systems for Wastewater Processing on Long Term and Deep Space Missions
Kimberly L. Cook (2003)
Evolutionary genetic analysis uncovers multiple species with distinct habitat preferences and antibiotic resistance phenotypes in the Stenotrophomonas maltophilia complex
Luz Edith Ochoa-Sánchez (2017)
Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites
Olaya Mediavilla (2019)
Environmental Escherichia coli occur as natural plant growth-promoting soil bacterium
Chandra Shekhar Nautiyal (2010)
Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere
Laura J. White (2017)
Genetic diversity and characterization of heavy metal-resistant-endophytic bacteria from two copper-tolerant plant species on copper mine wasteland.
Le-Ni Sun (2010)
Analysis of microbial community structures and functions in heavy metal-contaminated soils using molecular methods
Fabienne Gremion (2003)See more