Home LiteratureArticle Details
PMID: 19342429 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates.

Journal of experimental botany ·Vol. 60 ·No. 6 ·2009-00-00 ·Pages 1729-42

Micallef SA, Shiaris MP, Colón-Carmona A

Abstract

Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant-microbe interactions in the rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number of naturally occurring ecotype accessions exist, lacks mycorrhizal associations and is hence an ideal model for rhizobacterial studies. Eight Arabidopsis accessions were found to exert a marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA). Community differences in species composition and relative abundance were both significant (P <0.001). The eight distinct and reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates of these variants were analysed by high performance liquid chromatography (HPLC) to try to establish whether the unique rhizobacterial assemblages among accessions could be attributed to plant-regulated chemical changes in the rhizosphere. Natural variation in root exudation patterns was clearly exhibited, suggesting that differences in exudation patterns among accessions could be influencing bacterial assemblages. Other factors such as root system architecture are also probably involved. Finally, to investigate the Arabidopsis rhizosphere further, the phylogenetic diversity of rhizobacteria from accession Cvi-0 is described.

MeSH Terms
Arabidopsis/metabolism,microbiology Bacteria/classification,genetics,isolation & purification Biodiversity DNA, Bacterial/genetics DNA, Ribosomal/genetics Molecular Sequence Data Phylogeny Plant Exudates/metabolism Plant Roots/metabolism,microbiology RNA, Ribosomal, 16S/genetics Soil Microbiology
Chemicals
DNA, Bacterial DNA, Ribosomal Plant Exudates RNA, Ribosomal, 16S
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Micallef Shirley A
Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
Shiaris Michael P
Colón-Carmona Adán
References (45)
45 references, click to expand
  1. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons.
    J Bacteriol. 2004 May;186(9):2629-35 PMID: 15090503
  2. Soil Type and Maize Cultivar Affect the Genetic Diversity of Maize Root-Associated Burkholderia cepacia Populations.
    Microb Ecol. 1999 Oct;38(3):273-284 PMID: 10541789
  3. Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls.
    Plant Physiol. 2003 May;132(1):146-53 PMID: 12746520
  4. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species.
    Appl Environ Microbiol. 1995 Jul;61(7):2798-801 PMID: 7618894
  5. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA.
    Nucleic Acids Res. 1989 Oct 11;17(19):7843-53 PMID: 2798131
  6. Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms.
    Oecologia. 2005 Mar;143(2):232-40 PMID: 15703913
  7. Metabolic profiling of root exudates of Arabidopsis thaliana.
    J Agric Food Chem. 2003 Apr 23;51(9):2548-54 PMID: 12696935
  8. Evaluation of root exudates of seven sorghum accessions.
    J Chem Ecol. 2003 Sep;29(9):2073-83 PMID: 14584676
  9. Genetic and Phenotypic Diversity of Bacillus polymyxa in Soil and in the Wheat Rhizosphere.
    Appl Environ Microbiol. 1992 Jun;58(6):1894-903 PMID: 16348720
  10. Variation of Microbial Rhizosphere Communities in Response to Crop Species, Soil Origin, and Inoculation with Sinorhizobium meliloti L33.
    Microb Ecol. 2000 Jul;40(1):43-56 PMID: 10977876
  11. Correlation of Pectolytic Enzyme Activity with the Programmed Release of Cells from Root Caps of Pea (Pisum sativum).
    Plant Physiol. 1990 Dec;94(4):1855-9 PMID: 16667927
  12. Biochemical and physiological mechanisms mediated by allelochemicals.
    Curr Opin Plant Biol. 2004 Aug;7(4):472-9 PMID: 15231272
  13. Characterization of bacterial community structure in rhizosphere soil of grain legumes.
    Microb Ecol. 2005 Apr;49(3):407-15 PMID: 16003473
  14. Living in a fungal world: impact of fungi on soil bacterial niche development.
    FEMS Microbiol Rev. 2005 Sep;29(4):795-811 PMID: 16102603
  15. Mediation of pathogen resistance by exudation of antimicrobials from roots.
    Nature. 2005 Mar 10;434(7030):217-21 PMID: 15759001
  16. Proton-transfer-reaction mass spectrometry as a new tool for real time analysis of root-secreted volatile organic compounds in Arabidopsis.
    Plant Physiol. 2004 May;135(1):47-58 PMID: 15141066
  17. Hidden branches: developments in root system architecture.
    Annu Rev Plant Biol. 2007;58:93-113 PMID: 17177637
  18. Toward an ecological classification of soil bacteria.
    Ecology. 2007 Jun;88(6):1354-64 PMID: 17601128
  19. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed.
    Appl Environ Microbiol. 2001 Oct;67(10):4742-51 PMID: 11571180
  20. Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics.
    Antonie Van Leeuwenhoek. 2004 Nov;86(4):339-47 PMID: 15702386
  21. Modification of rhizobacterial populations by engineering bacterium utilization of a novel plant-produced resource.
    Nat Biotechnol. 1997 Apr;15(4):363-8 PMID: 9094139
  22. Comprehensive chemical profiling of gramineous plant root exudates using high-resolution NMR and MS.
    Phytochemistry. 2001 May;57(2):209-21 PMID: 11382236
  23. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms.
    Appl Environ Microbiol. 1993 Apr;59(4):945-52 PMID: 8476298
  24. Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source.
    Mol Plant Microbe Interact. 2001 Jun;14(6):775-84 PMID: 11386373
  25. Root border-like cells of Arabidopsis. Microscopical characterization and role in the interaction with rhizobacteria.
    Plant Physiol. 2005 Jun;138(2):998-1008 PMID: 15908608
  26. Loss of non-host resistance of Arabidopsis NahG to Pseudomonas syringae pv. phaseolicola is due to degradation products of salicylic acid.
    Plant J. 2003 Feb;33(4):733-42 PMID: 12609045
  27. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices.
    Appl Environ Microbiol. 2006 Dec;72(12):7804-12 PMID: 17041161
  28. Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere.
    Microb Ecol. 2004 Jan;47(1):96-103 PMID: 15259274
  29. Wheat cultivar-specific selection of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations.
    Microb Ecol. 2004 Oct;48(3):338-48 PMID: 15692854
  30. A degradation product of the salicylic acid pathway triggers oxidative stress resulting in down-regulation of Bacillus subtilis biofilm formation on Arabidopsis thaliana roots.
    Planta. 2007 Jul;226(2):283-97 PMID: 17554552
  31. Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones.
    Appl Environ Microbiol. 2004 Mar;70(3):1787-94 PMID: 15006805
  32. Moving Waves of Bacterial Populations and Total Organic Carbon along Roots of Wheat.
    Microb Ecol. 1999 Feb;37(2):116-128 PMID: 9929400
  33. Rhizodeposition shapes rhizosphere microbial community structure in organic soil.
    New Phytol. 2007;173(3):600-610 PMID: 17244055
  34. Dynamics of bacterial and fungal communities on decaying salt marsh grass.
    Appl Environ Microbiol. 2003 Nov;69(11):6676-87 PMID: 14602628
  35. Genetically engineered plants producing opines alter their biological environment.
    Nat Biotechnol. 1997 Apr;15(4):369-72 PMID: 9094140
  36. Detection and in situ identification of representatives of a widely distributed new bacterial phylum.
    FEMS Microbiol Lett. 1997 Aug 1;153(1):181-90 PMID: 9252585
  37. Naturally occurring genetic variation in Arabidopsis thaliana.
    Annu Rev Plant Biol. 2004;55:141-72 PMID: 15377217
  38. Proteomic investigation of natural variation between Arabidopsis ecotypes.
    Proteomics. 2004 May;4(5):1372-81 PMID: 15188405
  39. Root-secreted malic acid recruits beneficial soil bacteria.
    Plant Physiol. 2008 Nov;148(3):1547-56 PMID: 18820082
  40. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'.
    Nucleic Acids Res. 2002 May 1;30(9):2083-8 PMID: 11972349
  41. Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family.
    Theor Appl Genet. 2005 Feb;110(4):742-53 PMID: 15678326
  42. The role of root border cells in plant defense.
    Trends Plant Sci. 2000 Mar;5(3):128-33 PMID: 10707079
  43. Microbial co-operation in the rhizosphere.
    J Exp Bot. 2005 Jul;56(417):1761-78 PMID: 15911555
  44. Heteroduplex resolution using T7 endonuclease I in microbial community analyses.
    Biotechniques. 2000 Apr;28(4):676-8, 680, 681 PMID: 10769745
  45. Bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates.
    Appl Environ Microbiol. 2000 Feb;66(2):801-9 PMID: 10653754
Article Info
Journal
Journal of experimental botany
Abbr.
J Exp Bot
ISSN
1460-2431
DOI
10.1093/jxb/erp053
Published
2009-00-00
Epub
2009-00-02
Pages
1729-42
Language
English
Region
England
NLM ID
9882906
PMCID
PMC2671628
Subset
IM
Databases
GENBANK
FJ712828, FJ712829, FJ712830, FJ712831, FJ712832, FJ712833, FJ712834, FJ712835, FJ712836, FJ712837, FJ712838, FJ712839, FJ712840, FJ712841, FJ712842, FJ712843, FJ712844, FJ712845, FJ712846, FJ712847, FJ712848, FJ712849, FJ712850, FJ712851, FJ712852, FJ712853, FJ712854, FJ712855, FJ712856, FJ712857, FJ712858, FJ712859, FJ712860, FJ712861, FJ712862, FJ712863, FJ712864, FJ712865, FJ712866, FJ712867, FJ712868, FJ712869, FJ712870, FJ712871, FJ712872, FJ712873, FJ712874, FJ712875, FJ712876, FJ712877, FJ712878, FJ712879, FJ712880, FJ712881, FJ712882, FJ712883, FJ712884, FJ712885, FJ712886
Corrections
CommentIn
PMID: 19386613
CommentIn
PMID: 19820328
External Links
PubMed source DOI: 10.1093/jxb/erp053 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2