Community structure of actively growing bacterial populations in plant pathogen suppressive soil

K. Hjort, A. Lembke, A.G.C.L. Speksnijder, K. Smalla, J.K. Jansson

    Research output: Contribution to journalArticleAcademicpeer-review

    52 Citations (Scopus)

    Abstract

    The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia, Kitasatospora, and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas-specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil
    Original languageEnglish
    Pages (from-to)399-413
    JournalMicrobial Ecology
    Volume53
    Issue number3
    DOIs
    Publication statusPublished - 2007

    Keywords

    • gradient gel-electrophoresis
    • 16s ribosomal-rna
    • bromodeoxyuridine immunocapture
    • plasmodiophora-brassicae
    • molecular-cloning
    • microbial ecology
    • chitinase gene
    • fungi
    • identification
    • amplification

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