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Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance

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Abstract:

Bacteria from forest soils were characterized by DNA sequence analysis of cloned 16S rRNA gene fragments (16S clones). Surface organic matter and mineral soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S). Phylogenetic analyses revealed that 87% of 580 16S clones were classified as Proteobacteria, Actinobacteria, Acidobacterium, Verrucomicrobia, Bacillus/Clostridium group, Cytophaga-Flexibacter-Bacteroides group, green nonsulfur bacteria, Planctomyces, and candidate divisions TM6 and OP10. Seventy-five 16S clones could not be classified into known bacterial divisions, and five 16S clones were related to chloroplast DNA. Members of Proteobacteria represented 46% of the clone library. A higher proportion of 16S clones affiliated with -Proteobacteria were from plot N compared with plot S. 16S rRNA gene fragments amplified with Pseudomonas-specific primers and cloned (Ps clones) were examined from mineral-soil samples from plots N and S from three LTSP installations. A significantly greater proportion of sequenced Ps clones from plot N contained Pseudomonas 16S rRNA gene fragments compared with Ps clones from plot S.Key words: bacterial diversity, 16S rRNA gene, forest soil.

Nous avons caractérisé des bactéries de sols forestiers par l'analyse des séquences d'ADN de fragments géniques clonés de l'ARNr 16S (clones 16S). Nous avons recueilli des échantillons de matière organique de surface et de sol minéralisé d'une installation de Productivité des Sols à Long Terme (LTSP) du Ministère des Forêts de la Colombie-Britannique pendant l'hiver et l'été à la suite de deux traitement perturbateurs : une récolte d'arbres entiers sans compactage du sol (terrains N) et une récolte d'arbres entiers plus un enlèvement complet de la matière organique de surface accompagné d'un compactage du sol lourd (terrains S). Des analyses phylogénétiques ont révélé que 87 % des 580 clones 16S pouvaient être classifiés dans les genres ou groupes Proteobacteria, Actinobacteria, Acidobacterium, Verrucomicrobia, Bacillus/Clostridium, CytophagaFlexibacter–Bacteroides, les bactéries vertes non sulfureuses, Planctomyces, et les divisions candidates TM6 et OP10. Soixante-quinze clones 16S n'ont pu être classifiés dans aucune division bactérienne connue et cinq clones 16S étaient apparentées à de l'ADN de chloroplaste. Les membres de Proteobacteria représentaient 46 % de la banque clonale. On a repéré des clones 16S associés à γ-Proteobacteria en plus forte proportion dans les terrains N que dans les terrains S. Des fragments géniques d'ARNr 16S amplifiés avec des amorces spécifiques à Pseudomonas puis clonées (clones Ps) ont été analysés à partir d'échantillons de sols minéralisés des terrains N et S situés dans trois installations LTSP. Une proportion significativement supérieure des clones Ps séquencés provenant de terrains N contenait des fragments géniques d'ARNr 16S de Pseudomonas comparativement aux clones Ps de terrains S.Mots clés : diversité bactérienne, gène de l'ARNr 16S, sols forestiers.[Traduit par la Rédaction]

Keywords: 16S rRNA gene; bacterial diversity; bactérienne; diversité; forest soil; gène de l'ARNr 16S; sols forestiers

Document Type: Research Article

Publication date: July 1, 2002

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  • Published since 1954, this monthly journal contains new research in the field of microbiology including applied microbiology and biotechnology; microbial structure and function; fungi and other eucaryotic protists; infection and immunity; microbial ecology; physiology, metabolism and enzymology; and virology, genetics, and molecular biology. It also publishes review articles and notes on an occasional basis, contributed by recognized scientists worldwide.
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