Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil Under Acacia Tortilis Subsp. Raddiana in Senegal

Syst Appl Microbiol. 2004 Mar;27(2):238-52. doi: 10.1078/072320204322881862.

Abstract

We used direct recovery of bacterial 16S rRNA gene sequences to investigate the bacterial diversity under Acacia tortilis subsp. raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with primers specific for bacterial 16S rRNA gene sequences. 16S rDNA clone libraries were constructed from two soil samples taken at two dates, i.e. June 25th 1999 (dry season) and August 28th 1999 (rainy season) at depths of 0.25-0.50 m and at 3 m distance from the stem. The 16S rDNA of 117 clones was partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity (100 phylotypes). Comparative sequence analysis of these clones identified members of the Gammaproteobacteria (35% of the phylotypes) as the most important group, followed by the Firmicutes division with 24%. Alphaproteobacteria, Betaproteobacteria, Acidobacteria and Actinobacteria were found to be less represented. Our data suggest that bacterial communities under Acacia tortilis subsp. raddiana might differ according to the season. The relative compositions of the populations is different in both samples: the Acidobacteria are present in a much higher percentage in the dry season than in the rainy season sample while the inverse effect is observed for the members of the other groups. Within the Gammaproteobacteria we found a shift between the dry season and the rainy season from pseudomonads to Acinetobacter and Escherichia related organisms.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acacia / microbiology*
  • Actinobacteria / genetics*
  • Base Sequence
  • Cloning, Molecular
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Electrophoresis, Polyacrylamide Gel
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • Proteobacteria / genetics*
  • RNA, Ribosomal, 16S / analysis*
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / genetics
  • Seasons
  • Senegal
  • Soil Microbiology*

Substances

  • DNA, Bacterial
  • RNA, Ribosomal, 16S