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Identification of dominant bacterial phylotypes in a cadmium-treated forest soil

Lazzaro, Anna, Widmer, Franco, Sperisen, Christoph, Frey, Beat
FEMS microbiology ecology 2008 v.63 no.2 pp. 143-155
Burkholderia, Streptomyces, bacterial communities, cadmium, clones, community structure, forest soils, genes, heavy metals, phylogeny, phylotype, polluted soils, quantitative polymerase chain reaction, restriction fragment length polymorphism, ribosomal RNA, soil pollution
The presence of heavy metals in soils can lead to changes in microbial community structure, characterized by the dominance of groups that are able to tolerate contamination. Such groups may provide good microbial indicators of heavy-metal pollution in soil. Through terminal restriction fragment length polymorphism (T-RFLP) profiling, changes in the bacterial community structure of an acidic forest soil that had been incubated with cadmium (Cd) for 30 days were investigated. T-RFLP revealed, in particular, three operational taxonomic units (OTUs) strongly dominating in relative abundance in the contaminated soil. By cloning of the amplified 16S rRNA genes and partial sequencing of 25 clones, these three dominant OTUs were phylogenetically characterized. One dominant OTU in the cadmium-contaminated soil was derived from Betaproteobacteria, genus Burkholderia, and the other two were from uncultured members of the class Actinobacteria, closely related to the genus Streptomyces. To confirm T-RFLP data, four primers were designed on the basis of this study's dominant sequences, targeting the OTUs corresponding to Burkholderia or Actinobacteria. Real-time PCR showed that Burkholderia target sequences were more abundant in cadmium-treated soil (7.8 x 10⁷± 3.0 x 10⁷ targets g⁻¹ soil) than in untreated soil (4.0 x 10⁶± 8.9 x 10⁵ targets g⁻¹ soil). It was concluded that the genus Burkholderia includes species that may be particularly dominant under cadmium contamination.