Comparison of 16S rRNA and 16S rDNA T-RFLP Approaches to Study Bacterial Communities in Soil Microcosms Treated with Chromate as Perturbing Agent
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Alessio Mengoni [1] ; Enrico Tatti [1] ; Francesca Decorosi [1] ; Carlo Viti [1] ; Marco Bazzicalupo [1] ; Luciana Giovannetti [1]
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[1] University of Florence
University of Florence
Firenze, Italia
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- Localización: Microbial ecology, ISSN-e 1432-184X, ISSN 0095-3628, Vol. 50, Nº. 3, 2005, págs. 375-384
- Idioma: inglés
- Texto completo no disponible (Saber más ...)
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Resumen
Transcripts of ribosomal RNA have been used for assessing the structure and dynamics of active bacterial populations; however, it remains unclear whether the information provided by community profiling derived from RNA is different from that derived from DNA, particularly when a selective pressure is applied on the bacterial community.
In the present work, terminal-restriction fragment length polymorphism (T-RFLP) community profiles based on DNA and RNA extracted from soil microcosms treated with a toxic concentration of chromate were compared.
Microcosms of a nonpolluted agricultural soil and of a heavy-metal-rich soil (serpentine) were treated with chromate and DNA and RNA were extracted. T-RFLP analysis was performed on amplified and retro-amplified 16SrRNA gene sequences, and band profiles obtained from samples of DNA and of RNA were compared. Some of the T-RFLP bands, identified as peculiar peaks in the profiles, were cloned and sequenced for taxonomic interpretation.
Results indicated that: (1) community profiles derived from RNA and DNA were partly overlapping; (2) there was a strong correlation between the dynamics shown by RNA- and DNA-based T-RFLP profiles; (3) chromate addition exerted a clear effect on both agricultural and serpentine soil bacterial communities, either at the DNA and at the RNA level; however, the profiles derived from RNA showed sharper differences between treated and control samples than that of DNA-based profiles.
