title: Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent.
abstract: 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.
authors.affiliation: Dipartimento di Biologia Animale e Genetica, Università degli Studi di Firenze, via Romana 17, I-50125, Florence, Italy. alessiome@unifi.it
authors.forename: Alessio
authors.initials: A
authors.lastname: Mengoni
authors.forename: Enrico
authors.initials: E
authors.lastname: Tatti
authors.forename: Francesca
authors.initials: F
authors.lastname: Decorosi
authors.forename: Carlo
authors.initials: C
authors.lastname: Viti
authors.forename: Marco
authors.initials: M
authors.lastname: Bazzicalupo
authors.forename: Luciana
authors.initials: L
authors.lastname: Giovannetti
mesh_terms: D000383:Agriculture; D017632:Asbestos, Serpentine; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D002840:Chromates; D004269:DNA, Bacterial / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012680:Sensitivity and Specificity; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D012989:Soil Pollutants; D013045:Species Specificity
chemical_list: D017632:Asbestos, Serpentine; D002840:Chromates; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil; D012989:Soil Pollutants