title: Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting.
abstract: In order to study microbial diversity in a polycyclic aromatic hydrocarbon-impacted soil, 14 bacterial strains were analyzed by 16S rRNA gene sequencing and amplified fragment length polymorphism (AFLP) analysis. Bacterial strains isolated from two different hydrocarbon-polluted sites were identified to the species level by 16S rRNA full-gene sequencing using MicroSeq 16S rRNA gene sequencing. Their genome was subsequently analyzed by high-resolution genotyping with AFLP analysis, in order to monitor species variability and to differentiate closely related strains. Cluster analysis based on AFLP fingerprinting showed intra-specific polymorphism, even among strains with 100% 16S rRNA gene sequence identity. The results show that AFLP is a powerful, highly reproducible and discriminatory tool for revealing genetic relationships in bacterial populations. The ability to differentiate and track related closely microbes is fundamental for studying structure and dynamics of microbial communities in contaminated ecosystems.
authors.affiliation: Environmental and Primary Prevention Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy. giuseppina.larosa@iss.it
authors.forename: G
authors.initials: G
authors.lastname: La Rosa
authors.forename: E
authors.initials: E
authors.lastname: De Carolis
authors.forename: M
authors.initials: M
authors.lastname: Sali
authors.forename: M
authors.initials: M
authors.lastname: Papacchini
authors.forename: C
authors.initials: C
authors.lastname: Riccardi
authors.forename: A
authors.initials: A
authors.lastname: Mansi
authors.forename: E
authors.initials: E
authors.lastname: Paba
authors.forename: C
authors.initials: C
authors.lastname: Alquati
authors.forename: G
authors.initials: G
authors.lastname: Bestetti
authors.forename: M
authors.initials: M
authors.lastname: Muscillo
mesh_terms: D001419:Bacteria / Q000235:genetics*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D007558:Italy; D010802:Phylogeny; D011084:Polycyclic Aromatic Hydrocarbons; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012988:Soil Microbiology; D012989:Soil Pollutants
chemical_list: D004269:DNA, Bacterial; D011084:Polycyclic Aromatic Hydrocarbons; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants