The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.Horizontal gene transfer, the intraspecies and interspecies exchange of genetic information, plays an important role in the evolution of bacteria (10,24,26,39,65). Three major mechanisms, transformation, transduction, and conjugation (9), provide bacterial populations with access to a "horizontal gene pool," enabling them to rapidly respond to environmental challenges (16, 34).The most important contributor to horizontal gene transfer is the heterogeneous group of mobile genetic elements that includes plasmids, insertion (IS) elements, transposons, integrons, phages, and genomic islands (10, 17). They are "selfish" elements that promote their own maintenance and distribution and, in addition, can function as vectors for accessory DNA elements. These accessory elements commonly consist of genes that are nonessential for survival but confer a phenotype, which is advantageous under particular environmental conditions. Prominent examples of such traits are antibiotic and heavy metal resistances, degradation of xenobiotic compounds, symbiosis and virulence determinants, resistance to radiation, and increased mutation frequency (15).A group of related conjugative DNA elements has been identified as carriers of antibiotic resistance genes in members of the ␥-Proteobacteria from dispersed global locations. R391, the archetype of this group, was originally detected in a South African Providencia rettgeri isolate (8); for many years, it was believed to be a plasmid and was assigned to a new incompatibility group, IncJ. Subsequently, other IncJ elements, conferring the same phenotype as that conferred by R391 (19, 20) (32), and Shewanella putrefaciens (pMERPH; mercury resistance) from the United Kingdom (48). Previous studies have exa...
Hexachlorocyclohexane (HCH) is a highly recalcitrant pesticide that persists in soils. Three novel HCHdegrading strains (DS2, DS2-2 and DS3-1) were isolated after enrichment from HCH-contaminated soil from Germany. These strains efficiently degraded the a a a a -, g g g g -and d d d d -isomers of HCH, while strain DS3-1 also degraded b b b b -HCH. Based on 16S rDNA analysis, strain DS3-1 was closely related to Sphingomonas taejonensis , while strains DS2 and DS2-2 were closely related to Sphingomonas flava and seven HCHdegrading strains recently isolated from HCH-contaminated Spanish soil. Hence, geographic origin of the strains was not reflected in their phylogenetic affiliation. Subsequently, lin genes involved in HCH degradation, virtually identical to those from Sphingomonas paucimobilis strains UT26 from Japan and B90A from India, were identified in strains DS3-1, DS2, DS2-2 and five of the strains from Spain. The conserved lin gene sequences and structural organization, as well as the close association with IS 6100 , suggest a shared lin gene origin and recent horizontal gene transfer among phylogenetically diverged Sphingomonas strains in remote geographic locations. The loss of the ability to degrade g g g g -HCH was associated with the deletion of the linA gene, probably due to recombination involving IS 6100 elements, of which several copies are located in the lin cluster region.
SummaryWe used a two‐step enrichment approach to isolate root‐colonizing hexachlorocyclohexane (HCH)‐degrading microorganisms. The first step consists of the use of classical liquid enrichment to isolate γ‐HCH degraders. The γ‐HCH‐degrading microbes were attached in mass to corn seeds sown in soil with γ‐HCH, and after plant development we rescued bacteria growing on root tips. Bacteria were then subjected to a second enrichment round in which growth on liquid medium with γ‐HCH and inoculation of corn seeds were repeated. We then isolated bacteria on M9 minimal medium with γ‐HCH from root tips. We were able to isolate four Sphingomonas strains, all of which degraded α‐, β‐, γ‐ and δ‐HCH. Two of the strains were particularly good colonizers of corn roots, reaching high cell density in vegetated soil and partly removing γ‐HCH. In contrast, these bacteria performed poorly in unplanted soils. This study supports the hypothesis that the removal of persistent toxic chemicals can be accelerated by combinations of plants and bacteria, a process generally known as rhizoremediation.
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