Amplified fragment length polymorphisms reveal genetic differentiation among strains of Xanthomonas albilineans.

Xanthomonas albilineans, the causative agent of leaf scald disease (LSD), colonizes the vascular system of sugarcane (Saccharum spp. hybrids). In this study X. albilineans strains from 28 countries were differentiated by using two methods of amplified fragment length polymorphism (AFLP). In the manual procedure, AFLP reactions were performed on 57 X. albilineans strains and after selective amplification using radiolabelled primers, the resulting products were separated using polyacrylamide gel electrophoresis. The autoradiographs were analyzed using GelCompar version 4.1 software (Applied Maths) to construct dendograms from similarity matrices. Fluorescent AFLP (FAFLP) was also employed on 52 X. albilineans strains using three fluorescently labelled primer combinations (automated AFLP). The FAFLP data was converted to a binary format using the Genemapper Software 3.7 (Applied Biosystems). Thereafter, dendograms were generated using the NTSYSpc. Software (USA). Distinct AFLP profiles were produced for the majority of the strains and were found to be useful in differentiating X. albilineans strains from various geographical locations. Fingerprints unique to each strain were reproducibly obtained and may be used to create a database for use in the identification of the various X. albilineans strains. It can be also concluded from the results obtained that the FAFLP has considerable technical advantages compared with the manual AFLP and also that the FAFLP is more sensitive than AFLP using radiolabelled primers in differentiating X. albilineans.

Aerobic biodegradation of dichloroethenes by indigenous bacteria isolated from contaminated sites in Africa.

The widespread use of tetrachloroethene (PCE) and trichloroethene (TCE) as dry cleaning solvents and degreasing agents for military and industrial applications has resulted in significant environmental contamination worldwide. Anaerobic biotransformation of PCE and TCE through reductive dechlorination frequently lead to the accumulation of dichloroethenes (DCEs), thus limiting the use of reductive dechlorination for the biotransformation of the compounds. In this study, seven bacteria indigenous to contaminated sites in Africa were characterized for DCE degradation under aerobic conditions. The specific growth rate constants of the bacterial isolates ranged between 0.346-0.552 d(-1) and 0.461-0.667 d(-1) in cis-DCE and trans-DCE, respectively. Gas chromatographic analysis revealed that up to 75% of the compounds were degraded within seven days with the degradation rate constants ranging between 0.167 and 0.198 d(-1). The two compounds were also observed to be significantly degraded, simultaneously, rather than sequentially, when present as a mixture. Phylogenetic analysis of the 16S rRNA gene sequences of the bacterial isolates revealed their identity as well as their relation to other environmentally-important bacteria. The observed biodegradation of DCEs may contribute to PCE and TCE removal at the aerobic fringe of groundwater plumes undergoing reductive dechlorination in contaminated sites.

Microbial community profiling in cis- and trans-dichloroethene enrichment systems using denaturing gradient gel electrophoresis.

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the 16S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

Analysis of the mechanisms of fluoroquinolone resistance in urinary tract pathogens.

OBJECTIVES: To characterize the mechanisms of fluoroquinolone resistance in urinary tract pathogens exhibiting a multiple antibiotic resistance phenotype as well as a high-level resistance to fluoroquinolones. METHODS: Nineteen Escherichia coli urinary tract infection pathogens exhibiting high-level resistance to fluoroquinolones were characterized in this study. Alterations in outer membrane proteins (OMPs) and lipopolysaccharide (LPS) were analysed by PAGE. Changes to the quinolone resistance-determining regions (QRDRs) of GyrA and ParC were determined by PCR and DNA sequencing. The presence of the qnrA gene was determined by PCR amplification. Ciprofloxacin uptake was determined spectrophotometrically using the quinolone accumulation assay. RESULTS: OMP analysis showed decreased expression, the absence of certain proteins or the presence of proteins with altered molecular weights when compared with wild-type strains. Most isolates possessed a smooth LPS phenotype. Isolates had double mutations in GyrA codons 83 and 87, in addition to a ParC alteration at Ser-80/Glu-84. Isolates accumulated varying levels of ciprofloxacin, and upon the addition of carbonyl cyanide m-chlorophenylhydrazone, increased accumulation was observed in all instances. E. coli isolates with a rough LPS phenotype appeared to accumulate higher levels of ciprofloxacin compared with those with a smooth LPS phenotype expressing OmpF normally, or even those not possessing OmpF. All E. coli isolates tested demonstrated active efflux of ciprofloxacin. Plasmid-mediated quinolone resistance (presence of the qnrA gene) was observed in 36.8% of isolates. CONCLUSIONS: A combination of target gene alterations, altered OM permeability, presence of the qnrA gene and active efflux appear to act together to produce a high-level, multiresistance phenotype.

Biostimulation and bioaugmentation enhances aerobic biodegradation of dichloroethenes.

The accumulation of dichloroethenes (DCEs) as dominant products of microbial reductive dechlorination activity in soil and water represent a significant obstacle to the application of bioremediation as a remedial option for chloroethenes in many contaminated systems. In this study, the effects of biostimulation and/or bioaugmentation on the biodegradation of cis- and trans-DCE in soil and water samples collected from contaminated sites in South Africa were evaluated in order to determine the possible bioremediation option for these compounds in the contaminated sites. Results from this study indicate that cis- and trans-DCE were readily degraded to varying degrees by natural microbial populations in all the soil and water samples tested, with up to 44% of cis-DCE and 41% of trans-DCE degraded in the untreated soil and water samples in two weeks. The degradation rate constants ranged significantly (P<0.05) between 0.0938 and 0.560 wk(-1) and 0.182 and 0.401 wk(-1), for cis- and trans-DCE, respectively, for the various treatments employed. A combination of biostimulation and bioaugmentation significantly increased the biodegradation of both compounds within two weeks; 14% for cis-DCE and 18% for trans-DCE degradation, above those observed in untreated soil and water samples. These findings support the use of a combination of biostimulation and bioaugmentation for the efficient biodegradation of these compounds in contaminated soil and water. In addition, the results clearly demonstrate that while naturally occurring microorganisms are capable of aerobic biodegradation of cis- and trans-DCE, biotransformation may be affected by several factors, including isomer structure, soil type, and the amount of nutrients available in the water and soil.

Molecular profiling demonstrates limited diversity amongst geographically separate strains of Ustilago scitaminea.

Intraspecies diversity within Ustilago scitaminea isolates from South Africa, Reunion Island, Hawaii and Guadeloupe was assessed by RAPDs, bE mating-type gene detection, rDNA sequence analysis, microscopy and germination and morphological studies. Except for sequence data, the other analyses yielded no differences in the isolates that could be used in a phylogenetic separation. Mycelial DNA of the SA isolate shared 100% sequence identity with that of mycelial DNA cultured from in vitro produced teliospores of the parent cultivar. Overall the ITS1 and ITS2 regions were found to have 96.1% and 96.9% sequence identity with a total of 17 and 21 base changes, respectively, amongst the isolates. The Reunion Island isolate was shown to be most distantly related by 3.6% to the other isolates, indicating a single clonal lineage. The lack of germination in teliospores from Guadeloupe may be attributed to changes in temperature and humidity during transportation.

Aerobic dechlorination of cis- and trans-dichloroethenes by some indigenous bacteria isolated from contaminated sites in Africa.

The innate toxicity of dichloroethenes (DCEs) and their tendency to be reduced to vinyl chloride (VC) (a known human carcinogen) is a cause for environmental concern. Aerobic bacteria capable of growth on cis- and trans-DCEs as sole carbon and energy sources were isolated by enrichment culture technique and identified to belong to the genera; Bacillus, Pseudomonas and Acinetobacter. Axenic and mixed cultures of the bacterial isolates utilized DCEs at concentrations above the maximum contaminant level allowable in drinking water by the Environmental Protection Agency. Their specific growth rate constant ranged significantly (P < 0.05) between 0.346-0.552 and 0.461-0.667 d(-1); while the maximum specific substrate utilization rate ranged significantly (P < 0.05) between 20.01-29.79 and 31.40-42.83 nmol h(-1) (mg of protein)(-1) in cis- and trans-DCE, respectively. The optimum growth was observed at 30 degrees C and at a pH of 7.0 with up to 96% of the stoichiometric-expected chloride released. Serial adaptation positively affected the growth yields and dehalogenase activities of the organisms with multiple antibiotic patterns also demonstrated by the isolates. These findings therefore indicated the important roles that these organisms may play in the bioremediation of sites polluted with chlorinated ethene compounds in Africa.