Polymerase chain reaction for verification of fluorescent colonies of Erwinia chrysanthemi and Pseudomonas putida WCS358 in immunofluorescence colony staining

Effects of ecological factors on the survival and physiology of Ralstonia solanacearum bv. 2 in irrigation water

The fate of Ralstonia solanacearum bv. 2, the causative agent of brown rot in potato, in aquatic habitats of temperate climate regions is still poorly understood. In this study, the population dynamics and the physiological response of R. solanacearum bv. 2 were tested in sterile pure water and in agricultural drainage water obtained from waterways near potato cropping fields in The Netherlands. The behaviour of five different biovar 2 isolates in drainage water at 20 degrees C was very similar among strains. One typical isolate with consistent virulence (strain 1609) was selected for further studies. The effects of temperature, light, canal sediment, seawater salts, and the presence of competing microorganisms on the survival of strain 1609 were assessed. Moreover, the impacts of the physiological state of the inoculum and the inoculum density were analyzed. The population dynamics of strain 1609 in sterile pure water were also characterized. In sterile pure water, the fate of R. solanacearum 1609 cells depended strongly on temperature, irrespective of inoculum density or physiological state. At 4 degrees C and 44 degrees C, strain 1609 CFU numbers showed declines, whereas the strain was able to undergo several cell divisions at 12 degrees C, 20 degrees C, and 28 degrees C. At 20 degrees C and 28 degrees C, repeated growth took place when the organism was serially transferred, at low inoculum density, from grown water cultures into fresh water devoid of nutrients. Both at low and high cell densities and regardless of physiological state, R. solanacearum 1609 cells persisted as culturable cells for limited periods of time in drainage water. A major effect of temperature was found, with survival being maximal at 12 degrees C, 20 degrees C, and 28 degrees C. Temperatures of 4 degrees C, 36 degrees C, or 44 degrees C induced accelerated declines of the culturable cell numbers. The drainage water biota had a strong effect on survival at 12 degrees C, 20 degrees C, and 28 degrees C, as the persistence of strain 1609 was significantly enhanced in sterile drainage water systems. Furthermore, there was a negative effect of incident light, in a light:dark regime, on the survival of R. solanacearum 1609 in natural drainage water. Also, levels of seawater salts realistic for drainage water in coastal areas were detrimental to strain survival. Ralstonia solanacearum 1609 showed considerable persistence in canal sediment saturated with drainage water, but died out quickly when this sediment was subjected to drying. Evidence was obtained for the conversion of R. solanacearum 1609 cells to nonculturable cells in water microcosms kept at 4 degrees C, but not in those kept at 20 degrees C. A substantial fraction of the cells found to be nonculturable were still viable, as evidenced by the direct viable count and by staining with the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride. The potential occurrence of viable-but-nonculturable cells in natural waters poses a problem for the detection of R. solanacearum by cultivation-based methods.

Survival of Ralstonia solanacearum Biovar 2, the Causative Agent of Potato Brown Rot, in Field and Microcosm Soils in Temperate Climates

ABSTRACT After outbreaks of potato brown rot in three different fields in the Netherlands, the fate of the brown rot pathogen, Ralstonia solanacearum biovar 2, was monitored in soil by immunofluorescence colony staining (IFC) supported by R. solanacearum division-2 specific polymerase chain reaction. In selected areas of all fields, the R. solanacearum population densities were initially on the order 10(4) to 10(6) per g of topsoil. These population densities then declined progressively over time. In two fields, however, the pathogen persisted for periods of 10 to 12 months. The survival of a selected R. solanacearum biovar 2 isolate, strain 1609, in three soils, a loamy sand and two different silt loam soils, was further studied in soil microcosm experiments. The effects of temperature and soil moisture content were assessed. At 12 or 15 and 20 degrees C, a gradual decline of the population densities was observed in all three soils, from the established 10(5) to 10(6) CFU g(-1) of dry soil to significantly reduced levels, occasionally bordering the limit of detection (10(2) CFU g(-1)of dry soil), in periods of approximately 90 to 210 days. Soil type affected the rate of population decline at 20 degrees C, with the greatest decline occurring in loamy sand soil. In all three soils, the survival of IFC-detectable R. solanacearum 1609 cells at 4 degrees C was severely impaired, reflected in an accelerated decline of CFU counts, to undetectable numbers. Moreover, indications were found for the occurrence of viable but nonculturable strain 1609 cells in the loamy sand as well as in one silt loam soil under these conditions. In addition, a single freezing-thawing cycle caused a significant additional reduction of the culturable R. solanacearum 1609 populations in the three soils, though detectable populations remained. Moderate soil moisture fluctuations of approximately pF 2 did not affect the survival of R. solanacearum 1609 in soil. Severe drought, however, drastically reduced the populations of strain 1609 CFU in all three soils.

THE THREE DS OF PCR-BASED GENOMIC ANALYSIS OF PHYTOBACTERIA: Diversity, Detection, and Disease Diagnosis

The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-based genomic fingerprinting methods, especially when combined with computer-assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a high-resolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.

Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes

Conserved regions about 420 bp long of the pelADE cluster specific to Erwinia chrysanthemi were amplified by PCR and used to differentiate 78 strains of E. chrysanthemi that were obtained from different hosts and geographical areas. No PCR products were obtained from DNA samples extracted from other pectinolytic and nonpectinolytic species and genera. The pel fragments amplified from the E. chrysanthemi strains studied were compared by performing a restriction fragment length polymorphism (RFLP) analysis. On the basis of similarity coefficients derived from the RFLP analysis, the strains were separated into 16 PCR RFLP patterns grouped in six clusters, These clusters appeared to be correlated with other infraspecific levels of E. chrysanthemi classification, such as pathovar and biovar, and occasionally with geographical origin. Moreover, the clusters correlated well with the polymorphism of pectate lyase and pectin methylesterase isoenzymes. While the pectin methylesterase profiles correlated with host monocot-dicot classification, the pectate lyase polymorphism might reflect the cell wall microdomains of the plants belonging to these classes.