Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR

Variation in Genotype and Aggressiveness of Ralstonia solanacearum Race 1 Isolated from Tomato in Taiwan

ABSTRACT A population of Ralstonia solanacearum race 1 from tomato (Lycopersicon esculentum) was analyzed for genetic polymorphism and aggressiveness on tomato. The 46 strains were collected from main tomato-growing areas in Taiwan. Genetic analysis was achieved by two polymerase chain reaction (PCR)-based methods: REP-, ERIC-, and BOX-PCR (collectively as rep-PCR) and random amplified polymorphic DNA (RAPD) techniques. RAPD (with three 10-mers) and rep-PCR revealed 35 and 30 haplotypes, respectively, that were grouped in 14 clusters and 3 clusters, respectively. Distribution of strains into genetic clusters did not appear related to biovar or geographic origin in considering RAPD, rep-PCR, or composite data. Although strains were more dissimilar based on RAPD data than on rep-PCR data, the two techniques gave complementary results for strain clustering. A set of 40 strains representing the main haplotypes was inoculated on six tomato cultivars differing in their bacterial wilt resistance. Six groups differing in general level of aggressiveness and cultivar specificity were detected. Although populations were highly diverse in both genotype and aggressiveness, no association was found between the two characteristics. Although the sample sizes in this study were not adequate to draw definite conclusions about population structure, these results will be valuable for future population genetic studies on R. solanacearum.

Phenotypic and genetic diversity among Bacillus sphaericus strains isolated in Brazil, potentially useful as biological control agents against mosquito larvae

Thirty mosquitocidal strains of Bacillus sphaericus isolated from different sources and localities in Brazil were characterized phenotypically and genetically to determine their relationship. Among the strains tested, 93.3% were shown to be resistant to lincomycin, 96.6% to novobiocin, 60% to chloramphenicol and all strains were resistant to streptomycin. Resistance to HgCl2, NiSO4.6H2O and CuSO4 was observed in 83.3, 86.6 and 100% of the strains, respectively. All strains were inhibited by the presence of CoSO4. Tolerance to ethanol and variable responses to different amounts of creolin, phenol and xylol was also observed. Amplification of DNA of each of 30 isolates using repetitive primers allowed the identification of 5 groups of similar strains in BOX-PCR and 8 groups in REP-PCR. Using cloned toxin genes from B. sphaericus as probes in hybridization studies, 83% of the strains studied hybridized to the bin probe and 90% to the mtx probe. A comparison of the 30 strains by similarity matrix analysis using the data obtained in all approaches used in this study resulted in 22 groups (16 groups among the 24 high-toxicity strains) at 100% similarity, indicating a high degree of diversity among the strains tested. Some of the strains studied here, which are resistant to different stress conditions, should be considered for further ecological studies.

Bacterial Blight of Leek: A New Disease in California Caused by Pseudomonas syringae

During 1996 and 1997, a new and damaging disease of leek (Allium porrum) was observed on greenhouse-produced transplants and field-grown plants in California. Symptoms were water-soaked lesions at leaf tips, which eventually expanded down the length of the leaf and resulted in brown, elongated, stripe-like lesions with yellow margins. Diseased leaves eventually wilted. A blue fluorescent pseudomonad was consistently recovered from lesions, and biochemical and physiological tests indicated that it was Pseudomonas syringae. Pathogenicity tests established that representative strains of this P. syringae induced disease symptoms in leek that were similar to those observed on leek plants in the greenhouse and field, and that this bacterium caused similar symptoms in onion, chives, and garlic plants. Representative strains were further characterized by fatty acid analysis, repetitive bacterial sequence-polymerase chain reaction (rep-PCR), and rDNA sequencing. Fatty acid analysis confirmed that these isolates were P. syringae, but did not provide a clear pathovar designation. Rep-PCR analysis revealed that all the California leek P. syringae strains had identical DNA fingerprints and that these strains were indistinguishable from those of known strains of P. syringae pv. porri. In addition, the rDNA sequence of the spacer region between 16S and 23S rDNA genes was identical among the California leek P. syringae strains and P. syringae pv. porri. Together, these results established that the new leek disease in California is caused by P. syringae pv. porri. P. syringae pv. porri was recovered from a commercial leek seed lot imported into California, which suggests that the pathogen was introduced in association with seed. Commercial leek production in California is favorable for development of this disease because transplants are produced in greenhouses with high plant densities, overhead irrigation, and mowing of plants.

Functional analysis of the Pseudomonas syringae rulAB determinant in tolerance to ultraviolet B (290-320 nm) radiation and distribution of rulAB among P. syringae pathovars

The effect of the plasmid-encoded rulAB (resistance to ultraviolet radiation) determinant on responses of Pseudomonas syringae to ultraviolet-B (UV-B) radiation and the distribution of rulAB among pathovars of P. syringae were determined. The cloned rulAB determinant and the native rulAB+ plasmid pPSR1 both conferred approximately a 10-fold increase in survival on P. syringae pv. syringae FF5 following increasing doses of UV-B radiation. rulAB+ P. syringae strains also maintained significantly larger epiphytic populations on leaf surfaces irradiated with UV-B. rulAB-insertional mutants, constructed in two native rulAB+ strains, were from 10- to 100-fold more sensitive to UV-B radiation. The UV tolerance phenotype and the rulAB genes were widely distributed among P. syringae pathovars isolated from varied plant hosts throughout the world and within a broad range of genotypic backgrounds of P. syringae pv. syringae. With one exception, the rulAB determinant was harboured on pPT23A-like plasmids; these replicons are indigenous residents of the species P. syringae and also tend to encode determinants of importance in host-pathogen interactions.

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.

Typing of Listeria monocytogenes strains by repetitive element sequence-based PCR

Listeria monocytogenes strains possess short repetitive extragenic palindromic (REP) elements and enterobacterial repetitive intergenic consensus (ERIC) sequences. We used repetitive element sequence-based PCR (rep-PCR) to evaluate the potential of REP and ERIC elements for typing L. monocytogenes strains isolated from humans, animals, and foods. On the basis of rep-PCR fingerprints, L. monocytogenes strains were divided into four major clusters matching origin of isolation. rep-PCR fingerprints of human and animal isolates were different from those of food isolates. Computer evaluation of rep-PCR fingerprints allowed discrimination among the tested serotypes 1/2a, 1/2b, 1/2c, 3b, and 4b within each major cluster. The index of discrimination calculated for 52 epidemiologically unrelated isolates of L. monocytogenes was 0.98 for REP- and ERIC-PCR. Our results suggest that rep-PCR can provide an alternative method for L. monocytogenes typing.

Diversity Within Streptomyces ipomoeae Based on Inhibitory Interactions, rep-PCR, and Plasmid Profiles

ABSTRACT Streptomyces soil rot is a destructive disease of sweetpotato (Ipomoea batatas) that causes yield loss resulting from decay of the feeder root system and reduced quality due to the presence of necrotic lesions on the storage roots. It is managed by the use of resistant cultivars, but variability of the pathogen has not been previously assessed. This study compared 36 strains of the pathogen Streptomyces ipomoeae from different locations in the United States and Japan. The strains could be separated into three groups on the basis of their ability to inhibit the growth of one another in in vitro assays. Although some strains contained plasmids of approximately 18, 42, or 270 kb in size, plasmid profiles did not correspond to inhibition grouping. Fingerprinting by repetitive element-based polymerase chain reaction (rep-PCR) using outwardly facing primers for the BOX, enterobacterial repetitive intergenic consensus (ERIC), and repetitive extragenic palindromic (REP) sequences indicated relatively high genomic homogeneity within S. ipomoeae. However, cluster analysis of similarity coefficients among strains using rep-PCR data revealed clusters that correlated with the inhibition grouping. The neotype strain of S. ipomoeae had lower similarity values by rep-PCR than any of the other strains and could not be grouped by inhibitory interactions.

Relatedness of strains of xanthomonas fragariae by restriction fragment length polymorphism, DNA-DNA reassociation, and fatty acid analyses

The levels of relatedness of strains of Xanthomonas fragariae collected over several years from locations in Canada and the United States were compared by determining fatty acid methyl ester profiles, restriction fragment length polymorphisms (RFLP) based on pulsed-field gel electrophoresis (PFGE) analysis, and DNA-DNA reassociation values. Based on qualitative and quantitative differences in fatty acid profiles, the strains were divided into nine groups and four groups by the MIDI "10% rule" and unweighted pair analysis, respectively. Restriction analysis of genomic DNA by PFGE with two endonucleases (XbaI and SpeI) revealed four distinct profiles. When a third endonuclease (VspI) was used, one group was divided into three subgroups. The profile of the American Type Culture Collection type strain differed from the profile of every other strain of X. fragariae. Considerable diversity was observed within X. fragariae, although the majority of the strains represented a clonal population. The four groups based on fatty acid profiles were similar to the four groups based on RFLP, but neither method related groups to the geographic origins of the strains. The DNA-DNA reassociation values were high for representative strains, providing evidence that all of the strains belong to the same species.

Genetic characterization of pseudomonas syringae pv. syringae strains from stone fruits in california

Strains of Pseudomonas syringae pv. syringae were isolated from healthy and diseased stone fruit tissues sampled from 43 orchard sites in California in 1995 and 1996. These strains, together with P. syringae strains from other hosts and pathovars, were tested for pathogenicity and the presence of the syrB and syrC genes and were genetically characterized by using enterobacterial repetitive intergenic consensus (ERIC) primers and PCR. All 89 strains of P. syringae pv. syringae tested were moderately to highly pathogenic on Lovell peach seedlings regardless of the host of origin, while strains of other pathovars exhibited low or no pathogenicity. The 19 strains of P. syringae pv. syringae examined by restriction fragment length polymorphism analysis contained the syrB and syrC genes, whereas no hybridization occurred with 4 strains of other P. syringae pathovars. The P. syringae pv. syringae strains from stone fruit, except for a strain from New Zealand, generated ERIC genomic fingerprints which shared four fragments of similar mobility. Of the P. syringae pv. syringae strains tested from other hosts, only strains from rose, kiwi, and pear generated genomic fingerprints that had the same four fragments as the stone fruit strains. Analysis of the ERIC fingerprints from P. syringae pv. syringae strains showed that the strains isolated from stone fruits formed a distinct cluster separate from most of the strains isolated from other hosts. These results provide evidence of host specialization within the diverse pathovar P. syringae pv. syringae.

Comparison of paenibacillus azotofixans strains isolated from rhizoplane, rhizosphere, and non-root-associated soil from maize planted in two different brazilian soils

Paenibacillus azotofixans is a nitrogen-fixing bacterium often found in soil and in the rhizospheres of different grasses. In this study, two Brazilian clay soils were planted with cross-hybrid maize (BR-201) and four stages of plant growth were analyzed to characterize the P. azotofixans populations present in the rhizoplanes, rhizospheres, and non-root-associated soils (herein called nonrhizospheres). A total of 106 strains were isolated and identified as P. azotofixans with an API 50CH kit, by classical biochemical tests, and via the use of specific primers based on the 16S rRNA gene in PCRs. To compare the isolated strains, phenotypic characteristics were determined and three different probes were used in hybridization experiments: two nif probes and one probe comprising a 0.58-kb fragment cloned from the P. azotofixans C3L4 genome. These results were used to construct a dendrogram, in which two main clusters could be observed. One cluster contained exclusively strains from Varzea soil, and the other contained the majority of strains from Cerrado soil. The 60 strains from Varzea soil and the 46 strains from Cerrado soil were further analyzed with REP and BOX primers, respectively. Based on the patterns obtained, it was possible to identify 21 different groups among strains from Varzea soil and 4 different groups among strains from Cerrado soil. These different patterns were tested by multivariate analysis of variance, and differences in the populations of P. azotofixans during the four stages of plant growth were demonstrated. Moreover, strains isolated from the rhizoplanes, rhizospheres, and nonrhizospheres of maize planted in Cerrado and Varzea soils were shown to be statistically different; the diversity of P. azotofixans strains was affected by the soil type.

Cloning, nucleotide sequence, and expression in Escherichia coli of levansucrase genes from the plant pathogens Pseudomonas syringae pv. glycinea and P. syringae pv. phaseolicola

Plant-pathogenic bacteria produce various extracellular polysaccharides (EPSs) which may function as virulence factors in diseases caused by these bacteria. The EPS levan is synthesized by the extracellular enzyme levansucrase in Pseudomonas syringae, Erwinia amylovora, and other bacterial species. The lsc genes encoding levansucrase from P. syringae pv. glycinea PG4180 and P. syringae pv. phaseolicola NCPPB 1321 were cloned, and their nucleotide sequences were determined. Heterologous expression of the lsc gene in Escherichia coli was found in four and two genomic library clones of strains PG4180 and NCPPB 1321, respectively. A 3. 0-kb PstI fragment common to all six clones conferred levan synthesis on E. coli when further subcloned. Nucleotide sequence analysis revealed a 1,248-bp open reading frame (ORF) derived from PG4180 and a 1,296-bp ORF derived from NCPPB 1321, which were both designated lsc. Both ORFs showed high homology to the E. amylovora and Zymomonas mobilis lsc genes at the nucleic acid and deduced amino acid sequence levels. Levansucrase was not secreted into the supernatant but was located in the periplasmic fraction of E. coli harboring the lsc gene. Expression of lsc was found to be dependent on the vector-based Plac promoter, indicating that the native promoter of lsc was not functional in E. coli. Insertion of an antibiotic resistance cassette in the lsc gene abolished levan synthesis in E. coli. A PCR screening with primers derived from lsc of P. syringae pv. glycinea PG4180 allowed the detection of this gene in a number of related bacteria.

rep-PCR-Mediated Genomic Fingerprinting: A Rapid and Effective Method to Identify Clavibacter michiganensis

ABSTRACT The genomic DNA fingerprinting technique known as repetitive-sequence-based polymerase chain reaction (rep-PCR) was evaluated as a tool to differentiate subspecies of Clavibacter michiganensis, with special emphasis on C. michiganensis subsp. michiganensis, the pathogen responsible for bacterial canker of tomato. DNA primers (REP, ERIC, and BOX), corresponding to conserved repetitive element motifs in the genomes of diverse bacterial species, were used to generate genomic fingerprints of C. michiganensis subsp. michiganensis, C. michiganensis subsp. sepedonicus, C. michiganensis subsp. nebraskensis, C. michiganensis subsp. tessellarius, and C. michiganensis subsp. insidiosum. The rep-PCR-generated patterns of DNA fragments observed after agarose gel electrophoresis support the current division of C. michiganensis into five subspecies. In addition, the rep-PCR fingerprints identified at least four types (A, B, C, and D) within C. michiganensis subsp. michiganensis based on limited DNA polymorphisms; the ability to differentiate individual strains may be of potential use in studies on the epidemiology and host-pathogen interactions of this organism. In addition, we have recovered from diseased tomato plants a relatively large number of naturally occurring avirulent C. michiganensis subsp. michiganensis strains with rep-PCR fingerprints identical to those of virulent C. michiganensis subsp. michiganensis strains.

Characterization of isolates of Paenibacillus larvae subsp. larvae from diverse geographical origin by the polymerase chain reaction and BOX primers

Ninety-nine strains of Paenibacillus larvae subsp. larvae, the causal agent of American Foulbrood disease (AFB) of honeybees, were isolated from different regions of Argentina and other countries. The isolates were characterized on the basis of DNA fingerprints by a polymerase chain reaction technique (PCR) with BOX sequence-specific primers. Isolates from Argentina generated three groups of patterns (designated A, B, and C), while P. larvae subsp. larvae strains obtained from other countries yielded two distinguishable patterns (coincident with A and B). Strains from U.S. A. and Germany were identical and related to Group A, while all Czech and English isolates belonged to Group B. Strains from France, Poland, Italy, Sweden, and New Zealand showed two different patterns (A and B). Comparisons of the biochemical type and genotype of isolates rendered no obvious linkage between both features. These results suggest that AFB in Argentina resulted from multiple sources of contaminated material.

Isolation, characterization, and transfer of cryptic gene-mobilizing plasmids in the wheat rhizosphere

A set of self-transmissible plasmids with IncQ plasmid-mobilizing capacity was isolated by triparental exogenous isolation from the wheat rhizosphere with an Escherichia coli IncQ plasmid host and a Ralstonia eutropha recipient. Three plasmids of 38 to 45 kb, denoted pIPO1, pIPO2, and pIPO3, were selected for further study. No selectable traits (antibiotic or heavy-metal resistance) were identified in these plasmids. The plasmids were characterized by replicon typing via PCR and hybridization with replicon-specific probes and other hybridizations. pIPO1 and pIPO3 were similar to each other, whereas pIPO2 was different. None of these plasmids belonged to any known incompatibility group. pIPO2 was selected for further work, and a mini-Tn5-tet transposon was inserted to confer selectability. Plasmid pIPO2 had a broad IncQ plasmid mobilization and self-transfer range among the alpha, beta, and gamma subclasses of the Proteobacteria but did not show productive transfer to gram-positive bacteria. Plasmid pIPO2 mobilized IncQ plasmid pIE723 from Pseudomonas fluorescence to diverse indigenous proteobacteria in the rhizosphere of field-grown wheat. Transfer of pIE723 to indigenous bacteria was not observed in the absence of added pIPO2. A specific PCR primer system and a probe were developed for the detection of pIPO2-type plasmids in soil and rhizosphere. Analysis of soil DNA provided evidence for the presence of pIPO2 in inoculated wheat rhizosphere soil in the field study, as well as in the rhizosphere of uninoculated wheat plants growing in soil microcosms. The system failed to identify major reservoirs of pIPO2 in a variety of other soils.

Rapid Population Analysis of Magnaporthe grisea by Using rep-PCR and Endogenous Repetitive DNA Sequences

ABSTRACT DNA samples from Magnaporthe grisea isolates were fingerprinted by using repetitive element-based polymerase chain reaction (rep-PCR) with two outwardly directed primer sequences from Pot2, an element found in approximately 100 copies in the fungal genome. Variable length fragments, defining the sequences lying between these elements, were generated, and fingerprint patterns specific for individual strains were established. "Long PCR" conditions, including higher pH (9.2) and increased extension time (10 min) were used to amplify DNA fragments ranging from 400 bp to longer than 23 kb. Polymorphisms specific to M. grisea strains were generated, allowing inference of their genetic relationships. Segregation analysis was used to confirm single-locus inheritance for the fragments amplified by rep-PCR. Cluster analysis revealed robust groupings that corresponded to previously determined MGR586 restriction fragment length polymorphism lineages of the rice-infecting strains of the pathogen. We have also demonstrated the utility of rep-PCR to differentiate isolates that infect rice from those that infect nonrice hosts. DNA fingerprinting by Pot2 rep-PCR provides an efficient means to monitor the population dynamics of the blast pathogen. Because of the method's low cost and ease in application, it is now feasible to conduct large-scale population studies to understand the impact of host genotypes on pathogen evolution.

Diversity among xanthomonads pathogenic on pepper and tomato

Xanthomonas campestris pv. vesicatoria, causal agent of bacterial spot of tomato and pepper, had been considered for nearly 70 years to be a relatively homogeneous organism. However, in the past decade this bacterium was determined to be composed of two genetically and phenotypically distinct groups. The two groups, designated A and B, were distinguished based on amylolytic activity, expression of unique protein bands, reaction on differential hosts (tomato races T1 and T2), reaction patterns with monoclonal antibodies, DNA restriction profiles, and DNA:DNA hybridization. The A and B groups were placed into X. axonopodis pv. vesicatoria and X. vesicatoria, respectively. A third group, designated C, was pathogenically (race T3) and serologically distinct from A and B strains, and formed unique DNA restriction profiles. DNA:DNA hybridization data suggest that C is distinct but related to A strains and may represent a subspecies of A. A final group, designated D, consisted of X. gardneri, an organism identified in Yugoslavia in 1957, and also found in Costa Rica. Group D was determined to be genetically distinct from strains within the other two groups; it represents a third Xanthomonas species pathogenic on tomato and pepper.

Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.

Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species

Horizontal transfer of genes of selective value in an environment 6 years after their introduction into a watershed has been observed. Expression of the gene pheA, which encodes phenol monooxygenase and is linked to the pheBA operon (A. Nurk, L. Kasak, and M. Kivisaar, Gene 102:13-18, 1991), allows pseudomonads to use phenol as a growth substrate. Pseudomonas putida strains carrying this operon on a plasmid were used for bioremediation after an accidental fire in the Estonia oil shale mine in Estonia in 1988. The water samples used for studying the fate of the genes introduced were collected in 1994. The same gene cluster was also detected in Pseudomonas strains isolated from water samples of a nearby watershed which has been continuously polluted with phenols due to oil shale industry leachate. Together with the more frequently existing counterparts of the dmp genes (V. Shingler, J. Powlowski, and U. Marklund, J. Bacteriol. 174:711-724, 1992), the pheA gene was also represented in the phenol-degrading strains. The area where the strains containing the pheA gene were found was restricted to the regular route of phenolic leachate to the Baltic Sea. Nine Pseudomonas strains belonging to four different species (P. corrugata, P. fragi, P. stutzeri, and P. fluorescens biotypes B, C, and F) and harboring horizontally transferred pheBA operons were investigated. The phe genes were clustered in the same manner in these nine phe operons and were connected to the same promoter as in the case of the original pheBA operon. One 10.6-kb plasmid carrying a pheBA gene cluster was sequenced, and the structure of the rearranged pheBA operon was described. This data indicates that introduced genetic material could, if it encodes a beneficial capability, enrich the natural genetic variety for biodegradation.

Differentiation of Erwinia amylovora strains by pulsed-field gel electrophoresis

Erwinia amylovora strains, isolated from several host plants in various geographic regions during different years, were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of the DNA from lysed, agar-embedded cells with rare-cutting restriction enzymes. The banding patterns obtained with enzyme XbaI digests revealed significant differences among strains from different areas. North American strains E9 and Ea-Rb, a Rubus strain, were highly divergent from other E. amylovora strains. French strains were different from central European and English strains. E. amylovora strains from central Europe and New Zealand had identical PFGE patters, as had strains from Egypt, Greece, and Turkey. PFGE of genomic DNA from American and English strains gave rise to dissimilar patterns. Patterns of some American strains resembled those from strains isolated in other parts of the world. The restriction fragment length polymorphisms observed by PFGE analysis can be used to group strains and may give hints about the course of distribution of the plant disease. From the sizes of the restriction fragments obtained, a molecular mass of approximately 4.5 Mb was calculated for the genome of E. amylovora.

Development of a diagnostic DNA probe for xanthomonads causing bacterial spot of peppers and tomatoes

Xanthomonas vesicatoria and Xanthomonas axonopodis pv. vesicatoria, causal agents for bacterial spot of tomatoes and peppers, are difficult to distinguish from other xanthomonads found on field-grown plants. A genomic subtraction technique with subtracter DNA from nonpathogenic epiphytic xanthomonads was used to enrich for sequences that could serve as diagnostic probes for these pathogens. A 1.75-kb PstI-NotI fragment (KK1750) that preferentially hybridized to X. vesicatoria DNA and X. axonopodis pv. vesicatoria DNA was identified and cloned into pBluescriptII KS+. It hybridized to 46 (89%) of the 52 geographically diverse bacterial spot-causing xanthomonad (bsx) strains included in this study. The six probe-negative strains were genotypically and pathologically distinct from the other bsx strains studied. Two of these strains, DC91-1 and DC91-2, resembled X. campestris pv. raphani in that they also infected radish plants. X. vesicatoria strains gave stronger hybridization signals than did most X. axonopodis pv. vesicatoria strains. In a survey of 110 non-bsx plant-associated bacteria, including 44 nonvesicatoria phytopathogenic xanthomonads and 43 epiphytic xanthomonad strains, only 8 were probe positive, but the responses were weak. Further testing revealed that one of these strains was actually a tomato pathogen. Pulsed-field gel electrophoresis and Southern blot analysis of 46 bsx strains indicated that KK1750 sequences could be either plasmid-borne (10.9%), chromosome-borne (43.4%), or present on both replicons (45.7%). KK1750, unique in its ability to hybridize to both X. axonopodis pv. vesicatoria and X. vesicatoria strains, should facilitate disease diagnosis for these important plant pathogens.

Association of mercury resistance with antibiotic resistance in the gram-negative fecal bacteria of primates

Gram-negative fecal bacterial from three longitudinal Hg exposure experiments and from two independent survey collections were examined for their carriage of the mercury resistance (mer) locus. The occurrence of antibiotic resistance was also assessed in both mercury-resistant (Hgr) and mercury-susceptible (Hgs) isolates from the same collections. The longitudinal studies involved exposure of the intestinal flora to Hg released from amalgam "silver" dental restorations in six monkeys. Hgr strains were recovered before the installation of amalgams, and frequently these became the dominant strains while amalgams were installed. Such persistent Hgr strains always carried the same mer locus throughout the experiments. In both the longitudinal and survey collections, certain mer loci were preferentially associated with one genus, whereas other mer loci were recovered from many genera. In general, strains with any mer locus were more likely to be multiresistant than were strains without mer loci; this clustering tendency was also seen for antibiotic resistance genes. However, the association of antibiotic multiresistance with mer loci was not random; regardless of source, certain mer loci occurred in highly multiresistant strains (with as many as seven antibiotic resistances), whereas other mer loci were found in strains without any antibiotic resistance. The majority of highly multiresistant Hgr strains also carried genes characteristic of an integron, a novel genetic element which enables the formation of tandem arrays of antibiotic resistance genes. Hgr strains lacking antibiotic resistance showed no evidence of integron components.

Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints

Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNA(IIe)) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus-specific PCR followed by BOX- and tDNA-PCR; it enabled us to assign new diazotrophic isolates originating from fungal resting stages (sclerotia) to known species of Azoarcus. The assignment was confirmed by phylogenetic analysis of 16S rDNA sequences. Additionally, the phylogenetic distances and the lack of monophyly suggested emendment of the genus Azoarcus: the unnamed species Azoarcus groups C and D and a new group (E) of Azoarcus, which was detected in association with fungi, are likely to have the taxonomic rank of three different genera. According to its small subunit rRNA, the sclerotium-forming basidiomycete was related to the Ustilagomycetes, facultatively biotrophic parasites of plants. Since they occurred in a field which was under cultivation with rice and wheat, these fungi might serve as a niche for survival for Azoarcus in the soil and as a source for reinfection of plants.

Epidemiological typing of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is increasingly recognized as a cause of hospital-acquired infection and respiratory tract colonization in cystic fibrosis patients. A number of methods have been described for the typing of strains in epidemiological studies. Pulsed-field gel electrophoresis (PFGE) of total chromosomal DNA cleaved by low-frequency restriction site endonucleases (XbaI, SpeI) is highly discriminatory and defines populations at the strain level. Other molecular methods such as ribotyping with restriction endonucleases (BamHI, ClaI, BelI, EcoRI) can be used to subdivide the species but with reduced discrimination compared with PFGE. Polymerase chain reaction (PCR) fingerprinting techniques utilizing random primers or those directed against repeat motifs (ERIC, REP) are rapid and offer high discrimination for the study of outbreaks. A consistent finding from a number of incidents is the high diversity of strain types of S. maltophilia identified and the low incidence of cross-infection between patients.

Amplification of anonymous DNA fragments using pairs of long primers generates reproducible DNA fingerprints that are sensitive to genetic variation

The reproducibility and potential applications of anonymous amplification protocols can be improved by using pairs of primers, each of 18 to 24 bases, to replace the single 8 to 10 base primers normally used in randomly amplified polymorphic DNA (RAPD) or DNA amplification fingerprinting (DAF) methods. Amplification using large primer pairs (LP-RAPD) generates 5 to 30 bands that can be resolved on standard agarose gels. Complex fingerprints can be readily generated from viruses, bacteria, fungi, plants, invertebrates and vertebrates. We also present evidence that a number of polymerase chain reaction (PCR) methods, including those based on the use of enterobacterial repetitive intergenic consensus (ERIC-PCR) or microsatellite primed (MP-PCR) sequence, may in essence operate by the same mechanism as LP-RAPD. Using standard LP-RAPD protocols, reproducible fingerprints can be generated from a single specimen using different thermocyclers, regardless of the mechanism used for thermocycling (air-cooled, Peltier effect, or robotic arm). LP-RAPD is sensitive to intraspecific and interspecific genetic variation, demonstrated here by analysis of mites and apple cultivars. Approximately 50% of LP-RAPD products are expected to have different primers at either end. Polymorphic bands with this arrangement can be recovered from the gel and directly sequenced using the LP-RAPD primers themselves. The efficiency of sequencing is improved by the length of the LP-RAPD primers. This method has the potential to allow the production of allele-specific species markers in less than two days.

A novel means to develop strain-specific DNA probes for detecting bacteria in the environment

A simple means to develop strain-specific DNA probes for use in monitoring the movement and survival of bacteria in natural and laboratory ecosystems was developed. The method employed amplification of genomic DNA via repetitive sequence-based PCR (rep-PCR) using primers specific for repetitive extragenic palindromic (REP) elements, followed by cloning of the amplified fragments. The cloned fragments were screened to identify those which were strain specific, and these were used as probes for total genomic DNA isolated from microbial communities and subjected to rep-PCR. To evaluate the utility of the approach, we developed probes specific for Burkholderia cepacia G4 and used them to determine the persistence of the strain in aquifer sediment microcosms following bioaugmentation. Two of four probes tested were found to specifically hybridize to DNA fragments of the expected sizes in the rep-PCR fingerprint of B. cepacia G4 but not to 64 genetically distinct bacteria previously isolated from the aquifer. One of these probes, a 650-bp fragment, produced a hybridization signal when as few as 10 CFU of B. cepacia G4 were present in a mixture with 10(6) CFU nontarget strains, indicating that the sensitivity of these probes was comparable to those of other PCR-based detection methods. The probes were used to discriminate groundwater and microcosm samples that contained B. cepacia G4 from those which did not. False-positive results were obtained with a few samples, but these were readily identified by using hybridization to the second probe as a confirmation step. The general applicability of the method was demonstrated by constructing probes specific to three other environmental isolates.

Phylogenetic characterization of bacteria in the subsurface microbial culture collection

The Subsurface Microbial Culture Collection (SMCC) was established by the U.S. Dept. of Energy (DOE) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. Selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16S ribosomal RNA (rRNA) gene nucleotide sequences. Among these isolates were members of six major phylogenetic groups of bacteria: the high-G+C and low-G+C Gram-positive bacteria; the alpha-, beta-, and gamma-subdivisions of the Proteobacteria; and the Flexibacter/Cytophaga/Bacteroides group. A small number of the SMCC strains may be members of new bacterial genera, but most of them could be placed with reasonable confidence into more than 35 previously described genera. The majority of the Gram-positive isolates were species of Arthrobacter, Bacillus, or Streptococcus, whereas Acinetobacter, Comamonas, Pseudomonas, Sphingomonas, and Variovorax were among the most frequently encountered Gram-negative genera. A high proportion of the strains were placed in fewer than 10 genera, implying that there is substantial duplication within the SMCC at the genus level. When groups of isolates assigned to Acinetobacter, Arthrobacter, or Sphingomonas were analyzed in more detail, however, it was found that each group consisted of subgroups of strains that probably differed at the species level. Restriction endonuclease analysis (applied to the strains from one sample site) indicated that additional diversity was present at the strain level. Most of the SMCC isolates assigned to some genera (e.g., Acinetobacter) were very closely related to previously described species in those genera, but most of the isolates assigned to other genera (e.g., Arthrobacter and Sphingomonas) appeared (or were shown) to be new species, thereby indicating that a reasonable amount of novelty is present within the SMCC at the species level.

Movement of Xanthomonas oryzae pv. oryzae in Southeast Asia Detected Using PCR-Based DNA Fingerprinting

ABSTRACT Two outwardly directed primers complementary to sequences in IS1112, a repetitive element isolated from Xanthomonas oryzae pv. oryzae, were used to fingerprint DNA from a set of 71 bacterial blight pathogen strains using polymerase chain reaction (PCR), PCR-based restriction analysis, and ligation-mediated PCR. To allow amplification of long DNA fragments, standard amplification conditions were altered to increase the pH, add dimethylsulfoxide, decrease denaturation time, and increase extension time. Bands ranging in size from 100 bp to 7 kb and in number from 13 to 48 bands per strain were amplified. The three methods revealed useful polymorphisms among individual strains and allowed their genetic relationships to be efficiently deduced. Good correlation was found between the major clusters obtained by the three methods. The PCR method gave the most robust clusters and was most efficient in terms of speed, simplicity, and economy. Using PCR and restriction fragment length polymorphism to compare strains of the bacterial blight pathogen from Indonesia and the Philippines, we found that, whereas there is regional differentiation of the pathogen populations, the predominant strains in the pathogen collections from both countries are closely related. This indicates the occurrence of regional movement, perhaps as a consequence of germ plasm exchange.

Application of repetitive sequence-based PCR (inter-LINE PCR) for the analysis of genomic rearrangements and for the genome characterization on different taxonomic levels

Oligonucleotide primers derived from consensus LINE-sequences generated highly reproducible, species-specific PCR product patterns suitable for the identification of genomic rearrangements and for the discrimination on different taxonomic levels of higher and lower eukaryotes and even prokaryotes.

Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen

Genetic relationships among 25 isolates of Xanthomonas fragariae from diverse geographic regions were determined by three PCR methods that rely on different amplification priming strategies: random amplified polymorphic DNA (RAPD) PCR, repetitive extragenic palindromic (REP) PCR, and enterobacterial repetitive intergenic consensus (ERIC) PCR. The results of these assays are mutually consistent and indicate that pathogenic strains are very closely related to each other. RAPD, ERIC, and REP PCR assays identified nine, four, and two genotypes, respectively, within X. fragariae isolates. A single nonpathogenic isolate of X. fragariae was not distinguishable by these methods. The results of the PCR assays were also fully confirmed by physiological tests. There was no correlation between DNA amplification product patterns and geographic sites of isolation, suggesting that this bacterium has spread largely through exchange of infected plant germ plasm. Sequences identified through the RAPD assays were used to develop three primer pairs for standard PCR assays to identify X. fragariae. In addition, we developed a stringent multiplexed PCR assay to identify X. fragariae by simultaneously using the three independently derived sets of primers specific for pathogenic strains of the bacteria.

Repetitive element sequence-based PCR for species and strain discrimination in the genus Listeria

Repetitive element sequence-based PCR (rep-PCR) was used to generate DNA fingerprints for Listeria spp. Two primer sets (REP 1R-I REP 2-I and ERIC 1R ERIC 2) used in respectively REP- and ERIC-PCR revealed that bacteria of the genus Listeria possess short repetitive extragenic palindromic elements and enterobacterial repetitive intergenic consensus sequences. Specific band profiles obtained by ERIC-PCR enabled the identification of Listeria species. With both REP- and ERIC-PCR the L. monocytogenes serotypes 1/2a, 1/2b, 1/2c, 3b and 4b could be clearly distinguished from each other. Within the serotype 1/2a, REP-PCR showed a higher discriminative potential than ERIC-PCR and a comparable discriminative potential as RAPD combining 3-4 primers.

Repetitive element sequence based polymerase chain reaction for typing of Brucella strains

A collection of 40 Brucella strains, including 19 clinical B.canis isolates, was analyzed using ERIC-PCR and REP-PCR. PCR amplification using primers REP 1R-I and REP 2-I provided distinct patterns for Brucella spp. All Brucella strains could be discriminated at least to the species level. ERIC-PCR, employing ERIC 1R and ERIC 2 as primers was less discriminative for Brucella, only allowing a discrimination to the genus level with occasional discrimination between individual strains. It can be concluded that rep PCR is a promising fingerprinting method for the evaluation of an outbreak.

Characterization of Rhizobium 'hedysari' by RFLP analysis of PCR amplified rDNA and by genomic PCR fingerprinting

The taxonomic and discriminatory power of RFLP analysis of PCR amplified parts of rhizobial rrn operons was compared to those of genomic PCR fingerprinting with arbitrary and repetitive primers. For this purpose, the two methods were applied for characterization of a group of bacterial isolates referred to as Rhizobium 'hedysari'. As outgroups, representatives of the family Rhizobiaceae, belonging to the Rhizobium galegae, Rhizobium meliloti, Rhizobium leguminosarum and Agrobacterium tumefaciens species were used. By the RFLP analysis of the PCR products corresponding to the variable 5'-half of the 23S rRNA gene and of the amplified spacer region between the 16S and 23S rRNA genes all Rh. 'hedysari' strains studied were tightly clustered together while the outgroups were placed in an outer position. The PCR products of the 3' end parts of the 23S rDNA did not show significant RFL polymorphism and no species differentiation on their basis was possible. In parallel, analysis of the same strains was performed by PCR amplification of their DNA with 19, 18 and 10 bp long arbitrary primers (AP-PCR) as well as with single primers corresponding to several bacterial repetitive sequences (rep-PCR). By both AP and rep-PCR an identification of every particular strain was achieved. In general, all primers provided taxonomic results that are in agreement with the species and group assignments based on the RFLP analysis of the rrn operons. On the basis of the results presented here it can be concluded that AP and rep-PCR are more informative and discriminative than rDNA and RFLP analysis of the rhizobial strains studied.

Polymorphism in Brucella strains detected by studying distribution of two short repetitive DNA elements

Thirty-four Brucella reference or field strains representing all the species and biovars were studied by repetitive element sequence-based PCR, a PCR using primers complementary to two enterobacterial short repetitive sequences: repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus sequences. All the stains showed a positive amplification, suggesting that the Brucella genome contains such sequences. Repetitive extragenic palindromic PCR was less discriminating than enterobacterial repetitive intergenic consensus PCR in terms of distinguishing strains, but a combination of the two methods was able to distinguish all the isolates, except for some strains belonging to biovars 3 and 9 of Brucella abortus. Repetitive element sequence-based PCR appears to be a simple and useful method for the study of brucellosis epidemiology.

Comparative usefulness of ribotyping, exotoxin A genotyping, and SalI restriction fragment length polymorphism analysis for Pseudomonas aeruginosa lineage assessment

Ribotyping, exotoxin A genotyping (EAGP), and restriction fragment length polymorphism (RFLP) analysis of total DNA with SalI (SalI RFLP) were compared for intraspecies discrimination of 93 Pseudomonas aeruginosa isolates. Type-ability of all methods was 100% and the results of typing with each method remained unchanged during laboratory manipulation. Clonal groups defined with each molecular method were largely coincident and, in those cases where inconsistencies were detected, isolates were analyzed by transverse alternating field gel electrophoresis (TAFE) and arbitrarily primed polymerase chain reaction (AP-PCR). SalI RFLP analysis was highly discriminative so as to distinguish unrelated isolates of close lineage. However, it was not a good method to identify isolates of unrelated lineage because SalI RFLP appeared to be subjected to convergent evolution. The index of discrimination suggested by Hunter and Gaston was determined to assess the discriminatory power of the molecular methods utilized either alone or in several combinations. Combined use of ribotyping and SalI RFLP analysis reached the highest index of discrimination (0.982) and proved to be a very valuable tool for epidemiological differentiation of P. aeruginosa isolates.

Genetic diversity of Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 in Kenya

Genetic diversity among isolates of the bacterial plant pathogen Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 biovar II of Kenya was determined by PCR with repetitive sequences (ERIC and BOX repetitive primer sets) and pulsed-field gel electrophoresis of genomic DNA digested by rare-cutting restriction endonucleases (RC-PFGE). The study comprised 46 isolates collected during 1992 from the major potato-growing regions of Kenya (45 were identified as race 3 biovar II, and 1 belonged to race 3 biovar N2) and 39 reference isolates from 19 other countries. RC-PFGE identified 10 distinct profile types among the Kenyan race 3 biovar II isolates (29 of the isolates exhibited identical profiles) and a further 27 distinct profile types among the reference isolates. ERIC and BOX primer sets were unable to differentiate race 3 biovar II isolates within the Kenyan population but differentiated a further two distinct profile types among the reference isolates. The race 3 biovar N2 isolate had a highly distinct RC-PFGE and repetitive sequence PCR profile. Statistical analysis of the data identified biogeographic trends consistent with conclusions drawn from previous studies on the origin and worldwide dissemination of race 3 biovar II isolates; however, genomic fingerprinting by RC-PFGE revealed a level of genetic diversity previously unrealized.

Strain-specific fingerprints of Rhizobium galegae generated by PCR with arbitrary and repetitive primers

Strain-specific genomic patterns of Rhizobium galegae were generated by PCR using both arbitrary and repetitive (BOX, ERIC and REP) primers. The identification of the strains was achieved also by RFLP analysis. However, the PCR genomic fingerprinting has significant advantages: it is not only simpler and faster, but it is also much more discriminative because it deals with the full bacterial genome and not only with parts of it as is the case with RFLP. In addition, both kinds of PCR fingerprinting (using arbitrary or repetitive primers) generated highly specific and reproducible patterns when parallel reactions with total bacterial DNA, extracted from independent liquid cultures were performed. The latter shows that AP- and rep-PCR are convenient for controlling the production and application of Rhizobium inoculants.