Strain characterization and 16S-23S probe development for differentiating geographically dispersed isolates of the phytopathogen Ralstonia solanacearum

Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors

Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of 17 isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a Select Agent in the United States, were thus analyzed to get insight into the phylogeography of this pathogen. Thirteen of fourteen isolates from Europe, Africa, and Asia were found to belong to a single clonal lineage while isolates from South America were genetically diverse and tended to carry ancestral alleles at the analyzed genomic loci consistent with a South American origin of R3bv2. The R3bv2 isolates share a core repertoire of 31 type III-secreted effector genes representing excellent candidates to be targeted with resistance genes in breeding programs to develop durable disease resistance. Toward this goal, 27 R3bv2 effectors were tested in eggplant, tomato, pepper, tobacco, and lettuce for induction of a hypersensitive-like response indicative of recognition by cognate resistance receptors. Fifteen effectors, eight of them core effectors, triggered a response in one or more plant species. These genotypes may harbor resistance genes that could be identified and mapped, cloned, and expressed in tomato or potato, for which sources of genetic resistance to R3bv2 are extremely limited.

Phylogeny and population structure of brown rot- and Moko disease-causing strains of Ralstonia solanacearum phylotype II

The ancient soilborne plant vascular pathogen Ralstonia solanacearum has evolved and adapted to cause severe damage in an unusually wide range of plants. In order to better describe and understand these adaptations, strains with very similar lifestyles and host specializations are grouped into ecotypes. We used comparative genomic hybridization (CGH) to investigate three particular ecotypes in the American phylotype II group: (i) brown rot strains from phylotypes IIB-1 and IIB-2, historically known as race 3 biovar 2 and clonal; (ii) new pathogenic variants from phylotype IIB-4NPB that lack pathogenicity for banana but can infect many other plant species; and (iii) Moko disease-causing strains from phylotypes IIB-3, IIB-4, and IIA-6, historically known as race 2, that cause wilt on banana, plantain, and Heliconia spp. We compared the genomes of 72 R. solanacearum strains, mainly from the three major ecotypes of phylotype II, using a newly developed pangenomic microarray to decipher their population structure and gain clues about the epidemiology of these ecotypes. Strain phylogeny and population structure were reconstructed. The results revealed a phylogeographic structure within brown rot strains, allowing us to distinguish European outbreak strains of Andean and African origins. The pangenomic CGH data also demonstrated that Moko ecotype IIB-4 is phylogenetically distinct from the emerging IIB-4NPB strains. These findings improved our understanding of the epidemiology of important ecotypes in phylotype II and will be useful for evolutionary analyses and the development of new DNA-based diagnostic tools.

Genetic diversity of Ralstonia solanacearum strains from China assessed by PCR-based fingerprints to unravel host plant- and site-dependent distribution patterns

Bacterial wilt caused by Ralstonia solanacearum is a serious threat to crop production in China. A collection of 319 R. solanacearum strains isolated from 14 different diseased host plants collected in 15 Chinese provinces was investigated by BOX fingerprints in order to test the influence of the site and the host plant on their genetic diversity. Phylotype, fliC-RFLP patterns and biovar were determined for all strains and the sequevar for 39 representative strains. The majority of strains belonged to the Asian phylotype I, shared identical fliC-RFLP patterns and were assigned to four biovars (bv3:123; bv4:162; bv5:3; and bv6:11). Twenty strains were phylotype II, assigned to biovar 2, and had distinct fliC-RFLP patterns. BOX-PCR fingerprints generated from the genomic DNA of each strain revealed a high diversity of the phylotype I strains, where 28 types of BOX fingerprints could be distinguished. While many BOX clusters comprised isolates from different provinces and several host plants, some groups contained isolates that were plant or site specific. All phylotype II isolates originating from 10 provinces belonged to sequevar 1 and displayed identical BOX patterns as the potato brown rot strains from various regions of the world.

Ralstonia solanacearum ΔPGI-1 strain KZR-5 is affected in growth, response to cold stress and invasion of tomato

The survival and persistence of Ralstonia solanacearum biovar 2 in temperate climates is still poorly understood. To assess whether genomic variants of the organism show adaptation to local conditions, we compared the behaviour of environmental strain KZR-5, which underwent a deletion of the 17.6 kb genomic island PGI-1, with that of environmental strain KZR-1 and potato-derived strains 1609 and 715. PGI-1 harbours two genes of potential ecological relevance, i.e. one encoding a hypothetical protein with a RelA/SpoT domain and one a putative cellobiohydrolase. We thus assessed bacterial fate under conditions of amino acid starvation, during growth, upon incubation at low temperature and invasion of tomato plants. In contrast to the other strains, environmental strain KZR-5 did not grow on media that induce amino acid starvation. In addition, its maximum growth rate at 28°C in rich medium was significantly reduced. On the other hand, long-term survival at 4°C was significantly enhanced as compared to that of strains 1609, 715 and KZR-1. Although strain KZR-5 showed growth rates (at 28°C) in two different media, which were similar to those of strains 1609 and 715, its ability to compete with these strains under these conditions was reduced. In singly inoculated tomato plants, no significant differences in invasiveness were observed among strains KZR-5, KZR-1, 1609 and 715. However, reduced competitiveness of strain KZR-5 was found in experiments on tomato plant colonisation and wilting when using 1:1 or 5:1 mixtures of strains. The potential role of PGI-1 in plant invasion, response to stress and growth in competition at high and moderate temperatures is discussed.

Deciphering phenotypic diversity of Ralstonia solanacearum strains pathogenic to potato

Based on the phylotype classification, we questioned how genetically and phenotypically diverse strains of Ralstonia solanacearum pathogenic to potato may be. We studied 129 European and Mediterranean strains along with 57 reference strains known to cover genetic diversity in this species. Phylogeny analysis was done on endoglucanase gene sequences. Pathogenicity to potato, tomato, and eggplant was established at 24 to 30°C and 15 to 24°C, whereas tests on banana were conducted at 24 to 30°C. The ability to cause wilt on species of Solanaceae was shared by strains in all four phylotypes. Brown rot phylotypes IIB-1 and IIB-2 and phylotype IIB-27 established latent infections in banana, and Moko disease-causing phylotypes IIA-6, IIB-3, and IIB-4 were virulent to susceptible potato and tomato, addressing the question of host adaptation mechanisms, which may have undergone a similar bottleneck evolution. Cold-tolerance ability is only shared on species of Solanaceae among brown rot phylotype IIB-1, which gathered the majority of European and Mediterranean strains. We surveyed strain LNPV24.25 as the first report of an emerging phylotype IIB-4NPB strain in France. These findings showed that pathogenicity traits of genetically identified strains still need to be understood, especially in the perspective of post-genomics comparative analysis, to understand bacterial speciation in the R. solanacearum species complex.

A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization

Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato.

Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways

A novel set of Ralstonia solanacearum biovar 2 isolates was obtained, at several sampling occasions, from Dutch waterways, sediment and bittersweet plants and their genetic and phenotypic diversity was investigated. As reference strains, two previously-described strains obtained from diseased potato plants, denoted 1609 (The Netherlands) and 715 (Bangladesh), were included in the analyses. All novel isolates showed BOX and GTG5 PCR based genomic profiles similar to those of the reference strains. Also, PCR-restriction fragment length polymorphism analysis of the phcA and hrp genomic regions, as well as sequence analysis of six selected genomic loci, revealed great homogeneity across the strains. In contrast, pulsed field gel electrophoresis of restricted genomic DNA revealed the distribution of all strains across four groups, denoted pulsotypes A through D (pulsotypes C and D had one representative each). Moreover, pulsotype B, consisting of five strains, could be separated from the other pulsotypes by a divergent genomic fingerprint when hybridized to a probe specific for insertion element ISRso3. Representatives of pulsotypes A, B and C were selected for growth and metabolic studies. They showed similar growth rates when grown aerobically in liquid media. Assessment of their metabolic capacity using BIOLOG GN-2 revealed a reduced utilization of compounds as compared to the reference strains, with some variation between strains.

Specific and sensitive detection of Ralstonia solanacearum in soil with quantitative, real-time PCR assays

AIMS

The aim of this study was to develop a sensitive and an effective method suitable for large-scale detection and quantification of Ralstonia solanacearum in soil.

METHODS AND RESULTS

Based on the specific sequence of R. solanacearum strain G1000, the primer pair R.sol1-R.sol2 and the TaqMan probe Rs-pro were designed, and specific and sensitive PCR detection methods were successfully established. The detection limit was 100 fg microl(-1) DNA in conventional PCR and 1.2 fg microl(-1) in real-time PCR. By combining real-time PCR with the modified protocols to extract DNA from soil, it was possible to achieve real-time detection of R. solanacearum in soil, and the degree of sensitivity was 100 fg microl(-1). To detect inhibition in soil samples, an exogenous internal positive control (IPC) was included preventing false negative results, and IPC was successfully amplified from all samples tested. The methodology developed was used to detect the presence of R. solanacearum in tobacco fields in China.

CONCLUSIONS

The real-time PCR combined with the protocol to extract DNA from soil led to the development of a specific, sensitive and rapid detection method for R. solanacearum in soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The real-time PCR improves the detection sensitivity and specificity and provides an important tool for routine detection of R. solanacearum in soil samples and for epidemiological and ecological studies.

Integrated approach for detection of nonculturable cells of Ralstonia solanacearum in asymptomatic Pelargonium spp. cuttings

Ralstonia solanacearum (biovar 2, race 3) is a soil and water-borne pathogen that causes serious diseases in several solanaceous hosts. It can also infect geranium plants, posing an important threat to their culture when latently infected cuttings are imported from countries where the pathogen is endemic. R. solanacearum can be present in very low numbers in asymptomatic geranium cuttings, and/or in a particular stressed physiological state that escapes direct isolation on the solid media usually employed. Consequently, an integrated protocol has been developed to analyze asymptomatic geranium cuttings routinely. The first screening tests include isolation and co-operational-polymerase chain reaction (Co-PCR), based on the simultaneous and co-operational action of three primers from 16S rRNA of R. solanacearum. This method was selected as the most sensitive one, able to detect only 1 cell/ml including nonculturable cells. When isolation is negative but Co-PCR is positive, the bioassay in tomato plants is proposed, since stressed bacterial cells or those present in low numbers that do not grow on solid media can be recovered from inoculated tomato plants and retain pathogenicity. This methodology has been demonstrated to be useful and has allowed us to assess the relevance of the physiological status of bacterial cells and its implications in detection. It also reveals the risk of introducing R. solanacearum through asymptomatic geranium material when relying only on bacterial isolation.

The effects of the presence of stored product pests on the microfauna of a flour community

AIMS

To determine the effect that the presence of some beetles have on the species of bacteria found in their flour.

METHODS AND RESULTS

Bacteria were isolated from flour that either did not contain beetles, contained Tribolium beetles in different environments, or contained either Stegobium paniceum or Lasioderma serricorne. These bacteria were tentatively identified by both the gas chromatography-fatty acid methyl esters (GC-FAME) method and partial sequencing of the 16S rRNA gene. All samples contained Bacillus species including the controls, but the non-Tribolium beetles and a Tribolium beetle line known to have low benzoquinones also contained Enterococcus and Enterobacter species. Additionally an unidentified bacteria isolate in the Enterobacteriaceae was also found in the L. serricorne sample. Our results also suggest incongruent identifications when using the GC-FAME method vs sequencing.

CONCLUSIONS

Certain species of bacteria can be introduced by the presence of insect pests, but the diversity of species is far less in stocks of Tribolium beetles.

SIGNIFICANCE AND IMPACT OF THE STUDY

Stored product pests can alter the bacterial community. Isolated species from this study show a strong genetic relationship to each other, suggesting an isolated evolving system. A unique bacteria was also isolated. GC and sequencing methods of identification are compared.

In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus

Ralstonia solanacerum and Clavibacter michiganensis subsp. sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes in silico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about in silico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.

Specific and sensitive detection of Ralstonia solanacearum in soil on the basis of PCR amplification of fliC fragments

Ralstonia solanacearum is the causative agent of bacterial wilt in many important crops. A specific and sensitive PCR detection method that uses primers targeting the gene coding for the flagella subunit, fliC, was established. Based on the first fliC gene sequence of R. solanacearum strain K60 available at GenBank, the Ral_fliC PCR primer system was designed; this system yielded a single 724-bp product with the DNAs of all of the R. solanacearum strains tested. However, R. pickettii and four environmental Ralstonia isolates also yielded amplicons. The Ral_fliC PCR products obtained with 12 strains (R. solanacearum, R. pickettii, and environmental isolates) were sequenced. By sequence alignment, Rsol_fliC primers specific for R. solanacearum were designed. With this primer system, a specific 400-bp PCR product was obtained from all 82 strains of R. solanacearum tested. Six strains of R. pickettii and several closely related environmental isolates yielded no PCR product; however, a product was obtained with one Pseudomonas syzygii strain. A GC-clamped 400-bp fliC product could be separated in denaturing gradient gels and allowed us to distinguish P. syzygii from R. solanacearum. The Rsol_fliC PCR system was applied to detect R. solanacearum in soil. PCR amplification, followed by Southern blot hybridization, allowed us to detect about one target DNA molecule per PCR, which is equivalent to 10(3) CFU g of bulk soil(-1). The system was applied to survey soils from different geographic origins for the presence of R. solanacearum.