Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Background

Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains.

Results

These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences.

Conclusions

This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1474-8) contains supplementary material, which is available to authorized users.     

Isolation of Endophytic Actinomycetes from Different Cultivars of Tomato and their Activities Against Ralstonia solanacearum in Vitro

The populations of endophytic actinomycetes from healthy and wilting tomato plants (tomato cultivars resistant and susceptible to Ralstonia solanacearum) grown in three different sites from Guangzhou, Guangdong Province, South China were investigated by cultivation methods. Most of the isolates belonged to streptomycetes. The Aureus group of Streptomyces was the most frequently isolated group. The population composition of Streptomyces varied according to tomato cultivars, physiological status and soil types. The proportions of antagonistic Streptomyces strains from healthy plants were higher than that from wilting plants (P < 0.05), although the difference among the proportions of antagonistic Streptomyces strains from different cultivars of healthy tomato was not significant, the similar result was found from wilting plants. No significant difference was found in the proportions of siderophere-producing Streptomyces strains from the same site (P > 0.05), but the difference was found from the different sampling sites (P < 0.05). The percentage of bacterial cell wall-degrading streptomycetes from wilting tomato was higher than that from healthy plants (P < 0.05). These results indicated that the cultivar of the host plant, physiological status and sampling sites would influence the proportion of endophytic streptomycetes with different physiological traits. Diversity of endophytic Streptomyces and their physiological diversity should be involved in developing potential biocontrol agents.     

Heat shock,with recovery,promotes protection of Nicotiana tabacum during subsequent exposure to Ralstonia solanacearum

Host–pathogen interactions in plants are complex and potentially influenced by heat shock/stress (HS). Host HS proteins (HSPs) induced prior to bacterial exposure may facilitate the folding of newly synthesized defense proteins and promote incompatible host–pathogen interactions. We hypothesized that a non-lethal HS, with recovery, promotes protection of Nicotiana tabacum during subsequent exposure to avirulent soilborne necrotrophic pathogen Ralstonia solanacearum. The objective of this study included investigating the effects of HS with or without recovery on the outcome of bacterial exposure to a virulent and avirulent biovar of R. solanacearum in N. tabacum cell suspensions. This was assessed by quantifying host Hsp70/Hsc70 levels, mitochondrial electron (e⁻) transport activity as a marker of viability, and phosphatidylserine externalization and DNA fragmentation as markers of apoptosis. Our findings support the hypothesis that HS, with recovery, promotes protection of N. tabacum during subsequent exposure to R. solanacearum, suggesting a role for Hsp70/Hsc70 in the observed protection of e⁻ transport, increased apoptosis, and DNA fragmentation.     

Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum

Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease.     

Fertile Solanum tuberosum+S. commersonii somatic hybrids as sources of resistance to bacterial wilt caused by Ralstonia solanacearum

 The wild potato relative Solanum commersonii is reported to carry resistance to bacterial wilt disease caused by Ralstonia solanacearum. To overcome sexual incompatibilites due to differences in ploidy and endosperm balance numbers, somatic hybrids were made that combine the S. tuberosum and S. commersonii genomes. The resulting somatic hybrid plants are vigorous, but their disease resistance level and their fertility was unknown. We therefore tested the S. commersonii and S. tuberosum source material cv Superior, potato cv Atlantic and six somatic hybrid lines for resistance to a virulent strain of R. solanacearum (race 3, biovar 2) at 28°C. As expected, S. commersonii was significantly more wilt-resistant than the cultivated potatoes. In five of the six somatic hybrid lines, disease resistance levels were similar to that of the resistant S. commersonii parent. The resistance level of the sixth somatic hybrid was intermediate, significantly different from both S. commersonii and S. tuberosum. In controlled crosses, the somatic hybrids in this study proved both to be male- and female-fertile and were self-compatible. More importantly, the somatic hybrids can be crossed with S. tuberosum to produce viable seeds. Received: 23 June 1998 / Accepted: 13 October 1998     

Genetic Analysis of Resistance to Meloidogyne chitwoodi Introgressed from Solanum hougasii into Cultivated Potato

An accession of Solanum hougasii, a wild tuber-bearing potato species native to Mexico, was found to be resistant to races 1 and 2 of Meloidogyne chitwoodi. A resistant selection was selfed and its progeny possessed the same combined resistance uniformly. A selected resistant seedling from the selfed progeny was crossed to cultivated tetraploid potato (S. tuberosum) to form an F₁ hybrid, and was backcrossed to cultivated tetraploid potato to form a BC₁ population in which resistance to the two races segregated. Progeny of the BC₁ were tested in inoculation experiments with four replicates for each progeny genotype for each race of nematode. Resistance was evaluated on the basis of extracted egg counts from the entire root system of pot-grown plants. Considering resistance to each race separately, for race 1, non-host (Rf ≤ 0.1) status was exhibited by approximately half of the BC₁. About one-third of the progeny showed non-host status to race 2. Egg production among progeny that showed non-host status for both races was higher with race 2 than with race 1. Analysis of co-segregation established that genetic control for the two races appears to be independently segregating. Although genes for resistance to race 1 derived from S. bulbocastanum and S. fendleri were previously described, this report is the first analysis showing independent genetic control in Solanum spp. for resistance to race 2 of M. chitwoodi only.     

Characterization of Resistance in a Somatic Hybrid of Solanum bulbocastanum and S. tuberosum,to Meloidogyne chitwoodi

A somatic hybrid, CBP-233, between resistant Solanum bulbocastanum (SB-22) and susceptible S. tuberosum (R4) was tested for resistance to Meloidogyne chitwoodi race 1. One week after inoculation, only 0.04-0.4% of the initial inoculum (Pi, 5,000 eggs) as second stage-juveniles infected SB-22 and CBP-233 root systems, compared to 2% in R4. After 8 weeks, the number of M. chitwoodi in SB-22 and CBP-233 roots remained lower (0.3-1.5% of Pi) compared to R4, which increased from 2% to ca. 27%. Development of M. chitwoodi was delayed on SB-22 and CBP-233 by at least 2 weeks, and only half of the infective nematodes established feeding sites and matured in resistant clones compared to 99% in susceptible R4. Necrotic tissue surrounded nematodes that failed to develop in SB-22 and CBP-233. The reproductive factor (ratio of final number of eggs recovered from roots to Pi) was <0.01 for both SB-22 and CBP-233 and 46.8 for R4. Delaying inoculation of CBP-233 from 1 to 3 months after planting did not increase the chance or rate of tuber infection. Only a few M. chitwoodi developed to maturity on CBP-233 tubers and deposited a small number of eggs. SB-22 rarely produced tubers in these experiments, and like CBP-233 were resistant to M. chitwoodi. It appeared that the mechanisms of resistance to M. chitwoodi in roots and tubers of CBP-233 are similar.     

Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

Background and Aims

Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations.

Methods

Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers.

Key Results

As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions.

Conclusions

This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts.     

Control of Globodera tabacum solanacearum by Alternating Host Resistance and Nematicide

The feasibility of alternating use of resistant vs. susceptible flue-cured tobacco cultivars to improve control of Globodera tabacum subsp, solanacearum (TCN) was investigated at two Virginia locations in 1984-86. Post-harvest TCN population densities were reduced in each year of the study when fenamiphos was used with a TCN-resistant cultivar (NC 567), relative to susceptible cultivars (K 326 or Mc 944). Using NC 567 with fenamipbos also reduced preplant TCN population densities in the next growing season. Egg population densities before planting in 1986 were significantly lower in plots planted with NC 567 in 1984, even when a susceptible cultivar had been planted in 1985. Use of fenamiphos with NC 567 in 1984 and 1985 further reduced preplant egg population densities in 1986. Economic returns were significantly greater in 1984 when NC 567 was used with fenamiphos, rather than a susceptible cultivar. Treatments involving fenamiphos and (or) NC 567 in 1984 and 1985 resulted in higher economic returns in 1986 than did treatments using a susceptible cultivar without fenamiphos in both previous years. Economic returns were highest in 1986 when fenamiphos and NC 567 were used in 1984 and 1985 and a susceptible cultivar was planted in 1986.     

Understanding Reaction of Potato (Solanum tuberosum) to Ralstonia solanacearum and Relationship of Wilt Incidence to Latent Infection

Bacterial wilt caused by Ralstonia solanacearum is one of the most important diseases affecting more than 200 plant species, including solanaceous crops. The pathogen is known to cause complicated symptoms ranging from visible to latent ones. Understanding crop's reaction to the pathogen and the underlying relatedness of latent infection to wilt incidence is of paramount importance. Thus, a number of potato cultivars including improved and otherwise were evaluated under greenhouse and field conditions. Accordingly, twenty‐eight of the cultivars tested under greenhouse conditions were resistant to the pathogen with scores ranging from 0.77 to 1.17 of 5. Nonetheless, under field conditions, only 2 of 28 cultivars found to be ‘resistant’ under greenhouse conditions, showed adequate resistance to the pathogen, indicating the significant impact of environment on the activity of the pathogen and reaction of the crop. Percentage wilt incidence and latent infection showed significant (P < 0.05) positive correlation, with r = 0.9438. Thus, evaluation of crop's performance based on the combination of the parameters like field wilt incidence and proportion of latent infection gave us better picture of the overall crop feat, than using wilt incidence as a sole parameter of evaluation as has been the case in most studies. Moreover, the established correlation of latent infection with field wilt incidence will also help us understand the disease epidemiology and design effective management measures, accordingly.     

Enhanced Hatching of Globodera tabacum solanacearum Juveniles by Root Exudates of Flue-cured Tobacco

Stimulation of hatching of a tobacco cyst nematode (Globodera tabacum solanacearum) by root exudates from resistant NC 567 and susceptible K 326 cultivars of flue-cured tobacco, Nicotiana tabacum, was investigated. Root exudates were collected by soaking seedlings in deionized water for 2 hours at 22 °C in the dark. Fifteen mature and uniformly sized cysts were exposed at 15, 20, or 25 °C to undiluted root exudate, root exudate diluted 1:1 or 1:3 with deionized water, or deionized water alone. Hatched juveniles were counted and removed at weekly intervals during 42 and 53 days of exposure in experiments conducted in 1994 and 1995, respectively. Root exudates from both susceptible cultivar K 326 and resistant cultivar NC 567 stimulated more hatching than deionized water at 25 °C in 1994, and at all three tested temperatures in 1995. In 1994, dilution of root exudates 1:3 reduced stimulation of hatching at 25 °C compared to undiluted exudate. Hatching at 25 °C was similarly stimulated by exposure to undiluted root exudate and exudate diluted 1:1. In 1995, both dilutions reduced stimulation of hatching by root exudates at all the temperatures.