Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields.

Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.

Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806T Isolated from Soil Polluted by Crude Oil in China.

Here, we report the draft genome sequence of Tepidibacter mesophilus strain JCM 16806T, which was isolated from an oil field. It is composed of 3,310,272 bp and contains 3,160 protein-coding genes, 8 5S rRNAs, 3 16S rRNAs, and 69 tRNAs.

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse.

The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA. A difference in prokaryotic community structures between soil samples with and without bacterial wilt was only observed in the upper soil layer despite apparent similarities in the communities at the phylum level. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and several Archaea were more abundant in soil samples without disease symptoms, whereas taxa in another eight phyla were more abundant in soil samples with disease symptoms. Furthermore, some prokaryotic taxa were abundant specifically in the lower layer of soil, regardless of whether disease was present. These prokaryotic taxa may suppress or accelerate the pathogenesis of bacterial wilt and are good targets for future studies on disease control.

l-Histidine Induces Resistance in Plants to the Bacterial Pathogen Ralstonia solanacearum Partially Through the Activation of Ethylene Signaling.

Wilt disease in plants, which is caused by the soil-borne bacterial pathogen Ralstonia solanacearum, is one of the most devastating plant diseases. We previously detected bacterial wilt disease-inhibiting activity in an extract from yeast cells. In the present study, we purified this activity and identified one of the substances responsible for the activity as the amino acid histidine. The exogenous application of l-histidine, but not d-histidine, inhibited wilt disease in tomato and Arabidopsis plants without exhibiting any antibacterial activity. l-Histidine induced the expression of genes related to ethylene (ET) biosynthesis and signaling as well as the production of ET in tomato and Arabidopsis plants. l-Histidine-induced resistance to R. solanacearum was partially abolished in ein3-1, an ET-insensitive Arabidopsis mutant line. Resistance to the fungal pathogen Botrytis cinerea, which is known to require ET biosynthesis or signaling, was also induced by exogenously applied l-histidine. These results suggest that l-histidine induces resistance to R. solanacearum and B. cinerea partially through the activation of ET signaling in plants.

Sensitive quantitative detection of Ralstonia solanacearum in soil by the most probable number-polymerase chain reaction (MPN-PCR) method.

We developed a sensitive quantitative assay for detecting Ralstonia solanacearum in soil by most probable number (MPN) analysis based on bio-PCR results. For development of the detection method, we optimized an elution buffer containing 5 g/L skim milk for extracting bacteria from soil and reducing contamination of polymerase inhibitors in soil extracts. Because R. solanacearum can grow in water without any added nutrients, we used a cultivation buffer in the culture step of the bio-PCR that contained only the buffer and antibiotics to suppress the growth of other soil microorganisms. To quantify the bacterial population in soil, the elution buffer was added to 10 g soil on a dry weight basis so that the combined weight of buffer, soil, and soil-water was 50 g; 5 mL of soil extract was assumed to originate from 1 g of soil. The soil extract was divided into triplicate aliquots each of 5 mL and 500, 50, and 5 µL. Each aliquot was diluted with the cultivation buffer and incubated at 35 °C for about 24 h. After incubation, 5 µL of culture was directly used for nested PCR. The number of aliquots showing positive results was collectively checked against the MPN table. The method could quantify bacterial populations in soil down to 3 cfu/10 g dried soil and was successfully applied to several types of soil. We applied the method for the quantitative detection of R. solanacearum in horticultural soils, which could quantitatively detect small populations (9.3 cfu/g), but the semiselective media were not able to detect the bacteria.

Transcriptional profile of tomato roots exhibiting Bacillus thuringiensis-induced resistance to Ralstonia solanacearum.

KEY MESSAGE: Activation of SA-dependent signaling pathway and suppression of JA-dependent signaling pathway seem to play key roles inB. thuringiensis-induced resistance toR. solanacearumin tomato plants. Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with a filter-sterilized cell-free filtrate (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1(P6) gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with CF on their roots suggested that the B. thuringiensis-induced defense system was activated in the leaf, stem, and main root tissues, but not in the lateral root tissue. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main roots but not in the CF-treated lateral roots. This distinct activation of the defense reaction and suppression of R. solanacearum were reflected by the differences in the transcriptional profiles of the main and lateral tissues in response to the CF. In CF-treated main roots, but not CF-treated lateral roots, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related gene expression was either down-regulated or not induced in response to the CF. On the other hand, genes encoding ethylene (ET)-related proteins were induced equally in both the main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play key roles in B. thuringiensis-induced resistance to R. solanacearum in tomato.

Transcriptome analysis of quantitative resistance-specific response upon Ralstonia solanacearum infection in tomato.

Bacterial wilt, caused by the soil-borne bacterium Ralstonia solanacearum, is a lethal disease of tomato, but the molecular mechanisms of the host resistance responses to R. solanacearum remain unclear. In this study, we report the first work describing the transcriptome of cultivar resistance and susceptible tomato cultivar after inoculation with R. solanacearum. To elucidate the characteristics of resistance early in the interaction, we analyzed microarrays for resistant cultivar LS-89 and susceptible cultivar Ponderosa 1 day after stem inoculation. No change in gene expression was detected for Ponderosa, but expression levels of over 140 genes, including pathogenesis-related, hormone signaling and lignin biosynthesis genes, increased in LS-89. Expression of ß-1,3-glucanase genes increased substantially. In an immunohistochemical study, glucanase in LS-89 accumulated in the xylem and pith tissues surrounding xylem vessels filled with R. solanacearum. The expression of these genes also increased in four other resistant cultivars, but changed little in four susceptible cultivars in response to R. solanacearum, suggesting that similar reactions occur in other cultivars. These gene expression profiles will serve as fundamental information to elucidate the molecular mechanisms in the resistance response to R. solanacearum in tomato.

Identification of natural diterpenes that inhibit bacterial wilt disease in tobacco, tomato and Arabidopsis.

The soil-borne bacterial pathogen Ralstonia solanacearum invades a broad range of plants through their roots, resulting in wilting of the plant, but no effective protection against this disease has been developed. Two bacterial wilt disease-inhibiting compounds were biochemically isolated from tobacco and identified as sclareol and cis-abienol, labdane-type diterpenes. When exogenously applied to their roots, sclareol and cis-abienol inhibited wilt disease in tobacco, tomato and Arabidopsis plants without exhibiting any antibacterial activity. Microarray analysis identified many sclareol-responsive genes in Arabidopsis roots, including genes encoding or with a role in ATP-binding cassette (ABC) transporters, and biosynthesis and signaling of defense-related molecules and mitogen-activated protein kinase (MAPK) cascade components. Inhibition of wilt disease by sclareol was attenuated in Arabidopsis mutants defective in the ABC transporter AtPDR12, the MAPK MPK3, and ethylene and abscisic acid signaling pathways, and also in transgenic tobacco plants with reduced expression of NtPDR1, a tobacco homolog of AtPDR12. These results suggest that multiple host factors are involved in the inhibition of bacterial wilt disease by sclareol-related compounds.

Enhanced defense responses in Arabidopsis induced by the cell wall protein fractions from Pythium oligandrum require SGT1, RAR1, NPR1 and JAR1.

The cell wall protein fraction (CWP) is purified from the non-pathogenic biocontrol agent Pythium oligandrum and is composed of two glycoproteins (POD-1 and POD-2), which are structurally similar to class III elicitins. In tomato plants treated with CWP, jasmonic acid (JA)- and ethylene (ET)-dependent signaling pathways are activated, and resistance to Ralstonia solanaceraum is enhanced. To dissect CWP-induced defense mechanisms, we investigated defense gene expression and resistance to bacterial pathogens in Arabidopsis thaliana ecotype Col-0 treated with CWP. When the leaves of Col-0 were infiltrated with CWP, neither visible necrosis nor salicylic acid (SA)-responsive gene (PR-1 and PR-5) expression was induced. In contrast, JA-responsive gene (PDF1.2 and JR2) expression was up-regulated and the resistance to R. solanaceraum and Pseudomonas syringae pv. tomato DC3000 was enhanced in response to CWP. Such CWP-induced defense responses were completely compromised in CWP-treated coi1-1 and jar1-1 mutants with an impaired JA signaling pathway. The induction of defense-related gene expression after CWP treatment was partially compromised in ET-insensitive ein2-1 mutants, but not in SA signaling mutants or nahG transgenic plants. Global gene expression analysis using cDNA array also suggested that several other JA- and ET-responsive genes, but not SA-responsive genes, were up-regulated in response to CWP. Further analysis of CWP-induced defense responses using another eight mutants with impaired defense signaling pathways indicated that, interestingly, the induction of JA-responsive gene expression and enhanced resistance to two bacterial pathogens in response to CWP were completely compromised in rar1-1, rar1-21, sgt1a-1, sgt1b (edm1) and npr1-1 mutants. Thus, the CWP-induced defense system appears to be regulated by JA-mediated and SGT1-, RAR1- and NPR1-dependent signaling pathways.

Colonization of Pythium oligandrum in the tomato rhizosphere for biological control of bacterial wilt disease analyzed by real-time PCR and confocal laser-scanning microscopy.

It recently has been reported that the non-plant-pathogenic oomycete Pythium oligandrum suppresses bacterial wilt caused by Ralstonia solanacearum in tomato. As one approach to determine disease-suppressive mechanisms of action, we analyzed the colonization of P. oligandrum in rhizospheres of tomato using real-time polymerase chain reaction (PCR) and confocal laser-scanning microscopy. The real-time PCR specifically quantified P. oligandrum in the tomato rhizosphere that is reliable over a range of 0.1 pg to 1 ng of P. oligandrum DNA from 25 mg dry weight of soil. Rhizosphere populations of P. oligandrum from tomato grown for 3 weeks in both unsterilized and sterilized field soils similarly increased with the initial application of at least 5 x 10(5) oospores per plant. Confocal microscopic observation also showed that hyphal development was frequent on the root surface and some hyphae penetrated into root epidermis. However, rhizosphere population dynamics after transplanting into sterilized soil showed that the P. oligandrum population decreased with time after transplanting, particularly at the root tips, indicating that this biocontrol fungus is rhizosphere competent but does not actively spread along roots. Protection over the long term from root-infecting pathogens does not seem to involve direct competition. However, sparse rhizosphere colonization of P. oligandrum reduced the bacterial wilt as well as more extensive colonization, which did not reduce the rhizosphere population of R. solanacearum. These results suggest that competition for infection sites and nutrients in rhizosphere is not the primary biocontrol mechanism of bacterial wilt by P. oligandrum.

Mutations in the lrpE gene of Ralstonia solanacearum affects Hrp pili production and virulence.

The Ralstonia solanacearum hrpB-regulated gene lrpE (hpx5/brg24) encodes a PopC-like leucine-rich repeat (LRR) protein that carries 11 tandem LRR in the central region. Defects in the lrpE gene slightly reduced the virulence of R. solanacearum on host plants and changed the bacterial morphology leading to the formation of large aggregates in a minimal medium. The aggregation in the deltalrpE background required the presence of a functional Hrp type III secretion system. In wild-type R. solanacearum, Hrp pili disappeared from the bacterial surface at the end of the exponential growth phase, when the pili form into long bundles. However, even in the late growth phase, bundled Hrp pili were still observed on the cell surface of the deltalrpE mutant. Such bundles were entangled and anchored the mutant cells in the aggregates. In contrast to PopC, LrpE accumulated in bacterial cells and did not translocate into plant cells as an effector protein. The expression levels of hrp genes increased three- to fivefold in the deltalrpE background compared with those in the wild type. We propose that LrpE may negatively regulate the production of Hrp pili on the cell surface of R. solanacearum to disperse bacterial cells from aggregates. In turn, dispersal may contribute to the movement of the pathogen in the plant vascular system and, as a consequence, the pathogenicity of R. solanacearum.

Beta-cyanoalanine synthase as a molecular marker for induced resistance by fungal glycoprotein elicitor and commercial plant activators.

ABSTRACT The biocontrol agent Pythium oligandrum produces glycoprotein elicitor in the cell wall fraction, designated CWP, and induces resistance to a broad range of pathogens. To understand the mechanism of CWP-induced resistance to pathogens, gene expression at the early stage of CWP treatment in tomato roots was analyzed using a cDNA array. At 4 h after CWP treatment, 144 genes were up-regulated and 99 genes were down-regulated. In the 144 up-regulated genes, nine genes exhibited about eightfold increased expression. Analysis of the response of these nine genes to three commercial plant activators indicated that a high level of one gene, beta-cyanoalanine synthase gene (LeCAS) encoding hydrogen cyanide (HCN) detoxification enzyme, was stably induced in tomato roots by such treatment. However, expression of LeCAS was not significantly induced in tomato roots at 4 h by abiotic stresses, whereas only a very low level of induction of such expression by cold stress was observed. This LeCAS expression was also induced after exogenous treatment with a low level of 1-amino-cyclopropane-1-carboxylate as the precursor of ethylene, but not with either salicylic acid or methyl jas-monate. The induction of LeCAS expression in CWP-treated and plant activator-treated roots is likely to be caused by the detoxification of HCN during ethylene production. Transient activation of LeCAS expression caused by ethylene production in tomato roots may be a general phenomenon in fungal elicitor-induced and synthetic plant activator-induced resistance. LeCAS seems to be useful for screening possible novel plant activators for plant protection against pathogens.

Ralstonia solanacearum Race 3, Biovar 2 Strains Isolated from Geranium Are Pathogenic on Potato.

Ralstonia solanacearum race 3, biovar 2 is a soilborne bacterium that causes potato brown rot disease in temperate and subtropical climates. Recent outbreaks of this disease in Europe have caused serious losses, but the pathogen had not been identified in the United States. However, in 1999, strains of R. solanacearum were isolated from wilting geraniums growing in Wisconsin greenhouses. Physiological and biochemical tests of the Wisconsin strains and a similar strain from South Dakota demonstrated that the strains belong to R. solanacearum subgroup biovar 2, which is largely synonymous with the race 3 subgroup, a classification based on host range. These results were confirmed by polymerase chain reaction analyses in which race 3, biovar 2-specific primers amplified a fragment of the expected size. This is the first report of race 3, biovar 2 in the United States, and it is the first known occurrence of race 3, biovar 2 in Wiscon-sin. The geranium strains were highly pathogenic on both geranium and potato. The presence of R. solanacearum race 3, biovar 2 in the United States raises concern that the bacterium could move from ornamental plants into potato fields, where it could cause both direct economic damage and quarantine problems. A commercial indirect enzyme-linked immunosorbent assay for R. solanacearum produced some false negatives for these strains, indicating that current indexing may not be sufficient to identify this destructive pathogen.