Assessment of the phenotypic and genotypic diversity of endophytic strains of Bacillus and closely related genera from Carpinus betulus in the Hyrcanian forests of Iran

BACKGROUND

Identification and characterization of the endophytic microorganism, is gaining their underestimated significance in influencing health, performance, and other biological attributions of plants in general and forest tree species in particular. Because of the scarcity of information on the endophytic microbiome of the Hyrcanian forests species, including hornbeam (Carpinus betulus L.) trees, as a major constituent thereof, the present study aimed at the identification and partial characterization of the endophytic Bacillus species of Carpinus betulus as the first step in this context.

METHODS AND RESULTS

Shoot samples were collected from the Hyrcanian forest locations of Mazandaran and Golestan provinces in Iran. Bacterial strains were isolated from the surface-disinfected shoot segments and subjected to phenotypic characterization. Following assessment of the genetic diversity of the isolates by BOX-PCR fingerprinting, the representative isolates of each of the 15 groups were used for further characterization. Analysis of the nucleotide sequences of the 16S rDNA and HSP60 gene of the isolates led to the identification of 10 species. The predominant species was B. cereus followed by B. subtilis. The other species encountered were B. thuringiensis, Priestia filamentosa, B. velezensis, B. mojavensis, B. amyloliquefaciens, B. safensis, P. aryabhattai, and Gottfriedia acidiceleris. Most isolates possessed characteristics which could contribute to the biocontrol potential of the isolates, including formation of biofilm, production of hydrogen cyanide, tolerant to relatively high concentration of sodium chloride, and antibacterial activity.

CONCLUSIONS

Ten Bacillus species were identified as the prevailing endophytic species of C. betulus in the Hyrcanian forest of northern Iran, most turned up to possess biological activities involved in biocontrol capability of the isolates against some plant pathogens. These potentially capable bacteria could be implemented in the promotion of plant growth as well as in the biological control of pathogens. This is the first report on the characterization and elucidation of the diversity of the potentially beneficial endophytic species of Bacillus and the closely related genera living in the internal tissues of hornbeam trees.

Efficacy of ergosterol peroxide obtained from the endophytic fungus Acrophialophora jodhpurensis against Rhizoctonia solani

AIM

To investigate antifungal activity of the extract and major metabolite of the endophytic fungus Acrophialophora jodhpurensis (belonging to Chaetomiaceae) against crown and root rot caused by Rhizoctonia solani (teleomorph: Thanatephorus cucumeris), as an important pathogen of tomato.

METHODS AND RESULTS

The endophytic fungus A. jodhpurensis, has high inhibitory effect against R. solani AG4-HG II in vitro and in vivo. The media conditions were optimized for production of the endophyte's metabolites. The highest amounts of secondary metabolites were produced at pH 7, 30°C temperature, and in the presence of 0.5% glucose, 0.033% sodium nitrate, and 1 gl-1 asparagine as the best carbon, nitrogen, and amino acid sources, respectively. The mycelia were extracted by methanol and the obtained extract was submitted to various chromatography techniques. Phytochemical analysis via thin-layer chromatography (TLC) and nuclear magnetic resonance (NMR) spectroscopy showed that ergosterol peroxide was the major component in the extract of this endophyte. Antifungal activities of the methanolic extract and ergosterol peroxide in the culture media were studied against R. solani. Minimum inhibitory concentrations of the extract and ergosterol peroxide against the pathogen were 600 and 150 µg ml-1, respectively. Ergosterol peroxide revealed destructive effects on the pathogen structures in microscopic analyses and induced sclerotia production. Histochemical analyses revealed that it induced apoptosis in the mycelia of R. solani via superoxide production and cell death. Application of ergosterol peroxide in the leaf disc assay reduced the disease severity in tomato leaves.

CONCLUSIONS

Antifungal metabolites produced by A. jodhpurensis, such as ergosterol peroxide, are capable of controlling destructive Rhizoctonia diseases on tomato.

Evaluating the Antivirulence Effects of New Thiazolidinedione Compounds Against Pseudomonas aeruginosa PAO1

Pseudomonas aeruginosa is an opportunistic pathogen that causes several serious health problems and numerous forms of virulence. During the treatment of P. aeruginosa infections, the development of multidrug-resistant isolates creates significant clinical problems. Using antivirulence compounds to disrupt pathogenicity rather than killing the bacterium may be an interesting strategy to overcome this problem, because less harsh conditions will exist for the development of resistance. To reduce pathogenicity and biofilm formation, newly synthesized analogs of imidazolyl (8n) and previously synthesized analogs (8a-8m) with a similar backbone [the 5-(imidazolyl-methyl) thiazolidinediones] were tested against pyoverdine and pyocyanin production, protease activity, and biofilm formation. Compared to the positive control group, the best compounds reduced the production of pyoverdine (8n) by 89.57% and pyocyanin (8i) by 22.68%, and protease activity (8n) by 2.80% for PAO1 strain, at a concentration of 10 μM. Moreover, the biofilm formation assay showed a reduction of 87.94% (8i) for PAO1, as well as 30.53% (8d) and 44.65% (8m) for 1074 and 1707 strains, respectively. The compounds used in this study did not show any toxicity in the human dermal fibroblasts and 4T1 cells (viability higher than 90%). The in silico study of these compounds revealed that their antivirulence activity could be due to their interaction with the PqsR, PqsE, and LasR receptors.

Acrophialophora jodhpurensis: an endophytic plant growth promoting fungus with biocontrol effect against Alternaria alternata

In this study, efficiency of the endophytic fungal isolate Msh5 was evaluated on promoting tomato plant growth and controlling Alternaria alternata, the causal agent of early blight in tomatoes. Morphological and molecular (ITS and tub2 sequences) analyses revealed that the fungal isolate, Msh5, was Acrophialophora jodhpurensis (Chaetomium jodhpurense Lodha). This beneficial fungus was capable of producing indole-3-acetic acid (IAA), urease, siderophore, extracellular enzymes, and solubilized phosphate. Under laboratory conditions, the Msh5 isolate of A. jodhpurensis inhibited A. alternata growth in dual culture, volatile and non-volatile metabolites assays. The supernatant of this endophytic fungus was capable of reducing spore germination and altering the hyphal structure of A. alternata and the spores produced germ tubes showed vacuolization and abnormal structure compared to the control. Also, the effect of A. jodhpurensis on plant growth parameters (such as shoot and root weight and length) and suppressing A. alternata was investigated in vivo via seed inoculation with spores of A. jodhpurensis using 1% sugar, 0.5% carboxymethyl cellulose (CMC) or 0.5% molasses solution as stickers. Colonization of tomato roots by the endophytic fungus resulted in significant increasing plant growth parameters and reduction in the progress of the diseases caused by A. alternata compared to the controls. Among the different coating materials used as stickers, sugar was found to be the most effective for enhancing plant growth parameters and decreasing the disease progress. Therefore, A. jodhpurensis isolate Msh5 can be suggested as a potential biofertilizer and biocontrol agent for protecting tomato plants against A. alternata.

The Arac-like transcriptional regulator YqhC is involved in pathogenicity of Erwinia amylovora

AIMS

This study aimed to identify virulence-associated genes and functions that affect disease development on pear caused by Erwinia amylovora EaUMG3 isolated from Iran.

METHODS AND RESULTS

A mini-Tn5 transposon library was generated in EaUMG3. An E. amylovora mutant that had lost its ability to cause lesions on immature pear fruits, was selected for further analysis. This mutant was shown to have a transposon insertion in yqhC, a gene belongs to the AraC family of transcriptional regulators. A mutant of the wild-type EaUMG3 carrying an unmarked deletion of the yqhC gene was created using pDMS197. The Ea∆yqhC mutant showed reduced disease progression on immature pear fruits and pear plants, reduced motility and significantly lower levels of the virulence factors siderophore and amylovoran. Complementation with yqhC cloned in pBBR1MCS restored disease progression and the level of virulence factors to near wild type.

CONCLUSION

YqhC transcriptional regulator is necessary for full virulence of E. amylovora. In addition, this regulator affects virulence factors such as siderophore production, amylovoran production, and motility.

SIGNIFICANCE AND IMPACT OF STUDY

The identification of a novel transcriptional regulator with strong impact in the pathogenesis of E. amylovora, an organism causing significant economic losses in fruit production.

Farnesol altered morphogenesis and induced oxidative burst-related responses in Rhizoctonia solani AG1-IA

Farnesol induces morphological changes characteristic of apoptosis in filamentous fungi. Growth-inhibitory effect and induced features of apoptosis on Rhizoctonia solani AG1-IA were observed in our study by addition of exogenous farnesol to the culture. The obtained results implied that farnesol triggered apoptosis-like features, such as production of reactive oxygen species (ROS), in R. solani AG1-IA and that there was increased superoxide dismutase (SOD) activity in the presence of farnesol, as well as decreased fungal biomass. Light microscopic analysis showed that farnesol disrupted the cytoplasm and deformed the hyphae of R. solani AG1-IA. The diameter of the hyphal cross-section in the fungus treated with farnesol decreased compared with control. Transmission electron microscopy (TEM) showed marked alternations in the cell wall, cell membrane, parenthesome, septum, and septal pore of the fungal cells. The findings of this work suggest that farnesol is deleterious to R. solani and has potential for use as an antifungal compound against this destructive phytopathogenic fungus.

The role of nitric oxide in basal and induced resistance in relation with hydrogen peroxide and antioxidant enzymes

Nitric oxide (NO) is one of the main signal molecules, which is involved in plant growth and development and can change regular physiological activity in biotic and abiotic stresses. In this study, the role of NO in induced resistance with Pseudomonas fluorescent (CHA0) and basal resistance against Rhizoctonia solani in bean plant was investigated. Our results revealed that P. fluorescent and R. solani can increase NO production at 6h post inoculation (hpi). Also, using the NO donor S-nitroso-N-acetyl D-penicillamine (SNAP) led to increase NO and bean plant resistance against R. solani. Utilizing the NO scavenger, 2-(4-carboxyphenyl)-4,4,5,5-tetramethy-limidazoline-1-oxyl-3-oxide (cPTIO), not only decreased basal resistance but also reduced induced resistance. In continue, the activity of antioxidant enzymes was studied in the former treatments. SNAP, CHA0 and R. solani increased the activity of peroxidase (POX), catalase (CAT) and ascorbate peroxidase (APX) at 6, 12 and 24h post inoculation (hpi). In contrast, using cPTIO and R. solani simultaneously (cPTIO+R) showed reduction in activity of POX and APX at 6 hpi. The cPTIO+R treatment increased POX, APX and CAT activity at 12 and 24 hpi. Hydrogen peroxide (H₂O₂) monitoring in the leaf discs clarified that SNAP can increase H₂O₂ production like CHA0 and R. solani. On the other hand, SNAP increased the resistance level of leaf discs against R. solani. Treating the leaf discs with cPTIO led to decrease resistance against the pathogen. These leaf discs showed reduction in H₂O₂ production at 6 hpi and suddenly enhanced H₂O₂ generation was observed at 24hpi. This study showed that CHA0 can increase NO level in bean plants. NO induced H₂O₂ generation and regulated redox state of the host plant. This interaction resulted in significant defense against the pathogen.

CitB is required for full virulence of Xanthomonas oryzae pv. oryzae

To identify novel virulence associated genes in Xanthomonas oryzae pv. oryzae (Xoo), a Xoo isolate (XooIR42), obtained from north of Iran, was selected to generate a mini-Tn5 transposon mutation library. One mutant (XooM176) that indicated reduced virulence on rice plants, while grew similar to wild type was selected. This mutant had an insertion in a coding region with 96% amino acid identity to a response regulator of Xoo KACC10331, citB (Xoo_RS12710). Genome analysis of Xoo KACC10331 indicated several genes including a flagelin protein (FlgL) and a chemotaxis protein (Xoo_RS12720) which were identified as virulence genes 4297 and 1403 nucleotides from the citB, respectively. The swarming motility, resistance to hydrogen peroxide, induced a hypersensitive response, in planta growth and pathogenicity were reduced in XooM176 mutant compared to that of wild-type. A plasmid containing the full citB gene of Xoo KACC10331was sufficient to complement the XooM176 mutant for lesion formation and resistance to hydrogen peroxide. We therefore propose that Xoo requires CitB for full pathogenicity in rice plants and also for protection against oxidative stress.

Genetic and Virulence Analysis of Rhizoctonia spp. Associated with Sugar Beet Root and Crown Rot in the Northeast Region of Iran

Rhizoctonia spp. are the main causal agents of root and crown rot on sugar beet. In this study, isolates of Rhizoctonia spp. were obtained from diseased sugar beet in Iran over 2 years. Of 68 isolates, 61 were R. solani and 7 were R. cerealis. The anastomosis group (AG) of all isolates was determined on glass slides against the testers. Characterization of intraspecific groups (ISGs) of R. solani isolates revealed that, of 61 isolates, 43 were AG2-2 IIIB and 18 were AG2-2 IV. Amplified fragment length polymorphism (AFLP) analyses were used to investigate genetic structure of Rhizoctonia populations. Principal coordinate plots and cluster analysis differentiated R. solani from R. cerealis isolates and separated the R. solani isolates belonging to different ISGs. AFLP data indicated that the R. solani and R. cerealis populations are not clonal. Analysis of molecular variance in AG2-2 IIIB isolates showed that geographic region was the main factor determining genetic structure of the populations. Sampling year had no significant effect on the genotypes. Pathogenicity tests on Beta vulgaris 'FD0432' revealed that R. solani AG2-2 IIIB and AG2-2 IV isolates were more virulent than R. cerealis.

Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa

BACKGROUND

Small colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch.

METHODOLOGY/PRINCIPAL FINDINGS

One SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10(-5) on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS). Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM), the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAO-SCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexAB-oprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels.

CONCLUSIONS

By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the Pseudomonas quinolone signal quorum sensing system.

New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution

Peach latent mosaic viroid isolates from peach and plum in Iran have been compared with an Australian isolate from nectarine. Thirteen sequence variants 336-338 nt in size were obtained. All variants clustered phylogenetically with variants reported from several hosts and countries. A total nucleic acid extract, a slightly longer than full-length RT-PCR amplicon, and a recombinant plasmid clone from the Australian isolate were all infectious to, and symptomatic in, mechanically inoculated peach seedlings. The infectious clone generated two progeny viroid molecules, which each showed 10 different mutations compared with the parent clone inoculated 30 days previously.

A survey on basal resistance and riboflavin-induced defense responses of sugar beet against Rhizoctonia solani

We examined basal defense responses and cytomolecular aspects of riboflavin-induced resistance (IR) in sugar beet-Rhizoctonia solani pathsystem by investigating H(2)O(2) burst, phenolics accumulation and analyzing the expression of phenylalanine ammonia-lyase (PAL) and peroxidase (cprx1) genes. Riboflavin was capable of priming plant defense responses via timely induction of H(2)O(2) production and phenolics accumulation. A correlation was found between induction of resistance by riboflavin and upregulation of PAL and cprx1 which are involved in phenylpropanoid signaling and phenolics metabolism. Application of peroxidase and PAL inhibitors suppressed not only basal resistance, but also riboflavin-IR of sugar beet to the pathogen. Treatment of the leaves with each inhibitor alone or together with riboflavin reduced phenolics accumulation which was correlated with higher level of disease progress. Together, these results demonstrate the indispensability of rapid H(2)O(2) accumulation, phenylpropanoid pathway and phenolics metabolism in basal defense and riboflavin-IR of sugar beet against R. solani.

Riboflavin induces resistance in rice against Rhizoctonia solani via jasmonate-mediated priming of phenylpropanoid pathway

Vitamins are plant growth regulators and activators of defense responses against pathogens. The cytomolecular mechanisms involved in the induction of resistance by chemicals especially vitamins on monocotyledonous plants are largely unknown. Here, we show that riboflavin, which acts as a defense activator in rice against economically important sheath blight caused by Rhizoctonia solani, primed the expression of lipoxygenase (LOX) as a key gene in octadecanoid pathway, and enhanced lignification. Exogenous jasmonic acid (JA) application on rice induces resistance against R. solani in a manner similar to riboflavin. Application of jasmonate-deficient rice mutant hebiba and using a LOX inhibitor revealed the main role of octadecanoid pathway in riboflavin-induced resistance (IR). In riboflavin-treated inoculated plants, upregulation of phenylalanine ammonia-lyase (PAL) expression, as a major marker of phenylpropanoid pathway, was detected downstream of LOX upregulation. Co-application of riboflavin and 5, 8, 11, 14-eicosatetraynoic acid (ETYA) on rice leaves revealed no upregulation of PAL and no priming in lignification. Furthermore, lower levels of PAL transcripts and lignin were detected in hebiba compared with control. These findings indicate the role of octadecanoid pathway in the induction of phenylpropanoid metabolism leading to lignification as a novel mechanism of riboflavin-IR in Oryza sativa-R. solani pathosystem.

The PA4204 gene encodes a periplasmic gluconolactonase (PpgL) which is important for fitness of Pseudomonas aeruginosa

In Pseudomonas aeruginosa, the PA4204 gene encodes a protein with a signal peptide and a COG2706 domain of the type present in 3-carboxy-cis,cis-muconate lactonizing enzymes. A molecular model based on the structure of the Escherichia coli YbhE phosphogluconate lactonizing enzyme shows that the enzyme has a beta-propeller ('doughnut') structure and a central active site comprising one histidine, one glutamic acid and two arginines. Inactivation of the P. aeruginosa PA4204 gene had profound phenotypic effects, resulting in slowly growing small colonies which frequently gave rise to larger colonies. The small colonies did not produce pyocyanin, produced reduced amounts of N-acylhomoserine lactones, and had extremely low levels of 2-alkyl-4-quinolones (AQs), while the larger colonies produced pyocyanin and higher amounts of AQs, including the pseudomonas quinolone signal (PQS), compared with the wild-type strain. Mutagenesis of His 182 in PA4204 resulted in the inability of this protein to restore pyocyanin production in the PA4204 isogenic mutant, suggesting that this enzyme may share an active site with other lactonizing enzymes. The protein with signal peptide was expressed as a His fusion in E. coli and purified. Two forms were observed, suggesting that the protein is translocated. The purified enzyme cleaved (S)-5-oxo-2-tetrahydrofurancarboxylic acid and d-glucono-delta-lactone, demonstrating lactonase activity. Decreased expression of the cytoplasmic phosphogluconolactonase gene (pgl) was observed in the small-colony mutant, and the mutant could not grow in the presence of mannitol or gluconate, suggesting functions in the detoxification of a gluconolactone and in sugar metabolism.