Jonathan Gerbore

Pythium oligandrum: an example of opportunistic success.

Pythium oligandrum, a non-pathogenic soil-inhabiting oomycete, colonizes the root ecosystem of many crop species. Whereas most members in the genus Pythium are plant pathogens, P. oligandrum distinguishes itself from the pathogenic species by its ability to protect plants from biotic stresses in addition to promoting plant growth. The success of P. oligandrum at controlling soilborne pathogens is partly associated with direct antagonism mediated by mycoparasitism and antimicrobial compounds. Interestingly, P. oligandrum has evolved with specific mechanisms to attack its prey even when these belong to closely related species. Of particular relevance is the question of how P. oligandrum distinguishes between self- and non-self cell wall degradation during the mycoparasitic process of pathogenic oomycete species. The ability of P. oligandrum to enter and colonize the root system before rapidly degenerating is one of the most striking features that differentiate it from all other known biocontrol fungal agents. In spite of this atypical behaviour, P. oligandrum sensitizes the plant to defend itself through the production of at least two types of microbe-associated molecular patterns, including oligandrin and cell wall protein fractions, which appear to be closely involved in the early events preceding activation of the jasmonic acid- and ethylene-dependent signalling pathways and subsequent localized and systemic induced resistance. The aim of this review is to highlight the expanding knowledge of the mechanisms by which P. oligandrum provides beneficial effects to plants and to explore the potential use of this oomycete or its metabolites as new disease management strategies.

Analyses of the Temporal Dynamics of Fungal Communities Colonizing the Healthy Wood Tissues of Esca Leaf-Symptomatic and Asymptomatic Vines

Esca, a Grapevine Trunk Disease (GTD), is of major concern for viticulture worldwide. Our study compares the fungal communities that inhabit the wood tissues of vines that expressed or not foliar esca-symptoms. The trunk and rootstock tissues were apparently healthy, whether the 10 year-old plants were symptomatic or not. The only difference was in the cordon, which contained white rot, a typical form of esca, in 79% of symptomatic plants. Observations over a period of one year using a fingerprint method, Single Strand Conformation Polymorphism (SSCP), and the ITS-DNA sequencing of cultivable fungi, showed that shifts occurred in the fungal communities colonizing the healthy wood tissues. However, whatever the sampling time, spring, summer, autumn or winter, the fungi colonizing the healthy tissues of asymptomatic or symptomatic plants were not significantly different. Forty-eight genera were isolated, with species of Hypocreaceae and Botryosphaeriaceae being the most abundant species. Diverse fungal assemblages, made up of potentially plant-pathogenic and -protective fungi, colonized these non-necrotic tissues. Some fungi, possibly involved in GTD, inhabited the non-necrotic wood of young plants, but no increase in necrosis areas was observed over the one-year period.

Draft Genome Sequence of Biocontrol Agent Pythium oligandrum Strain Po37, an Oomycota

ABSTRACT The oomycota Pythium oligandrum Po37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of the P. oligandrum Po37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.

Bio-suppression of Sclerotinia Stem Rot of Tomato and Biostimulation ofPlant Growth Using Tomato-associated Rhizobacteria

A collection of 25 rhizobacterial strains, recovered from rhizospheric soils around healthy tomato plants grown in Rhizoctonia-infested fields, belonging to Bacillus amyloliquefaciens, B. thuringiensis, B. megaterium, B. subtilis, Enterobacter cloacae, Chryseobacterium jejuense, and Klebsiella pneumoniae was screened for its suppressive effects of Sclerotinia Stem Rot of tomato caused by Sclerotinia sclerotiorum and plant growth-promoting ability. The inhibitory effects of diffusible and volatile metabolites from these rhizobacteria against pathogen mycelial growth depended significantly upon strains tested. Growth inhibition caused by diffusible and volatile compounds was of about 37-57% and 24-54%, respectively. All strains tested had totally suppressed myceliogenic germination of sclerotia and improved germination of bacterized tomato seeds as compared to the untreated controls. The screening of their disease-suppressive and plant growth-promoting abilities revealed 72-100% decrease in Sclerotinia Stem Rot severity and significant increments in plant height by 52-67%, roots fresh weight by about 66-88% and aerial part weight by 47-75%, compared to S. sclerotiorum-inoculated and untreated control. The most promising strains combining disease-suppressive and growth-promoting abilities were B. subtilis B10 (KT921327) and B14 (KU161090), B. thuringiensis B2 (KU158884), B. amyloliquefaciens B13 (KT951658) and B15 (KT923051), and E. cloacae B16 (KT921429).

Biocontrol of Rhizoctonia Root Rot in Tomato and Enhancement of PlantGrowth using Rhizobacteria Naturally associated to Tomato

In the present study, 25 rhizobacterial isolates, obtained from rhizosphere of healthy tomato plants collected from various tomato-growing sites in Tunisia, were tested in vitro and in vivo against Rhizoctonia solani. This bacterial collection, composed of isolates belonging to Bacillus spp., Enterobacter cloacae, Chryseobacterium jejuense, and Klebsiella pneumoniae, was assessed for its antifungal potential against R. solani the causative agent of Rhizoctonia Root Rot disease in various crops including tomato. Antifungal activity of diffusible and volatile metabolites derived from these isolates was tested against target pathogen using dual and distance culture bioassays, respectively. Growth inhibition rates, recorded after 5 days of incubation at 25°C, depended significantly upon tested bacterial isolates and screening methods and reached 34-59% and 18-45% for diffusible and volatile metabolites, respectively. The screening of disease-suppressive and plant growth-promoting abilities of these tomato-associated rhizobacteria showed 47-100% decrease in disease severity and significant increments in plant height by 62-76%, roots fresh weight by 53-86%, and aerial parts fresh weight by 34-67% compared to pathogen-inoculated and untreated control. B. thuringiensis B2 (KU158884), B. subtilis B10 (KT921327) and E. cloacae B16 (KT921429) were found to be the most efficient isolates in decreasing R. solani radial growth, suppressing disease severity, and enhancing plant growth.

Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium

ABSTRACT The complete genome of Bacillus methylotrophicus strain B25, isolated in Switzerland, was sequenced. Its size is 3.85 Mb, and several genes that may contribute to plant growth-promoting activities were identified in silico.

Comparative Efficacy of Three Tomato-Associated Rhizobacteria used Singly or in Combination in Suppressing Rhizoctonia Root Rot and Enhancing Tomato Growth

Three indigenous tomato-associated rhizobacteria strains -Bacillus subtilis str. B2 KT921327, B. thuringiensis str. B10 KU158884 and Enterobacter cloacae str. B16 KT921429 - were tested singly and in combination as substrate drench for Rhizoctonia Root Root suppression and plant growth promotion on two tomato cultivars during two cropping seasons. All bacteria-based treatments were found to be more effective in suppressing disease than the fungicide on both cultivars and in both cropping seasons. The disease-suppression and growth-promotion abilities of the treatments tested varied significantly depending on pathogen presence or absence, bacterial strains, tomato cultivars and cropping years. Overall, for all trials and cultivars combined, disease suppression potential, as compared to the untreated controls, ranged between 74.72 and 83.94% using three-strain mixture relative to 60.46-85.01% achieved using single strains. Height increment in disease free plants achieved with mixtures varied between 17.02 and 45.69% compared to 7.55 and 44.76% noted using single strains. Plants grown in R. solaniinoculated peat and challenged with three-strain mixture were 49.46 to 76.74% higher than controls whereas those grown in peat amended with single strains showed 42.28-83.58% height increase. Increment of aerial parts and root fresh weights on disease free plants were 42.31-78.09% and 45.03-91.21% for plants treated with mixture compared to 33.70-82.48% and 20.52-92.39% recorded using strains singly, respectively. On inoculated plants, these parameters were enhanced by 61.2-95.44% and 59.13-98.5% using mixed treatment and by 48.41-97.02% and by 51.5-99.05%, respectively, using single-train-based treatments. Analysis of the microbial populations revealed no differences between Single Strand Conformational Polymorphism (SSCP) profiles when neither the rhizobacteriabased treatment nor the pathogen inoculation was considered. The microbial communities differed only depending on cultivars grown.

Characterization of Tomato-associated Rhizobacteria Recovered fromVarious Tomato-growing Sites in Tunisia

In the present study, a total of 200 rhizobacterial isolates were obtained from rhizosphere of healthy tomato plants grown in fields with a history of severe soilborne diseases and mainly crown and root rots. Screened their capacity to suppress in vitro growth of Sclerotinia sclerotiorum and Rhizoctonia solani, 69 and 57 isolates out of the 200 tested were shown able to inhibit significantly the mycelial growth of target pathogens by 11-62% relative to control. The 25 most effective isolates, leading to suppression of both fungi by more than 45% over control, were selected and subjected to morphological, biochemical, molecular, and metabolic characterizations. This collection of tomato-associated rhizobacteria exhibited a great morphological and biochemical diversity. Sequencing of 16S rRNA and rpoB genes led to the identification of four genera namely Bacillus, Chryseobacterium, Enterobacter, and Klebsiella. The most frequent species were B. amyloliquefaciens, B. thuringiensis, B. megaterium, B. subtilis, E. cloacae, C. jejuense, and K. pneumoniae. Screening for their plant growth-promoting properties, 20 isolates were shown able to produce siderophore, 18 had solubilized phosphate, and 19 were capable to synthesize indole-3- acetic acid (IAA). PCR amplification of lipopeptide biosynthetic genes revealed the presence of genes encoding fengycin A and bacillomycin D biosynthesis in 18 and 16 isolates, respectively. Metabolic characterization performed using Biolog™ Ecoplates indicated that tomato-associated rhizobacteria displayed a large metabolic activity and they were able to use a wide range of carbon sources with the increase of the incubation duration. Based on their metabolic profiles, these rhizobacterial isolates were grouped into eight major clusters generated at the different sampling times (24, 48 and 120 h of incubation). Average well-color development (AWCD) values were found to be positively correlated with the Shannon diversity index.

Evaluation of the Effectiveness of Tomato-Associated RhizobacteriaApplied Singly or as Three-Strain Consortium for Biosuppression ofSclerotinia Stem Rot in Tomato

In the present study, the capacity of three native tomato-associated rhizobacteria (Bacillus subtilis B2, B. thuringiensis B10, and Enterobacter cloacae B16) to suppress Sclerotinia Stem Rot in tomato and to improve growth was investigated in two tomato cultivars. The three bacterial strains were tested against S. sclerotiorum either singly or as consortium and their efficacy was compared to a fungicide control. All bacteria-based treatments were found to be more effective in suppressing disease than chemical fungicide on both cultivars and in both year trials. The disease-suppression and growth-promoting abilities of the treatments tested varied significantly depending on bacterial strains used, tomato cultivars grown, and year trial. Overall, all three strains suppressed the disease more effectively than the chemical fungicide. Indeed, for both year trials and cultivars combined, disease suppression potential, as compared to pathogen-inoculated and untreated control, ranged between 80.79 and 88.01% using the three-strain consortium relative to 70.00-82.07% achieved with single strains and 32.13-58.97% using fungicide. Plants grown in S. sclerotiorum-infected peat and challenged with the three-strain consortium were 38.36 to 80.95% taller than control ones whereas height increment noted using single strains and fungicide was of about 32.35- 79.01 and 29.62-51.85%, respectively. Aerial parts and root fresh weights of pathogen-inoculated and treated plants were enhanced by 51.59-74.69% and 54.00-78.12% using mixed strains and by 39.12-76.83% and 42.02-77.01%, respectively, using single strains compared to 24.04-53.05 and 12.74-67.05% noted on chemically treated plants. The effect of the three biocontrol agents was also examined on the composition of microbial communities inhabiting the rhizosphere of tomato plants. Results of the single strand conformational polymorphism (SSCP)-based profiling revealed that rhizosphere communities differed between cultivars only. However, the introduction of S. sclerotiorum or biocontrol agents did not cause detectable perturbations in the composition of fungal and bacterial communities inhabiting roots of treated tomato plants.