Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA.We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens

Sporulation rate in culture and mycoparasitic activity, but not mycohost specificity, are the key factors for selecting Ampelomyces strains for biocontrol of grapevine powdery mildew (Erysiphe necator)

To develop a new biofungicide product against grapevine powdery mildew, caused by Erysiphe necator, cultural characteristics and mycoparasitic activities of pre-selected strains of Ampelomyces spp. were compared in laboratory tests to the commercial strain AQ10. Then, a 2-year experiment was performed in five vineyards with a selected strain, RS1-a, and the AQ10 strain. This consisted of autumn sprays in vineyards as the goal was to reduce the number of chasmothecia of E. necator, and, thus, the amount of overwintering inocula, instead of targeting the conidial stage of the pathogen during spring and summer. This is a yet little explored strategy to manage E. necator in vineyards. Laboratory tests compared the growth and sporulation of colonies of a total of 33 strains in culture; among these, eight strains with superior characteristics were compared to the commercial product AQ10 Biofungicide® in terms of their intrahyphal spread, pycnidial production, and reduction of both asexual and sexual reproduction in E. necator colonies. Mycoparasitic activities of the eight strains isolated from six different powdery mildew species, including E. necator, did not depend on their mycohost species of origin. Strain RS1-a, isolated from rose powdery mildew, showed, togetherwith three strains from E. necator, the highest rate of parasitism of E. necator chasmothecia. In field experiments, each strain, AQ10 and RS1-a, applied twice in autumn, significantly delayed and reduced early-season development of grapevine powdery mildew in the next year. Therefore, instead of mycohost specificity of Ampelomyces presumed in some works, but not confirmed by this study, the high sporulation rate in culture and the mycoparasitic patterns became the key factors for proposing strain RS1-a for further development as a biocontrol agent of E. necator

Biocontrol Potential of Forest Tree Endophytes

Peer reviewe

Chapitre 14: Phytopathogènes et stratégies de contrôle en aquaponie

peer reviewedAmong the diversity of plant diseases occurring in aquaponics, soil-borne pathogens, such as Fusarium spp., Phytophthora spp. and Pythium spp., are the most problematic due to their preference for humid/aquatic environment conditions. Phytophthora spp. and Pythium spp. which belong to the Oomycetes pseudo-fungi require special attention because of their mobile form of dispersion, the so-called zoospores that can move freely and actively in liquid water. In coupled aquaponics, curative methods are still limited because of the possible toxicity of pesticides and chemical agents for fish and beneficial bacteria (e.g. nitrifying bacteria of the biofilter). Furthermore, the development of biocontrol agents for aquaponic use is still at its beginning. Consequently, ways to control the initial infection and the progression of a disease are mainly based on preventive actions and water physical treatments. However, suppressive action (suppression) could happen in aquaponic environment considering recent papers and the suppressive activity already highlighted in hydroponics. In addition, aquaponic water contains organic matter that could promote establishment and growth of heterotrophic bacteria in the system or even improve plant growth and viability directly. With regards to organic hydroponics (i.e. use of organic fertilisation and organic plant media), these bacteria could act as antagonist agents or as plant defence elicitors to protect plants from diseases. In the future, research on the disease suppressive ability of the aquaponic biotope must be increased, as well as isolation, characterisation and formulation of microbial plant pathogen antagonists. Finally, a good knowledge in the rapid identification of pathogens, combined with control methods and diseases monitoring, as recommended in integrated plant pest management, is the key to an efficient control of plant diseases in aquaponics.Cos

Systemic Induction Of Phytoalexins In Cucumber In Response To Treatments With Fluorescent Pseudomonads

The Pseudomonas putida isolate BTP1 and its sid2 mutant M3 were recently reported to protect cucumber against Pythium aphanidermatum root rot. This protection was mainly associated with an accumulation of antifungal phenolics in the treated roots. In this study, analyses of root extracts from split-root experiments showed that these phytoalexins were produced systemically. Indeed, several antifungal molecules accumulated similarly in both treated and nontreated root parts of plants protected against P. aphanidermatum with BTP1 or M3. In addition, analyses of leaf samples also revealed increased amounts of fungitoxic molecules in PGPR-treated plants, although the nature of these molecules appeared to be different from those detected in roots. The antifungal compounds isolated both from roots and leaves were mainly detected in acid-hydrolyzed extracts containing aglycones. These results suggest that PGPR can elicit phytoalexins systemically in cucumber and that the overall defence response is not based on a single phytoalexin but is chemically complex and organ-specific

Protection Of Cucumber Against Pythium Root Rot By Fluorescent Pseudomonads: Predominant Role Of Induced Resistance Over Siderophores And Antibiosis

Four Pseudomonas strains were evaluated for their intrinsic properties conferring their ability to protect long English cucumber against Pythium aphanidermatum in hydroponic culture. Two of the strains, BTP1 and its siderophorenegative mutant M3, increased plant yield as compared with the non-inoculated control plants. Strain BTP7 was intermediate in its biocontrol activity while strain ATCC 17400 failed to reduce disease development. The role of pyoverdines could not be confirmed since treatment with either BTP1 or its siderophore-negative mutant M3 provided similar suppression of Pythium disease. In addition, no siderophores were detected in the nutrient solution. BTP1 did not inhibit pathogen growth in vitro on several media, suggesting that antibiosis was not a mechanism of suppression. Quantification of root bacterial populations did not indicate differences among the strains. On the other hand, roots treated with either BTP1 or its sid¹ mutant M3 contained more antifungal phenolics than roots from any other treatments including controls. These results suggest that antifungal compounds induced by inoculation of cucumber roots with the fluorescent Pseudomonas strains BTP1 and M3 participate actively in the protection of cucumber plants against P. aphanidermatu