Genetic diversity of[i] Rhizoctonia solani[/i] associated with potato tubers in France

Affiche, résuméThe plant pathogenic soil-borne fungus Rhizoctonia solani causes severe damages in crops all around the world. Tubers of potato are frequently affected by R. solani leading to the downgrading of the production. Generally the isolates involved in the sclerotia occurring at the surface of the tuber are assigned to the anastomosis group (AG) 3 but a more precise characterization of the diversity of this deleterious group is needed to set up appropriate control strategies. The diversity of 73 French isolates from the mains potato seed production areas and 31 isolates originating from 9 other countries was assessed according to 3 molecular approaches. Three phylogenetic trees were built up based on the sequences of the internal transcribed spacer (ITS) region and the gene tef-1α as well as the comparison of the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed 3 different AGs among our collection (60 AG 3, 8 AG 2-1 and 5 AG 5). Grouping of the isolates belonging to the same AG was confirmed by the sequencing of the gene tef-1α used for the first time to study the genetic diversity of R. solani. About 42 % of the ITS sequences and 73 % of the gene tef-1α sequences contained polymorphic sites where several nucleotides are possible, suggesting that the cells of R. solani strains contain several copies of ITS and gene tef-1α within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1α sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover, there was no relationship between the geographical origins of the strains or the potato variety from which they were isolated and their genetic diversity. This important and under evaluated genetic diversity as the lack of population structure suggest important genetic mixings leading to a constant evolution within R. solani and could explain the difficulties to control it successfully

Current Status of Fusarium oxysporum Formae Speciales and Races

Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species

Build up of patches caused by Rhizoctonia solani

International audienceRhizoctonia solani is a complex species that is composed of different anastomosis groups (AG). Although these different AGs show differences in their host ranges, generally R. solani is a phytopathogenic species with a wide spectrum of hosts. It has the ability to grow as a saprotroph, which further complicates its behaviour as a parasite. The losses caused by R. solani are very important and need a sustainable management strategy. The patchy appearance of the disease caused by this pathogen is well-known. The patches show within and between season dynamics. The factors which affect the spread of the disease can be grouped into three main categories: host plant, pathogen and environment. However, each of the categories in its detail may depend on or react with the other categories. There are a number of factors that may be involved in dynamics of patches. These potential mechanisms are discussed. It is essential to know about the mechanisms involved to develop an effective control strategy. Although more work is needed to investigate different mechanisms of parasitism deployed by different AGs in different hosts, it seems that many mechanisms external to the host are operating at the same time which necessitates an integrative research approach to study and control the diseases caused by R. solani

Fungal genes and metabolites associated with the biocontrol of soil-borne plant pathogenic fungi

SPEIPMThis handbook compiles authoritative information about fungal metabolites and their chemistry and biotechnology. The first in the reference work series “Phytochemicals”, and written by a team of international expert authors, this book provides reference information ranging from the description of fungal natural products, over their use e.g. as anticancer agents, to microbial synthesis, even spanning to the production of secondary metabolites on industrial scale. On the other hand it also describes global health issues related to aflatoxin production in foods and agriculture, including perspectives for detoxification. The handbook characterizes different compound classes derived from fungal secondary metabolites, like ergot alkaloids and aflatoxins. The discussion puts a special emphasis on how potentially useful compounds can be obtained and what applications they can find, on the one hand, and how potential dangers can be encountered on the other hand. The comprehensive chapters in this handbook will thus appeal to readers from diverse backgrounds in chemistry, biology, life sciences, and even medicine, who are working or planning to work with fungal (secondary) metabolites and their application. They provide the readers with rich sources of reference information on important topics in this field. The first authoritative summary and reference work on fungal (secondary) metabolites, their chemistry and biotechnological use and applications Covering aspects from beneficial use, to potential health issues of fungal metabolites Reference information for readers from various backgrounds: chemists, biologists, life scientists, medical scienti The biocontrol of plant pathogenic fungi includes two complementary approaches depending on whether the aim is to control soil-borne or air-borne pathogenic fungi. In the first case, natural biotic interactions within the indigenous microflora should be stimulated to regulate inoculum density and the infectious activity of pathogen populations. This strategy can be enhanced by inoculating one or more previously selected biocontrol agents. In the second case, one or more previously selected biocontrol agents can be sprayed on plant foliage to interfere with the development of the targeted pathogen through different mechanisms involving particular enzymes or metabolites. Selecting the most effective biological control agents implies (i) knowing the mechanisms of their interactions with the pathogens and (ii) checking that the environment in which the biocontrol agent is introduced will permit the expression of these mechanisms. The common thread of this chapter is the impressive diversity of metabolites and proteins produced by fungi and involved in interactions between pathogenic and nonpathogenic fungi. Many metabolites and proteins were discovered empirically or by chance a few decades ago, and what we knew about them was they inhibited the growth of pathogenic models on agar medium. Fungi producing these metabolites were not well-known fungal species and were not used as biocon- trol agents. However, the demonstration of their intense metabolic activity paved the way for more investigations in this area and led to deciphering the mechanisms of interactions between fungal strains. Thus, in recent years a large number of enzymes, signal molecules, secondary metabolites, large-size proteins, as well as new metabolic pathways have been revealed by genomics, and it is now possible to understand why some strains can control a given pathogen more than others or stimulate plant defense reactions. To date, the most studied fungi include many strains of the genus Trichoderma but also the species Chlonostachys rosea, Coniothyrium minitans, Verticillium biguttatum, and the oomycete Pythium oligandrum. All of them are successfully used as biocontrol agents. This chapter does not aim to provide a comprehensive catalog, but rather to associate these metabolites and proteins to the modes of action involved in pathogen control. The state of the art presented in this review suggests promising prospects for rational, appropriate, and effective use of the biocontrol potential offered by the huge diversity of fungal metab- olites and proteins

Genetic diversity of <em>Fusarium oxysporum</em> and related species pathogenic on tomato in Algeria and other Mediterranean countries

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceIn order to characterize the pathogen(s) responsible for the outbreak of fusarium diseases in Algeria, 48 Fusarium spp. isolates were collected from diseased tomato in Algeria and compared with 58 isolates of Fusarium oxysporum originating from seven other Mediterranean countries and 24 reference strains. Partial sequences of the translation elongation factor EF-1a gene enabled identification of 27 isolates as F. oxysporum, 18 as F. commune and three as F. redolens among the Algerian isolates. Pathogenicity tests confirmed that all isolates were pathogenic on tomato, with disease incidence greater at 28 degrees C than at 24 degrees C. All isolates were characterized using intergenic spacer (IGS) DNA typing, vegetative compatibility group (VCG) and PCR detection of the SIX1 (secreted in xylem 1) gene specific to F. oxysporum f. sp. lycopersici (FOL). No DNA polymorphisms were detected in the isolates of F. redolens or F. commune. In contrast, the 27 Algerian isolates of F. oxysporum were shown to comprise nine IGS types and 13 VCGs, including several potentially new VCGs. As none of the isolates was scored as SIX1+, the 27 isolates could be assigned to F. oxysporum f. sp. radicis-lycopersici (FORL). Isolates from Tunisia were also highly diverse but genetically distinct from the Algerian isolates. Several Tunisian isolates were identified as FOL by a PCR that detected the presence of SIX1. The results show that isolates from European countries were less diverse than those from Tunisia. Given the difference between Algerian populations and populations in other Mediterranean countries, newly emergent pathogenic forms could have evolved from local non-pathogenic populations in Algeri

Interest of cultural practices to manage soilborne diseases

National audienc

Fungal proteins and genes associated with biocontrol mechanisms of soil-borne pathogens : a review

SPEIPMSoil suppressiveness to soil-borne diseases relies mainly on microbial interactions. Some of them, e.g. antibiosis and mycoparasitism, are directly deleterious to pathogenic fungi; others indirectly affect microbial populations, pathogens included, when quite active non pathogenic microorganisms intensively exploit trophic or spatial resources. The mechanisms that govern the suppressive nature of the various known suppressive soils are often hypothetical. The objective of this article is to review the fungal proteins and corresponding genes directly or indirectly involved in antagonistic relationships between pathogens and non-pathogens and associated with biocontrol of soil-borne pathogens. The current hypothesis is that they contribute to soil suppressiveness. We assigned the proteins encoded by these genes to five function-based groups. The first group contains the proteins involved in host recognition and signaling pathways and the transcription factors involved in biocontrol activities. Proteins that protect antagonistic fungi against their own toxins and against other microorganisms are also included in this first group. The second group lists enzymes and proteins involved in the biosynthesis pathway of secondary metabolites, such as peptaibols, terpenes, polyketides, and gliotoxins that have antifungal activity towards soil-borne plant pathogens. The third group deals with proteins and molecules involved in competition for nutrients and root colonization. The fourth one contains the fungal cell wall-degrading enzymes secreted by antagonistic fungi during mycoparasitism. They are mainly chitin-degrading enzymes, glucanases and proteases. Finally, the last group gathers fungal proteins and molecules that induce plant defense reactions and prevent infection by plant pathogens. We conclude that the proteins involved or simply associated with the specific suppression of pathogens are not all known yet, but genes encoding a number of them or facilitating their expression are identified. Selecting candidate genes among them may help to understand the underlying mechanisms of soil suppressiveness when using metatranscriptomic analyses to identify functional groups

Root Interactions with Nonpathogenic Fusarium oxysporum Hey Fusarium oxysporum, What Do You Do in Life When You Do Not Infect a Plant?

In this review, we tried to present Fusarium oxysporum in an ecological context rather than to confine it in the too classic double play of the nonpathogenic fungus that protects the plant against the corresponding forma specialis. Moreover, F. oxysporum is sometimes one, sometimes the other, and only the fungus can reveal its hidden face, according to it is or not in front of the target plant. Despite the quality and richness of the studies conducted to date, molecular approaches highlight some of the evolutionary mechanisms that explain the polyphyletic nature of this species, but still they do not identify a nonpathogenic F. oxysporum. This soilborne fungus has primarily an intense saprophytic life, and it finds its place in the functioning of the ecosystem of which it actively occupies all compartments, thanks to an impressive metabolic flexibility and a high enzyme potential. This adaptability is exploited by F. oxysporum first to get carbon from different organic sources and energy through variable strategies including nitrate dissimilation under severe anaerobic conditions and also to colonize extreme environments, some of which being dramatically anthropized. This adaptability is also exploited by man for bioremediation of polluted sites, for detoxification of xenobiotic compounds including pesticides, and furthermore for industrial and biotechnological processes. The presence of the fungus in water distribution networks of city stresses again the adaptable nature of the fungus, but more precisely, this highlights the presence of clonal populations worldwide and raises the question of the role of man in the transfer of biological resources. We conclude in a provocative manner by asking if nonpathogenic F. oxysporum would not be the all-purpose fungal tool needed to ensure a good soil functioning

Fusarium diversity in soil using a specific molecular approach and a cultural approach

International audienceFusarium species are ubiquitous in soil. They cause plant and human diseases and can produce mycotoxins. Surveys of Fusarium species diversity in environmental samples usually rely on laborious culture-based methods. In the present study, we have developed a molecular method to analyze Fusarium diversity directly from soil DNA. We designed primers targeting the translation elongation factor 1-alpha (EF-1 alpha) gene and demonstrated their specificity toward Fusarium using a large collection of fungi. We used the specific primers to construct a clone library from three contrasting soils. Sequence analysis confirmed the specificity of the assay, with 750 clones identified as Fusarium and distributed among eight species or species complexes. The Fusarium oxysporum species complex (FOSC) was the most abundant one in the three soils, followed by the Fusarium solani species complex (FSSC). We then compared our molecular approach results with those obtained by isolating Fusarium colonies on two culture media and identifying species by sequencing part of the EF-1 alpha gene. The 750 isolates were distributed into eight species or species complexes, with the same dominant species as with the cloning method. Sequence diversity was much higher in the clone library than in the isolate collection. The molecular approach proved to be a valuable tool to assess Fusarium diversity in environmental samples. Combined with high throughput sequencing, it will allow for in-depth analysis of large numbers of sample

Soil suppressiveness to plant diseases

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