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International audience; Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural and practical taxonomic option available.

Here, we report a chromosome-level genome assembly of Fusarium oxysporum strain Fo47 (12 pseudomolecules; contig N50: 4.52Mb), generated using a combination of PacBio long-read, Illumina pair-ended and Hi-C sequencing data. Although F. oxysporum causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and widely used as a biocontrol agent for plant disease control. The Fo47 genome carries a single accessory chromosome of 4.23 Mb, compared to the reference genome of F. oxysporum f.sp. lycopersici strain Fol4287. The high-quality assembly and annotation of the Fo47 genome will be a valuable resource for studying the mechanisms underlying the endophytic interactions between F. oxysporum and plants, as well as deciphering the genome evolution of the F. oxysporum species complex.

International audience; Aphanomyces euteiches Drechs is a pathogenic soil-borne oomycete that causes root rot of legumes, one of the most serious diseases affecting legume production worldwide. There is currently no registered pesticide and no available resistant pea cultivar. Avoidance of infested fields based on disease risk assessment prior to pea sowing remains the main method available to manage the disease, but time-consuming bioassays are required to assess disease severity on susceptible plants grown in field soil samples. Direct quantification of A. euteiches inoculum in the soil by targeting multicopy genomic sequences of the internal transcribed spacer 1 with a qPCR-based method has been proposed as a rapid alternative for disease prediction. However, the method lacks sensitivity to accurately quantify low inoculum levels from naturally infested fields. We developed a suitable methodology based on droplet digital PCR (ddPCR) to quantify low A. euteiches inoculum levels in naturally infested soils. The methodology was validated on 200 soil samples taken from four naturally infested fields in the main pea cropping area in the north of France. The comparative analysis of inoculum density and disease severity of the 50 samples within each of the four fields revealed a non-homogeneous distribution of the A. euteiches population; this explains why the disease is visible in the form of foci. A significant relationship between pea root rot disease severity determined by bioassays and A. euteiches inoculum density was highlighted, and a linear mixed model is proposed to predict disease severity from inoculum density.

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (∼80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.One-sentence summaryMultiomics analysis reveals the regulatory plasticity of plants in response to beneficial and antagonistic microbes, resulting in distinct phenotypes and rewired transcriptional networks.

International audience; Fusarium graminearum is a plant-pathogenic fungus that causes the devastating disease “Fusarium head blight” (FHB) in cereal crops such as wheat (Triticum aestivum). It also contaminates grains with mycotoxins, including deoxynivalenol (DON), which turn toxic to humans and animals. This fungus overwinters in crop residues left in the field. The fate of mycotoxins in these crop residues in the soil and their ecological role are still unexplored. Therefore, our objective was to assess whether mycotoxins are maintained in the soil, impact the soil biome and benefit the survival of F. graminearum. A six-month study in microcosms was performed to examine the fate of DON in F. graminearum-contaminated wheat straw and soil, and its impact on soil communities. DON was extracted from straw and soil mixtures, and quantified by high-performance liquid chromatography (HPLC). Fusarium graminearum and total fungal and bacterial molecular biomasses were quantified using real-time polymerase chain reaction (Q-PCR). Nematode and earthworm densities were quantified through binocular observations. Changes in the genetic structure of fungi, bacteria, protozoa, and nematodes communities were determined by terminal restriction fragment length polymorphism (T-RFLP) analyses. Results revealed that DON disappeared from the straw and the soil over time. The rate of disappearance was accelerated when straw was incorporated into the soil and when microcosms contained earthworms. Fungal and bacterial biomass, first stimulated during the incorporation of straw, decreased after 2 weeks and until the end of the experiment (24 weeks). It decreased more strongly in the presence of DON. This negative impact of DON was temporary and at the end of the experiment, the bacterial and fungal biomass was higher in the treatments that received DON than in the other treatments while the population of F. graminearum was unaffected. Similarly, DON modified the community structures of fungi, bacteria and protozoa to various extents but not that of nematodes. DON-contaminated straw was found attractive for earthworms, and its presence stimulated their reproduction or cocoon hatching. The major conclusion is that DON briefly affected soil communities, disappeared over time and gave no observable advantage to soil-borne F. graminearum populations.

Rhizoctonia crown and root rot causes severe damage on sugar beet. We collected twenty-seven isolates of Rhizoctonia solani from diseased sugar beets in France and Belgium over two years. All of them were pathogenic on sugar beet but displayed variable aggressiveness levels. Based on their internal transcribed spacer (ITS) sequences, we identified them as belonging to the anastomosis group (AG) 2-2. All isolates were further classified within the subgroup AG-2-2 IIIB based on their ability to grow at 35 degrees C. As we observed genetic diversity within and among isolates, we clarified heterogeneity within isolates by cloning their ITS region and sequencing 129 clones. The genetic variability levels among clones of a same isolate and among isolates were similar, suggesting that the 27 isolates were closely related. Reference isolates of R. solani AG-2-2 IIIB were genetically more diverse than the isolates collected in our study. The collection of R. solani established in this study provides resources for future investigations on the diversity and evolution of pathogenic populations and for breeding programs.

International audience; Orobanchaceae-broomrapes-are a family of parasitic plants that represent an ecological and agronomic challenge because some of them cause significant damage to many monocots or dicots. Weedy broomrapes infest different crops in the Mediterranean basin, leading to substantial yield losses. Besides, they quickly adapt to new host plants, so that new crops are more and more under threat. Control methods are lacking because as plant parasites they cannot be considered as a common weed in agriculture. It is therefore important to characterize the main drivers of their regulation to identify sustainable management strategies. We reviewed all the possible interactions of Orobanchaceae species with surrounding organisms in an agricultural landscape, with a focus on the Orobanche and Phelipanche genera. Our main findings are that (1) broomrapes successfully co-evolve with their host through tight interactions ranging from the molecular to the tissue level, resulting in a unique strategy in their interactions with their host; (2) broomrapes have to face natural regulatory mechanisms such as host plant defenses, allelopathic interferences, and pest attacks from both the rhizosphere and phyllosphere; (3) alternative methods combining these natural mechanisms with existing conventional methods should be used to control broomrape. Conventional methods have shown limited results with parasitic weeds. By considering their life cycle and biotic and abiotic environment, management methods will target their weak point(s). Combining different control methods needs to be considered in an integrated weed management system. Furthermore, future studies on biocontrol will bring out new products to be used in addition to cultural techniques. Modeling approaches would help predict the evolution of broomrape-infested plots and the available potential management strategies.

International audience; Ancient ecological legacies and past land use changes may inform on the present structure of biological communities. However, regions providing such successive ecosystems are scarce. In France, the Landes de Gascogne area provides such ecological shifts since a few ancient moorland, peatland and oak areas prior the afforestation with maritime pine (Pinus pinaster) 160 years ago still remain. Focusing on soil-borne parasites such as plant-parasitic nematodes (PPN), because forests were recently increasingly impacted by the introduction of intensive agriculture, this study is therefore aimed at comparing the diversity and the community patterns of these organisms at different scales (intra- and intersites) and between different successive ecosystems. The understory vegetation as well as the pedoclimatic characterization of the sampled sites were also considered. Common diversity indices were not impacted by this transition from ancient to past ecosystems. Although the most colonizer nematodes prevailed in all the ecosystems, PPN community structures significantly diverged between both ecosystems. In the logged pine forests, the sediment legacy could have primarily impacted the diversity. Moreover, the PPN diversity would mainly respond to the soil hydromorphicity that determined the associated understory vegetation. Consequently, a significant shift in community structure from moorlands to logged pine to logged pine forests was observed, regarding especially high pathogenic species such as Pratylenchus spp. Thus, analyzing PPN community structure highlights the PPN potential risk to consider during the introduction of intensive cropping systems.

International audience; The use of bioherbicides containing fungal active ingredients or natural fungal molecules is one of the possible solutions to reduce the use of chemical products. This paper focuses on studies of bioherbicides, including both living fungi and natural fungal molecules, published in the last 45 years, and their associated weed targets; current problems in the development of bioherbicides are also discussed. Bibliometric methods based on the Web of Science database were used to analyse relevant articles published between 1973 and 2018. Overall analysis suggested that interest in bioherbicides extends over the preceding thirty years, when many potential microorganisms and natural fungal molecules were proposed. Furthermore, analysis of about 229 articles indicated an encouraging exploitable potential, although there is a real gap between the number of experimental studies and the small number of products currently on the market. A dozen fungal‐based bioherbicides are on the market in the United States and Canada, while countries, such as China and South Africa, have one, and none is available in Europe. The active ingredients in these bioherbicides are living fungi, but no fungal molecule‐based product is thus far on the market. Reasons for this gap include production hurdles, formulation process, ecological fitness, duration of herbicidal effects, and costly and time‐consuming registration procedures. However, it is clear that analysis of fungus–plant interactions provides a promising source of bioherbicides that may be applied to appropriate cropping systems for environment‐friendly, sustainable weed control.

Aims Pathogenic gain-of-function variants in CACAN1C cause type-8 long QT syndrome (LQT8). We sought to describe the electrocardiographic features in LQT8 and utilize molecular modelling to gain mechanistic insights into its genetic culprits. Methods and results Rare variants in CACNA1C were identified from genetic testing laboratories. Treating physicians provided clinical information. Variant pathogenicity was independently assessed according to recent guidelines. Pathogenic (P) and likely pathogenic (LP) variants were mapped onto a 3D modelled structure of the Cav1.2 protein. Nine P/LP variants, identified in 23 patients from 19 families with non-syndromic LQTS were identified. Six variants, found in 79% of families, clustered to a 4-residue section in the cytosolic II–III loop region which forms a region capable of binding STAC SH3 domains. Therefore, variants may affect binding of SH3-domain containing proteins. Arrhythmic events occurred in similar proportions of patients with II–III loop variants and with other P/LP variants (53% vs. 48%, P = 0.41) despite shorter QTc intervals (477 ± 31 ms vs. 515 ± 37 ms, P = 0.03). A history of sudden death was reported only in families with II–III loop variants (60% vs. 0%, P = 0.03). The predominant T-wave morphology was a late peaking T wave with a steep descending limb. Exercise testing demonstrated QTc prolongation on standing and at 4 min recovery after exercise. Conclusion The majority of P/LP variants in patients with CACNA1C-mediated LQT8 cluster in an SH3-binding domain of the cytosolic II–III loop. This represents a ‘mutation hotspot’ in LQT8. A late-peaking T wave with a steep descending limb and QT prolongation on exercise are commonly seen.

Fusarium oxysporum f. sp. cyclaminis (Focy) is the most damaging pathogen of cyclamen (Cyclamen persicum). Control measures are limited and not efficient enough to ensure a healthy production. The development of a tool allowing the early detection of Focy and an effective control method relies on the knowledge of Focy diversity. We obtained 27 Focy strains from international collections, and recovered 24 additional F. oxysporum isolates from cyclamen. A pathogenicity test revealed 15 pathogenic isolates out of the 24 isolates from cyclamen, with substantial differences in aggressiveness among isolates. The other nine were non-pathogenic endophytic strains of cyclamen. We described the genetic diversity of pathogenic and non-pathogenic strains by sequencing part of the translation elongation factor 1-alpha gene and the full-length nuclear ribosomal intergenic spacer region. We found high genetic diversity within the forma specialis, with 42 Focy strains distributed into six two-locus sequence types (ST). No relationship was found between genotypic grouping, geographic origin and aggressiveness within the collection of strains. Genetic diversity was much higher among non-pathogenic strains: the nine strains were distributed into nine ST, all of them distinct from pathogenic ST. As both pathogenic strains and endophytic strains can be present in cyclamen, an efficient tool to detect Focy is badly needed.

Phenotypic traits are regularly used to diagnose the development of Fusarium head blight (FHB) in the field, whereas mycotoxin accumulation in wheat grains can only be accurately evaluated through costly methods, such as high–performance liquid chromatography (HPLC). The aim of this study was to determine whether: (i) the results provided by existing commercial decision support tools could be anticipated using phenotypic measurements, including a novel technique of computer–assisted image analysis of spikes; and (ii) these measurements could avoid using HPLC. We monitored the FHB development during two consecutive years in highly contaminated plots in the Burgundy region (France). Contamination by crop residues was simulated through a field inoculation with barley grains artificially colonized by Fusarium graminearum. The development of the disease on spikes and harvested grains was assessed on one tolerant and two susceptible wheat varieties. The accumulated amounts of mycotoxins were measured in harvested grains using HPLC. As expected, the measured traits revealed that the inoculum responsible for infection on spikes mainly came from residues left on the soil surface, and the susceptible varieties were more diseased than the tolerant variety. Weather conditions had a strong effect on disease development. The novel computer–assisted image analysis technique had a better prediction power of deoxynivalenol accumulation, was more objective and time–saving than classical visual symptom assessments. This assessment method could be suitable to supplement the use of existing prediction tools and might avoid systematic and costly mycotoxin measurements in likely infected plots.

International audience; Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.

International audience; In the context of a shift towards pesticide reduction in arable farming, weed management remains a challenging issue. Integrated Weed Management currently recommends agronomic practices for weed control, but it does not integrate the use of biodiversity-based options, enhancing the biological regulation of weeds. Here, wereview existing knowledge related to three potentially beneficial interactions, of crop–weed competition, weed seed granivory, and weed interactions with pathogenic fungi. Our main finding are the following : (1) promoting cropped plant–weed competition by manipulating cropped cover could greatly contribute to weed reduction ; (2) weed seed granivory by invertebrates can significantly lower weed emergence, although this effect can be highly variable because seed predation is embedded within complex multitrophic interactions that are to date not fully understood ; (3) a wide range of fungi are pathogenic to various stages of weed development, but strain efficacy in field trials does not often match that in controlled conditions. We present a framework that superimposes biodiversity-based options for weed biocontrol on a classical Integrated Weed Management system. We then describe the current state of knowledge on interactions between agronomic practices and the organisms at play and between the different biological components of the system. We argue that further advances in our understanding of biodiversity-based options and their performance for weed biocontrol will require farm-scale experimental trials.

International audience; Background Global agriculture is undergoing a phase of agroecological transition. This transition will be characterized by adoption of agroecological cropping practices and by an increased diversity of soil management/tillage practices. However, very little is known as to whether or not crop seed germination and seedling emergence (hereafter referred to as SGE) will be affected under these cropping practices. Scope This paper first proposes a conceptual scheme which integrates key abiotic and biotic factors affecting crop SGE. Subsequently, the key mechanistic factors affecting SGE (i.e. intrinsic factors related to the seeds, and extrinsic factors related to the biotic and abiotic conditions of the seedbed), and how crop management practices can influence SGE through alterations of these direct mechanistic factors are discussed. This is done with special emphasis on how agricultural practices, particularly those related to agro-ecology, may impact SGE. Conclusions Crop SGE are affected by five major groups of drivers, namely seed and seedling characteristics, seedbed physical components, seedbed chemical components, seedbed biological components, and cropping systems. Although the crop SGE failure frequently occurs under field conditions, very little quantitative information is available in the literature on the real economic impact, the precise cause/s and ranking of factors associated with this failure. Re-seeding is often practiced for a number of crops to compensate the lack of SGE with significant direct and indirect costs for farmers. Little information exists in the literature concerning how SGE will be affected under agroecological cropping systems, such as conservation agriculture, or organic farming, or under climate-driven changes. Field observation, experimental and modeling studies are needed to fill the current knowledge gaps on the economic impact, precise cause/s and ranking of different stress factors associated with SGE failure.

Certain amino acids induce inhibitory effects in plant growth due to feedback inhibition of metabolic pathways. The inhibition patterns depend on plant species and the plant developmental stage. Those amino acids with inhibitory action on specific weeds could be utilized as herbicides, however, their use for weed control has not been put into practice. Orobanche minor is a weed that parasitizes red clover. O. minor germination is stimulated by clover root exudates. The subsequent seedling is an obligated parasite that must attach quickly to the clover root to withdraw its nutrients. Early development of O. minor is vulnerable to amino acid inhibition and therefore, a series of in vitro, rhizotron, and field experiments were conducted to investigate the potential of amino acids to inhibit O. minor parasitism. In in vitro experiments it was found that among a collection of 20 protein amino acids, lysine, methionine and tryptophan strongly interfere with O. minor early development. Field research confirmed their inhibitory effect but revealed that methionine was more effective than lysine and tryptophan, and that two successive methionine applications at 308 and 543 growing degree days inhibited O. minor emergence in red clover up to 67%. We investigated additional effects with potential to influence the practical use of amino acids against broomrape weeds, whether the herbicidal effect may be reversible by other amino acids exuded by host plants or may be amplified by inducing host resistance barriers against O. minor penetration. This paper suggests that amino acids may have the potential to be integrated into biorational programs of broomrape management., This work was funded by INRA ‘Division Santé des Plantes et Environnement. Appel à projets scientifiques 2015. Catégorie Biocontrôle’. MF-A was supported by the Marie-Curie FP7 COFUND People Programme, through the award of an AgreenSkills fellowship (under grant agreement n° PCOFUND-GA-2010-267196).

Fusarium head blight (FHB) is a devastating disease of cereals caused by Fusarium fungi. The disease is of great economic importance especially owing to reduced grain quality due to contamination by a range of mycotoxins produced by Fusarium. Disease control and prediction is difficult because of the many Fusarium species associated with FHB. Different species may respond differently to control methods and can have both competitive and synergistic interactions. Therefore, it is important to understand how agricultural practices affect Fusarium at the community level. Lower levels of Fusariwn mycotoxin contamination of organically produced cereals compared with conventionally produced have been reported, but the causes of these differences are not well understood. The aim of our study was to investigate the effect of agricultural factors on Fusarium abundance and community composition in different cropping systems. Winter wheat kernels were collected from 18 organically and conventionally cultivated fields in Sweden, paired based on their geographical distance and the wheat cultivar grown. We characterised the Fusarium community in harvested wheat kernels using 454 sequencing of translation elongation factor 1-alpha amplicons. In addition, we quantified Fusariwn spp. using real-time PCR to reveal differences in biomass between fields. We identified 12 Fusariwn operational taxonomic units (OTUs) with a median of 4.5 OTUs per field. Fusarium graminearum was the most abundant species, while F. avenaceum had the highest occurrence. The abundance of Fusariwn spp. ranged two orders of magnitude between fields. Two pairs of Fusariurt species co-occurred between fields: F. poae with F. tricinctwn and F. culmorwn with F. sporofrichoides. We could not detect any difference in Fusariwn communities between the organic and conventional systems. However, agricultural intensity, measured as the number of pesticide applications and the amount of nitrogen fertiliser applied, had an impact on Fusariwn communities, specifically increasing the abundance of F. tricinctwn. There were geographical differences in the Fusarium community composition where F. graminearwn was more abundant in the western part of Sweden. The application of amplicon sequencing provided a comprehensive view of the Fusarium community in cereals. This gives us better opportunities to understand the ecology of Fusarium spp., which is important in order to limit FHB and mycotoxin contamination in cereals.

We present a case of total occlusion of the superior vena cava (SVC) with extensive thrombosis of the adjacent large veins secondary to multiple abandoned pacemaker leads with a superimposed chronic lead infection by Corynebacterium jeikeium. A surgical lead extraction was performed with an extensive en-bloc resection of the SVC together with the right subclavian vein and the right innomate vein. No venous reconstruction was required because of an unobstructed runoff via a well-developed azygos system.

Genome sequencing of Fusarium oxysporum revealed that pathogenic forms of this fungus harbour supernumerary chromosomes with a wide variety of genes, many of which likely encode traits required for pathogenicity or niche specialization. Specific transcription factor gene families are expanded on these chromosomes including the EBR1 family (Enhanced Branching). The significance of the EBR1 family expansion on supernumerary chromosomes and whether EBR1 paralogues are functional is currently unknown. EBR1 is found as a single copy in F.graminearum and other fungi but as multiple paralogues in pathogenic F.oxysporum strains. These paralogues exhibit sequence and copy number variation among different host-specific strains and even between more closely related strains. Relative expression of the EBR1 paralogues depends on growth conditions and on the presence of the single EBR1 gene in the core genome. Deletion of EBR1 in the core genome in different F.oxysporum strains resulted in impaired growth, reduced pathogenicity and slightly reduced biocontrol capacities. To identify genes regulated by EBR1, the transcriptomes of wild-type and Deltaebr1 strains were compared for both F.oxysporum and F.graminearum. These studies showed that in both species, EBR1 regulates genes involved in general metabolism as well as virulence.

The protective Fusarium oxysporum strain Fo47 is effective in controlling Fusarium wilt in tomato. Previous studies have demonstrated the role of direct antagonism and involvement of induced resistance. The aim of the present study was to investigate whether priming of plant defense responses is a mechanism by which Fo47 controls Fusarium wilt. An in vitro design enabled inoculation of the tap root with Fo47 and the pathogenic strain (Fol8) at different locations and different times. The expression levels of six genes known to be involved in tomato defense responses were quantified using reverse-transcription quantitative polymerase chain reaction (qPCR). Three genes—CHI3, GLUA, and PR-1a—were overexpressed in the root preinoculated with Fo47, and then challenged with Fol8. The genes GLUA and PR-1a were upregulated in cotyledons after inoculation of Fo47. Fungal growth in the root was assessed by qPCR, using specific markers for Fo47 and Fol8. Results showed a reduction of the pathogen growth in the root of the tomato plant preinoculated with Fo47. This study demonstrated that priming of tomato defense responses is one of the mechanisms of action of Fo47, which induces a reduced colonization of the root by the pathogen.

Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. IMPORTANCE We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution.

Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium -specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology.

SPEIPM; This 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.

Aims To evaluate the effect of the type of crop residues on the colonization dynamic of Fusarium graminearum in soil. Methods and Results The ability of F. graminearum to survive in the presence of various crop residues was assessed on Petri dishes and in microcosms. These microcosms comprised soil that had or had not been previously disinfested with or without amendment with various crop residues. The colonization dynamic of F. graminearum was monitored through real–time PCR. Fusarium graminearum development was higher in disinfested soil than in non-disinfested one. The fungal growth was enhanced to various extents according to the type of crop residues, except for mustard residues which inhibited it. The biochemical and physical properties of the residues were likely to account for the differences in the survival of F. graminearum. Conclusions F. graminearum is a poor competitor in soil but it can use maize, wheat, and rape residues to ensure its survival. Conversely alfalfa, which is assimilated by microorganisms very easily, avoids long-lasting survival of the fungus. And finally mustard producing glucosinolates could be used as an intermediate crop to reduce the inoculum amount. Significance and Impact of Study This study is contributing to the knowledge about F. graminearum saprotophic abilities and proposes interesting paths to limit its survival in soil. This article is protected by copyright. All rights reserved.

International audience; The intensive use of synthetic herbicides is questioned for many reasons. Bioherbicides, as integrated weed management tools, however, have the potential to offer a number of benefits such as increased target specificity and rapid degradation. Despite the efforts to identify effective bioherbicide agents in laboratory and field, only thirteen bioherbicides are currently available on the market. Since 1980, the number of biopesticides has increased around the world, while the market share of bioherbicides represents less than 10% of all biopesticides. Nevertheless, weed management implemented at the cropping systems scale needs bioherbicides because of legislation to drive weed management away from heavy reliance on chemicals, the global increase in organic agriculture, the need of both organic and conventional agriculture to increase weed control efficiency, concerns about herbicide resistance, and concern from the public about environmental safety of herbicides. Consequently, we review here the existing products on the market and describe their history, mode of action, efficacy and target weeds. This review is unique because we also discuss the role of bioherbicides in integrated weed management: to manage soil weed seedbanks with seed-targeted agents in addition to primary tillage, to increase the efficacy of mechanical weeding because bioherbicides are more effective on seedlings, to increase the suppression effect of crop cultivars by first slowing weed growth, to terminate cover crops particularly in conservation agriculture, and finally to manage herbicide resistant populations. (C) 2016 Elsevier Ltd. All rights reserved.

SPE IPM; Ornamentals include all decorative plants suitable for indoor or outdoor uses. A large variety of plants is produced and sold on a worldwide market. One of the most destructive pathogenic microorganisms for ornamental production is the soil-borne fungus Fusarium oxysporum. Many F. oxysporum pathogenic strains can infect numerous ornamental plants during production and/or post harvest storage. Once the disease has broken out, plants are rarely suitable for commercialization. No curative control method is currently available. The best management of the diseases can only be achieved through an integrative approach in which biological control can play a major role in complement of varietal selection for resistance, provided that lines are available, which is rarely the case. Biological control methods on ornamentals are limited to the use of microbial biological control agents and botanicals, i.e. essential oils or plant extracts. An overview of the studies about botanical and microorganism use against F. oxysporum on ornamentals highlighted that the use of these methods is less than 2 decades and that they arouse increasing interest. Microorganism and botanical sources are countless; consequently, the choice of a screening method to select good candidates is critical. Both microorganisms and botanicals display various modes of action that are not all fully understood, especially for botanicals. As soon as a promising microorganism or botanical candidate is identified, different parameters linked to the development of the product (mode of application, dose, formulation, production) need to be defined and standardized to optimize the quality of the final product. These steps also determine the success or failure of a product on the market. Once the product has been elaborated, the registration process can start. Depending on the country, requirements are different and the whole process is more or less tedious. However, 26 biological control products are currently available for F. oxysporum control on ornamentals, and the biological control market is growing. Moreover, biological control methods can be combined with one another or with other control methods but much additional research is required to develop methodologies for incorporating biologicals into other control strategies for ornamental disease management.

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.

In 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-1α 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°C than at 24°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 Algeria.

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/256699; Nonpathogenic Fusarium oxysporum endophytes from healthy banana roots were evaluated for their ability to reduce Fusarium wilt of banana (Panama disease). Isolates were identified morphologically and by using species-specific primers. Pathogenicity was confirmed by inoculating banana plantlets in the greenhouse. Nonpathogenic F. oxysporum isolates were grouped into 14 haplotype groups by polymerase chain reaction restriction fragment length polymorphism analysis of the intergenic spacer region, and representative isolates evaluated for biocontrol of F. oxysporum f. sp. cubense. In the greenhouse, 10 nonpathogenic F. oxysporum isolates were able to significantly reduce Fusarium wilt of banana. The isolate that protected banana plantlets best in the greenhouse, a nonpathogenic F. oxysporum from the root rhizosphere, and Pseudomonas fluorescens WCS 417 were then field tested. When the putative biological control organisms were tested in the field, neither the nonpathogenic F. oxysporum, P. fluorescens, nor combinations thereof reduced Fusarium wilt development significantly. A number of factors could contribute to the lack of field protection, including soil microbial and chemical composition and reduced survival of biocontrol organisms in banana roots. A lack of knowledge regarding the etiology of Fusarium wilt of ‘Cavendish’ banana in the subtropics and the effect of F. oxysporum f. sp. cubense race and banana cultivar in protection of banana by biocontrol organisms should be further investigated.

Being able to identify specifically a biological control agent at the strain level is not the only requirement set by regulations (EC)1107/2009, it is also necessary to study the interactions of the agent with the plant and the pathogen in the rhizosphere. Fo47 is a soil-borne strain of Fusarium oxysporum which has the capacity to protect several plant species against the pathogenic formae speciales of F. oxysporum inducing wilts. A strain-specific sequence-characterized amplified region marker has been designed which makes it possible to distinguish Fo47 from other strains of F. oxysporum. In addition, a real-time PCR assay has been developed to quantify Fo47 in root tissues. The proposed assay has been validated by following the dynamics of root colonization of tomato plants grown in soil infested with Fo47. Results showed that with the method it is possible to quantify Fo47 in roots in the absence or presence of the pathogen and in the absence or in presence of the native microbial communities.

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/256699; International audience; Potato crop is the fourth main food crop in the world and it will certainly feed a big part of the global population in the next years. The economical outlets for this crop are great; however, numerous diseases either soil- or air-borne can cause huge losses in the production. Worldwide, about 40 soil-borne diseases affect potato and cause severe damages especially on tubers, the economically most important part of the plant. The occurrence and development of soil-borne diseases depend on very diverse factors affecting either the pathogen or the plant. Favorable conditions for potato diseases development are frequently the same as the conditions needed for potato growth: temperature between 10°C and 25°C, high humidity, medium pH, etc. Adapted cultural practices such as a rotation longer than 4 years, appropriate fertilization and water management, an adapted delay between haulm killing and harvest, and dry and cool conditions for tuber storage are good ways to control potato diseases. In most cases, potato pathogens develop specific survival forms, dissemination ways and host penetration methods. The genetic variability of the pathogens implies the use of adapted diagnostic and control methods. Decision support systems developed to predict yield losses allow choosing good control methods such as the use of healthy seeds, adapted pesticides, cultural practices, and biological control agents for each potato disease. The complexity of the interactions between a pathogen and its host, influenced by biotic and abiotic factors of the environment, make the control of the diseases often very difficult. However, deep knowledge of pathosystems allows setting up integrated pest management systems allowing the production of healthy and good quality potatoes.

Rhizoctonia 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.

International audience; The relationships between biotic changes and local decrease in soil conduciveness in disease patches towards the disease incited by Rhizoctonia solani AG 2-2 in a sugar beet field in France were investigated. Soil samples from healthy and diseased areas were analysed for bacterial and fungal densities, molecular and physiological microbial community structures, and antagonistic abilities of Trichoderma isolates collected from diseased and healthy areas. Although the inoculum density was higher inside the disease patches, the respective soil was less conducive towards disease incited by R. solani AG 2-2. It was concluded that the pathogen was present in healthy areas but did not incite disease in field conditions. Conversely, the response of the microflora to previous development of R. solani in diseased areas prevented further pathogenic activity. Indeed, genetic and physiological structures of the fungal communities and physiological structures of the bacterial communities were modified in disease patches compared to healthy areas. The terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the peaks corresponding to R. solani and Trichoderma spp. were higher inside the patches than in the healthy areas. Trichoderma isolates from the disease patches were more antagonistic than those from the healthy areas. These results suggest that disease caused by R. solani AG 2-2 induced changes in genetic and physiological structure of microbial populations and development of antagonists. The decreased conduciveness inside the patches may help explain patch mobility in the following season.

IFN regulatory factor 7 (IRF7) has been described as the master regulator of type I IFN responses and has been shown to be critical for innate antiviral immunity in vivo. In addition to type I IFN, NK cell responses are involved in the control of viral replication during acute viral infection. To investigate the role of IRF7 in the context of a viral infection that induces a strong NK cell response, the murine cytomegalovirus (MCMV) infection model was used. WT, IRF7-deficient and IRF3/IRF7-double deficient mice were infected with MCMV. The systemic IFN-alpha response to MCMV was entirely dependent on IRF7, but independent of IRF3. However, peak IFN-beta production during MCMV infection was not affected by the lack of IRF7 or both IRF7 and IRF3. Despite the complete lack of IFN-alpha production IRF7- and IRF3/IRF7-deficient mice were surprisingly efficient in controlling MCMV replication and were only modestly more susceptible to MCMV infection than WT mice. NK cell cytotoxicity was unimpaired and NK cell IFN-gamma production was enhanced in IRF7-deficient mice correlating with increased levels of bioactive IL-12. Owing to these compensatory mechanisms IRF7-dependent antiviral immune responses were not essential for resistance against acute MCMV infection in vivo.

Dendritic cells which are located at the interface of innate and adaptive immunity are targets for infection by many different DNA and RNA viruses. Dendritic cell subpopulations express specific nucleic acid recognition receptors belonging to the Toll-like receptor family (TLR3, 7, 8, 9) and the cytosolic RNA helicase family (RIG-I, MDA5, LGP2). Activation of dendritic cells by viral DNA and RNA via these receptors is essential for triggering the innate antiviral immune response and shaping the ensuing adaptive antiviral immunity. This review will summarize our current knowledge of viral nucleic acid recognition and signaling by Toll-like receptors and RNA helicases focusing on recent evidence for their specific functions in antiviral defense in vivo.

International audience; Root and stem rot (RSR) is a very detrimental disease of vanilla worldwide. Fusarium oxysporum is frequently associated with the disease but other Fusarium species are also reported. In this international study, 52 vanilla plots were surveyed in three of the most important vanilla producing countries (Madagascar, Reunion Island and French Polynesia) in order to determine the aetiology of RSR disease. Subsets from the 377 single-spored Fusarium isolates recovered from rotten roots and stems in the surveys were characterized by molecular genotyping (EF1α and IGS gene sequences) and pathogenicity assays on Vanilla planifolia and V. ×tahitensis, the two commercially grown vanilla species. Fusarium oxysporum was shown to be the principal species responsible for the disease, representing 79% of the isolates recovered from the RSR tissues, 40% of which induced severe symptoms on inoculated plantlets. Fusarium oxysporum isolates were highly polyphyletic regardless of geographic origin or pathogenicity. Fusarium solani, found in 15% of the samples and inducing only mild symptoms on plantlets, was considered a secondary pathogen of vanilla. Three additional Fusarium species were occasionally isolated in the study (F. proliferatum, F. concentricum and F. mangiferae) but were nonpathogenic. Histopathological preparations observed in wide field and multiphoton microscopy showed that F. oxysporum penetrated the root hair region of roots, then invaded the cortical cells where it induced necrosis in both V. planifolia and V. ×tahitensis. The hyphae never invaded the root vascular system up to 9 days post-inoculation. As a whole, the data demonstrated that RSR of vanilla is present worldwide and that its causal agent should be named F. oxysporum f. sp. radicis-vanillae. (Résumé d'auteur)

Knowing that actin microfilaments play a key role in the mobilization of the defence-associated cellular responses, the aim of this study was to compare changes affecting the actin cytoskeleton in tomato cells after inoculation with germinated microconidia of a biocontrol (Fo47, Fom24) or a pathogenic (Fol8) strain of Fusarium oxysporum. Actin microfilaments were observed by labelling with TRITC-phalloidin combined with fluorescence microscopy. Results showed that only tenuous changes in the actin cytoskeleton architecture occurred after inoculation with the biocontrol strains whereas the actin cytoskeleton was significantly altered after inoculation with the pathogenic one. In the two types of interaction, cell death occurs and can be considered as one key component of cell defence responses. A pharmacological approach using cytochalasins was chosen to determine whether the inhibition of actin polymerization differently affects the kinetics of tomato cell death. Data showed that cytochalasins reduced cell death induced by the biocontrol strain Fo47, and in contrast, increased cell death induced by the pathogenic strain Fol8, suggesting that the pathway leading to cell death differs in the protective and compatible interactions.

Fusarium 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 samples

N2O is a powerful greenhouse gas contributing both to global warming and ozone depletion. While fungi have been identified as a putative source of N2O, little is known about their production of this greenhouse gas. Here we investigated the N2O-producing ability of a collection of 207 fungal isolates. Seventy strains producing N2O in pure culture were identified. They were mostly species from the order Hypocreales order—particularly Fusarium oxysporum and Trichoderma spp.—and to a lesser extent species from the orders Eurotiales, Sordariales and Chaetosphaeriales. The N2O 15N site preference (SP) values of the fungal strains ranged from 15.8‰ to 36.7‰ and we observed a significant taxa effect, with Penicillium strains displaying lower SP values than the other fungal genera. Inoculation of 15 N2O-producing strains into pre-sterilized arable, forest and grassland soils confirmed the ability of the strains to produce N2O in soil with a significant strain-by-soil effect. The copper-containing nitrite reductase gene (nirK) was amplified from 45 N2O-producing strains and its genetic variability showed a strong congruence with the ITS phylogeny, indicating vertical inheritance of this trait. Taken together, this comprehensive set of findings should enhance our knowledge of fungi as a source of N2O in the environment.

Background and Aim. Humic substances (HS) comprise the majority of dead and living organic carbon, including organisms. In the environment, they are considered to be chemically inert or at least refractory. Recent papers, however, show that HS (including natural organic matter – NOM, isolated by reverse osmosis) are natural chemicals which interact with aquatic organisms. They are taken up and cause a variety of stress defense reactions which are well known from man-made chemicals. These reactions include chaperon activation, induction and modulation of biotransformation enzymes, or induction of antioxidant defense enzymes. One specific reaction with freshwater plants is the reduction of photosynthetic oxygen release. In this contribution, we compare the susceptibilities (cell yield) of two closely related coccal green algae, Monoraphidium convolutum and M. minutum, towards various NOM isolates.

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/256699; One of the most serious diseases of banana is fusarium wilt, caused by Fusarium oxysporum f.sp. cubense (Foc). The objectives of this study were to isolate and identify nonpathogenic F. oxysporum strains from soils suppressive to banana wilt, and to determine the diversity of these isolates. More than 100 Fusarium strains were isolated from the rhizosphere of banana plants and identified to species level. Pathogenicity testing was carried out to confirm that these isolates were nonpathogens of banana. A PCR-based RFLP analysis of the intergenic spacer region of the ribosomal RNA operon was used to characterize the nonpathogens. The isolates were also compared with isolates of Foc from South Africa and the known biological control isolate of F. oxysporum, Fo47. The species-specific primers FOF1 and FOR1, in addition to morphological features, were used to confirm the identity of F. oxysporum isolates included in the PCR-RFLP analysis. Twelve different genotypes could be distinguished, identified by a six-letter code allocated to each isolate following digestion with the restriction enzymes HaeIII, HhaI, HinfI, MspI, RsaI and ScrfI. Eleven of these included nonpathogenic F. oxysporum isolates, and these groups could all be distinguished from the genotype that included Foc. Fo47 was included in one of the genotype groups consisting of nonpathogenic F. oxysporum isolates from South Africa.

The most common approach to biological control consists of selecting antagonistic microorganisms, studying their modes of action and developing a biological control product. Despite progress made in the knowledge of the modes of action of these biological control agents (BCAs), practical application often fails to control disease in the fields. One of the reasons explaining this failure is that the bio-control product is used the same way as a chemical product. Being biological these products have to be applied in accordance with their ecological requirements. Another approach consists of induction of plant defence reactions. This can be done by application of natural substances produced by or extracted from microorganisms, plants, or algae. Since they do not aim at killing the pathogens, these methods of disease control are totally different from chemical control. Although promising, these methods have not been sufficiently implemented under field conditions. A third approach consists of choosing cultural practices that might decrease the incidence or severity of diseases. These methods include the choice of an appropriate crop rotation with management of the crop residues, application of organic amendments and the use of new technology such as the biological disinfestation of soils. Biological control practices need an integrative approach, and more knowledge than chemical control.

A collection of 76 plant-pathogenic and 41 saprophytic Fusarium oxysporum strains was screened for sensitivity to 2,4-diacetylphloroglucinol (2,4-DAPG), a broad-spectrum antibiotic produced by multiple strains of antagonistic Pseudomonas fluorescens. Approximately 17% of the F. oxysporum strains were relatively tolerant to high 2,4-DAPG concentrations. Tolerance to 2,4-DAPG did not correlate with the geographic origin of the strains, formae speciales, intergenic spacer (IGS) group, or fusaric acid production levels. Biochemical analysis showed that 18 of 20 tolerant F. oxysporum strains were capable of metabolizing 2,4-DAPG. For two tolerant strains, analysis by mass spectrometry indicated that deacetylation of 2,4-DAPG to the less fungitoxic derivatives monoacetylphloroglucinol and phloroglucinol is among the initial mechanisms of 2,4-DAPG degradation. Production of fusaric acid, a known inhibitor of 2,4-DAPG biosynthesis in P. fluorescens, differed considerably among both 2,4-DAPG-sensitive and -tolerant F. oxysporum strains, indicating that fusaric acid production may be as important for 2,4-DAPG-sensitive as for -tolerant F. oxysporum strains. Whether 2,4-DAPG triggers fusaric acid production was studied for six F. oxysporum strains; 2,4-DAPG had no significant effect on fusaric acid production in four strains. In two strains, however, sublethal concentrations of 2,4-DAPG either enhanced or significantly decreased fusaric acid production. The implications of 2,4-DAPG degradation, the distribution of this trait within F. oxysporum and other plant-pathogenic fungi, and the consequences for the efficacy of biological control are discussed.

Strains of non-pathogenic Fusarium oxysporum and Pseudomonas fluorescens are effective biocontrol agents against Fusarium diseases. Use of strain Fo47 of F. oxysporum in combination with strain C7 of P. fluorescens improves disease control in comparison to application of Fo47 alone. To develop a product based on a combination of these two strains, it would be beneficial to produce and formulate both organisms together. When an irradiated peat was inoculated with these strains either alone or in combination, they grew actively and reached similar maximum population densities irrespective of the initial inoculum concentration (1×103 and 1×106 g−1 of peat) and mode of inoculation. These populations survived well with only a slight decrease in population densities after 11 months storage at 25°C. A bioassay was performed to evaluate peat and microbial suspension inocula of C7 and Fo47 alone or in combination against the flax pathogen, F. oxysporum f. sp. lini. Biocontrol activity of the peat-produced inocula ...

SPE IPM MERS EA; International audience; Members of the Fusarium group were recently detected in water distribution systems of several hospitals in the world. An epidemiological investigation was conducted over 2 years in hospital buildings in Dijon and Nancy (France) and in non-hospital buildings in Dijon. The fungi were detected only within the water distribution systems of the hospital buildings and also, but at very low concentrations, in the urban water network of Nancy. All fungi were identified as Fusarium oxysporum species complex (FOSC) and Fusarium dimerum species complex (FDSC) by sequencing part of the translation elongation factor 1- alpha (TEF-1a) gene. Very low diversity was found in each complex, suggesting the existence of a clonal population for each. Density and heterogeneous distributions according to buildings and variability over time were explained by episodic detachments of parts of the colony from biofilms in the pipes. Isolates of these waterborne populations as well as soilborne isolates were tested for their ability to grow in liquid medium in the presence of increasing concentrations of sodium hypochlorite, copper sulfate, anti-corrosion pipe coating, at various temperatures (4 e42 C) and on agar medium with amphotericin B and voriconazole. The waterborne isolates tolerated higher sodium hypochlorite and copper sulfate concentrations and temperatures than did soilborne isolates but did not show any specific resistance to fungicides. In addition, unlike waterborne isolates, soilborne isolates did not survive in water even supplemented with glucose, while the former developed in the soil as well as soilborne isolates. We concluded the existence of homogeneous populations of FOSC and FDSC common to all contaminated hospital sites. These populations are present at very low densities in natural waters, making them difficult to detect, but they are adapted to the specific conditions offered by the complex water systems of public hospitals in Dijon and Nancy and probably other localities in the world.

The insecticide chlordecone is a contaminant found in most of the banana plantations in the French West Indies. This study aims to search for fungal populations able to grow on it. An Andosol heavily contaminated with chlordecone, perfused for 1 year in a soil-charcoal system, was used to conduct enrichment cultures. A total of 103 fungal strains able to grow on chlordecone-mineral salt medium were isolated, purified, and deposited in the MIAE collection (Microorganismes d'Intérêt Agro-Environnemental, UMR Agroécologie, Institut National de la Recherche Agronomique, Dijon, France). Internal transcribed spacer sequencing revealed that all isolated strains belonged to the Ascomycota phylum and gathered in 11 genera: Metacordyceps, Cordyceps, Pochonia, Acremonium, Fusarium, Paecilomyces, Ophiocordyceps, Purpureocillium, Bionectria, Penicillium, and Aspergillus. Among predominant species, only one isolate, Fusarium oxysporum MIAE01197, was able to grow in a liquid culture medium that contained chlordecone as sole carbon source. Chlordecone increased F. oxysporum MIAE01197 growth rate, attesting for its tolerance to this organochlorine. Moreover, F. oxysporum MIAE01197 exhibited a higher EC50 value than the reference strain F. oxysporum MIAE00047. This further suggests its adaptation to chlordecone tolerance up to 29.2 mg l(-1). Gas chromatography-mass spectrometry (GC-MS) analysis revealed that 40 % of chlordecone was dissipated in F. oxysporum MIAE01197 suspension culture. No chlordecone metabolite was detected by GC-MS. However, weak amount of (14)CO2 evolved from (14)C10-chlordecone and (14)C10-metabolites were observed. Sorption of (14)C10-chlordecone onto fungal biomass followed a linear relationship (r (2) = 0.99) suggesting that it may also account for chlordecone dissipation in F. oxysporum MIAE01197 culture.

SPEIPM; Soil 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.

Reports in the literature show that the dietary fatty acid (FA) composition is reflected in fish muscle, their internal organs and eggs. Fish eggs are used in toxicity tests to determine the subchronic toxicity of various substances. In toxicity tests, physico-chemical test parameters have been standardized. However, parental age and diet may also influence results of toxicity tests and if so would also require standardization. Our investigations hitherto indicate that the FA composition of eggs and testes in zebrafish is caused by the FA composition of fish diet. Diets with different ratios of n-3/n-6 polyunsaturated fatty acids led to different contents of these FA in the reproductive organs and finally to variations in the fertilization rates. This rate is elevated in the eggs of zebrafish (Danio rerio Hamilton-Buchanan) if the quotient of n-3/n-6 is low.

The enrichment of water bodies with plant nutrients often results in mass growths of cyanobacteria which can produce a range of toxins. Cyanobacterial toxins have adverse effects on fish, birds, and mammals, and are being increasingly recognized as animal and human health hazards. The effects of cyanobacterial toxins on plants, particularly aquatic macrophytes, are little understood. The uptake of microcystin-LR (MC-LR) by Ceratophyllum demersum was detected with approximately 11.2% of the applied 14C-labelled microcystin being taken up after 7 days of exposure. The effects of various concentrations of this toxin on the detoxication enzyme glutathione S-transferase (microsomal and soluble forms) were investigated. Microsomal glutathione S-transferase activity was increased in C. demersum exposed to concentrations of MC-LR above 0.12 μg/L, but reduced at concentrations above 1.0 μg/L, whereas soluble glutathione S-transferase activity was increased by exposure to MC-LR concentrations above 0.5 μg/L. No reduction of soluble GST activity was observed. The activity of both microsomal and soluble GST systems, freshly prepared from a range of plants, was inhibited in the presence of 0.5 μg/L MC-LR. The results indicate a detoxication pathway for MC-LR in aquatic plants. ©1999 John Wiley & Sons, Inc. Environ Toxicol 14: 111–115, 1999