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PEOPLE@HES-SO – Annuaire et Répertoire des compétences
PEOPLE@HES-SO – Annuaire et Répertoire des compétences

PEOPLE@HES-SO
Annuaire et Répertoire des compétences

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Lefort François

Lefort François

Professeur HES ordinaire

Compétences principales

Biocontrôle

Génomique

Métagénomique

Phytopathologie

Microbiologie et bactériologie

Biologie végétale

Profilage génétique

  • Contact

  • Enseignement

  • Publications

  • Conférences

Contrat principal

Professeur HES ordinaire

Bureau: H1.02 - Lullier /DI36- Genève

Haute école du paysage, d'ingénierie et d'architecture de Genève
Rue de la Prairie 4, 1202 Genève, CH
hepia
Domaine
Agronomie et économie forestière
Filière principale
Agronomie
BSc HES-SO en Agronomie - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • Génétique
BSc HES-SO en Agronomie - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • responsable des thèses de bachelor en agronomie
BA HES-SO en Architecture - Haute école du paysage, d'ingénierie et d'architecture de Genève
  • Amélioration des plantes
  • Santé des plantes
  • Biotechnologie végétale appliquée
  • Phytopathologie
MA BFH/HES-SO en Architecture - HES-SO Master
  • Landscape genetics
  • Journal Club E1

2025

Quick in vitro Screening of PGPMs for salt tolerance and evaluation of induced tolerance to saline stress in tomato culture
Article scientifique ArODES

Lucas Arminjon, François Lefort

Microorganisms,  2025, 13, 2, 246

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Résumé:

Soil salinity, affecting 20–50% of irrigated farmland globally, poses a significant threat to agriculture and food security, worsened by climate change and increasing droughts. Traditional methods for managing saline soils—such as leaching, gypsum addition, and soil excavation—are costly and often unsustainable. An alternative approach using plant growth-promoting microorganisms (PGPMs) offers promise for improving crop productivity in saline conditions. This study tested twenty-three bacterial strains, one yeast, and one fungal strain, isolated from diverse sources including salicornia plants, sandy soils, tomato stems or seeds, tree leaves, stems, and flowers. They were initially submitted to in vitro selection tests to assess their ability to promote plant growth under salt stress. In vitro tests included auxin production, phosphate solubilization, and co-culture of microorganisms and tomato seedlings in salt-supplemented media. The Bacillus sp. strain 44 showed the highest auxin production, while Bacillus megaterium MJ had the strongest phosphate solubilization ability. Cryptococcus sp. STSD 4 and Gliomastix murorum (4)10-1(iso1) promoted germination and the growth of tomato seedlings in an in vitro co-culture test performed on a salt-enriched medium. This innovative test proved particularly effective in selecting relevant strains for in planta trials. The microorganisms that performed best in the various in vitro tests were then evaluated in vivo on tomato plants grown in greenhouses. The results showed significant improvements in growth, including increases in fresh and dry biomass and stem size. Among the strains tested, Gliomastix murorum (4)10-1(iso1) stood out, delivering an increase in fresh biomass of 94% in comparison to the negative control of the salt modality. These findings highlight the potential of specific PGPM strains to enhance crop resilience and productivity in saline soils, supporting sustainable agricultural practices.

2024

Response of biofilm structure to long-term exposure to CeO2 nanoparticles in a trickling bioreactor for the removal of phenol, nitrogen, and phosphorus
Article scientifique ArODES

Mahkameh Amirbandeh, Seyed Morteza Zamir, François Lefort, Julien Crovadore, Bita Bakhshi

International Biodeterioration & Biodegradation,  2024, 195, 105880

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Résumé:

The long-term exposure of cerium oxide nanoparticles (CeO2 NPs) at 5, 20, and 50 mg/L to the biofilm and its impact on the treatment of synthetic wastewater, containing phenol, in a trickling bioreactor (TBR) were examined. An increase of 38.1 % in the reactive oxygen species (ROS) production and 29.0 % in the lactate dehydrogenase (LDH) release indicated that CeO2 NPs were toxic to the microorganisms at 50 mg/L and disrupted the integrity of the microbial membrane within the community. Phenol biodegradation, total nitrogen (TN), and total phosphorus (TP) removal slightly changed from 98.6, 53.7, and 13.0 % in the absence of NPs to respectively 96.5, 49.7, and 9.0 % in the presence of 50 mg/L CeO2 NPs. High-throughput sequencing after prolonged 30-day exposure to CeO2 NPs showed that the microbial community could self-regulate the population by adjusting species composition in response to the presence of NPs. The relative abundance of some sensitive species such as Castellaniella defragrans declined from 39.5 to 0.6 % in the presence of NPs. However, other species such as Comamonadaceae bacterium thrived and became more prevalent. The TBR effectively removed phenol, TN, and TP in the presence of CeO2 NPs, benefiting from the cells immobilization that limited the access of NPs to the deep layers of biofilm.

Validating indigenous farmers’ practice in the management of the fall armyworm spodoptera frugiperda (J. E. Smith) in maize cropping systems in Africa
Article scientifique ArODES

Saliou Niassy, Evanson Rigan Omuse, John Emanuel Khang'ati, Ines Bächinger, David Mfuti Kupesa, Xavier Cheseto, Benjamin W. Mbatha, Robert S. Copeland, Samira Abuelgasim Mohamed, Mphatso Gama, Joyce Mulila Mitti, Yeneneh Belayneh, Nicolas Delabays, François Lefort, Sunday Ekesi, Sevgan Subramanian

Life,  14, 2, 180

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Résumé:

Before the invasion of the fall armyworm (FAW) Spodoptera frugiperda into Africa, smallholder farmers had been using indigenous practices such as applying fish soup to plants to manage stemborer pests. Although farmers have since begun adapting this practice against FAW, no attempt has been made to scientifically evaluate this practice. Therefore, we assessed the efficacy of applying fish soup to maize plants that were artificially infested with FAW under semi-field conditions. Our results showed that foliar damage is inversely correlated with the concentration of a fish soup and sugar solution, with the highest (100%) concentration resulting in the lowest foliar damage and the highest plant recovery. The FAW foliar damage results for maize plants treated with 100%, 50%, 10% fish soup and sugar, and distilled water were 46.3 ± 5.6, 51.1 ± 5.0, 71.6 ± 5.2, and 99.4 ± 0.4%, respectively, whereas plant recovery results from the same treatments were 35.2 ± 3.7, 31.1 ± 5.4, 20.0 ± 4.6, and 0.0 ± 0.0%, respectively. A concentration of fish soup and sugar solution of at least 25.9% was required to achieve the lowest foliar damage of 17.8% and peak plant recovery of 73.6%. Fish soup and sugar solutions attracted a wide range of insects, including potential natural enemies (predators and parasitoids) of FAW, in a dose-dependent manner. Maize plants treated with fish soup and sugar showed higher chlorophyll content and better growth than the control did. Proximate and chemical analysis showed that fish soup contains essential plant growth nutrients (e.g., nitrogen, phosphorus, and calcium). Through GC-MS analyses, we identified 76 volatile organic compounds in fish soup, of which 16 have been reported as insect attractants, highlighting their potential ecological significance. Therefore, the indigenous pest management practices for FAW, such as the use of fish soup, deserve particular attention. These practices could contribute to food security and improve the livelihoods of vulnerable communities. Further field validation studies, economic analyses, product development, and optimisation are therefore required to optimise the use of fish soup based on fish waste.

2023

Bioprospecting of a Metschnikowia pulcherrima indigenous strain for Chasselas winemaking in 2022 vintage
Article scientifique ArODES

Frederico Sizzano, Marie Blackford, Hélène Berthoud, Laurent Amiet, Sébastien Bailly, Frédéric Vuichard, Christine Monnard, Stefan Bieri, Jean-Laurent Spring, Yannick Barth, Corentin Descombes, François Lefort, Marilyn Cléroux, Scott Simonin, Charles Chappuis, Gilles Bourdin, Benoît Bach

Foods,  12, 24, 4485

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Résumé:

Interest in Metschnikowia (M.) pulcherrima is growing in the world of winemaking. M. pulcherrima is used both to protect musts from microbial spoilage and to modulate the aromatic profile of wines. Here, we describe the isolation, characterization, and use of an autochthonous strain of M. pulcherrima in the vinification of Chasselas musts from the 2022 vintage. M. pulcherrima was used in co-fermentation with Saccharomyces cerevisiae at both laboratory and experimental cellar scales. Our results showed that M. pulcherrima does not ferment sugars but has high metabolic activity, as detected by flow cytometry. Furthermore, sensory analysis showed that M. pulcherrima contributed slightly to the aromatic profile when compared to the control vinifications. The overall results suggest that our bioprospecting strategy can guide the selection of microorganisms that can be effectively used in the winemaking process.

Proposition d'un indice de performance cultural (IPC) agroécologique
Article professionnel ArODES

Zsolt Maurer, François Lefort, Julian Tugwell, Kim Schneider

Vignes Vergers,  2023, 12, 12-16

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Résumé:

Un nouvel indice opérationnel, l’Indice de Performance Cultural (IPC), a été créé comme outil d’aide à la décision pour les choix des agriculteurs dans leurs plans de culture. Cet indice évalue le rapport entre la quantité d'engrais azoté absorbée par les plantes et la matière fraîche vendable, tout en tenant compte des coûts du marché des engrais et des prix des produits disponibles à la vente au détail. L'IPC identifie les espèces produisant le chiffre d'affaires de production le plus important par mètre carré en utilisant la plus petite quantité d'engrais azoté. Cet indice est basé sur le principe agroécologique qui encourage l'utilisation d'espèces ou de variétés adaptées à un faible niveau d'intrants. Les légumes les plus performants ont été identités en intégrant l'IPC dans le plan cultural d'une exploitation agricole de la région de Genève à titre d’exemple.

Isolation, identification and evaluation of the effects of native entomopathogenic fungi from Côte d’Ivoire on Galleria mellonella
Article scientifique ArODES

Fatoumatou Fofana, Corentin Descombes, Assiri Patrice Kouamé, François Lefort

Microorganisms,  2023, vol. 11, no. 8, article no. 2104

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Résumé:

The fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), is a polyphagous pest highly damaging to maize and other food crops in Africa, particularly in Côte d’Ivoire. Chemical pesticides not only have often proved to be unsuccessful, but cause adverse effects on the environment and human health; therefore, entomopathogenic fungi could represent an alternative biocontrol solution. Against this background, fungi were isolated from soil samples collected in maize fields in three regions of Côte d’Ivoire, by the methods of soil dilution and baiting with Galleria mellonella. The resulting 86 fungal isolates were phenotypically and genetically identified. The pathogenicity of seven isolates of Metarhizium spp., three isolates of Beauveria bassiana and two isolates of Trichoderma sp. was evaluated on fifth instar larvae (L5) of G. mellonella. Larval mortality rates and the median lethal time (LT50) were determined seven days after inoculation for each of these selected isolates. The median lethal concentration (LC50) was determined for a selection of isolates. Beauveria bassiana isolate A214b was the most effective, causing 100% mortality, with an LT50 of 2.64 days and an LC50 of 1.12 × 104 conidia mL−1. Two other promising isolates, A211 and A214a, belonging to B. bassiana, caused 100% mortality with LT50 values of 3.44 and 4.04 days, respectively. Mortality caused by Metarhizium isolates varied from 65.38% to 100%, with Metarhizium anisopliae isolate T331 causing 100% mortality with an LT50 of 3.08 days at an LC50 of 3.33 × 104 conidia mL−1. Trichoderma sp. isolates were the least pathogenic ones. Beauveria bassiana and Metarhizium isolates showed to be virulent against the model Lepidopteran G. mellonella and will be tested on S. frugiperda.

Attraction of Frankliniella occidentalis females towards the aggregation pheromone neryl (S)-2-methylbutanoate and airomones in a y-olfactometer
Article scientifique ArODES

Charles J. F. Chappuis, Marilyn Cléroux, Corentin Descombes, Yannick Barth, François Lefort

Insects,  2023, vol. 14, no. 6, article no. 562

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Résumé:

An understanding of insect olfaction allows for more specific alternative methods of pest control. We evaluated the responses of the western flower thrips (WFT, Frankliniella occidentalis) in a Y-olfactometer to estimate gas-phase concentrations of the aggregation pheromone neryl (S)-2-methylbutanoate and known kairomones such as methyl isonicotinate, (S)-(-)-verbenone, and p-anisaldehyde. The gas-phase concentrations of these compounds were obtained from the release rates measured in dynamic headspace cells. The compounds were collected from the headspace using dried solid-phase extraction (SPE) cartridges and analyzed with a triple quadrupole GC-MS/MS. We observed that the aggregation pheromone significantly attracted WFT females at doses of 10 and 100 µg, whereas methyl isonicotinate and p-anisaldehyde significantly attracted WFT females at the highest dose. Verbenone did not produce any significant results. A completely different picture was obtained when the gas-phase concentrations were considered. The minimal gas-phase concentrations of the pheromone required to attract WFT females was 0.027 ng/mL, at least 100 times lower than that of the other two compounds. The relevance and implications of our results are discussed in light of the insect’s biology and pest management methods.

Levures contre pourritures des fruits :
Article professionnel ArODES
évaluation de levures indigènes contre les maladies post-récolte

Guillaume Thébault, Yannick Barth, François Lefort

Objectif,  98, 15-17

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Résumé:

La réduction du risque phytosanitaire posé par les pesticides chimiques de synthèse nécessite d’évaluer toutes les solutions alternatives dont les microorganismes. Ici, nous avons évalué 25 souches de levures indigènes isolées en Suisse romande comme agents de lutte biologique contre trois importants pathogènes post-récolte des fruits à pépins: Botrytis cinerea, Penicillium expansum et Penicillium digitatum.

2022

Impact of invading species on biodiversity :
Article scientifique ArODES
diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland

Anne Mondino, Julien Crovadore, François Lefort, Sylvain Ursenbacher

Global Ecology and Conservation,  2022, vol. 38, article no. e02239

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Résumé:

Next-generation sequencing is increasingly used in conservation biology to resolve complex interactions between species, either diet or gut parasites studies. We applied a recent long metabarcoding method to elucidate the green whip snake’s (Hierophis viridiflavus) prey consumption based on DNA extracted from stomach contents. Illegally introduced in Canton of Vaud (Switzerland), three populations of the green whip snake have strongly developed in two regions, East (Chablais) and North. We suspect that this introduced species is threatening part of the local herpetofauna, especially the Asp viper and the Western green lizard in this region. Consequently, an extermination program has been implemented from 2016 to mitigate Hierophis viridiflavus expansion and its impact arising from its generalist diet. Stomach contents of 94 individuals removed from introduction sites were analysed by long metabarcoding. Our study revealed the consumption of 67 prey belonging to 9 species, primarily small mammals and reptiles. The recurrent presence of two parasitic nematodes was also discovered. Although cannibalistic behaviour could not be highlighted with this approach, a scavenging behaviour was suspected based on the presence of an insect used in forensic entomology (Calliphora vicina). These results confirm the opportunistic feeding behaviour of Hierophis viridiflavus and its ability to predate on threatened species. Although 86.6 % of preys were not listed on the Swiss Red List, the impact on the Asp viper population can be important (up to 20 % of consumed preys) and could partially explain its strong decline.

Dietary modulation of the human gut microbiota and metabolome with flaxseed preparations
Article scientifique ArODES

Karin Kleigrewe, Martina Haack, Martine Baudin, Thomas Ménabréaz, Julien Crovadore, mahmoud Masri, Michael Beyrer, Wilfried Andlauer, François Lefort, Corinna Dawid, Thomas B. Brück, Wolfram M. Brück

International Journal of Molecular Sciences,  2022, vol. 23, no. 18, article no. 10473

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Résumé:

Flaxseeds are typically consumed either as whole flaxseed, ground flaxseed, flaxseed oil, partially defatted flaxseed meal, or as a milk alternative. They are considered a rich source of vitamins, minerals, proteins and peptides, lipids, carbohydrates, lignans, and dietary fiber, which have shown hypolipidemic, antiatherogenic, anticholesterolemic, and anti-inflammatory property activity. Here, an in vitro batch culture model was used to investigate the influence of whole milled flaxseed and partially defatted milled flaxseed press cake on the gut microbiota and the liberation of flaxseed bioactives. Microbial communities were profiled using 16S rRNA gene-based high-throughput sequencing with targeted mass spectrometry measuring lignan, cyclolinopeptide, and bile acid content and HPLC for short-chain fatty acid profiles. Flaxseed supplementation decreased gut microbiota richness with Firmicutes, Proteobacteria, and Bacteroidetes becoming the predominant phyla. Secoisolariciresinol, enterodiol, and enterolactone were rapidly produced with acetic acid, butyric acid, and propionic acid being the predominant acids after 24 h of fermentation. The flaxseed press cake and whole flaxseed were equivalent in microbiota changes and functionality. However, press cake may be superior as a functional additive in a variety of foods in terms of consumer acceptance as it would be more resistant to oxidative changes.

Shall the wild boar pass? :
Article scientifique ArODES
a genetically assessed ecological corridor in the Geneva region

Fanny Alexandra Laura Kupferschmid, Julien Crovadore, Claude Fischer, François Lefort

Sustainability,  2022, vol. 14, article no. 7463

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Résumé:

Landscape fragmentation caused by road infrastructures represents a major threat to the genetic diversity of a region. The resulting genetic isolation between subpopulations may lead to consanguinity, and consequently to population collapse and extinction. However, the construction of wildlife crossings can help maintain connectivity. In the present paper, we evaluated the genetic spatial structuring of populations of wild boars (Sus scrofa) in three areas of the Geneva region connected by an ecological corridor. Those areas are cut off either by a highway that is crossed by a wildlife overpass or by an anthropized sector. Genetic profiling with 9 nuclear microsatellite markers yielded 61 single profiles, which allowed for clustering, parentage, and linkage disequilibrium analyses, uncovering the populations’ genetic structure. We also evaluated whether the genetic structure was affected by the sex of individuals. In our analyses, all individuals clustered into a single genetic group, suggesting that no structure limited significantly the gene flow in the region. However, a recent admixture indicated a potential increase in the gene flow between two of the subpopulations due to the wildlife overpass, while the other part of the ecological corridor was not or was only partially functional. Genetic distances between males were significantly higher than between females, although the role of sex remains unclear as to its influence on population genetics. Finally, in order to avoid a subregion becoming fully isolated, urbanization planning should consider this genetic evaluation and proceed with further monitoring, especially by focusing on species more sensitive to landscape fragmentation.

No reduction in yield of young robusta coffee when grown under shade trees in ecuadorian amazonia
Article scientifique ArODES

Kevin Piato, Cristian Subia, François Lefort, Jimmy Pico, Dario Calderon, Lindsey Norgrove

Life,  2022, vol. 12, no. 6, article no. 807

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Résumé:

Little is known on what impact shade trees have on the physiology of Coffea canephora (robusta coffee) under tropical humid conditions. To fill this gap, a field experiment was conducted in the Ecuadorian Amazon to investigate how growth, nutrition (leaf N), phenological state (BBCH-scale) and yield of 5-year-old robusta coffee shrubs are affected by the presence or absence of leguminous trees, the type (organic v conventional) and intensity of management. The experiment was a factorial 5 × 4 design with four cropping systems: intensive conventional (IC), moderate conventional (MC), intensive organic (IO) and low organic (LO), and with five shading systems in a split-plot arrangement: full sun (SUN), both Erythrina spp. and Myroxylon balsamum (TaE), M. balsamum (TIM), E. spp. (ERY) and Inga edulis (GUA). Three monthly assessments were made. Cherry yields of coffee shrubs under moderate shade (c. 25%) were similar to those under high light exposure. Coffee shrubs grown with either E. spp. or I. edulis were taller (+10%) and had higher leaf N concentrations (22%) than those grown without consistent shade. Unless receiving c. 25% of shade, coffee shrubs grown under organic cropping systems showed reduced growth (25%). No correlation was found between height, cherry yield and leaf N. Both shading and cropping systems affected leaf N concentration, also depending on phenological state and yield. Further research is needed to confirm our findings in the long-term as well as to elucidate how leguminous trees may induce physiological responses in robusta coffee under humid tropical conditions.

Endophytic PGPR from tomato roots :
Article scientifique ArODES
isolation, in vitro characterization and in vivo evaluation of treated tomatoes (Solanum lycopersicum L.)

Bastien Cochard, Basile Giroud, Julien Crovadore, Romain Chablais, Lucas Arminjon, François Lefort

Microorganisms,  2022, vol. 10, no. 4. article no. 765

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Résumé:

Plant-growth-promoting rhizobacteria (PGPR) are soil bacteria colonizing the rhizosphere and the rhizoplane which have an effect on plant growth through multiple chemical compounds. Rhizobacteria with beneficial effects for plants could therefore be used to reduce the dependence on synthetic chemical fertilizers in conventional agriculture. Within this study, 67 endophytic fungi and 49 bacteria were isolated from root samples from 3 different commercial productions: an off-ground tomato production in a greenhouse, an organic production and a conventional production, both in a soil tunnel. Following morphological selection, 12 fungal and 33 bacterial isolates were genetically identified. Thirteen bacterial isolates belonging to nine potential PGPR species were then applied to tomato seedlings established in sterile substrate. The ability of these bacteria to produce indole acetic acid (IAA) and solubilize phosphate was also evaluated. They all were IAA producers and solubilized phosphate. The most interesting strains for growth promotion were found to be the isolates Pseudomonas palleroniana B10, Bacillus subtilis B25, Bacillus aryabhattai B29 and Pseudomonas fluorescens B17. The isolates P. fluorescens B17, B. aryabhattai B29, B. subtilis B18 and Pseudomonas moraviensis B6 also increased root growth. This study proposed a quick protocol for isolating and testing potential endophytic PGPR that should be characterized further for the direct and indirect mechanisms of growth promotion.

Évaluation agronomique :
Article professionnel ArODES
de trois biostimulants microbiens en production hors sol de chêne rouvre, quercus petraea

Bastien Cochard, Lucas Arminjon, François Lefort

Objectif,  2022, vol. 96, pp. 15-17

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Résumé:

Le développement de la production biologique en pépinière est considéré comme un défi majeur en horticulture. Le renoncement aux intrants de synthèse et aux substrats enrichis en tourbe oblige les professionnels à revoir leur modèle de production sans impacter la productivité et la qualité, garants de viabilité économique. La difficulté est de trouver des alternatives efficaces aux engrais minéraux enrobés et à la tourbe, toujours massivement utilisés. Les biostimulants microbiens seraient un moyen intéressant pour faciliter l'absorption d'éléments nutritifs et limiter l'effet des stress plus propices à apparaître en hors-sol. Plusieurs biostimulants homologués par le FIBL sont disponibles, mais le manque de retour sur leur l'efficacité limite leur utilisation. Dans le cadre de cet essai, trois biostimulants commerciaux ont été évalués sur quarante chênes rouvres. La circonférence des troncs fut mesurée à intervalle régulier sur une période de 23 mois. Les gains de croissance observés en comparaison au contrôle étaient compris entre 11,33 % et 34,40 %.

2021

From strain characterization to field authorization :
Article scientifique ArODES
highlights on Bacillus velezensis strain B25 beneficial properties for plants and its activities on phytopathogenic fungi

Pierre Joly, Alexandra Calteau, Aurélie Wauquier, Rémi Dumas, Mylène Beuvin, David Vallenet, Julien Crovadore, Bastien Cochard, François Lefort, Jean-Yves Berthon

Microorganisms,  2021, vol. 9, no. 9, article no. 1924

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Résumé:

Agriculture is in need of alternative products to conventional phytopharmaceutical treatments from chemical industry. One solution is the use of natural microorganisms with beneficial properties to ensure crop yields and plant health. In the present study, we focused our analyses on a bacterium referred as strain B25 and belonging to the species Bacillus velezensis (synonym B. amyloliquefaciens subsp. plantarum or B. methylotrophicus), a promising plant growth promoting rhizobacterium (PGPR) and an inhibitor of pathogenic fungi inducing crops diseases. B25 strain activities were investigated. Its genes are well preserved, with their majority being common with other Bacillus spp. strains and responsible for the biosynthesis of secondary metabolites known to be involved in biocontrol and plant growth-promoting activities. No antibiotic resistance genes were found in the B25 strain plasmid. In vitro and in planta tests were conducted to confirm these PGPR and biocontrol properties, showing its efficiency against 13 different pathogenic fungi through antibiosis mechanism. B25 strain also showed good capacities to quickly colonize its environment, to solubilize phosphorus and to produce siderophores and little amounts of auxin-type phytohormones (around 13,051 µg/mL after 32 h). All these findings combined to the fact that B25 demonstrated good properties for industrialization of the production and an environmental-friendly profile, led to its commercialization under market authorization since 2018 in several biostimulant preparations and opened its potential use as a biocontrol agent.

Revitalization of the Greek Vitis database :
Article scientifique ArODES
a multimedia web-backed genetic database for germplasm management of Vitis resources in Greece

Androniki C. Bibi, John Marountas, Yiannis Kouklinos, Dimitris Kafetzopoulos, François Lefort, Kalliopi Roubelakis-Angelakis

Journal of Wine Research,  2021, vol. 32, no. 1

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Résumé:

Lefort and Roubelakis-Angelakis ([2000. The Greek Vitis Database: A multimedia web-backed genetic database for germplasm management of Vitis resources in Greece. Journal of Wine Research, 11(3), 233–242. https://doi.org/10.1080/713684241)] were the first to develop a Greek Vitis multimedia web-backed service at the Laboratory of Plant Physiology and Biotechnology of the University of Crete 20 years ago. This service was named Greek Vitis Database (GVD) and it provided free access to six databases, gathering information about Greek cultivars of Vitis vinifera: an information database; a nuclear single sequence repeats (nSSR) microsatellite profiles database; a chloroplast microsatellite (cpSSR) database; a combined nSSR – cpSSR profiles database; an ampelographic database; and a rootstock database. Information and descriptive images were combined with SSR profiles. Although simple sequence repeats are still the markers of choice for compilation, standardization and exchange of information regarding grapevine genetic resources, the advances in computing technology through the years made the GDV inactive. This report is to announce the renovation and revitalization of GVD using new computing technologies. The GVD can now be accessible at http://greekvitisdb.biology.uoc.gr or in the previous address http://www.biology.uoc.gr/gvd redirected.

Neofusicoccum parvum, a new agent of sequoia canker and dieback identified in Geneva, Switzerland
Article scientifique ArODES

Martine Haenzi, Bastien Cochard, Romain Chablais, Julien Crovadore, François Lefort

Forests,  This article belongs to the Special Issue Pests and Pathogens of Urban Trees

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Résumé:

Fungi were isolated in pure cultures from decaying giant sequoias in Geneva (Switzerland). Isolates were genetically identified by ITS rDNA sequencing. Young giant sequoia trees were artificially infected with a pure culture of Botryosphaeria parva. Henle-Koch’s Postulates demonstrated that Botryosphaeria parva was pathogenic to Sequoiadendron giganteum. When analysing the microorganisms associated to canker and dieback symptoms in a giant sequoias (Sequoiadendron giganteum) in Geneva, the fungus Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, teleomorph Botryosphaeria parva (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, was isolated, whereas such symptoms are commonly associated to Fusicoccum aesculi (teleomorph Botryosphaeria dothidea). These two fungal species belong to the same genus Botryosphaeria of the Botryosphaeriaceae family. Because Neofusicoccum parvum was causing cankers and diebacks in other woody species around the world, we extended the analysis to other trees displaying sequoia dieback symptoms in order to evaluate the involvement of Neofusicoccum parvum in such increasing symptoms in sequoias in Geneva. Dried twigs, trunk, and branch cankers from diseased trees were sampled on several distinct sites. From all samples, isolated fungi in pure cultures showed a phenotype typical of Botryosphaeriaceae species. Isolates were then genetically identified at the species level. Subsequently Neofusicoccum parvum was inoculated to young giant sequoia trees, re-isolated in pure culture from provoked symptoms, and re-identified to fulfil Henle-Koch’s postulates. The identification confirmed that Neofusicoccum parvum was present on all sites, while Fusicoccum aesculi was retrieved only once alone. The inoculation of Neofusicoccum parvum isolates on young sequoias demonstrated for the first time that this fungus was able to develop cankers in Sequoiadendron giganteum. Neofusicoccum parvum could, therefore, be the major cause for dying of giant sequoias in the Geneva Lake area.

Draft genome sequences of 3 strains of Apilactobacillus kunkeei isolated from the bee gut microbial community
Article scientifique ArODES

Julien Crovadore, Romain Chablais, François Raffini, Bastien Cochard, Martine Haenzi, François Gérard, Karl Kristian Jensen, François Lefort

Microbiology Resource Announcements,  2021, vol. 10, no. 13, article no. e00088-21

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Résumé:

Apilactobacillus kunkeei is a fructophilic lactic acid bacterium found in fructose-rich environments such as flowers, fruits, fermented food, honey, and honeydew, as well as in the guts of fructose-feeding insects. We report here the draft genome sequences of three Apilactobacillus kunkeei strains isolated from the gut microbial community of three honeybees.

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Article scientifique ArODES

V. I. Risovannya, S. M. Goryslavets, François Lefort

Magarach Vinogradstvo i Vinodelie,  2021, vol. 23, no. 4, pp. 330-335

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The assessment results of genetic diversity of 24 local varieties of the South of Russia, maintained in the ampelographic collection of the FSBSI Institute Magarach are presented. DNA typing of cultivars and assessment of allelic diversity was performed using 9 nuclear (nSSR) and 3 chloroplast (cpSSR) microsatellite loci. The level of polymorphism of nSSR loci was 100%. A total of 73 alleles were identified with an average of 9.1 alleles per locus. The minimal number of alleles was observed in the ssrVrZAG64 and ssrZag83 loci. The biggest number of alleles was found in the ssrVvUCH29 locus (13 alleles), the size range of which was 203 bp-309 bp. As a result of polymorphism analysis of cpSSR loci, 4 chlorotypes were identified: A, B, C, D. Chlorotype D is the most widespread in the group of the studied cultivars (58%). The article discusses the origin of varieties based on the analysis of their haplotypes. Based on the results of the analysis of allelic polymorphism of nSSR loci, a matrix of genetic distances was calculated, the values of which were in the range of 0.33-0.94, and a dendrogram, reflecting the relationship between the samples, was constructed. According to the degree of genetic similarity, 3 main clusters were distinguished, in which differentiation or a tendency towards differentiation by ecological-geographical groups was observed.

Organic farming practices and shade trees reduce pest infestations in robusta coffee systems in Amazonia
Article scientifique ArODES

Kevin Piato, Cristian Subia, Jimmy Pico, Dario Calderon, Lindsey Norgrove, François Lefort

Life,  2021, vol. 11, no. 5, article no. 413

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Coffee agroforestry systems could reconcile agricultural and environmental objectives. While pests and diseases can reduce yield, their interactions with shade and nutrition have been rarely researched, and are particularly lacking in perennial systems. We hypothesized that intermediate shade levels could reduce coffee pests while excess shade could favor fungal diseases. We hypothesized that organic rather than mineral fertilization would better synchronize with nutrient uptake and higher nutrient inputs would be associated with reduced pest and disease damage due to higher plant vigor, yet effects would be less obvious in shaded plots as coffee growth would be light-limited. Using three-year-old trees of Coffea canephora var. Robusta (robusta coffee) in the Ecuadorian Amazon, we compared a full-sun system with four shading methods creating different shade levels: (1) Myroxylon balsamum; (2) Inga edulis; (3) Erythrina spp.; or, (4) Erythrina spp. plus Myroxylon balsamum. Conventional farming at either (1) moderate or (2) intensified input and organic farming at (3) low or (4) intensified input were compared in a split-plot design with shade as the main plot factor and farming practice as the sub-plot factor. The infestation of the following pests and disease incidences were evaluated monthly during the dry season: brown twig beetle (Xylosandrus morigerus), coffee leaf miner (Leucoptera coffeella), coffee berry borer (Hypothenemus hampei), anthracnose disease (Colletotrichum spp.), thread blight (Pellicularia koleroga), and cercospora leaf spot (Cercospora coffeicola). Coffee berry borer and brown twig beetle infestation were both reduced by 7% in intensified organic treatments compared to intensified conventional treatments. Colonization of coffee berry borer holes in coffee berries by the entomopathogenic fungus Beauveria bassiana was also assessed. Brown twig beetle infestation was significantly higher under full sun than under Inga edulis, yet no other shade effects were detected. We demonstrate for the first time how intensified input use might promote pest populations and thus ultimately lead to robusta coffee yield losses.

The role of Desmodium intortum , Brachiaria sp. and Phaseolus vulgaris in the management of fall armyworm Spodoptera frugiperda (J. E. Smith) in maize cropping systems in Africa
Article scientifique ArODES

Laetitia Scheidegger, Saliou Niassy, Charles Midega, Xavier Chiriboga, Nicolas Delabays, François Lefort, Roger Zürcher, Girma Hailu, Zeyaur Khan, Sevgan Subramanian

Pest Management Science,  2021, vol. 77, no. 5,, pp. 2350-2357

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The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a serious pest of maize. Farming systems such as push‐pull or maize‐legume intercropping have been reported to reduce FAW infestations significantly. However, the exact mechanisms involved in FAW management have not been practically elucidated. We therefore assessed larval host preference, feeding and survival rate when exposed to four host plants commonly used in push‐pull and legume intercropping. We also compared adult moths' oviposition preference between maize and other grasses used as trap crops in push‐pull. The larval orientation and settlement study showed that maize was the most preferred host plant followed by bean, desmodium and Brachiaria brizantha cv Mulato II. The larval arrest and dispersal experiment showed that mean number of larvae was significantly higher on maize than on Desmodium or B. brizantha cv Mulato II. However, no significant differences were found between maize and bean after 24 h. Maize was the most consumed plant, followed by bean, desmodium and finally brachiaria. The mean percentage of survival to the pupation stage was significantly higher on maize. The study on FAW oviposition preference showed no significant differences in egg deposited between maize and other grasses. However, B. brizantha cv Xaraes, which received more eggs than maize, could be a promising alternative to B. brizantha cv Mulato II for the control of FAW. The study provides a better understanding of the mechanisms involved in the control of fall armyworm under the push‐pull and maize legume intercropping.

Microbiological control of carpocoris fuscispinus (hemiptera : pentatomidae), a pest of onion and leek seed crops
Article scientifique ArODES

Falc Zollinger, Romain Chablais, Julien Crovadore, Bastien Cochard, Martine Haenzi, Pierre-Yves Bovigny, François Lefort

AGROFOR International Journal,  2021, vol. 6, no. 1, pp. 65-72

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Facades represent an important part of urban envelop in dense areas. They play a major role in the thermal comfort of pedestrians as well as on the city (in)-ability to stay reasonably fresh during the day or to cool at night. This study focuses on differences in thermal comportment of different kind of vertical éléments – heavy or light, pale or dark, absorbent - reflective or transparent based on measurements of different real situations. The study shows the differences between vertical surface’s temperatures but also highlights the differences of speed at which surfaces reach their highest temperature and so the time necessary to cool after solar exposure. Finally, it also underlines the ability of reflective surfaces (eg. glass facades) to worsen the comfort of pedestrians by adding up to 40% of incoming solar radiation intensity. Findings from this study show that surfaces do not only affect the apparent temperature by adding up to several degrees but also to a lesser extent the urban heat island effect. These results show the importance of material and constructive choices regarding the mitigation of exacerbation of global warming in cities.

2020

Detection of fungi and oomycetes by volatiles using E-nose and SPME-GC/MS platforms
Article scientifique ArODES

Jérémie Loulier, François Lefort, Marcin Stocki, Monika Asztemborska, Rafal Szmigielski, Krzysztof Siwek, Tomasz Grzywacz, Tom Hsiang, Slawomir Sluraski, Tomasz Oszako, Marcin Klisz, Rafal Tarakowski, Justyna Anna Nowakowska

Molecules,  2020, vol. 25, no. 23, article no. 5749

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Fungi and oomycetes release volatiles into their environment which could be used for olfactory detection and identification of these organisms by electronic-nose (e-nose). The aim of this study was to survey volatile compound emission using an e-nose device and to identify released molecules through solid phase microextraction–gas chromatography/mass spectrometry (SPME–GC/MS) analysis to ultimately develop a detection system for fungi and fungi-like organisms. To this end, cultures of eight fungi (Armillaria gallica, Armillaria ostoyae, Fusarium avenaceum, Fusarium culmorum, Fusarium oxysporum, Fusarium poae, Rhizoctonia solani, Trichoderma asperellum) and four oomycetes (Phytophthora cactorum, P. cinnamomi, P. plurivora, P. ramorum) were tested with the e-nose system and investigated by means of SPME-GC/MS. Strains of F. poae, R. solani and T. asperellum appeared to be the most odoriferous. All investigated fungal species (except R. solani) produced sesquiterpenes in variable amounts, in contrast to the tested oomycetes strains. Other molecules such as aliphatic hydrocarbons, alcohols, aldehydes, esters and benzene derivatives were found in all samples. The results suggested that the major differences between respective VOC emission ranges of the tested species lie in sesquiterpene production, with fungi emitting some while oomycetes released none or smaller amounts of such molecules. Our e-nose system could discriminate between the odors emitted by P. ramorum, F. poae, T. asperellum and R. solani, which accounted for over 88% of the PCA variance. These preliminary results of fungal and oomycete detection make the e-nose device suitable for further sensor design as a potential tool for forest managers, other plant managers, as well as regulatory agencies such as quarantine services.

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle ( Emys orbicularis , L. 1758)
Article scientifique ArODES

Charlotte Ducotterd, Julien Crovadore, François Lefort, Jean-François Rubin, Sylvain Ursenbacher

Molecular Ecology Resources,  2021, vol. 21, no. 2, pp. 433-447

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High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.

Effects of shade trees on robusta coffee growth, yield and quality :
Article scientifique ArODES
a meta-analysis

Kevin Piato, François Lefort, Cristian Subia, Carlos Caicedo, Jimmy Pico, Lindsey Nogrove

Agronomy for Sustainable Development,  2020, vol. 40, article no. 38

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Productivity of coffee plantations is threatened by both climate change and decreasing revenues of coffee growers. Using shade trees might protect against temperature variability, erosion and excessive radiation but there may be trade-offs in productivity and quality. While impacts of shade trees on arabica (Coffea arabica) have been reviewed, a global synthesis on robusta (Coffea canephora) coffee is lacking. We assessed how shade affects robusta growth and productivity, and what are the interactions and trade-offs. We conducted a systematic literature search in Web of Science and CAB Abstracts on 16 December 2019. Thirty papers fulfilled our inclusion criteria of being experimental studies on the impact of overstory trees with approximately half being from Brazil or India. Shade improved robusta tree growth and yield with some contrasting effects on physicochemical and biochemical properties. Shade (> 30%) was associated with reduced beverage quality. Significant interactions between shade and location, rainfall level and robusta clone were found. Among the clones tested, 06V, C153, LB1, GG229 and JM2 showed a higher productivity and growth (from + 17 to + 280%) under moderate shade (41–65%). This is the first meta-analysis of the effects of shade on robusta coffee. By synthesizing data from different studies, we highlight for the first time that the effect of shade on robusta coffee depends on tree age. Shade had positive impacts on older robusta trees (mean of 16 years), while the impact of shade on younger trees was either insignificant or negative. We highlight the importance of both clone type and tree ages. Research gaps included a lack of knowledge on the effects of shade with respect to coffee and shade tree age as well as interactive effects. More in-depth studies are needed to understand the mechanisms of how shade trees affect robusta coffee.

Draft genome sequence of bacillus licheniformis strain UASWS1606, a plant biostimulant for agriculture
Article scientifique ArODES

Julien Crovadore, Bastien Cochard, Damien Grizard, Romain Chablais, Marine Baillarguet, Morgane Comby, François Lefort

Microbiology Resource Announcements,  2020, vol. 9, no. 7, article no. e00740-20

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Bacillus licheniformis is a well-known industrial bacterium. New strains show interesting properties of biostimulants and biological control agents for agriculture. Here, we report the draft genome sequence, obtained with an Illumina MiniSeq system, of strain UASWS1606 of the bacterium Bacillus licheniformis, which is being developed as an agricultural biostimulant.

The feeding behaviour of the European pond turtle (Emys orbicularis, L. 1758) is not a threat for other endangered species
Article scientifique ArODES

Charlotte Ducotterd, Julien Crovadore, François Lefort, Antoine Guisan, Sylvain Ursenbacher, Jean-François Rubin

Global Ecology and Conservation,  2020, vol. 23, article no. e01133

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Molecular technologies, such as metabarcoding, have become powerful tools for conservation purposes. Here, we present a non-invasive study analyzing the diet of one population of European pond turtle (Emys orbicularis) during its whole activity period and of four other populations during the same period, based on faecal sample, and using for the first time on this species, a long metabarcoding approach. Emys orbicularis is an emblematic freshwater species of wetlands in Europe. In several countries, this species is endangered and, in Switzerland, Emys orbicularis is ranked as critically endangered on the Swiss Red List. A national conservation program was created to reintroduce this species and raised the question if this reintroduced species could be a threat for other endangered species. We developed a new method of long metabarcoding analysis, using universal PCR primers to determine prey species occurrence in the faeces. The analysis conducted on 174 faeces collected on 142 individuals revealed 1153 preys from 270 species. Emys orbicularis consumed plants throughout the year with a more diverse diet during the reproduction period (April–June). This study therefore not only determines precisely the omnivorous and opportunistic diet of the Emys orbicularis, but also shows that this species is not a threat to its environment, as 85.5% of the consumed species were not list on the Swiss Red List. Moreover, it also demonstrated that the genetic analyses of faeces could be an efficient tool to determine trophic interaction with a high level of precision, yielding promising perspectives for food web ecology.

Draft genome sequences of pseudomonas koreensis strain UASWS1668, bacillus megaterium strain UASWS1667, and paenibacillus sp. strain UASWS1643, considered potential plant growth-promoting rhizobacteria
Article scientifique ArODES

Julien Crovadore, Bastien Cochard, Romain Chablais, Martine Haenzi, François Raffini, François Lefort

Microbiology Resource Announcements,  2020, vol. 9, no.33, article no. e00768-20

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Plant growth-promoting rhizobacteria (PGPR) include species in the genera Bacillus, Paenibacillus, and Pseudomonas. We report here the draft genome sequences of the strains Pseudomonas koreensis UASWS1668 and Bacillus megaterium UASWS1667, isolated from a horse chestnut tree, and Paenibacillus sp. Strain UASWS1643, isolated from a tomato stem. Auxin production and phosphate solubilization were biochemically confirmed.

Reservoir of the European chestnut diversity in Switzerland
Article scientifique ArODES

S. Pereira-Lorenzo, Y. Bischofberger, M. Conedera, P. Piattini, Julien Crovadore, Romain Chablais, A. Rudow, S. Hatt, A. M. Ramos-Cabrer, T. Barreneche, François Lefort

Biodiversity and Conservation,  2020, vol. 29, pp. 2217-2234

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In Switzerland, chestnut forests cover about 27,100 ha, plus some 6800 ha of mixed stands. Due to environmental and historical reasons, most of these still existing forests are located in the Swiss Southern Alps, whereas in the northern parts of the country the chestnut cultivation and the related knowledge strongly regressed since the Little Ice Age period. Nevertheless, Switzerland still hosts valuable genetic resources of the sweet chestnut tree. The present genetic study bases on a nationwide inventory, identification and precise localisation of old and/or grafted chestnut trees for conservation purposes. The main objectives were: (1) to evaluate the genetic diversity and the genetic structure of Castanea sativa in Switzerland, and (2) to define a program of conservation including the proposal of a defined core collection. We genetically analysed a pre-selection of 962 accessions (out of 14,165 inventoried trees throughout Switzerland), profiling them with 24 microsatellites. We identified 675 different genotypes out of 962 accessions with a 29.8% of repetitiveness due to clonality. A structural analysis based on a Bayesian method allowed to identify two main clusters, one mostly related to the genetic group from southern Europe (Reconstructed Panmictic Population RPP1) and a second one (RPP2) which revealed to be independent and genetically different from other European groups of chestnut cultivars. The Swiss RPP2 represents a new genetic group, and consequently a complement to genetic resources of chestnut tree in Europe. Genetic analysis allowed defining a core collection of 46 genotypes, which should be used in priority for the Swiss conservation program.

2019

Oregano essential oil vapour prevents Plasmopara viticola infection in grapevine (Vitis Vinifera) and primes plant immunity mechanisms
Article scientifique ArODES

Markus Rienth, Julien Crovadore, Sana Ghaffari, François Lefort

PLOS ONE,

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The reduction of synthetic fungicides in agriculture is necessary to guarantee a sustainable production that protects the environment and consumers’ health. Downy mildew caused by the oomycete Plasmopara viticola is the major pathogen in viticulture worldwide and responsible for up to 60% of pesticide treatments. Alternatives to reduce fungicides are thus utterly needed to ensure sustainable vineyard-ecosystems, consumer health and public acceptance. Essential oils (EOs) are amongst the most promising natural plant protection alternatives and have shown their antibacterial, antiviral and antifungal properties on several agricultural crops. However, the efficiency of EOs highly depends on timing, application method and the molecular interactions between the host, the pathogen and EO. Despite proven EO efficiency, the underlying processes are still not understood and remain a black box. The objectives of the present study were: a) to evaluate whether a continuous fumigation of a particular EO can control downy mildew in order to circumvent the drawbacks of direct application, b) to decipher molecular mechanisms that could be triggered in the host and the pathogen by EO application and c) to try to differentiate whether essential oils directly repress the oomycete or act as plant resistance primers. To achieve this a custommade climatic chamber was constructed that enabled a continuous fumigation of potted vines with different EOs during long-term experiments. The grapevine (Vitis vinifera) cv Chasselas was chosen in reason of its high susceptibility to Plasmopara viticola. Grapevine cuttings were infected with P. viticola and subsequently exposed to continuous fumigation of different EOs at different concentrations, during 2 application time spans (24 hours and 10 days). Experiments were stopped when infection symptoms were clearly observed on the leaves of the control plants. Plant physiology (photosynthesis and growth rate parameters) were recorded and leaves were sampled at different time points for subsequent RNA extraction and transcriptomics analysis. Strikingly, the Oregano vulgare EO vapour treatment during 24h post-infection proved to be sufficient to reduce downy mildew development by 95%. Total RNA was extracted from leaves of 24h and 10d treatments and used for whole transcriptome shotgun sequencing (RNA-seq). Sequenced reads were then mapped onto the V. vinifera and P. viticola genomes. Less than 1% of reads could be mapped onto the P. viticola genome from treated samples, whereas up to 30% reads from the controls mapped onto the P. viticola genome, thereby confirming the visual observation of P. viticola absence in the treated plants. On average, 80% of reads could be mapped onto the V. vinifera genome for differential expression analysis, which yielded 4800 modulated genes. Transcriptomic data clearly showed that the treatment triggered the plant’s innate immune system with genes involved in salicylic, jasmonic acid and ethylene synthesis and signaling, activating Pathogenesis-Related-proteins as well as phytoalexin synthesis. These results elucidate EO-host-pathogen interactions for the first time and indicate that the antifungal efficiency of EO is mainly due to the triggering of resistance pathways inside the host plants. This is of major importance for the production and research on biopesticides, plant stimulation products and for resistance-breeding strategies.

Caractérisation génétique de la variété "Petite poire à grappe" utilisée pour la production de Poire à Botzi AOP
Article scientifique ArODES

Nicolas Garnier, Dominique Ruggli, Julien Crovadore, Bastien Cochard, Romain Chablais, François Lefort

Revue suisse Viticulture, Arboriculture, Horticulture : arboriculture,  2019, vol. 51, no. 4, pp. 248-255

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La Poire à Botzi est le seul fruit frais à bénéficier aujourd’hui en Suisse d’une appellation d’origine protégée (AOP). Cette poire est produite à partir de la variété Petite poire à grappe et donne des fruits de petit calibre de différentes couleurs qui se récoltent à partir du mois d’août. Il s’agit d’une ancienne variété de poire cultivée dans le canton de Fribourg, se consommant sous forme de poires cuites, notamment lors de la fête traditionnelle de la Bénichon. La caractérisation génétique de cette variété a été réalisée à l’aide de marqueurs microsatellites sur des individus provenant de l’ensemble du territoire couvert par l’AOP (vergers basse-tige, pépinières, arbres haute-tige traditionnels). Cette étude a permis d’évaluer la diversité génétique de cette variété de poire et a révélé qu’il n’existe qu’un seul génotype de Petite poire à grappe, exprimant plusieurs phénotypes selon les conditions environnementales.

Facteurs influençant la présence de Scaphoideus titanus, vecteur de la flavescence dorée, dans le vignoble genevois
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Stefano Bilotta, François Lefort, Sophie Rochefort, Pascale Deneulin, Valeria Trivellone, Patrik Kehrli

Revue suisse Viticulture, Arboriculture, Horticulture,  2019, vol. 51, no. 2, pp. 134-140

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La cicadelle Scaphoideus titanus est actuellement le principal vecteur connu de la transmission épidémique de la flavescence dorée. Cette étude a été réalisée durant l’été 2017 dans le but d’identifier les facteurs biotiques et abiotiques influençant la présence de cette cicadelle dans le vignoble du canton de Genève. Nos captures montrent que S. titanus est présent dans toutes les parcelles échantillonnées et confirme sa distribution sur la quasi-totalité du vignoble genevois. L’abondance de S. titanus diffère selon l’orientation des lignes et diminue avec la pente de la parcelle. Nos données indiquent également que la densité de S. titanus est plus élevée lorsque la surface viticole est importante dans les environs. Dans le cadre de prospections de S. titanus, en Suisse, cette étude recommande donc d’échantillonner des parcelles bien ensoleillées au milieu de grands vignobles à faible pente.

2018

Whole-genome sequence of pseudomonas putida strain 1312, a potential biostimulant developed for agriculture :
Article scientifique ArODES
a potential biostimulant developed for agriculture

Julien Crovaodre, Damien Grizard, Bastien Cochard, Romain Chablais, Philippe Blanc, François Lefort

Microbiology Resource Announcements,  2018, vol. 7, no. 10, article no. e01073-18

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We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments.

Whole-genome sequences of two arthrobacter sp. Strains, 4041 and 4042, potentially usable in agriculture and environmental depollution
Article scientifique ArODES

Julien Crovadore, Damien Grizard, Romain Chablais, Bastien Cochard, Philippe Blanc, François Lefort

Microbiology Resource Announcements,  2018, vol. 7, no. 10, article no. e01054-18

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We report here the draft genome sequences of Arthrobacter sp. strains 4041 and 4042, both of which possibly belong to the diverse Arthrobacter agilis species and are potentially usable as plant biostimulants for agriculture and as depolluting bacteria for the environment.

Whole-genome sequence of pseudomonas sp. strain 1239, isolated from soil in western France
Article scientifique ArODES

Julien Crovadore, Damien Grizard, Romain Chablais, Bastien Cochard, Philippe Blanc, François Lefort

Microbiology Resource Announcements,  2018, vol. 7, no. 10, article no. e01097-18

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We report here the draft genome sequence of Pseudomonas sp. strain 1239, a bacterium that is potentially usable as a biostimulant for agriculture or in depollution. Its genome encodes resistance to mercury, heavy metals, and several antibiotics. It is potentially able to produce marinocine, a broad-spectrum antibiotic.

Whole-genome sequence of pseudomonas aeruginosa Strain 4014, isolated from soil in France
Article scientifique ArODES

Julien Crovadore, Damien Grizard, Romain Chablais, Bastien Cochard, Philippe Blanc, François Lefort

Microbiology Resource Announcements,  2018, vol. 7, no. 10, article no. e01089-18

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Résumé:

We report here the draft genome sequence of strain 4014 of Pseudomonas aeruginosa, a common human pathogen, isolated from soil in France. This sequence predicts resistance to multiple antibiotics, including vancomycin.

The emerging pathogen of chestnut gnomoniopsis castaneae :
Article scientifique ArODES
the challenge posed by a versatile fungus

G. Lione, R. Danti, P. Fernandez-Conradi, J. V. Ferreira-Cardoso, François Lefort, G. Marques, J. B. Meyer, S. Prospero, L. Radócz, C. Robin, T. Turchetti, A. M. Vettraino, P. Gonthier

European Journal of Plant Pathology,  2019, vol. 153, pp. 671-685

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Résumé:

Gnomoniopsis castaneae is an emerging fungal pathogen currently scored as the major nut rot agent on chestnut, although it is also associated with cankers on both chestnut and hazelnut, as well as with necrosis on chestnut galls and leaves. Described for the first time in 2012, G. castaneae has been reported in several countries across Europe, Asia and Australasia, often in relation to severe outbreaks. The goal of this review is to provide a comprehensive summary of the state of the art about G. castaneae, highlighting the main results achieved by the research and stressing the most relevant knowledge gaps that still need to be filled. This overview includes topics encompassing the taxonomy of the fungal pathogen, its host range and geographic distribution, the symptomatology and the diagnostic methods available for its detection, its impact, biology, ecology and epidemiology. The main interactions between G. castaneae and other organisms are also discussed, as well as the possible control strategies. In these past few years, relevant progresses in the knowledge of G. castaneae have been achieved, yet the complexity of the challenges that this pathogen poses to chestnut growers and to the scientific community advocates for further advances.

Écologie saisonnière d'une espèce du genre Monophadnus (Hymenoptera : Tenthredinidae) sur Helleborus spp. et tentative de lutte biologique
Article scientifique ArODES

Lucas Malacari, Gaël Pétremand, Bastien Cochard, François Lefort, Sophie Rochefort

Revue d'écologie,  2018, 73, 2, pp. 122-131

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Depuis plusieurs années, un insecte du genre Monophadnus (Hymenoptera, Tenthredinidae : Blennocampinae) cause de sérieux dégâts aux collections de plantes du genre Helleborus des Conservatoire et Jardin Botaniques de Genève (CJB). Cette étude avait pour objectif de mieux connaître l’écologie saisonnière de cette espèce grâce à la mise en place d'élevages et à des observations in situ. Des essais de lutte biologique ont été également menés avec des champignons entomopathogènes des espèces Beauveria bassiana et Isaria farinosa, ainsi qu’avec un insecticide biologique, l’azadirachtine, extrait d’Azadirachta indica (NeemAzal®T/S). Seuls le NeemAzal®T/S à la concentration de 0,5 % et Isaria farinosa à 107 spores/ml ont permis de réduire significativement la population de cette espèce de Monophadnus provoquant des mortalités de 40 à 50 % plus élevées que dans le procédé témoin.

Plant organic farming research – current status and opportunities for future development
Article scientifique ArODES

Ivan Tsvektov, Atanas Atanassov, Mariana Vlahova, Lucien Carlier, Nikolai Christov, François Lefort, Krasimir Rusanov, Ilian Badjakov, Ivayla Dincheva, Mark Tchamitchian, Goritsa Rakleova, Liliya Georgieva, Lucius Tamm, Anelia Iantcheva, Joelle Herfoth-Rahmé, Epaminondas Paplomatas, Ivan Atanassov

Biotechnology Biotechnological Equipment,  2018, 32, 1

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Résumé:

This paper reviews the recent development of the scientific, legislative, economic and environmental aspects of plant organic farming. The impact of organic farming on biodiversity and soil fertility is discussed in comparison with conventional systems. A significant barrier for wide application and future development of organic farming is the existing diversity of national and international policy instruments in this sector. Special attention is paid to up-to-date research techniques that could help solve a number of the problems typically faced in plant organic farming. It is argued that organic farming is still not productive enough to be considered fully sustainable. This underlines the necessity of strong support for more effective implementation of scientific research innovations and improvement of the networking between all stakeholders – organic producers, scientists and corresponding policy makers at the national and international level.

2017

New strains of entomopathogenic fungi isolated from organic orchards in Geneva
Article scientifique ArODES

Etienne Laurent, Julien Crovadore, Pauline Deneux, Bastien Cochard, Pegah Pelleteret, Romain Chablais, Pierre-Yves Bovigny, François Lefort

Communications in agricultural and applied biological science,  2017, vol. 82, no. 2, pp. 207-212

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During the past century, agriculture went through significant ameliorations which resulted in a general yield increase, to which chemical pesticides greatly contributed. However, their negative environmental impacts had been early documented, and it is now established that these chemicals cannot represent a solution for a sustainable agriculture. Chemical residues in food, micro-pollutants in soils and water, selection of resistance of pathogens and pests are all harsh consequences impacting human health and biodiversity. Entomopathogenic fungi represent an interesting alternative to chemicals for crop protection against phytophagous insects and participate to a sustainable phytosanitary control. In this work, new fungal strains were isolated from soils of organic apple tree orchards and natural spaces, in the Canton of Geneva, with a baiting method using larvae of Galleria mellonella. All 71 collected isolates were genetically identified by PCR amplifications and sequencing of the rDNA ITS sequence. Out of these 71 isolates, 40 isolates belonged to entomopathogenic species. The baiting method with Galleria mellonella proved to be very efficient and showed that natural and untreated environments were generally richer in species and isolates. Interesting fungal strains belonging to the genera Beauveria, Metarhizium and Paecilomyces were isolated. Twelve of the most interesting isolates were then tested on the aphid pest Myzus Persicae. In a separate experiment, seven isolates of Metarhizium sp. were tested against the aphid Acyrthosiphon pisum. Experiments on the two aphids showed a strong virulence and entomotoxicity of some of the isolates. A mortality between 86.67% and 100% was recorded on Myzus persicae with 4 strains (2 Beauveria bassiana, 1 Metarhizium sp., 1 Paecilomyces sp.). The filtrates with spores were the most efficient against Myzus persicae. The filtrates without spores of the seven Metharizium sp. strains tested on Acyrthosiphon pisum caused a mortality of 100% after 7 days (control: mortality of 5% after 7 days) highlighting a very interesting potential of entomotoxicity of these fungi.

Inventaire de scolytinae (coleoptera, curculionidae) potentiellement associés au dépérissement de jeunes chênes sessiles dans le canton de Genève :
Article scientifique ArODES
inventaire et proposition de mesures de conservation

François Lefort, Gaël Pétremand, Pegah Pelleteret, Pierre-Yves Bovigny

Bulletin de la Société Vaudoise des Sciences Naturelles,  2017, vol. 96, pp. 77-84

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Résumé:

Des dépérissements ont été observés sur de jeunes chênes sessiles (Quercus petraea) plantés en alignement le long des routes dans le canton de Genève. Les insectes de la sous-famille des Scolytinae (Coleoptera, Curculionidae), présents sur des arbres affaiblis, peuvent être associés à des symptômes de dépérissement. Afin d'identifier les espèces potentiellement' impliquées, des piégeages ont été réalisés en 2006 et 2010 dans 13 communes genevoises. Durant ces deux campagnes de piégeage, dix espèces de Scolytinae, appartenant à sept genres, ont pu être identifiées. Scolytus intricatus et Anisandrus dispar ont été les deux principales espèces collectées.

Whole-genome sequences of 14 strains of bradyrhizobium canariense and 1 strain of bradyrhizobium japonicum isolated from lupinus spp. In algeria
Article scientifique ArODES

Djamel Chekireb, Julien Crovadore, Andreas Brachmann, Romain Chablais, Bastien Cochard, François Lefort

Genome Announcements,  2017, vol. 5, no. 29, article no. e00676-17

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Résumé:

We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense, isolated from root nodules of Lupinus microanthus and Lupinus angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root nodules from Lupinus angustifolius in Algeria. These sequences add to the known diversity of this agronomically important genus.

Metagenomes of soils samples from an established perennial cropping system of asparagus treated with biostimulants in Southern France
Article scientifique ArODES

Julien Crovadore, Ali Asaff Torres, Raúl Rodríguez Heredia, Bastien Cochard, Romain Chablais, François Lefort

Genome Announcements,  2017, vol. 5, no. 24, article no. e00511-17

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Résumé:

We report here the metagenomes of soils samples from a perennial cropping system of asparagus that was treated with two biostimulants. Two treatments were compared to an untreated control. Control soils samples were taken at the beginning and at end of the experiment.

Deeper insight in beehives :
Article scientifique ArODES
metagenomes of royal jelly, pollen, and honey from lavender, chestnut, and fir honeydew and epiphytic and endophytic microbiota of lavender and rose flowers

Julien Crovadore, François Gérard, Romain Chablais, Bastien Cochard, Karl Kristian Bergman Jensen, François Lefort

Genome Announcements,  2017, vol. 5, no. 22, article no. e00425-17

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Résumé:

Microbiota of beehive products are very little known. We report here for the first time six metagenomes of royal jelly, pollen, and different types of honey from wild and cultivated lavender, chestnut, and fir honeydew. Four metagenomes of epiphytic and endophytic microbiota of lavender and rose flowers are also reported.

Behaviour, morphology & molecular characterization of a monophadnus sawfly species (hymenoptera: tenthredinidae) feeding on helleborus spp. in western Switzerland
Article scientifique ArODES

Lucas Malacari, Gaël Pétremand, Sophie Rochefort, Bastien Cochard, Gautier Calmin, François Lefort

Archives des sciences et compte rendu des séances de la Société,  2017, vol. 69, pp. 137-144

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Résumé:

Comportement, morphologie et caractérisation moléculaire d’une espèce symphyte de Monophadnus (Hymenoptera : Tenthredinidae) se nourrissant sur diverses espèces d’Helleborus en Suisse Occidentale. – Depuis quelques années, une espèce non décrite de mouche à scie (Hymenoptera : Symphyta) cause d’importants dégâts aux collections d’hellébores des Conservatoire et Jardin botaniques de Genève, détruisant jusqu’à 80 % des plantes de certaines espèces. Ces mouches à scie, très voraces, ont été observées se nourrissant sur 14 espèces et sous-espèces d’hellébores. Cette étude avait pour objectif d’identifier cette espèce de mouche à scie laquelle a été morphologiquement identifiée comme appartenant au genre Monophadnus (Hymenoptera : Tenthredinidae). La description morphologique a été complétée par une identification moléculaire à plusieurs gènes, qui montre que cette espèce est génétiquement différente de M. monticola, souvent considérée comme un synonyme de M. latus, et de toutes les espèces pour lesquelles une description moléculaire est disponible. Il est probable que cette espèce soit M. latus sensu Lacourt 1999, ce qui pourrait être confirmé dans le futur par une révision du genre Monophadnus complétée par des identifications génétiques.

La lutte microbiologique :
Article professionnel ArODES
un aperçu de ses vastes possibilités d'utilisation en lutte phytosanitaire

François Lefort

Agroflash,  2017

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Résumé:

La lutte biologique est un concept devenu maintenant commun en horticulture, voire en agriculture.

Metagenomes and metatranscriptomes of activated sludge from a sewage plant, with or without aerobic granule enrichment
Article scientifique ArODES

Julien Crovadore, Vice Soljan, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort

Genome Announcements,  2017, vol. 5, no. 21, article no. e00372-17

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Résumé:

We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.

Metagenome-assembled genome sequence of rhodopseudomonas palustris strain eli 1980, commercialized as a biostimulant
Article scientifique ArODES

Julien Crovadore, Shoutao Xu, Romain Chablais, Bastien Cochard, Delvia Lukito, Gautier Calmin, François Lefort

Genome Announcements,  2017, vol. 5, no. 18, article no. e00221-17

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Insectes ravageurs émergents :
Article professionnel ArODES
établissement et optimisation d'un réseau de surveillance dans un contexte de réchauffement climatique

Gaël Pétremand, Olivier Vonlanthen, Vincent Gigon, Nicolas Delabays, Dominique Fleury, François Lefort, Sophie Rochefort

Revue suisse Viticulture, Arboriculture, Horticulture,  2017, vol. 5, pp. 272-279

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Das Blausieb befällt 150 Baumarten
Article professionnel ArODES

François Lefort, Sophie Rochefort, Camille Minguely

Wald und Holz,  2017, vol. 4, pp. 46-47

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Résumé:

Besonders in Baumschulen und jungen Obstkulturen ist das Blausieb (auch Kastanienbohrer genannt) gefürchtet, denn die holzfressende Raupe von Zeuzera pyrina kann in zahlreichen Laubhölzern – z.B. auch Eichen – und Sträuchern leben.

Urban London plane tree dieback linked to fungi in the botryosphaeriaceae
Article scientifique ArODES

Pegah Pelleteret, Julien Crovadore, Bastien Cochard, Sabrina Pasche, Pierre-Yves Bovigny, Romain Chablais, François Lefort

Urban Forestry Urban Greening,  2017, vol. 22, pp. 74-83

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Résumé:

Since the first report of the stain canker agent Ceratocystis platani in 2001 in Geneva, dieback of London plane trees (Platanus × acerifolia) has focused greater attention and an epidemiological monitoring has been implemented, as part of a compelling state directive for stain canker management. Genetic identification was carried out in order to ascertain the presence or absence of C. platani. We report here observations recorded between 2011 and 2013, of samplings from a total of 6 plane trees in 4 locations. Identification of bacteria and fungi was performed by sequencing of the rDNA ITS region for fungi, and of the 16S rRNA gene for bacteria. Fungi belonging to the Botryosphaeriaceae species occurred in almost every sampling, whereas Ceratocystis platani was only isolated in 2 trees. The 4 botryosphaeriaceous species, Diplodia mutila, Dothiorella sp., Diplodia seratia and Neofusicoccum parvum, could be responsible for the observed plane cankers, while other fungi could participate in the dieback symptoms. Since these species have been reported as canker agents on other tree species in Europe, artificial infections were carried out with pure cultures of Dothiorella sp., Diplodia mutila and Neofusicoccum parvum on young plane trees. Only Neofusicoccum parvum managed to provoke cork canker symptoms after a few months, but D. mutila and N. parvum were found in internal necrotic tissues. This is the first report of Dothiorella sp., Diplodia mutila and Neofusicoccum parvum associated with plane tree dieback in Switzerland and the first report of pathogenicity of Neofusicoccum parvum in plane trees. This survey showed that most cases of plane tree dieback in the Geneva region were not caused by C. platani and that other fungi could be responsible for similar symptoms.

Bioactive compound profile and antioxidant activity of fruits from six goji cultivars cultivated in Switzerland
Article scientifique ArODES

Agnieszka Kosinska-Cagnazzo, Brian Weber, Romain Chablais, José F. Vouillamoz, Bence Molnar, Julien Crovadore, François Lefort, Wilfried Andlauer

Journal of Berry Research,  2017, vol. 7, no. 1, pp. 43-59

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Résumé:

Goji berries, traditionally used in Chinese medicine, are nowadays gaining popularity in the Western world. The efforts are made to establish their cultivation in Europe. Goji berries might derive from two closely related species: Lycium barbarum and Lycium chinense, however, plant species is rarely stated by commercial suppliers. The aim of this study was to evaluate the antioxidant activity and the bioactive compounds profile of fruits from six goji berries cultivars cultivated in Switzerland and to provide their genetic characterisation. Goji fruits were cultivated at the experimental field of the Agroscope Research Center in Wallis, Switzerland. The genetic characterization was carried out by amplifying and sequencing two nuclear genes and one chloroplastic gene. The comparison with L. barbarum and L. chinense obtained from the Conservatory and Botanical Garden of Geneva (CBGG) was made. The profile of carotenoids and polyphenols was analysed using an HPLC-DAD. The antioxidant capacity was determined by ORAC and TEAC assays. DNA sequencing and phylogenetics confirmed that all the cultivars belonged to the Lycium genus. ‘Tibet’, ‘Red Life’, ‘Sweet Lifeberry’, ‘Big Lifeberry’ seemed to be closely related to a L. barbarum, whereas ‘Number One’ segregated closer to L. chinense. The individual Saxon, appeared genetically different from all other cultivars and the L. barbarum and L. chinense individuals from CBGG. Zeaxanthin esters were the predominant carotenoid in all six cultivars. ’Number One’ had the highest content of phenolic compounds such as rutin and ferulic, chlorogenic, caffeic and p-coumaric acid. The study confirmed the importance of combining the quantification of bioactive compounds with genetic characterisation in the analysis of goji species. The dissimilarity of ‘Number One’ and Saxon from four remaining cultivars investigated in this study was evident from the DNA sequencing and Principal Component Analysis of chemical results.

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents
Article scientifique ArODES

Julien Crovadore, Vice Soljan, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort

Heliyon,  October 2017, vol. 3, no. 10

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Résumé:

Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to7.6Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.

2016

Menaces sur le séquoia géant :
Article professionnel ArODES
champignons et changements climatiques

Martine Hänzi, François Lefort

Horticulture romande,  2016, vol. 12, pp. 17-19

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Résumé:

Originaire de l’ouest californien, le séquoia a été introduit en Europe au milieu du XIXe siècle. On en dénombre plus de 350 spécimens à Genève, principalement plantés dans les parcs, mais aussi dans de grandes propriétés privées. T

Whole-genome sequence of pseudomonas graminis strain UASWS1507, a potential biological control agent and biofertilizer isolated in Switzerland
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Romain Chablais, Bastien Cochard, Torsten Schulz, François Lefort

Genome Announcements,  2016, vol. 4, no. 5, article no. e01096-16

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Résumé:

We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species Pseudomonas graminis, isolated in Switzerland from an apple tree. This is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture.

Whole-genome sequence of bradyrhizobium elkanii strain UASWS1016, a potential symbiotic biofertilizer for agriculture
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Romain Chablais, Bastien Cochard, Torsten Schulz, François Lefort

Genome Announcements,  2016, vol. 4, no. 5, article no. e01095-16

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Résumé:

Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy. Fully equipped for ammonia assimilation, heavy metal resistances, and aromatic compounds degradation, it carries a large type IV secretion system, specific of plant-associated microbes. Deprived of toxins, it could be considered for agricultural and environmental uses.

Whole-genome sequence of mesorhizobium hungaricum sp. nov. strain UASWS1009, a potential resource for agricultural and environmental uses
Article scientifique ArODES

Julien Crovadore, Bastien Cochard, Gautier Calmin, Romain Chablais, Torsten Schulz, François Lefort

Genome Announcements,  2016, vol. 4, no. 5, article no. e01158-16

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Résumé:

We report here the whole-genome shotgun sequences of the strain UASWS1009 of the species Mesorhizobium hungaricum sp. nov., which are different from any other known Mesorhizobium species. This is the first genome registered for this new species, which could be considered as a potential resource for agriculture and environmental uses.

Whole-genome sequence of pseudomonas xanthomarina strain UASWS0955, a potential biological agent for agricultural and environmental uses
Article scientifique ArODES

Julien Crovadore, Bastien Cochard, Gautier Calmin, Romain Chablais, Torsten Schulz, François Lefort

Genome Announcements,  2016, vol. 4, no. 5, article no. e01136-16

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Résumé:

We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species Pseudomonas xanthomarina, isolated from sewage sludge. This genome was obtained with an Illumina MiniSeq and is the second genome registered for this species, which is considered as a promising resource for agriculture and bioremediation of contaminated soils.

Das Blausieb frisst Holz und ist nicht wählerisch
Article professionnel ArODES

Camille Minguely, Sophie Rochefort, François Lefort

gplus: Magazin für die grüne Branche,  2016, vol. 10, pp. 30-31

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Résumé:

Die holzfressenden Larven des Blausiebs sind besonders in Baumschulen und jungen Pflanzungen gefürchtete Schädlinge. Sie können sich in verschiedensten Bäumen und Sträuchern entwickeln.

First report of geosmithia langdonii and geosmithia spp. isolated from a decaying elm (Ulmus minor) in Geneva, Switzerland
Article scientifique ArODES

Martine Hänzi, Bastien Cochard, Romain Chablais, Julien Crovadore, François Lefort

Folia Forestalia Polonica,  2016, vol. 58, no. 2, pp. 96-102

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Résumé:

The mortality of a young elm Ulmus minor in 2014 in Geneva prompted a search for the microorganisms potentially involved. Symptoms included foliar chlorosis and wilting followed by defoliation of branches. Wood symptoms included a brown streaking of sap wood and brown stains in trunk and branches. The comparison of the resulting ITS rDNA sequences to the NCBI Nucleotide database allowed to identify 10 different organisms. The genus Geosmithia represented 48% of the isolates belonging to three species: Geosmithia langdonii (7 isolates) and 2 unknown morphologically and genetically different Geosmithia sp. 1 and sp. 2 (4 isolates). Geosmithia species are very little known ascomycetes, which have been recently shown to be opportunistic pathogens on broadleaved trees and conifers, living as saprobes in galleries of many bark beetle species. In the case described here, Geosmithia langdonii, and the unknown Geosmithia species were found in symptomatic wood while bark beetle galleries were found in close regions of the symptomatic wood. Geosmithia langdonii was the major fungus retrieved from the symptomatic wood and could have contributed, along with other identified fungal species, to a pathogenic complex producing symptoms similar to the ones of the Dutch Elm Disease and led to the dieback of this elm tree. Geosmithia langdonii and 2 yet unknown Geosmithia species (sp. 1 and sp. 2), different from any other reported Geosmithia species are reported from an elm tree in Switzerland for the first time.

Whole-genome sequence of enteractinococcus helveticum sp. nov. strain UASWS1574 isolated from industrial used waters
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort

Genome Announcements,  2016, vol. 4, no. 4, article no. e00756-16

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Résumé:

We report here the whole-genome shotgun sequences of the strain UASWS1574 of the undescribed Enteractinococcus helveticum sp. nov., isolated from used water. This is the first genome registered for the whole genus.

Xylella fastidiosa :
Article professionnel ArODES
une bactérie inquiétante pour l'agriculture marocaine

Younès Rechka, François Lefort

Agriculture du Maghreb,  2016, vol. 97,pp. 52-54

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Le rouge cryptogamique, ça mange du pin
Article professionnel ArODES

Martine Hänzi, Pierre-Yves Bovigny, Pegah Pelleteret, François Lefort

La Forêt,  2016, no. 16, pp. 13-15

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Résumé:

Des maladies fongiques des pins, le dépérissement des pousses dû à Sphaeropsis sapinea est le plus connu. Mais d’autres champignons peuvent causer des dépérissements à première vue semblables. Lophodermium seditiosum, agent de la maladie dite du «rouge cryptogamique» est l’un d’eux.

Biological control of the latent pathogen gnomoniopsis smithogylvyi in european chestnut grafting scions using bacillus amyloliquefaciens and trichoderma atroviride
Article scientifique ArODES

Sabrina Pasche, Julien Crovadore, Pegah Pelleteret, Mauro Jermini, Brigitte Mauch-Mani, Tomasz Oszako, François Lefort

Dendrobiology,  2016, vol. 75, pp. 113-122

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Résumé:

A search for endophytes in Castanea sativa Miller (Fagales: Fagaceae) grafting scions showed that a latent pathogenic fungus Gnomoniopsis smithogilvyi (Diaporthales: Gnomoniaceae) was present as the major component of the endophytic flora. Initially, the goal of this study was to develop a biological control method of Cryphonectria parasitica (Diaporthales: Valsaceae), the chestnut blight agent, by soaking chestnut scions before grafting in antagonists suspension. However, the healthy chestnut material used in in vitro and glasshouse experiments turned out to be naturally infected by a pathogen. At first view, the symptoms looked very similar to those caused by C. parasitica but some differences were noticed. DNA sequencing and application of Koch’s postulates revealed that G. smithogilvyi was the agent responsible of those symptoms. Preventive biocontrol experiments were carried out with chestnut tree scions soaked overnight in a liquid suspension of Bacillus amyloliquefaciens (Bacillales: Bacillaceae). This bacterium was then frequently found in the lower parts of scions (CF of 100% between 3.1 and 6 cm) and up to a height of 18 cm. It was observed that when B. amyloliquefaciens was present, the endophytic and opportunistic pathogenic fungus G. smithogil­vyi was not present. Conversely, the parts not colonized by the bacteria were always naturally infected by the endophytic fungus. This would indicate that the endophytic behavior of B. amyloliquefaciens inhibited the growth of G. smithogilvyi and reduced its presence in scions. A similar experiment, carried out with the Trichoderma atroviride (Hypocreales: Hypocreaceae), led to similar observations. Trichoderma atroviride was frequently isolated in the lower parts of scions (CF of 100% until 6 cm) and up to a height of 27 cm. Inoc­ulating B. amyloliquefaciens and T. atroviride as part of a preventive biocontrol treatment would allow these biological control agents to colonize the plant as endophytes and prevent the development of G. smithogilvyi.

Whole-genome sequences of seven strains of bacillus cereus isolated from foodstuff or poisoning incidents
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Jenna Tonacini, Romain Chablais, Bruno Schnyder, Ute Messelhäusser, François Lefort

Genome Announcements,  2016, vol. 4, no. 3, article no. e00435-16

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Résumé:

We present here the whole shotgun genome sequences of seven strains of Bacillus cereus isolated from foodstuff samples or food poisoning incidents.

Evaluation de biostimulants commerciaux en culture de tomates en sol
Article professionnel ArODES

Stefano Pedrazzi, Youness Rechka, Pegah Pelleteret, Romain Chablais, Julien Crovadore, François Lefort

Revue suisse Viticulture, Arboriculture, Horticulture,  2016, vol. 48, no. 6, pp. 358-364

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Sphaeropsis sapinea suit la grêle à la trace
Article professionnel ArODES

Martine Hänzi, François Lefort

La Forêt,  2016, vol. 5, pp. 10-13

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Résumé:

Sécheresse et grêle sont deux facteurs importants sur l’incidence du dépérissement des pousses de pin dû à Sphaeropsis sapinea, un champignon pathogène des pins mais aussi de nombreux autres conifères. Portrait de cet organisme débarqué chez nous à la fin du XXe siècle.

La zeuzère du poirier n'attaque pas seulement les poiriers !
Article professionnel ArODES

Camille Minguely, Sophie Rochefort, François Lefort

Horticulture romande,  2016, no. 4, pp. 32-35

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Résumé:

Ravageur particulièrement redoutable pour les pépinières et les jeunes plantations, les larves xylophages de la zeuzère peuvent se développer sur une très large gamme d'arbres et d'arbustes.

Complete genome sequence of bacillus methylotrophicus strain B25, a potential plant growth-promoting rhizobacterium
Article scientifique ArODES

Jonathan Gerbore, Aline Brutel, Arnaud Lemainque, Barbara Mairey, Claudine Médigue, David Vallenet, François Lefort, Damien Grizard

Genome Announcements,  2016, vol. 4, no. 2, article no. e00058-16

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Résumé:

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

Whole-genome sequence of bradyrhizobium elkanii strain UASWS1015, a highly ammonia-tolerant nitrifying bacterium
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Bastien Cochard, Romain Chablais, François Lefort

Genome Announcements,  2016, vol. 4, no. 2, article no. e00111-16

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Résumé:

Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome indicates that it is fully equipped for ammonia assimilation and aromatic compound degradation, and it displays a large type IV secretion system, which characterizes plant-associated microbes. Totally deprived of toxins, it could be considered for agricultural and environmental uses.

Propriétés antigerminatives des déchets de taille de Ginkgo biloba :
Article professionnel ArODES
une valorisation comme herbicide pour les espaces verts ?

Laura MacGillycuddy, François Lefort

Revue suisse Viticulture, Arboriculture, Horticulture,  2016, vol. 48, no. 3, pp. 204-206

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Résumé:

L’effet inhibiteur de la germination de divers extraits obtenus par macération de feuilles et de pseudo-fruits (ovules) de Ginkgo biloba a été testé in vitro sur des semences de cresson alénois, laitue, chou de Chine et haricot. Les résultats montrent une activité germinicide totale des extraits de pseudo-fruits sur toutes les espèces végétales testées. La possibilité d’une valorisation locale des déchets d’entretien des ginkgos, essence très répandue au sein des espaces verts citadins, est évoquée.

Gnomoniopsis smithogilvyi causes chestnut canker symptoms in castanea sativa shoots in switzerland
Article scientifique ArODES

Sabrina Pasche, Gautier Calmin, Guy Auderset, Julien Crovadore, Pegah Pelleteret, Brigitte Mauc-Mani, François Barja, Bernard Paul, Mauro Jermini, François Lefort

Fungal Genetics and Biology,  2016, vol. 87, pp. 9-21

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Résumé:

A screening of Castanea sativa scions for grafting for the presence of endophytes showed that the opportunistic fungal pathogen Gnomoniopsis smithogilvyi was the most abundant member of the endophytic flora. This fungus is known as a pathogen affecting chestnut fruits in Italy and Australia. Here, we present evidence that it causes cankers very similar to the ones due to Cryphonectria parasitica infection on twigs and scions of chestnut trees. We found natural infections of G. smithogilvyi in healthy grafted plants as well as in scions from chestnut trees. The identity of the fungus isolated from asymptomatic tissues was verified by applying Koch’s postulates and corroborated by DNA sequencing of four different gene regions. In contrast to C. parasitica that appears on the bark as yellow to orange pycnidia, stromata and slimy twisted tendrils, G. smithogilvyi forms orange to red and black pycnidia, gray stromata and cream-colored to beige slimy twisted tendrils on the bark. These Swiss strains are closely related to G. smithogilvyi strains from Australia and from New Zealand, Gnomoniopsis sp. and Gnomoniopsis castanea from New Zealand, Italy, France and Switzerland. While the strains from Ticino are genetically very close to G. smithogilvyi and G. castanea from Italy, the differences between the strains from Ticino and Geneva suggest two different origins. The present study supports the hypothesis that a single species named G. smithogilvyi, which is known to be the agent of chestnut rot, also causes wood cankers on chestnut.

Cas de suie de l'érable et de chancre du peuplier dans le canton de Genève
Article scientifique ArODES

Bastien Cochard, François Lefort

Schweizerische Zeitschrift für Fortwesen / Journal forestier suisse / rivista forestale svizzera / Swiss Forestry Journal,  2016, vol. 167, no. 2, pp. 98-104

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Résumé:

Durant l’été 2014, un cas de suie de l’érable sur un érable champêtre (Acer campestre) dû à Cryptostroma corticale et deux cas de chancre cytosporéen sur des peupliers euraméricains (Populus x euramericana) dû à Cytospora chrysosperma furent identifiés génétiquement pour la première fois sur le territoire genevois. Dans les deux cas les arbres présentaient des signes de dépérissement très avancés, accompagnés de symptômes spécifiques, tels que desquamation de l’écorce et plaques de suie noire dans le cas de l’érable, effilochement de l’écorce et coloration noire du bois sur plusieurs branches charpentières sur les peupliers. Un échantillonnage des zones symptomatiques et une mise en culture sur milieu gélosé furent réalisés afin d’isoler les éventuels champignons pathogènes. Les résultats de l’analyse moléculaire des différentes espèces, basée sur l’amplification de la région ITS de l’ADN ribosomique, permirent d’identifier la présence majoritaire de Cryptostroma corticale dans le cas de l’érable, et de Cytospora chrysosperma, sur les peupliers, deux champignons peu connus en Suisse et en Europe et peut-être associés aux changements climatiques.

Pyrale du buis :
Article professionnel ArODES
une piste pour un contrôle biologique

Laura MacGillycuddy, François Lefort

Horticulture romande,  2016, no. 1, pp. 20-21

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Résumé:

Ce nouveau ravageur fait l'objet de nombreuses recherches afin de trouver des solutions de lutte respectueuse de l'environnement. Les champignons entomophages montrent une voie de contrôle possible.

Nouvelles maladies fongiques d'espèces ligneuses identifiées à Genève
Article professionnel ArODES

Bastien Cochard, Sabrina Pasche, Marie Hänzi, Pegah Pelleteret, Julien Crovadore, François Lefort

Bulletin 2016 (Arboretum du Vallon d'Aubonne) : l'Arboretum au Pays du soleil levant,  2016, vol. 46, pp. 28-31

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Résumé:

Dans le cadre des activités de l'Observatoire cantonal des maladies des plantes ornementales, plusieurs espèces de champignons pathogènes inhabituelles ont été identifiées à Genève sur des arbres dépérissants.

2015

Les chenilles processionnaires :
Article professionnel ArODES
des larves de papillons à connaître et à surveiller

Bastien Cochard, Pegah Pelleteret, Pierre-Yves Bovigny, François Lefort

Bulletin 2015 (Arboretum du vallon d'Aubonne) : des arbres, des forêts et des hommes,  2015, no. 45, pp. 4-6

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Résumé:

En Suisse, les chenilles processionnaires du pin et du chêne posent de nombreux problèmes en forêt mais aussi dans les parcs publics et les jardins privés. Leur expansion géographique semble être en relation avec le réchauffement climatique. Il est donc nécessaire de mieux les connaître, afin d’en limiter les nuisances.

Whole-genome sequence of pseudomonas putida strain uasws0946, a highly ammonia-tolerant nitrifying bacterium isolated from sewage sludge aerobic granules
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Bastien Cochard, Romain Chablais, Damien Grizard, Jean-Yves Berthon, François Lefort

Genome Announcements,  2015, vol. 3, no. 5, article no. e01153-15

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Résumé:

We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.

Whole-genome sequences of 15 strains of staphylococcus aureus subsp. aureus isolated from foodstuff and human clinical samples
Article scientifique ArODES

Julien Crovadore, Gautier Calmin, Jenna Tonacini, Romain Chablais, Andreas Baumgartner, Bruno Schnyder, Elisabeth Hodille, François Lefort

Genome Announcements,  2015, vol. 3, no. 3, article no. e00684-15

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Résumé:

The whole-genome sequences of 15 strains of Staphylococcus aureus (10 strains isolated from foodstuff samples in Switzerland and five from human clinical samples) were obtained by Illumina sequencing. Most strains fit within the known diversity for the species, but one (SA-120) possessed a higher G+C content and a higher number of genes than usual.

Biocontrol endotherapy with trichoderma spp. and bacillus amyloliquefaciens against phytophthora spp.:
Article scientifique ArODES
a comparative study with phosphite treatment on quercus robur and fagus sylvatica

Gilles Berger, Katarzyna Czarnocka, Bastien Cochard, Tomasz Oszako, François Lefort

Journal of Agricultural Science and Technology,  2015, vol. 5, pp. 428-439

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Résumé:

Phytophthora species are particularly aggressive plant pathogens and are often associated with the decline of many tree species, including oak and beech. Several fungi and bacteria species are known as potential antagonists usable as biological control agents. Phosphonate (H3PO3), commonly branded as phosphite, has also been used in the past years to protect trees against invasive Phytophthora spp.. This study aimed at comparing the effects of selected antagonist microorganisms and phosphonate, when applied by microinjection or leaf treatment. Antagonistic species were first selected for their high inhibitory activity against problematic Phytophthora species, such as Phytophthora cactorum, P. quercina and P. plurivora attacking Quercus robur and Fagus sylvatica in Polish forests. Three endophytic species Trichoderma atroviride (two strains), T. harzianum and Bacillus amyloliquefaciens showed a high control activity, and their efficacy was then assessed in comparison with a phosphonate treatment. Two application methods were experimented in this study: injection of a solution of spores or phosphonate into the sap vessels of beech or a foliar treatment on oak. Phosphonate and two strains of Trichoderma significantly reduced the necrotic area on oak leaves inoculated with P. plurivora and one strain of T. atroviride significantly reduced necrotic areas on beech branches. These results are therefore promising of a novel way to control Phytophthora spp. in forest stands and nurseries.

First reports ofcryptostroma corticalecausing sooty bark disease inacersp. In canton Geneva, Switzerland
Article scientifique ArODES

Bastien Cochard, Julien Crovadore, Pierre-Yves Bovigny, Romain Chablais, François Lefort

New Disease Reports,  2015, vol. 31, no. 8

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Effets micro-organismes contre pythium spp. et sur la croissance de jeunes plants de lisianthus
Article professionnel ArODES

Yannick Fleury, François Lefort, Cédric Camps, Pascal Sigg

Revue suisse Viticulture, Arboriculture, Horticulture,  2015, vol. 47, no. 2, pp. 124-130

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2014

Chenille processionnaire du pin :
Article professionnel ArODES
la connaître pour mieux la contrôler

François Lefort, Pierre-Yves Bovigny, Bastien Cochard

La Forêt,  2014, no. 12, pp. 12-13

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Résumé:

La processionnaire du pin thaumetopoea pityocampa est le principal lépidoptère ravageur des pins dans nos régions tempérées. En plus de causer des dégâts aux pinaceae, elle pose un redoutable problème de santé pour les humains et les animaux.

Comment contrer biologiquement cylindrocladium buxicola et volutella buxi
Article professionnel ArODES

François Lefort, Pegah Pelleteret, Julien Crovadore, Gautier Calmin

La Forêt,  2014, no. 11, pp. 16-17

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Résumé:

Après un premier article sur la lutte contre la pyrale du buis, nous traitons ici d'essais de lutte biologique contre les champignons cylindrocladium buxicola et volutella buxi.

Kahlfrass in einer Saison
Article professionnel ArODES

Pierre-Yves Bovigny, Pegah Pelleteret, François Lefort

Wald und Holz,  2014, vol. 10, pp. 3-5

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Résumé:

Der Buchsbaum-Zünsler wurde 2007 in die Schweiz eingeschleppt und verursacht dort vielerorts grosse Schäden an Buchsbäumen. Inzwischen ist es wohl nicht mehr möglich, den Falter vollkommen auszurotten. Ihn zu kontrollieren, ist dennoch wichtig, um Schäden zu vermeiden und um dessen weitere Ausbreitung einzudämmen. Am effizientesten ist dabei der Bacillus thuringiensis. Aber auch andere biologische Methoden können in der Zukunft das Arsenal erweitern.

La lutte s'roganise contre la pyrale
Article professionnel ArODES

François Lefort, Pierre-Yves Bovigny, Bastien Cochard, Laura MacGillycuddy, Pegah Pelleteret

La Forêt,  2014, no. 10, pp. 12-15

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Résumé:

La pyrale du buis fait des ravages. Hors de l’espace forestier, les horticulteurs et les responsables de l’entretien des parcs et jardins et les pépiniéristes disposent d’un certain nombre de moyens de lutte, notamment biologiques. Le point avec les spécialistes de l’hepia.

Whole-genome shotgun sequence of arthrospira platensis strain paraca, a cultivated and edible cyanobacterium
Article scientifique ArODES

François Lefort, Gautier Calmin, Julien Crovadore, Jacques Falquet, Jean-Pierre Hurni, Magne Osteras, François Haldemann, Laurent Farinelli

Genome Announcements,

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Résumé:

Here we report the whole-genome shotgun sequence of a Peruvian strain of Arthrospira platensis (Paraca), a cultivated and edible haloalkaliphilic cyanobacterium of great scientific, technical, and economic potential.

La processionnaire du chêne
Article professionnel ArODES

Pegah Pelleteret, Pierre-Yves Bovigny, François Lefort

Horticulture romande,  2014, no. 6, pp. 2-3

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Whole-genome shotgun sequence of bacillus amyloliquefaciens strain UASWS BA1, a bacterium antagonistic to plant pathogenic fungi
Article scientifique ArODES

François Lefort, Gautier Calmin, Pegah Pelleteret, Laurent Farinelli, Magne Osteras, Julien Crovadore

Genome Announcements,

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Résumé:

We report here the whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS BA1, isolated from inner wood tissues of a decaying Platanus × acerifolia tree. This strain proved to be antagonistic to several plant pathogenic fungi and oomycetes and can be developed as a biological control agent in agriculture.

Pathogenicity of entomopathogenic fungi to the green peach aphid myzus persicae sulzer (aphididae) and the european tarnished bug Lygus rugulipennis poppius (miridae)
Article scientifique ArODES

François Lefort, Dominique Fleury, Isabelle Fleury, Cyrielle Coutant, Stefan Kuske, Patrick Kehrli, Pascal Maignet

Egyptian Journal of Biological Pest Control,  2014, vol. 24, no. 2, pp. 379-386

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Résumé:

To reduce economic losses, producers have no choice than controlling pests by chemical insecticides with their negative impact on the environment as well as on beneficial organisms. In this context, efficient and selective biological control agents such as entomopathogenic fungi should be integrated in pest management strategies. Screening experiments showed the pathogenicity of 16 fungal strains belong to the species Beauveria bassiana (Balsamo-Crivelli) Vuillemin, B. brongniartii (Sacc.) Petch, Metarhizium anisopliae (Metchnikoff) Sorokin, Lecanicillium lecanii (Zare and Gams) and Paecilomyces fumosoroseus Vassiljevsky against the two plant sap sucking pests, the green peach aphid, Myzus persicae Sulzerand and the European tarnished bug, Lygus rugulipennis Poppius. Bioassays established on treated Chinese cabbage leaves and bean pods for M. persicae and L. rugulipennis, respectively, allowed to evaluate the most pathogenic strains for controlling each pest. The two strains ART41 and ART2580 of B. bassiana showed highest pathogenicity on M. persicae with a mortality rate of 92 and 98%, respectively, seven days post treatment. Mortality rates of L. rugulipennis reached 92 and 98% seven days after treatment for the B. bassiana strains ART2580 and ART360BB, respectively. These results should be confirmed in open field experiments by exposing both insects to the suggested B. bassiana strains.

Whole-genome shotgun sequence of pseudomonas viridiflava, a bacterium species pathogenic to ararabidopsis thaliana
Article scientifique ArODES

François Lefort, Gautier Calmin, Julien Crovadore, Magne Osteras, Laurent Farinelli

Genome Announcements,

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Résumé:

We report here the first whole-genome shotgun sequence of Pseudomonas viridiflava strain UASWS38, a bacterium species pathogenic to the biological model plant Arabidopsis thaliana but also usable as a biological control agent and thus of great scientific interest for understanding the genetics of plant-microbe interactions.

Freshwater biodiversity under warming pressure in the Alps :
Article scientifique ArODES
a methodological framework for prioritization of restoration areas for small waterbodies

Beat Oertli, Christiane Ilg, Sandrine Angélibert, Janine Bolliger, Julien Crovadore, Eliane Demierre, Claire Julliand, Andréa Finger-Stich, Christel Forré, Pierre-André Frossard, François Lefort, Mathieu Mayencourt, Umberto Piantini, Sergio Schmid

eco.mont,  2014, vol. 6, pp. 23-34

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Résumé:

Freshwater biodiversity has shown to be highly vulnerable to climate warming. Boreo-alpine species are especially at risk in the Alps because they have to migrate to higher elevations to avoid local extinction. Effects of climate warming could be partly counteracted by creating new freshwater habitats: this would boost the population sizes of the endangered species and would increase the connectivity between Alpine waterbodies to facilitate the species’ upward dispersal and colonization of new habitats. Nevertheless, the localization of new habitats has to be carefully chosen, as successful restoration (or habitat creation) depends on many abiotic and ecological variables (e.g. habitats density and quality, connection between bodies of water, presence of targeted species, resistance of landscape to species movements). Furthermore, various socioeconomic drivers and actors determine the land and water uses in the Alps. Therefore we developed an innovative method for prioritization of areas for creation (or restoration) of small bodies of water, taking into account both ecological parameters (from species to landscape) and social ones. The method was developed in a test area (130 km2, in Canton Valais, Switzerland) representative of the Swiss Alpine landscapes and their associated socioeconomic activities. The proposed methodological framework consists of four steps which allow refining the geographical area to propose two or three small areas (some hectares) suitable for the creation of small water bodies. The first step investigates the regional scale, often several thousand km2, with a focus on environmental considerations: presence of historical or contemporary wetlands and waterbodies, presence of cold stenotherm species, and favourable landscape (in terms of land use) and socioeconomic context. The second step identifies areas of biological connectivity between source ponds and future host ponds for cold stenotherm species, taking into account the distance between source and host ponds and landscape resistance to the movements of propagules, finally highlighting the migration corridors. The third step checks the preselected areas with the aim of discarding catchments impaired by selective or diffuse pollutions. The fourth and final step is intended to enhance the probability of the project’s social acceptance: qualitative interviews and field observations are conducted on a local scale (often one km2) and options are evaluated with local stakeholders. Conducting the four successive and complementary steps ensures that the selected areas have a high potential for hosting the alpine biodiversity, and furthermore provide a favourable social framework for success in the short as well as the long term. Such a tool should promote and facilitate actions for conserving freshwater biodiversity in the Alps.

2013

Des champignons pour gérer les populations d'insectes ravageurs en arboriculture
Article professionnel ArODES

Dominique Fleury, Deborah Vuagnat, Isabelle Fleury, François Lefort

Objectifs,  2013, vol. 78, pp. 15-17

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2012

Selection and mass production of santalum album l. calli for induction of sesquiterpenes
Article scientifique ArODES

Julien Crovadore, Michel Schalk, François Lefort

Biotechnology Biotechnological Equipment,  2012, vol. 26, no. 2, pp. 2870-2874

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Résumé:

Young hypocotyl segments obtained from aseptically germinated seeds of Santalum album L. (5 weeks old) were used to induce callus formation. Growth of different calli types was induced on hypocotyls segments under different conditions. Resulting green calli were maintained on MS medium and Gamborg basal medium supplemented with 2,4D (2,4-Dichlorophenoxyacetic acid) (0.5 μM) and Kin (Kinetin) (10 μM). Numerous concentrations of 2,4D and Kin were tested in combination with inducers of the sesquiterpene metabolism and one promising callus type was selected for mass production. This interesting type of callus has been used for searching functional genes in the biosynthetic pathway leading to sesquiterpenes molecules.

2011

Alternaria jacinthicola, a new fungal species causing blight leaf disease on water hyacinth [eichhornia crassipes (martius) solms-laubach]
Article scientifique ArODES

Karim Dagno, Julien Crovadore, François Lefort, Rachid Lahlali, Ludivine Lassois, Haïssam Jijakli

Journal of Yeast and Fungal Research,  2011, vol. 2, no. 7, pp. 99-105

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Résumé:

Water hyacinth (Eichhornia crassipes) causes environmental, agricultural and health problems in Mali. This is particularly severe in the District of Bamako and the irrigation systems of the “Office du Niger” area. During two years survey for fungal pathogens of water hyacinth infested areas, isolate Mlb684 was collected from diseased plant. This fungal isolate was identified as a potential mycoherbicide for sustainable Management for water hyacinth. The aim of this study was to characterize isolate Mlb684. The characterization was based on a morphological description and a DNA sequence analysis. Various genes amplified from isolate Mlb684 were compared to those existing in Genbank. These genes were 18S ribosomal rDNA gene, ITS rDNA gene, elongation factor-1 alpha (EF1a) gene, calmodulin and actin genes. DNA sequence comparisons and morphological description provided enough evidences to show that isolate Mlb684 belonged to the Alternaria genus and was distinct from any other known Alternaria species. Based on these evidences, the new fungal isolate was called “Alternaria jacinthicola Dagno & M.H. Jijakli”. A specimen culture has been deposited in the Gembloux Agro Bio Tech Plant Pathology unit fungal collection, with Mlb684 reference and in the Industrial Fungal and Yeast Collection (BCCM/MUCL, Belgium) under the accession number: MUCL 53159 and all DNA sequences were deposited in GenBank (NCBI).

Conservation des fruits à pépins biologiques
Article professionnel ArODES

Dominique Fleury, Cyrielle Coutant, Pegah Cheikhravet, François Lefort

Revue suisse Viticulture, Arboriculture, Horticulture,  2011, vol. 43, no. 4, pp. 246-251

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2022

Suivi métatranscriptomique de l'évolution du microbiote du sol après traitement thermique
Conférence ArODES

Julien Crovadore, François Lefort

Actes du colloque "Stop aux invasives": projet de lutte contre les espèces végétales invasives "agissons pour la biodiversité", 14 octobre 2022, Saint-Julien-en-Genevois, France

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2020

Origanum vulgare vapor primes defence mechanisms in grapevine (Vitisvinifera) and hinders Plasmopara viticola infection
Conférence

Rienth Markus, Lefort François

International symposium on biocidal and non-biocidal plants to improve soil health, 22.03.2020 - 25.05.2022, Switzerland

2018

Metagenomics of aspargus field soils treated with biostimulants
Conférence ArODES

François Lefort, Julien Crovadore, Ali Asaff Torres, Jorge Verdin Ramos, Romain Chablais, Raul Rodriguez Heredia

Proceedings of XVe European Society for Agronomy Congress, 27-31 August 2018, Geneva, Switzerland

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2017

Evaluation of the presence of gnomoniopsis smithogilvyi (syn. castanea) in chestnuts, rootstocks and grafts of six varieties of chestnut trees
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, François Lefort

Proceedings of 15th Congress of the Mediterranean Phytopathological Union, 20-23 June 2017, Córdoba, Spain

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Assessment of biological control agents against gnomoniopsis smithogilvyi (syn. castanea), the fungus causing chestnut brown rot and canker
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, François Lefort

Proceedings of 15th Congress of the Mediterranean Phytopathological Union, 20-23 June 2017, Córdoba, Spain

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Evaluation of the presence of gnomoniopsis smith-ogilvyi (syn. castanea) in chestnuts, rootstocks and grafts of six varieties of chestnut trees
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, François Lefort

Abstracts of invited talks, oral and poster presentations given at the 15th Congress of the Mediterranean Phytopathological Union, June 20–23, 2017, in Córdoba, Spain ; Phytopathologia Mediterranea

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Assessment of biological control agents against gnomoniopsis smithogilvyi (syn. castanea), a fungal agent of chestnut brown rot and chestnut canker
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, François Lefort

Abstracts of invited talks, oral and poster presentations given at the 15th Congress of the Mediterranean Phytopathological Union, June 20–23, 2017, in Córdoba, Spain ; Phytopathologia Mediterranea

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Establishment of specific molecular diagnostic tests for gnomoniopsis smithogilvyi (syn. castanea) and cryphonectria parasitica
Conférence ArODES

M. Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, J.-B. Meyer, M. Jermini, François Lefort

Abstracts of invited talks, oral and poster presentations given at the 15th Congress of the Mediterranean Phytopathological Union, June 20–23, 2017, in Córdoba, Spain ; Phytopathologia Mediterranea

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Establishment of specific molecular diagnostic tests for Gnomoniopsis smithogilvyi (syn. castanea) and cryphonectria parasitica
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Joana Beatrice Meyer, Mauro Jermini, François Lefort

Proceedings of 15th Congress of the Mediterranean Phytopathological Union, 20-23 June 2017, Córdoba, Spain

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Molecular assessment of the latent endophytic pathogen Gnomoniopsis smithogilvyi in chestnuts, rootstocks and grafts of six varieties of chestnut trees
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, Tomasz Oszako, Justyna Anna Nowakowska, François Lefort

Proceedings of IUFRO Working Party Meeting 7.02.02 "Foliage, shoot and stem diseases of forest trees", 7-11 May 2017, Niagara Falls, Ontario, Canada

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Pseudomonas putida and Trichoderma harzianum may efficiently control the agent of chestnut brown rot and chestnut canker Gnomoniopsis smithogilvyi
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Mauro Jermini, Tomasz Oszako, François Lefort

Proceedings of IUFRO Working Party Meeting 7.02.02 "Foliage, shoot and stem diseases of forest trees", 7-11 May 2017, Niagara Falls, Ontario, Canada

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Molecular diagnostics of the chestnut canker agents Gnomoniopsis smithogilvyi and Cryphonectria parasitica in different tissues of Castanea sativa
Conférence ArODES

Matteo Conti, Julien Crovadore, Bastien Cochard, Romain Chablais, Joana Beatrice Meyer, Mauro Jermini, Tomasz Oszako, François Lefort

Proceedings of IUFRO Working Party Meeting 7.02.02 "Foliage, shoot and stem diseases of forest trees", 7-11 May 2017, Niagara Falls, Ontario, Canada

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