Job, Daniel

2015, Simon, Anaele, Bindschedler, Saskia, Job, Daniel, Wick, Lukas Y., Filippidou, Sevasti, Kooli, Wafa M., Verrecchia, Eric P., Junier, Pilar

Fungi and bacteria form various associations that are central to numerous environmental processes. In the so-called fungal highway, bacteria disperse along fungal mycelium. We developed a novel tool for the in situ isolation of bacteria moving along fungal hyphae as well as for the recovery of fungi potentially involved in dispersal, both of which are attracted towards a target culture medium. We present the validation and the results of the first in situ test. Couples of fungi and bacteria were isolated from soil. Amongst the enriched organisms, we identified several species of fast-growing fungi (Fusarium sp. and Chaetomium sp.), as well as various potentially associated bacterial groups, including Variovorax soli, Olivibacter soli, Acinetobacter calcoaceticus, and several species of the genera Stenotrophomonas, Achromobacter and Ochrobactrum. Migration of bacteria along fungal hyphae across a discontinuous medium was confirmed in most of the cases. Although the majority of the bacteria for which migration was confirmed were also positive for flagellar motility, not all motile bacteria dispersed using their potential fungal partner. In addition, the importance of hydrophobicity of the fungal mycelial surface was confirmed. Future applications of the columns include targeting different types of microorganisms and their interactions, either by enrichment or by state of the art molecular biological methods.

2009, Khammar, Nadia, Martin, Gaëtan, Ferro, Katia, Job, Daniel, Aragno, Michel, Verrecchia, Eric

Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64 × 10⁷ to 1.75 × 10⁸/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4 × 10⁶ (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate–carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO₂ sequestration.

2004, Job, Daniel

We studied the capacity of a selected strain of Gloeophyllum trabeum, alone or in combination with Resinicium bicolor, to defibrillate non treated deciduous wood at a semi industrial composting scale. Inoculum amount, aeration of the composted wood, type (freshly cut wood and wood stored since several years) and the quantity of wood used were analysed. The remaining cellular cohesion, lignin and holocellulose, as well as fungal biomass content in the wood after various treatments were determined. Results showed that G. trabeum rapidly colonised the non-sterile substrate and caused greater biodefibrillation compared with the control (non inoculated wood). Effects of the various treatments on biodefibrillation were compared and are discussed.

2004, Gonin, Yvan, Munnik, Frans, Farron, Gilles, Job, Daniel, Boschi, Pascal, Moratel, Jean-Louis, Mikhailov, Serguei

Les champignons sont connus pour être de bons accumulateurs de métaux, mais la localisation directe non-destructive des ces éléments dans les tissus fongiques requièrent des méthodes particulières. Le Laboratoire de Microbiologie de l'Université de Neuchâtel s'intéresse depuis longtemps à la culture des champignons et plus récemment à l'accumulation de métaux et de métalloïdes dans les fructifications. Afin de quantifier et de localiser les concentrations ainsi obtenues, il s'est approché du Centre d'Analyses par Faisceau Ionique (CAFI) au Locle, équipé d'un accélérateur de particules et d'une méthode de détection appropriée. Cet article décrit la méthode de mesure et les résultats obtenus sur une espèce particulière de champignon, YAgaricus blazei., Mushrooms are known to be good metal accumulators, but the nondestructive direct localization of these elements in fungal tissues requires particular methods. The Microbiology Laboratory of the University of Neuchatel has been interested for a long time in the culture of mushrooms and more recently in accumulation of metals and metalloids in fructifications. In order to quantify and to locate the concentrations obtained with this technique, the laboratory collaborated with the Ion Beam Analysis Center (CAFI) in Le Lode, equipped with a particle accelerator and a suitable detection instrument. This article describes the method of measurement and the results obtained on a particular mushroom species, Agaricus blazei.

2013, Bravo, Daniel, Cailleau, Guillaume, Bindschedler, Saskia, Simon, Anaele, Job, Daniel, Verrecchia, Eric, Junier, Pilar

2007, Küffer, Nicolas, Job, Daniel

Wood-inhabiting aphyllophoroid basidiomycetes are a species rich and ecologically significant group in nemoral and boreal forests. They are divided in three major morphological groups: corticioid, poroid and thelephoroid basidiomycetes. The species richness and species distribution depend on several features on different scales: the diversity of the provided substrate, i.e. dead wood, is of vital importance on a smaller scale. On a larger scale the direct (i.e. amount of dead wood, natural likeness) and indirect (i.e. forest fragmentation, distance between fungal populations) impact of forestry highly influences the fungal species richness, additionally to site specific (i.e. altitude, exposition, slope) and regional (i.e. biogeographical region) characteristics. For the quality of dead wood as substrate for wood-inhabiting fungi, three features are most essential: size of dead woody debris, degree of decomposition and host tree species. These characteristics and their combinations create a wide variety of niches subsequently colonised by a great number of fungal species. Especially the often neglected smallest fraction of dead woody debris, i.e. thin branches and twigs, are rich in species. Woody shrub species and thermophilic tree species host a particularly rich fungal species set, as many aphyllophoroid species are host-selective. Additionally, the amount of dead woody substrate is equally important, especially in managed forests. Evidently, the amount and the composition of dead woody substrate are strongly influenced by forest management practices, where most dead wood is cleared and a siteadapted tree cover is often ignored. On a larger scale, the management history of a forest is very important: the time since the last forestry intervention seems a good indicator to predict fungal species richness, at least when dealing with strongly managed Central European forests. Furthermore, if intensive forest management results in habitat fragmentation, the fungal species richness is heavily affected. Fragmentation may not only occur spatially, but also temporally: a break in the availability of the dead woody substrate disrupts the continuity of the fungal life cycle and so causes the local disappearance of populations. When considering the high degree of substrate specialisation of most fungal species, this temporal break in the substrate availability is a major threat for fungal populations in managed nemoral forests. Considering these findings, the remnant patches of natural forest in Central Europe should harbour a considerably higher amount of wood-inhabiting aphyllophoroid basidiomycetes. However, the results of this study are equivocal. Despite the presence of a higher quantity of dead wood and of more diverse dead wood as substrate, which clearly favours the woodinhabiting basidiomycetes, the analyses could not reveal statistically relevant differences.

2004, Job, Daniel

Use of coffee spent industry residues forproduction of Pleurotus ostreatus (Jacq.:Fr.) Kummerin solid state fermentation Studies were carried out to screen the industrial strain HK35 of Pleurotus ostreatus for its ability to develop fruiting bodies in solid state cultivation using several substrates containing 17.8 to 55% of coffee spent ground. Our results showed that only 55% of coffee spent ground was used in the substrate without detecting changes in fruiting body or on its biological efficiency of production.The chemical analyze of the caffeine in the substrate showed that this compound decreased about 59%? of the mycelium activity and no caffeine were found in fruiting bodies indicating its degradation by the fungal strain tested., Hemos estudiado la capacidad de la cepa industrial HK35 de Pleurotus ostreatus de fructificar en diferentes substratos que contienen de 17,8 a 55% de borra de café industrial. Nuestros resultados muestran que la incorporación al substrato de hasta un 55% de esta borra de café, no disminuye la capacidad de fructificar ni el rendimiento del pleuroto. Además, el análisis de la cafeína efectuado en el substrato indica que la misma es degradada hasta un 59 % por el micelio y que ésta no es incorporada en las fructificaciones recogidas indicando su degradación por el micelio.

2009, Bindschedler, Saskia, Milliere, Laure, Cailleau, Guillaume, Job, Daniel, Verrecchia, Eric P.

2006, Schiff Giovannini, Isabelle, Job, Daniel

Les champignons supérieurs sont une source encore peu explorée et exploitée de nouveaux produits naturels. Ils attirent toujours plus l’intérêt des milieux scientifiques et industriels. Dans ce contexte, nous voulions explorer le potentiel de champignons cultivés dans la recherche de nouveaux composés actifs. Nous avons obtenus les fructifications de 14 espèces de Basidiomycètes selon des techniques développées auparavant dans le laboratoire. De plus, nous avons testé la capacité à fructifier de 37 nouvelles souches de 27 espèces. Dans la plupart des expériences, seuls 4 substrats (A, B, C et D) variant principalement dans leur rapport C/N ont été utilisés. Quelques espèces ont été testées sur d’autres substrats, comme Agaricus blazei, seul saprophyte secondaire étudié durant ce travail. Nous avons obtenu la fructification de 59.5% des souches et 63% des espèces Plus la valeur C/N était basse plus il y avait d’espèces capables de former des fructifications : 56% sur le substrat A et 34.8% sur le substrat D. Certaines espèces présentaient une grande spécificité de substrat alors que d’autres pouvaient fructifier sur tous les substrats testés. Cependant un substrat adapté à une souche donnée ne convenait pas nécessairement à une autre souche de la même espèce. En conclusion l’initiation des primordia, la fructification, le rendement, mais aussi le temps jusqu’à la récolte dépendent du type de substrat, mais aussi de la souche utilisée. Le problème majeur durant la culture de champignons est le mycoparasite Trichoderma viride. A notre avis, l’aptitude à la compétition contre ce micromycète est une caractéristique à sélectionner parallèlement à la capacité à fructifier, lors du choix d’une nouvelle souche. Nous avons émis l’hypothèse qu’il est plus probable de trouver une molécule antifongique active contre ce pathogène chez des souches résistantes. Pour développer la méthode de sélection 5 souches de chacune des espèces Grifola frondosa et Fomitopsis pinicola ont été testées. Nous avons démontré que les tests en tubes de Téflon® étaient adéquats pour sélectionner des souches résistantes à un coût moindre et en un temps relativement court. De plus cela permet d’apporter des informations sur le comportement des souches sur les différents substrats. Les résultats ont montré qu’il y avait une grande variation de résistance entre souches et pour une même souche sur différents substrats. Un test autobiographique contre T. viride a été adapté de protocoles existants pour d’autres organismes. Les tests biologiques contre Bacillus subtilis, Cladosporium cucumerinum, Candida albicans, Biomphalaria glabrata et Aedes aegyptii, ainsi que contre le radical DPPH ont été réalisés sur 8 espèces à l’Institut de Pharmacognosie et Phytochimie de l’Université de Lausanne. Seul un petit nombre d’activités ont été décelées principalement dues à des acides gras. Nous avons comparé 5 souches de G. frondosa pour explorer la modulation chez les champignons. La variabilité morphologique, physiologique et chimique observée au sein d’une même espèce nous montre l’importance de conditions stables (souche, substrat, conditions de culture, traitement après récolte) dans la recherche de composés. Nous en concluons que ce travail est encourageant pour continuer dans cette ligne de recherche. Nous pouvons espérer un jour trouver de nouveaux arômes ou composés actifs étant donné le nombre d’espèces qui pourraient être testées. Il serait particulièrement intéressant de se focaliser sur des composés contre T. viride étant donné le manque de recherche actuellement réalisés sur ce sujet et le besoin urgent de nouveaux produits pour lutter contre ce pathogène.

2004, Casali, Sabrina, Job, Daniel