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- PublicationMétadonnées seulementEcological determinants of fungal diversity on deadwood in European forests(2008)
;Kuffer, Nicolas ; ;Senn-Irlet, Béatrice ;The fine-scale ecological determinants for wood-inhabiting aphyllophoroid basidiomycetes were investigated with statistical analyses of the occurrence of fruit bodies on woody debris collected in Switzerland and Ukraine. Three substrate descriptors were considered: diameter, degree of decomposition to those local environmental descriptors were detected. Three classes for diameter, as well as for degree of decomposition were thus delimited. They revealed the importance of very small sizes, which were not reported in the literature so far: the relevant diameter class limits were about 0.72 cm and 1.35 cm. Within the host tree species, a clear distinction between coniferous and broadleaf species was found. The next splits followed rather climatic determinants of tree distribution than taxonomical entities such as families or genera. The fidelity of the 59 fungal species to diameter classes, decomposition classes and host tree species was measured by the Dufrene-Legendre index and only significant responses after permutation tests were retained. This brought new insights on the ecology of many wood-inhabiting aphyllophoroid basidiomycetes. Redundancy Analysis was applied to investigate the response of fungal species to diameter and degree of decompostion of woody debris from the most common host tree species, Fagus sylvatica. This direct gradient analysis made it possible to reconstruct the succession of fungal species along the wood decomposition process.
- PublicationAccès libreBiologically induced mineralization in the tree Milicia excelsa (Moraceae) : its causes and consequences to the environment(2004)
;Braissant, Olivier ; ;Iroko trees (Milicia excelsa) in Ivory Coast and Cameroon are unusual because of their highly biomineralized tissues, which can virtually transform the trunk into stone. Oxalic acid (C2O4H2) and metal-oxalate play important roles in their ecosystems. In this study, the various forms of oxalate and carbonate mineralization reactions are investigated by using scanning electron microscopy and X-ray diffraction. Calcium oxalate monohydrate is associated with stem, bark and root tissues, whereas calcium oxalate dihydrate is found with wood rot fungi in soils, as well as in decaying wood. Laboratory cultures show that many soil bacteria are able to oxidize calcium oxalate rapidly, resulting in an increase in solution pH. In terms of M. excelsa, these transformations lead to the precipitation of calcium carbonate, not only within the wood tissue, but also within the litter and soil. We calculate that c. 500 kg of inorganic carbon is accumulated inside an 80-year-old tree, and c. 1000 kg is associated with its surrounding soil. Crucially, the fixation of atmospheric CO2 during tree photosynthesis, and its ultimate transformation into calcite, potentially represents a long-term carbon sink, because inorganic carbon has a longer residence time than organic carbon. Considering that calcium oxalate biosynthesis is widespread in the plant and fungal kingdoms, the biomineralization displayed by M. excelsa may be an extremely common phenomena.
- PublicationMétadonnées seulementExperimental calcium-oxalate crystal production and dissolution by selected wood-rot fungi(2011)
;Guggiari, Matteo ;Bloque, Raphael ; ; ;
- PublicationMétadonnées seulementFungi, bacteria and soil pH: the oxalate?carbonate pathway as a model for metabolic interaction(2012)
;Martin, Gaëtan ;Guggiari, Matteo ; ; ; ; ; ;
- PublicationAccès libreDiacetylphloroglucinol-producing pseudomonads do not influence AM fungi in wheat rhizosphere(2004)
;Gaur, Rachna ;Shani Noam ;Kawaljeet ;Johri, B. N. ;Rossi, PierreNatural agroecosystems are directly dependent on bene-ficial microorganisms present in bulk soil and rhizo-sphere for soil health and plant productivity. With the current thrust on use of microbial inoculants, espe-cially the biological control agents, it is necessary to assess their negative influence on such beneficial forms as AM fungi since they help the plant withstand various stresses. Among other molecules, pseudomonads pre-sent in the rhizosphere secrete the antifungal, 2,4-dia-cetylphloroglucinol (DAPG) and are currently in great demand as bioinoculants. Based on the cultural, bio-chemical, and molecular tools we show that DAPG producing pseudomonads recovered from wheat rhizo-sphere do not adversely affect AM colonization. Eva-luation of such effects on non-target organisms will help early acceptance of microbial inoculants in future.
- PublicationAccès libreBacteriophages as surface and ground water tracers
;Rossi, Pierre ;Dörfliger, Nathalie ;Kennedy, Keith ;Müller, ImreBacteriophages are increasingly used as tracers for quantitative analysis in both hydrology and hydrogeology. The biological particles are neither toxic nor pathogenic for other living organisms as they penetrate only a specific bacterial host. They have many advantages over classical fluorescent tracers and offer the additional possibility of multi-point injection for tracer tests. Several years of research make them suitable for quantitative transport analysis and flow boundary delineation in both surface and ground waters, including karst, fractured and porous media aquifers.
This article presents the effective application of bacteriophages based on their use in differing Swiss hydrological environments and compares their behaviour to conventional coloured dye or salt-type tracers. In surface water and karst aquifers, bacteriophages travel at about the same speed as the typically referenced fluorescent tracers (uranine, sulphurhodamine G extra). In aquifers of interstitial porosity, however, they appear to migrate more rapidly than fluorescent tracers, albeit with a significant reduction in their numbers within the porous media. This faster travel time implies that a modified rationale is needed for defining some gro und water protection area boundaries. Further developments of other bacteriophages and their documentation as tracer methods should result in an accurate and efficient tracer tool that will be a proven alternative to conventional fluorescent dyes.
- PublicationMétadonnées seulementUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
;Khammar, Nadia ;Martin, Gaëtan ;Ferro, Katia ; ;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 1.64x10(7) to 1.75x10(8)/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 6.4x10(6) (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. (c) 2008 Elsevier B.V. All rights reserved.
- PublicationAccès libreExperimental calcium-oxalate crystal production and dissolution by selected wood-rot fungi
;Guggiari, Matteo ;Bloque, Raphael ; ; ;Twenty-six species of white-rotting Agaricomycotina fungi (Basidiomycota) were screened for their ability to produce calcium-oxalate (CaOx) crystals in vitro. Most were able to produce CaOx crystals in malt agar medium in the absence of additional calcium. In the same medium enriched with Ca2+, all the species produced CaOx crystals (weddellite or whewellite). Hyphae of four species (Ganoderma lucidum, Polyporus ciliatus, Pycnoporus cinnabarinus, and Trametes versicolor) were found coated with crystals (weddellite/whewellite). The production of CaOx crystals during the growth phase was confirmed by an investigation of the production kinetics for six of the species considered in the initial screening (Pleurotus citrinopileatus, Pleurotus eryngii, Pleurotus ostreatus, P. cinnabarinus, Trametes suaveolens, and T. versicolor). However, the crystals produced during the growth phase disappeared from the medium over time in four of the six species (P. citrinopileatus, P. eryngii, P. cinnabarinus, and T. suaveolens). For P. cinnabarinus, the disappearance of the crystals was correlated with a decrease in the total oxalate concentration measured in the medium from 0.65 μg mm-2 (at the maximum accumulation rate) to 0.30 μg mm-2. The decrease in the CaOx concentration was correlated with a change in mycelia morphology. The oxalate dissolution capability of all the species was also tested in a medium containing calcium oxalate as the sole source of carbon (modified Schlegel medium). Three species (Agaricus blazei, Pleurotus tuberregium, and P. ciliatus) presented a dissolution halo around the growth zone. This study shows that CaOx crystal production is a widespread phenomenon in white-rot fungi, and that an excess of Ca2+ can enhance CaOx crystal production. In addition, it shows that some white-rot fungal species are capable of dissolving CaOx crystals after growth has ceased. These results highlight a diversity of responses around the production or dissolution of calcium oxalate in white-rot fungi and reveal an unexpected potential importance of fungi on the oxalate cycle in the environment.
- PublicationAccès libreExamination of Gould’s modified S1 (mS1) selective medium and Angle’s non-selective medium for describing the diversity of Pseudomonas spp. in soil and root environments(2003)
;Tarnawski, Sonia Estelle ;Hamelin, Jérôme ;Locatelli, Laurent ;Fromin, NathalieStudies on the diversity of environmental culturable Pseudomonas populations are dependent on the isolation procedure. This procedure includes the use of selective media which may influence the recovery of strains and thus the diversity described. In this study, we assessed the use of two agar isolation media for describing the diversity of soil- and root-inhabiting Pseudomonas associated with the perennial grass Molinia coerulea. A total of 382 Pseudomonas strains were recovered on either non-selective Angle’s medium, or on Gould’s modified S1 (mS1) Pseudomonas-selective medium. Their diversity was assessed by restriction analysis of PCR (polymerase chain reaction)-amplified 16S–23S rDNA internal transcript spacer sequences. The comparison of mS1- and Angle-recovered populations showed that the use of mS1 selective medium led to an underestimation of both Pseudomonas counts and diversity, especially in the soil environment.
- PublicationMétadonnées seulementLe sol vivant. Bases de pédologie, biologie des sols.(Lausanne: Presses Polytechniques et universitaires romandes, 2003)
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