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Job, Daniel
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Job, Daniel
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- PublicationMétadonnées seulementUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
; ; 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. - PublicationMétadonnées seulementEcological determinants of fungal diversity on deadwood in European forests(2008)
; ; 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.