Réponse des communautés microbiennes du sol à l'apport de résidus de culture : influence des pratiques agricoles et lien avec le fonctionnement biologique du sol

Abstract : The effect of the location of wheat residues (soil surface vs. incorporated in soil) on their decomposition and on soil bacterial communities was investigated by the means of a field experiment. Bacterial-Automated Ribosomal Intergenic Spacer Analysis (B-ARISA) of DNA extracts from residues, detritusphere (soil adjacent to residues), and bulk soil evidenced that residues constitute the zone of maximal changes in bacterial composition. However, the location of the residues influenced greatly their decomposition and the dynamics of the colonizing bacterial communities. Sequencing of 16S rRNA gene in DNA extracts from the residues at the early, middle, and late stages of degradation confirmed the difference of composition of the bacterial community according to the location. Bacteria belonging to the -subgroup of proteobacteria were stimulated when residues were incorporated whereas the -subgroup was stimulated when residues were left at the soil surface. Moreover, Actinobacteria were more represented when residues were left at the soil surface. According to the ecological attributes of the populations identified, our results suggested that climatic fluctuations at the soil surface select populations harboring enhanced catabolic and/or survival capacities whereas residues characteristics likely constitute the main determinant of the composition of the bacterial community colonizing incorporated residues. Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in a eleven-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass and genetic structure of the soil microbial communities. Wheat, alfalfa and rape residues were incorporated into the 0-15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near infrared spectroscopy (NIRS). Qualitative modifications in the genetic structure of the bacterial communities were determined by Bacterial-Automated Ribosomal Intergenic Spacer Analysis (B-ARISA). Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial communities dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic populations/bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process...
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Earth Sciences. Université de Bourgogne, 2010. French. <NNT : 2010DIJOS020>


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Noémie Pascault. Réponse des communautés microbiennes du sol à l'apport de résidus de culture : influence des pratiques agricoles et lien avec le fonctionnement biologique du sol. Earth Sciences. Université de Bourgogne, 2010. French. <NNT : 2010DIJOS020>. <tel-00582567>

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