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Aragno, Michel
Nom
Aragno, Michel
Affiliation principale
Email
Michel.Aragno@unine.ch
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Résultat de la recherche
Voici les éléments 1 - 10 sur 10
- PublicationAccès libreHow elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions(2006)
; ; Hamelin, JérômeThe response of total (DNA-based analysis) and active (RNA-based analysis) bacterial communities to a pCO2 increase under field conditions was assessed using two perennial grasses: the nitrophilic Lolium perenne and the oligonitrophilic Molinia coerulea. PCR- and reverse transcriptase-PCR denaturing gradient gel electrophoresis analysis of 16S rRNA genes generated contrasting profiles. The pCO2 increase influenced mainly the active and root-associated component of the bacterial community. Bacterial groups responsive to the pCO2 increase were identified by sequencing of corresponding denaturing gradient gel electrophoresis bands. About 50% of retrieved sequences were affiliated to Proteobacteria. Our data suggest that Actinobacteria in soil and Myxococcales (Deltaproteobacteria) in root are stimulated under elevated pCO2. - PublicationAccès librePhenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses(2006)
; Fromin, NathalieThe increasing atmospheric CO2 content (pCO2) is likely to modify the ecosystem functioning including rhizosphere bacteria that are directly dependent on rhizodeposition. This may include alteration of Pseudomonas populations that display phenotypic traits in relation with plant fitness. In the present study, 1228 Pseudomonas strains were isolated from the non-rhizosphere soil, rhizosphere soil and root fractions of perennial grassland systems: Lolium perenne and Molinia coerulea. Both plants were grown under ambient (36 Pa) and elevated (60 Pa) pCO2 in the Swiss Free Air CO2 Enrichment (FACE) system. Pseudomonas spp. were tested for their ability to produce auxin, siderophores and hydrogen cyanide, and to dissimilate nitrate. No effect of root proximity and elevated pCO2 was observed on the proportions of auxin producers. For L. perenne and M. coerulea, siderophore and hydrogen cyanide Pseudomonas producers were stimulated in the root fraction. In contrast lower frequencies of nitrate reducers were observed in the root fraction compared to non-rhizosphere soil. The frequencies of siderophore producers and nitrate dissimilating strains were higher, and those of hydrogen cyanide producers lower, under elevated pCO2 for L. perenne. This alteration of the phenotypic structure of Pseudomonas guild in the root fraction is discussed in relation with the physico-biochemical modifications of the rhizosphere condition via rhizodeposition and environmental changes occurring under elevated pCO2. - PublicationAccès libreWhite lupin has developed a complex strategy to limit microbial degradation of secreted citrate required for phosphate acquisition(2006)
; ; Martinoia, EnricoWhite lupins (Lupinus albus L.) respond to phosphate deficiency by producing special root structures called cluster roots. These cluster roots secrete large amounts of carboxylates into the rhizosphere, mostly citrate and malate, which act as phosphate solubilizers and enable the plant to grow in soils with sparingly available phosphate. The success and efficiency of such a P-acquisition strategy strongly depends on the persistence and stability of the carboxylates in the soil, a parameter that is influenced to a large extent by biodegradation through rhizosphere bacteria and fungi. In this study, we show that white lupin roots use several mechanisms to reduce microbial growth. The abundance of bacteria associated with cluster roots was decreased at the mature state of the cluster roots, where a burst of organic acid excretion and a drastic pH decrease is observed. Excretion of phenolic compounds, mainly isoflavonoids, induced fungal sporulation, indicating that vegetative growth, and thus potential citrate consumption, is reduced. In addition, the activity of two antifungal cell wall-degrading enzymes, chitinase and glucanase, were highest at the stage preceding the citrate excretion. Therefore, our results suggest that white lupin has developed a complex strategy to reduce microbial degradation of the phosphate-solubilizing agents. - PublicationAccès libreFrequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions(2005)
; Fromin, NathalieA total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil–associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatment. - PublicationAccès libreNitrogen fertiliser rate affects the frequency of nitrate-dissimilating Pseudomonas spp. in the rhizosphere of Lolium perenne grown under elevated pCO2 (Swiss FACE)(2005)
- PublicationAccès libreSecretion activity of white lupin’s cluster roots influences bacterial abundance, function and community structure(2005)
; Martinoia, EnricoWhite lupin (Lupinus albus L. cv. Amiga) reacts to phosphate deficiency by producing cluster roots which exude large amounts of organic acids. The detailed knowledge of the excretion physiology of the different root parts makes it a good model plant to study plant-bacteria interaction. Since the effect of the organic acid exudation by cluster roots on the rhizosphere microflora is still poorly understood, we investigated the abundance, diversity and functions of bacteria associated with the cluster roots of white lupin, with special emphasis on the influence of root proximity (comparing root, rhizosphere soil and bulk soil fractions) and cluster root growth stages, which are characterized by different excretion activities. Plants were grown for five weeks in microcosms, in the presence of low phosphate concentrations, on acidic sand inoculated with a soil suspension from a lupin field. Plate counts showed that bacterial abundance decreased at the stage where the cluster root excretes high amounts of citrate and protons. In vitro tests on isolates showed that the frequencies of auxin producers were highest in juvenile and mature cluster roots and significantly decreased in senescent cluster roots. However, no significant difference in the frequency of auxin producers was found between cluster and non cluster roots. The diversity and structure of bacterial communities were investigated by DGGE of 16S rDNA and 16S rRNA. The diversity and community structure were mostly influenced by root proximity and, to a lesser extent, by cluster root stage. The richness of bacterial communities decreased with root proximity, whereas the proportion of active populations increased. The high citrate and proton excretion occurring at the mature stage of cluster roots had a strong impact on the structure and richness of the bacterial communities, both in the root and in the rhizosphere soil. - 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)
; 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. - PublicationAccès libreStatistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns(2002)
; Rossi, PierreTechnical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities. - PublicationAccès librenifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass(2002)
- PublicationAccès libreSpecific PCR Amplification for the Genus Pseudomonas Targeting the 3′ Half of 16S rDNA and the Whole 16S–23S rDNA Spacer(2002)
; Fromin, NathalieA PCR protocol was developed for the selective amplification of a segment of the ribosomal RNA operon in Pseudomonas strains. Two specific conserved sequences suitable for PCR priming were identified in the middle of the 16S rDNA and at the very beginning of the 23S rDNA respectively. As a result, amplified region includes the 3′ half of the 16S rDNA with the whole 16S–23S rRNA Internal Transcripted Spacer (ITS1) sequence. The specificity of the primer set was checked on sequence databases and validated on collection strains and on one hundred soil bacterial isolates. Our results showed that both collection, soil-inhabiting Pseudomonas and some Pseudomonas-related Azotobacter DNAs could be amplified. This specific PCR for the detection of Pseudomonas strains was in good agreement with colony hybridisation using a Pseudomonas-specific probe. The targeted segment is relevant for a characterisation at the species (16S rDNA) as well as at the infraspecific (ITS1) levels. This PCR-based approach offers promising potential for the characterisation of environmental Pseudomonas populations.