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Université de Neuchâtel

Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil

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

In: Journal of Microbiological Methods, 2009, vol. 76, no. 2, p. 120-127

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...

Université de Neuchâtel

Secretion activity of white lupin’s cluster roots influences bacterial abundance, function and community structure

Weisskopf, Laure ; Fromin, Nathalie ; Tomasi, Nicola ; Aragno, Michel ; Martinoia, Enrico

In: Plant and Soil, 2005, vol. 268, no. 1, p. 181-194

White 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...

Université de Neuchâtel

How elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions

Jossi, Maryline ; Fromin, Nathalie ; Tarnawski, Sonia ; Kohler, Florian ; Gillet, François ; Aragno, Michel ; Hamelin, Jérôme

In: FEMS Microbiology Ecology, 2006, vol. 55, no. 3, p. 339-350

The 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...

Université de Neuchâtel

nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass

Hamelin, Jérôme ; Fromin, Nathalie ; Tarnawski, Sonia ; Teyssier-Cuvelle, Sylvie ; Aragno, Michel

In: Environmental Microbiology, 2002, vol. 4, no. 8, p. 477-481

Rhizosphere associative dinitrogen fixation could be a valuable source of nitrogen in many nitrogen limited natural ecosystems, such as the rhizosphere of Molinia coerulea, a hemicryptophytic perennial grass naturally occurring in contrasted oligonitrophilic soils. The diversity of the dinitrogen-fixing bacteria associated with this environment was assessed by a cloning–sequencing...

Université de Neuchâtel

Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Fromin, Nathalie ; Hamelin, Jérôme ; Tarnawski, Sonia ; Roesti, David ; Jourdain-Miserez, K. ; Teyssier-Cuvelle, Sylvie ; Gillet, F. ; Aragno, Michel ; Rossi, Pierre

In: Environmental Microbiology, 2002, vol. 4, no. 11, p. 634-643

Technical 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...

Université de Neuchâtel

Examination 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

Tarnawski, Sonia Estelle ; Hamelin, Jérôme ; Locatelli, Laurent ; Aragno, Michel ; Fromin, Nathalie

In: FEMS Microbiology Ecology, 2003, vol. 45, p. 97-104

Studies 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...

Université de Neuchâtel

Specific PCR Amplification for the Genus Pseudomonas Targeting the 3′ Half of 16S rDNA and the Whole 16S–23S rDNA Spacer

Locatelli, Laurent ; Tarnawski, Sonia Estelle ; Hamelin, Jérôme ; Rossi, Pierre ; Aragno, Michel ; Fromin, Nathalie

In: Systematic and Applied Microbiology, 2002, vol. 25, p. 220-227

A 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...

Université de Neuchâtel

Phenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses

Tarnawski, Sonia Estelle ; Hamelin, Jérôme ; Jossi, M. ; Aragno, Michel ; Fromin, Nathalie

In: Soil Biology and Biochemistry, 2006, vol. 38, p. 1193-1201

The 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...

Université de Neuchâtel

Nitrogen fertiliser rate affects the frequency of nitrate-dissimilating Pseudomonas spp. in the rhizosphere of Lolium perenne grown under elevated pCO2 (Swiss FACE)

Fromin, Nathalie ; Tarnawski, Sonia Estelle ; Roussel-Delif, L. ; Hamelin, Jérôme ; Baggs, E.M. ; Aragno, Michel

In: Soil Biology and Biochemistry, 2005, vol. 37, p. 1962-1965

The effect of elevated pCO2 (60 Pa) on the frequency of nitrate-dissimilating Pseudomonas (NDP) was investigated in the rhizosphere of fertilised Lolium perenne swards in the Swiss Free Air Carbon dioxide Enrichment (FACE) experiment. Numbers of cultivable root-associated Pseudomonas were greater under elevated (60 Pa) than under ambient (36 Pa) pCO2 in...

Université de Neuchâtel

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

Roussel-Delif, L. ; Tarnawski, Sonia Estelle ; Hamelin, Jérôme ; Philippot, L. ; Aragno, Michel ; Fromin, Nathalie

In: Microbial Ecology, 2005, vol. 49, p. 63 - 72

A 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-,...