showing 10 related works from this author
Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure
2011
Three soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15,000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant differenc…
Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR
2011
Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affec…
Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms
2010
Eight Erwinia strains, isolated from necrotic pear blossoms in València, Spain, were compared with reference strains of Erwinia amylovora and Erwinia pyrifoliae, both of which are pathogenic to species of pear tree, and to other species of the family Enterobacteriaceae using a polyphasic approach. Phenotypic analyses clustered the novel isolates into one phenon, distinct from other species of the genus Erwinia, showing that the novel isolates constituted a homogeneous phenotypic group. Rep-PCR profiles, PCR products obtained with different pairs of primers and plasmid contents determined by restriction analysis showed differences between the novel strains and reference strains of E. amylovo…
Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-inform…
2011
Communication orale, résuméCommunication orale, résumé; La diversité microbienne d’un sol est difficile à caractériser. Ceci s’explique par une accessibilité plus ou moins importante des populations au sein d’une matrice hétérogène et structurée, mais aussi par l’incapacité à résoudre une information constituée de 100 000 à 1 000 000 d’espèces différentes par gramme de sol. Toutefois, récemment, d’importantes avancées en biologie moléculaire ont permis de mieux caractériser la diversité des communautés microbiennes du sol in situ et ce sans a priori. Ainsi, la puissance des nouvelles générations de séquençage comme le pyroséquençage permettent de travailler en haut-débit afin d’obtenir plus…
Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-inform…
2012
National audience
Pseudomonas salomonii sp. nov., pathogenic on garlic, and Pseudomonas palleroniara sp. nov., isolated from rice
2002
International audience; A total of 26 strains, including 15 strains isolated from garlic plants with the typical symptoms of 'Café au lait' disease and 11 strains isolated from diseased or healthy rice seeds and sheaths infested by Pseudomonas fuscovaginae, were compared with 70 type or reference strains of oxidase-positive pathogenic or non-pathogenic fluorescent pseudomonads. The strains were characterized by using a polyphasic taxonomic approach. Numerical taxonomy of phenotypic characteristics showed that the garlic and rice strains were related to each other. However, they clustered into separate phenons, distinct from those of the other strains tested, and were different in several nu…
Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils.
2002
The taxonomic position of eight fluorescent Pseudomonas strains isolated from bulk and rhizospheric soils, and from water was examined. These eight strains clustered in one phenon together with Pseudomomas mandelii (CFBP 4844T), but could still be differentiated from this type strain by four phenotypic features. The eight stains exhibited internal DNA-DNA hybridization values ranging from 60 to 100%, with deltaTm below 5 degrees C (3.9 and 4.3 degrees C) for the lowest values (60 and 66%). The percentages of hybridization with type or reference strains of other Pseudomonas species tested ranged from 12 to 60% (deltaTm = 5.5 degrees C), indicating that the eight isolates studied constituted …
Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols
2012
La diversité microbienne d’un sol (que l’on estime à 100000 à 1000000 d’espè ces différentes par gramme de sol) est difficile à caractériser. Toutefois, d’importantes avancé es en biologie moléculaire (comme le développement du pyrosé quençage), ont permis d'obtenir plusieurs centaines de milliers de sé quences à partir d’un ADN métagénomique, permettant une meilleure caracté risation de la diversité des communautés microbiennes du sol. Toutefois, dans un contexte ou l’écologie microbienne du sol commence à s’accaparer les é chantillonnages de grande envergure (spatial et temporelle) afin de mieux hié rarchiser les processus et paramètres impliqués dans la diversification de ces communauté …
GnS-PIPE: an optimized bionformatic pipeline to efficiently assess microbial taxonomic diversity of complex environments using high throughput sequen…
2013
International audience; The rRNA genes (16S, 18S, ITS) are widely used to study microbial communities in soils, as they can be easily amplified from metagenomic DNA. Moreover, the recent development of high-throughput sequencing technologies allows the assessment of millions of sequences from a single metagenomic DNA. Some pipelines are already available (e.g. QIIME or Mothur) to efficiently treat such data. However, the development of bioinformatic tools must now be validated by various biological tests. This was particularly true for key steps to appraise microbial diversity and richness. Here, we present a new pipeline named GnS-PIPE, a software application performing bacterial, archaeal…
GnS-PIPE: an optimized bionformatic pipeline to efficiently assess microbial taxonomic diversity of complex environments using high throughput sequen…
2013
International audience; The rRNA genes (16S, 18S, ITS) are widely used to study microbial communities in soils, as they can be easily amplified from metagenomic DNA. Moreover, the recent development of high-throughput sequencing technologies allows the assessment of millions of sequences from a single metagenomic DNA. Some pipelines are already available (e.g. QIIME or Mothur) to efficiently treat such data. However, the development of bioinformatic tools must now be validated by various biological tests. This was particularly true for key steps to appraise microbial diversity and richness. Here, we present a new pipeline named GnS-PIPE, a software application performing bacterial, archaeal…