Papers by Claire Prigent-combaret
Comparaison de sols résistant ou non à la maladie du piétin-échaudage du blé par une approche puce à ADN taxonomique 16S ciblant les bactéries rhizosphériques phytoprotectrices du genre Pseudomonas
HAL (Le Centre pour la Communication Scientifique Directe), 2006
Abstract: Comparison of soils suppressive or not to take-all disease of wheat by 16S taxonomic mi... more Abstract: Comparison of soils suppressive or not to take-all disease of wheat by 16S taxonomic microarray targeting plant-protecting rhizosphere bacteria. Take-all is an important wheat disease caused by the soil-borne fungus Gaeumannomyces graminis var. tritici. Disease severity can be high, but a decline of take-all disease may take place in the following years in case of wheat monocropping. Microbial populations known to be associated to take-all decline (disease suppressiveness) include culturable antagonistic fluorescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol. The objective of this study was to assess changes in the diversity of rhizosphere pseudomonads linked with take-all decline of wheat, following a culture-independent approach based on the use of a 16S rRNA-based taxonomic microarray. The microarray contains about 700 probes, which target bacteria at various taxonomic levels. Certain probes (about 70) target pseudomonads, including groups of biocontrol Pseudomonas strains (about 20 probes). The latter were defined in this work after phylogenetic analysis of 16S rRNA sequences available in databases for biocontrol strains and other pseudomonads, based on Neighbor Joining (with Kimura 2 parameter) and Maximum Parcimony methods. The microarray probes were defined using ARB software (http://www.arb-home.de) and they were checked in silico. Most have a melting temperature of 65 ± 5 °C, GC > 50 %, no secondary structure or a secondary structure with a -2 kcal mol-1 and melting temperature < 50 °C, and they do not form stable homoduplex. The probes were spotted by 5' C6-NH2 covalent link on slides. Each basic pattern for the probe set is replicated three times per slide. Rhizosphere samples were collected at the INRA station of La Gruche (Brittany, France) from plots grown with wheat for one year (treatment PI; low level of takeall disease), five years (treatment PV; high level of disease) or ten years (treatment PX; low level of disease, suppressiveness reached). This experimental set-up enabled comparison of treatments under same conditions of soil composition, microclimate, wheat cultivar and farming techniques. Rhizosphere DNA was extracted and subjected to PCR using priming conditions designed in this work to target biocontrol pseudomonads. Cluster analysis of microarray data obtained after PCR of Pseudomonas populations in the wheat rhizosphere discriminated mainly between treatments PI and PX, treatment PV being in an intermediate position. The results are in accordance with quantitative PCR data obtained for the total pseudomonads. Overall, treatment PX appears to be associated with a particular composition in biocontrol pseudomonads (which comprise biocontrol strains producing 2,4- diacetylphloroglucinol). These findings indicate that the 16S taxonomic microarray is a promising tool for analysis of bacterial diversity associated with diseasesuppressive soils.
Molecular Plant-microbe Interactions, Feb 1, 2011
During evolution, plants have become associated with guilds of plant-growth-promoting rhizobacter... more During evolution, plants have become associated with guilds of plant-growth-promoting rhizobacteria (PGPR), which raises the possibility that individual PGPR populations may have developed mechanisms to cointeract with one another on plant roots. We hypothesize that this has resulted in signaling phenomena between different types of PGPR colonizing the same roots. Here, the objective was to determine whether the Pseudomonas secondary metabolite 2,4-diacetylphloroglucinol (DAPG) can act as a signal on Azospirillum PGPR and enhance the phytostimulation effects of the latter. On roots, the DAPG-producing Pseudomonas fluorescens F113 strain but not its phl-negative mutant enhanced the phytostimulatory effect of Azospirillum brasilense Sp245-Rif on wheat. Accordingly, DAPG enhanced Sp245-Rif traits involved in root colonization (cell motility, biofilm formation, and poly-β-hydroxybutyrate production) and phytostimulation (auxin production). A differential fluorescence induction promoter-trapping approach based on flow cytometry was then used to identify Sp245-Rif genes upregulated by DAPG. DAPG enhanced expression of a wide range of Sp245-Rif genes, including genes involved in phytostimulation. Four of them (i.e., ppdC, flgE, nirK, and nifX-nifB) tended to be upregulated on roots in the presence of P. fluorescens F113 compared with its phl-negative mutant. Our results indicate that DAPG can act as a signal by which some beneficial pseudomonads may stimulate plant-beneficial activities of Azospirillum PGPR.
Comparaison de sols résistant ou non à la maladie du piétin-échaudage du blé par une approche puce à ADN taxonomique 16S ciblant les bactéries rhizosphériques phytoprotectrices du genre
Abstract: Comparison of soils suppressive or not to take-all disease of wheat by 16S taxonomic mi... more Abstract: Comparison of soils suppressive or not to take-all disease of wheat by 16S taxonomic microarray targeting plant-protecting rhizosphere bacteria. Take-all is an important wheat disease caused by the soil-borne fungus Gaeumannomyces graminis var. tritici. Disease severity can be high, but a decline of take-all disease may take place in the following years in case of wheat monocropping. Microbial populations known to be associated to take-all decline (disease suppressiveness) include culturable antagonistic fluorescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol. The objective of this study was to assess changes in the diversity of rhizosphere pseudomonads linked with take-all decline of wheat, following a culture-independent approach based on the use of a 16S rRNA-based taxonomic microarray. The microarray contains about 700 probes, which target bacteria at various taxonomic levels. Certain probes (about 70) target pseudomonads, including groups of biocontrol Pseudomonas strains (about 20 probes). The latter were defined in this work after phylogenetic analysis of 16S rRNA sequences available in databases for biocontrol strains and other pseudomonads, based on Neighbor Joining (with Kimura 2 parameter) and Maximum Parcimony methods. The microarray probes were defined using ARB software (http://www.arb-home.de) and they were checked in silico. Most have a melting temperature of 65 ± 5 °C, GC > 50 %, no secondary structure or a secondary structure with a -2 kcal mol-1 and melting temperature < 50 °C, and they do not form stable homoduplex. The probes were spotted by 5' C6-NH2 covalent link on slides. Each basic pattern for the probe set is replicated three times per slide. Rhizosphere samples were collected at the INRA station of La Gruche (Brittany, France) from plots grown with wheat for one year (treatment PI; low level of takeall disease), five years (treatment PV; high level of disease) or ten years (treatment PX; low level of disease, suppressiveness reached). This experimental set-up enabled comparison of treatments under same conditions of soil composition, microclimate, wheat cultivar and farming techniques. Rhizosphere DNA was extracted and subjected to PCR using priming conditions designed in this work to target biocontrol pseudomonads. Cluster analysis of microarray data obtained after PCR of Pseudomonas populations in the wheat rhizosphere discriminated mainly between treatments PI and PX, treatment PV being in an intermediate position. The results are in accordance with quantitative PCR data obtained for the total pseudomonads. Overall, treatment PX appears to be associated with a particular composition in biocontrol pseudomonads (which comprise biocontrol strains producing 2,4- diacetylphloroglucinol). These findings indicate that the 16S taxonomic microarray is a promising tool for analysis of bacterial diversity associated with diseasesuppressive soils.
Molecular Plant-microbe Interactions, Jun 1, 2008
In the plant growth-promoting rhizobacterium Azospirillum brasilense Sp245, nitric oxide produced... more In the plant growth-promoting rhizobacterium Azospirillum brasilense Sp245, nitric oxide produced by denitrification could be a signal involved in stimulation of root branching, and the dissimilatory nitrite reductase gene nirK is upregulated on wheat roots. Here, it was found that Sp245 did not contain one copy of nirK but two (named nirK1 and nirK2), localized on two different plasmids, including one plasmid prone to rearrangements. Their deduced protein sequences displayed 99.2% identity but their promoter regions and upstream genetic environment differed. Phylogenetic studies revealed that nirK1 and nirK2 clustered next to most β-proteobacterial sequences rather than in the vicinity of other Azospirillum spp. and most α-proteobacterial sequences, regardless of whether DNA or deduced protein sequences were used. This points to past horizontal gene transfers. Analysis of the number of nonsynonymous and synonymous substitutions per site indicated that nirK has been subjected to neutral selection in bacteria. The use of transcriptional fusions with egfp, encoding an enhanced green fluorescent protein variant, revealed that both nirK1 and nirK2 promoter regions were upregulated in vitro under microaerobiosis or the presence of nitrite as well as on wheat roots. The analysis of nirK1 and nirK2 mutants revealed that the two genes were functional. Overall, results suggest that nirK has been acquired horizontally by A. brasilense Sp245 from a distant relative and underwent subsequent duplication; however, both paralogs remained functional and retained their upregulation by the plant partner.
[4] Monitoring gene expression in biofilms
Methods in Enzymology, 1999
ABSTRACT
Biocontrol of Plant Disease
Persistence of Shiga toxin-producing Escherichia coli O26 in cow slurry
Letters in Applied Microbiology, Jul 1, 2007
The main objective of this study was to evaluate the growth and survival of Shiga toxin-producing... more The main objective of this study was to evaluate the growth and survival of Shiga toxin-producing Escherichia coli (STEC) O26 in cow slurry; this serogroup is regarded as an important cause of STEC-associated diseases. Four STEC were examined by polymerase chain reaction (PCR) to determine whether they harbour key virulence determinants and also by pulsed-field gel electrophoresis (PFGE) to obtain overview fingerprints of their genomes. They were transformed with the pGFPuv plasmid and were separately inoculated at a level of 10(6) CFU ml(-1) in 15 l of cow slurry. All STEC O26 strains could be detected for at least 3 months in cow slurry without any genetic changes. The moisture content of the slurry decreased over time to reach a final value of 75% while the pH increased from 8.5 to 9.5 units during the last 50 days. STEC O26 strains were able to survive in cow slurry for an extended period. Long-term storage of waste slurry should be required to reduce the pathogen load and to limit environmental contamination by STEC O26.
Wheat-bacteria positive interactions: would ancient wheat genotypes be our hope for the future of agriculture?
HAL (Le Centre pour la Communication Scientifique Directe), Apr 23, 2017
Wheat-bacteria positive interactions: would ancient wheat genotypes be our hope for the future of... more Wheat-bacteria positive interactions: would ancient wheat genotypes be our hope for the future of agriculture?. 13. IWGS
HAL (Le Centre pour la Communication Scientifique Directe), 2001
The Escherichia coli OmpR/EnvZ two-component regulatory system, which senses environmental osmola... more The Escherichia coli OmpR/EnvZ two-component regulatory system, which senses environmental osmolarity, also regulates biofilm formation. Up mutations in the ompR gene, such as the ompR234 mutation, stimulate laboratory strains of E. coli to grow as a biofilm community rather than in a planktonic state. In this report, we show that the OmpR234 protein promotes biofilm formation by binding the csgD promoter region and stimulating its transcription. The csgD gene encodes the transcription regulator CsgD, which in turn activates transcription of the csgBA operon encoding curli, extracellular structures involved in bacterial adhesion. Consistent with the role of the ompR gene as part of an osmolarity-sensing regulatory system, we also show that the formation of biofilm by E. coli is inhibited by increasing osmolarity in the growth medium. The ompR234 mutation counteracts adhesion inhibition by high medium osmolarity; we provide evidence that the ompR234 mutation promotes biofilm formation by strongly increasing the initial adhesion of bacteria to an abiotic surface. This increase in initial adhesion is stationary phase dependent, but it is negatively regulated by the stationary-phase-specific sigma factor RpoS. We propose that this negative regulation takes place via rpoSdependent transcription of the transcription regulator cpxR; cpxR-mediated repression of csgB and csgD promoters is also triggered by osmolarity and by curli overproduction, in a feedback regulation loop.
Methylation of inorganic selenium by the bacterial thiopurine methyltransferase
HAL (Le Centre pour la Communication Scientifique Directe), 2002
International audienc
The Role of Microbial Metabolites in Biological Control
Springer eBooks, 2022
Horizontal Acquisition of Prokaryotic Genes for Eukaryote Functioning and Niche Adaptation
Springer eBooks, 2013
ABSTRACT Horizontal gene transfer (HGT) is a major mechanism of evolution, in that it is pervasiv... more ABSTRACT Horizontal gene transfer (HGT) is a major mechanism of evolution, in that it is pervasive and can dramatically affect lifestyle by allowing adaptation to specialized niches. Although research has mostly focused on HGT within prokaryotes, examples of inter-domain transfers from prokaryotes to eukaryotes are increasing, and such inter-domain HGT is emerging as a very significant component in ecological and evolutionary terms. Here, different cases of intra- and inter-domain HGT conferring an adaptive advantage to eukaryotes are reviewed to examine novel trends and HGT paradigms. Thus, HGT appears to play an important role in eukaryotic adaptation to specific environmental conditions, including in the ecological evolution toward parasitic lifestyles and pathogenesis. The diversity of prokaryotes and their genetic potential are emerging as a vast reservoir to foster rapid eukaryote evolution.
Control of the Cooperation Between Plant Growth-Promoting Rhizobacteria and Crops by Rhizosphere Signals
John Wiley & Sons, Inc. eBooks, Mar 18, 2013
ABSTRACT In the rhizosphere, an extensive communication takes place between plants and root-assoc... more ABSTRACT In the rhizosphere, an extensive communication takes place between plants and root-associated microorganisms, and involving an astonishing diversity of compounds released by plants (as root exudates) and rhizobacteria. These organic compounds may play a role as nutrients, toxins and/or signals, depending on the microbial partner as well as compound concentration. Therefore, they can be a major driver determining the assembly and functioning of rhizosphere communities. Until now, chemical signalling has been mostly studied during interaction between plants and pathogens, but recent work evidenced the involvement of several chemical signals in controlling the associative symbiosis between plant growth-promoting rhizobacteria (PGPR) and roots. In this review, recent findings about the identification of signals involved in the interaction of plants with PGPR, and of PGPR with each others, are presented. First, the focus is put on primary and secondary metabolites produced by plants, which may control the expression of PGPR genes, particularly those involved in plant-beneficial properties. Second, the role of signals released by PGPR, such as phytohormones, volatile organic compounds (VOC), N-acyl homoserine lactones (AHL) or antimicrobial compounds, on modulation of plant growth and health, is considered. Third, signal molecules involved in cross-talk between PGPR are examined. Finally, the spatial distribution of PGPR populations on roots is emphasized as a key factor influencing PGPR’s relationships with other rhizosphere-inhabiting partners.
Microbiology, Oct 1, 2007
Azospirillum strains have been used as plant-growth-promoting rhizobacteria (PGPR) of cereal crop... more Azospirillum strains have been used as plant-growth-promoting rhizobacteria (PGPR) of cereal crops, but their adaptation to the root remains poorly understood. Here, we used a global approach based on differential fluorescence induction (DFI) promoter trapping to identify genes of the wheat isolate Azospirillum brasilense Sp245 that are induced in the presence of spring wheat seed extracts. Fluorescence-based flow cytometry sorting of Sp245 cells was validated using PlacZ, PsbpA and PnifH promoters and egfp. A random promoter library was constructed by cloning 1-3 kb Sp245 fragments upstream of a promoterless version of egfp in the promoter-trap plasmid pOT1e (genome coverage estimated at threefold). Exposure to spring wheat seed extracts obtained using a methanol solution led to the detection of 300 induced DFI clones, and upregulation by seed extracts was confirmed in vitro for 46 clones. Sequencing of 21 clones enabled identification of seven promoter regions. Five of them displayed upregulation once inoculated onto spring wheat seedlings. Their downstream sequence was similar to (i) a predicted transcriptional regulator, (ii) a serine/threonine protein kinase, (iii) two conserved hypothetical proteins, or (iv) the copper-containing dissimilatory nitrite reductase NirK. Two of them were also upregulated when inoculated on winter wheat and pea but not on maize, whereas the three others (including PnirK) were upregulated on the three hosts. The amounts of nitrate and/or nitrite present in spring wheat seed extracts were sufficient for PnirK upregulation. Overall, DFI promoter trapping was useful to reveal Azospirillum genes involved in the interaction with the plant.
Long-term survival of Shiga toxin-producing Escherichia coli in cattle effluents and environment: An updated review
Veterinary Microbiology, Nov 1, 2008
Shiga toxin-producing Escherichia coli (STEC) are one of the most important emergent foodborne pa... more Shiga toxin-producing Escherichia coli (STEC) are one of the most important emergent foodborne pathogens. STEC are common as colonizers in the intestine of healthy cattle and are spread into the environment by fecal shedding or following the surface application of farm effluent on soil. The bacteria can be transmitted to humans through food, such as inadequately cooked ground beef or unpasteurized milk. During the last decade, a wide variety of environmentally related exposures have emerged as new routes of transmission. Major outbreaks due to the consumption of raw fruits and vegetables or accidental ingestion of soil or water contaminated by STEC have been increasingly reported. STEC survival in cattle effluents, soil, plants and water is discussed in the light of new knowledge regarding both biotic and abiotic factors which may affect their survival or enhance their dissemination in the environment. The ability to persist in cattle production environments contributes to the contamination and recontamination of cattle, as well as for human infection. Consequently, effective control strategies must be considered on cattle farms, in order to limit entry of STEC cells into the environment.
Biochemical and genomic comparison of inorganic phosphate solubilization in Pseudomonas species
Environmental Microbiology Reports, Dec 4, 2009
SummaryMobilization of insoluble soil inorganic phosphate by plant beneficial rhizobacteria is a ... more SummaryMobilization of insoluble soil inorganic phosphate by plant beneficial rhizobacteria is a trait of key importance to the development of microbial biofertilizers. In this study, the ability of several Pseudomonas spp. to solubilize Ca3(PO4)2 was compared. While all Pseudomonas spp. were found to facilitate a decrease in pH and solubilize inorganic phosphate by the production of extracellular organic acids, strains varied by producing either gluconic or 2‐ketogluconic acid. Furthermore, comparison between the Pseudomonas spp. of the genes involved in oxidative glucose metabolism revealed variations in genomic organization. To further investigate the genetic mechanisms involved in inorganic phosphate solubilization by Pseudomonas spp., a transposon mutant library of P. fluorescens F113 was screened for mutants with reduced Ca3(PO4)2 solubilization ability. Mutations in the gcd and pqqE genes greatly reduced the solubilization ability, whereas mutations in the pqqB gene only moderately reduced this ability. The combination of biochemical analysis and genomic comparisons revealed that alterations in the pqq biosynthetic genes, and the presence/absence of the gluconate dehydrogenase (gad) gene, fundamentally affect phosphate solublization in strains of P. fluorescens.
Plant and Soil, Feb 27, 2009
The rhizosphere is a complex environment where roots interact with physical, chemical and biologi... more The rhizosphere is a complex environment where roots interact with physical, chemical and biological properties of soil. Structural and functional characteristics of roots contribute to rhizosphere processes and both have significant influence on the capacity of roots to acquire nutrients. Roots also interact extensively with soil microorganisms which further impact on plant nutrition either directly, by influencing nutrient availability and uptake, or indirectly through plant (root) growth promotion. In this paper, features of the rhizosphere that are important for nutrient acquisition from soil are reviewed, with specific emphasis on the characteristics of roots that influence the availability and uptake of phosphorus and nitrogen. The interaction of roots with soil microorganisms, in particular with mycorrhizal fungi and non-symbiotic plant growth promoting rhizobacteria, is also considered in relation to nutrient availability and through the mechanisms that are associated with plant growth promotion.
Biological Controls in Horticulture
ANR BacterBlé: a project to study rhizobacterial benefits for adaptation of wheat to nitrogen limitation and drought
HAL (Le Centre pour la Communication Scientifique Directe), Jun 8, 2015
[15] First stages of biofilm formation: Characterization and quantification of bacterial functions involved in colonization process
Methods in Enzymology, 2001
Publisher Summary This chapter discusses the Bacterial colonization of abiotic materials and biof... more Publisher Summary This chapter discusses the Bacterial colonization of abiotic materials and biofilm formation, having important detrimental consequences in medicine (contamination of catheters, prostheses, indwelling devices, and artificial organs), and in many economic fields. There is therefore, a strong need to design surface coating methods able to interfere with the colonization process in order to prevent, or at least to delay, biofilm development. To reach this objective, increasing attention is being paid to the physiology and genetics of the initial stages of adhesion. Bacterial appendages and adhesins responsible for the linkage of the first pioneering cells to the surface (or the conditioning film) are potential targets for antiadhesion molecules grafted or smeared on the surface. The determination of the mechanisms resulting in the movement of bacteria toward surfaces—the identification of the functions involved in the sensing of the particular microenvironments encountered at interfaces, and the description of the regulatory networks allowing the developmental processes necessary for the structural development of biofilms—would help find nontoxic surface treatments able to lead the microorganisms away from the locations they usually contaminate. This would be particularly important in the field of indwelling medical devices. Any delay in the colonization process could successfully increase the capacities of the antibiotic therapy and the immunological defenses to eradicate the infection. This chapter describes methods to obtain and analyze bacterial mutants with altered adhesion properties.
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Papers by Claire Prigent-combaret