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Combes-Meynet E.,CNRS Microbial Ecology | Pothier J.F.,CNRS Microbial Ecology | Pothier J.F.,Research Station Agroscope Changins Wadenswil | Moenne-Loccoz Y.,CNRS Microbial Ecology | Prigent-Combaret C.,University Claude Bernard Lyon 1
Molecular Plant-Microbe Interactions | Year: 2011

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 pfl-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 pfel-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. © 2011 The American Phytopathoiogicai Society.

Walsh F.,Research Station Agroscope Changins Wadenswil
Frontiers in Microbiology | Year: 2013

There have been many calls for more information about the natural resistome and these have also highlighted the importance of understanding the soil resistome in the preservation of antibiotics for the treatment of infections. However, to date there have been few studies which have investigated the culturable soil resistome, which highlights the difficulties faced by microbiologists in designing these experiments to produce meaningful data. The World Health Organization definition of resistance is the most fitting to non-clinical environmental studies: antimicrobial resistance is resistance of a microorganism to an antimicrobial medicine to which it was previously sensitive. The ideal investigation of non-clinical environments for antibiotic resistance of clinical relevance would be using standardized guidelines and breakpoints. This review outlines different definitions and methodologies used to understand antibiotic resistance and suggests how this can be performed outside of the clinical environment. © 2013 Walsh.

Frapolli M.,ETH Zurich | Frapolli M.,University of Zurich | Pothier J.F.,University Claude Bernard Lyon 1 | Pothier J.F.,CNRS Microbial Ecology | And 4 more authors.
Molecular Phylogenetics and Evolution | Year: 2012

Plant-beneficial fluorescent Pseudomonas spp. play important ecological roles. Here, their evolutionary history was investigated by a multilocus approach targeting genes involved in synthesis of secondary antimicrobial metabolites implicated in biocontrol of phytopathogens. Some of these genes were proposed to be ancestral, and this was investigated using a worldwide collection of 30 plant-colonizing fluorescent pseudomonads, based on phylogenetic analysis of 14 loci involved in production of 2,4-diacetylphloroglucinol (phlACBDE, phlF, intergenic locus phlA/. phlF), hydrogen cyanide (hcnABC, anr) or global regulation of secondary metabolism (gacA, gacS, rsmZ). The 10 housekeeping loci rrs, dsbA, gyrB, rpoD, fdxA, recA, rpoB, rpsL, rpsG, and fusA served as controls. Each strain was readily distinguished from the others when considering allelic combinations for these 14 biocontrol-relevant loci. Topology comparisons based on Shimodaira-Hasegawa tests showed extensive incongruence when comparing single-locus phylogenetic trees with one another, but less when comparing (after sequence concatenation) trees inferred for genes involved in 2,4-diacetylphloroglucinol synthesis, hydrogen cyanide synthesis, or secondary metabolism global regulation with trees for housekeeping genes. The 14 loci displayed linkage disequilibrium, as housekeeping loci did, and all 12 protein-coding loci were subjected to purifying selection except for one positively-selected site in HcnA. Overall, the evolutionary history of Pseudomonas genes involved in synthesis of secondary antimicrobial metabolites important for biocontrol functions is in fact similar to that of housekeeping genes, and results suggest that they are ancestral in pseudomonads producing hydrogen cyanide and 2,4-diacetylphloroglucinol. © 2012 Elsevier Inc.

Costa F.,Research and Innovation Center | Cappellin L.,Research and Innovation Center | Zini E.,Research and Innovation Center | Patocchi A.,Research Station Agroscope Changins Wadenswil | And 4 more authors.
Plant Science | Year: 2013

The aroma trait in apple is a key factor for fruit quality strongly affecting the consumer appreciation, and its detection and analysis is often an extremely laborious and time consuming procedure. Molecular markers associated to this trait can to date represent a valuable selection tool to overcome these limitations. QTL mapping is the first step in the process of targeting valuable molecular markers to be employed in marker-assisted breeding programmes (MAB). However, a validation step is usually required before a newly identified molecular marker can be implemented in marker-assisted selection. In this work the position of a set of QTLs associated to volatile organic compounds (VOCs) was confirmed and validated in three different environments in Switzerland, namely Wädenswil, Conthey and Cadenazzo, where the progeny 'Fiesta. ×. Discovery' was replicated. For both QTL identification and validation, the phenotypic data were represented by VOCs produced by mature apple fruit and assessed with a Proton Transfer Reaction-Mass Spectrometer (PTR-MS) instrument. The QTL-VOC combined analysis performed among these three locations validated the presence of important QTLs in three specific genomic regions, two located in the linkage group 2 and one in linkage group 15, respectively, for compounds related to esters (m/. z 43, 61 and 131) and to the hormone ethylene (m/. z 28). The QTL set presented here confirmed that in apple some compounds are highly genetically regulated and stable across environments. © 2013 Elsevier Ireland Ltd.

Kellerhals M.,Research Station Agroscope Changins Wadenswil | Szalatnay D.,Research Station Agroscope Changins Wadenswil | Hunziker K.,Research Station Agroscope Changins Wadenswil | Duffy B.,Research Station Agroscope Changins Wadenswil | And 5 more authors.
Trees - Structure and Function | Year: 2012

Pome fruit genetic resources collections constitute a highly valuable resource not only for fruit breeding but also for direct use by nurseries, growers, and home gardeners. In order to use these resources efficiently and sustainably, reliable evaluation data on fruit and tree characteristics must be generated. Here we focus on pome fruit genetic resources evaluated phenotypically and genotypically for susceptibility to apple scab (Venturiainaequalis), powdery mildew (Podosphaeraleucotricha), fire blight (Erwiniaamylovora), pear rust (Gymnosporangiumsabinae) and storage diseases (e. g., Penicilliumexpansum). Examples are presented of several ongoing projects throughout Europe, with the aim to evaluate fruit genetic resources for disease susceptibility and potential use in breeding and for commercial use. The COST action 864 has fostered international cooperation in the evaluation of pome fruit genetic resources, and some of these evaluations therefore involve research groups from several of the participating countries. © 2011 The Author(s).

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