Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads.

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population. (Résumé d'auteur

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract\ud \ud \ud \ud Background\ud Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences.\ud \ud \ud \ud Results\ud Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations.\ud \ud \ud \ud Conclusions\ud This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.AI is funded by a PhD grant from INRA-SPE and region Pays de la Loire, France. EG was funded by a PhD grant from the French Ministry of National Education and Research and French Guyana. SC, EG, MA, EL and LDN are funded by the LABEX TULIP (ANR-10-LABX-41), LSG is funded by ANR-2010-GENM-013 Xanthomix

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Evolution de la flore adventice du vignoble de Côte-d'Or sous la pression des techniques d'entretien des cultures

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Matériau solide nanocomposite à base d’hexa- et octacyanometallates, son procédé de préparation et procédé de fixation de polluants minéraux le mettant en œuvre

Matériau solide nanocomposite comprenant des nanoparticules d'un polymère de coordination métallique à ligands CN comprenant des cations Mn+, où M est un métal de transition, et n est 2 ou 3; et des anions [M' (CN)m]x-, où M' est un métal de transition, x est 3 ou 4, et m est 6 ou 8; lesdits cations Mn+ du polymère de coordination étant liés par une liaison organométallique à un groupe organique d'un greffon organique fixé chimiquement à l'intérieur des pores d'un support en verre poreux. Procédé de préparation de ce matériau. Procédé de fixation d'un polluant minéral tel que le césium radioactif contenu dans une solution par mise en contact de ladite solution avec ledit matériau

Time-lapse seismic experiments to constrain hydrodynamic parameters at the stream-aquifer interface

International audienceVP/VS or Poisson’s ratio estimated from active seismic methods recently proved to be efficient in the imaging ofthe critical zone and associated hydrosystems. We suggest here a time-lapse application of this approach to provideboth spatial and temporal constraints on the hydrodynamic model of the Avenelles experimental basin (Seine etMarne, France). The preliminary studies of this hydrosystem relied on typical combined interpretation of sparsegeological and hydrological data. Geophysical surveys, performed throughout the watershed, helped delineatingthe different compartments and identifying their connectivity with the stream network. Once a basin-scale globalhydrogeological model established, hotspots were targeted with local high frequency monitoring stations to inves-tigate its stream-aquifer exchanges. At these stations, recorded data (bank piezometers, stream water temperatureand level, temperature profiles in the hyporheic zone) clearly showed contrasts in the dynamic of the hydrosystemalong the stream network. However, the nature of the compartments and their associated properties, observed at thebasin-scale, would not explain the data observed at the local scale. It highlighted the need for detailed descriptionof the hydrosystem, at the stream-aquifer interface. One specific hotspot was thus selected to perform soundingsand geophysical measurements of higher resolutions. Thanks to electrical resistivity tomography, P-wave refrac-tion and surface-wave seismic imaging, we provided a description of the local heterogeneities both in terms oflithology and water content. The seismic experiments were then repeated with a two-month time step. At eachtime step, pseudo-2D sections of Poisson’s ratio clearly showed strong spatial and temporal variations in satura-tion of the vadose zone. These results then helped providing updated constraints and boundary conditions to thehydrodynamic mode