Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884

Article de revue (Article scientifique dans une revue à comité de lecture)International audienceWe report the draft genome sequence of the flagellated strain CFBP 4884 of Xanthomonas fuscans subsp. fuscans, which was isolatedin an outbreak of common bacterial blight of beans along with non-flagellated strains. Comparative genomics will allowone to decipher the genomic diversity of strains cohabiting in epidemics.</p

The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

<p>Abstract</p> <p>Background</p> <p>The <it>Xanthomonadaceae </it>family contains two xylem-limited plant pathogenic bacterial species, <it>Xanthomonas albilineans </it>and <it>Xylella fastidiosa</it>. <it>X. fastidiosa </it>was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess <it>hrp </it>genes which encode a Type III secretion system found in most plant pathogenic bacteria. <it>X. fastidiosa </it>was excluded from the <it>Xanthomonas </it>group based on phylogenetic analyses with rRNA sequences.</p> <p>Results</p> <p>The complete genome of <it>X. albilineans </it>was sequenced and annotated. <it>X. albilineans</it>, which is not known to be insect-vectored, also has a reduced genome and does not possess <it>hrp </it>genes. Phylogenetic analysis using <it>X. albilineans </it>genomic sequences showed that <it>X. fastidiosa </it>belongs to the <it>Xanthomonas </it>group. Order of divergence of the <it>Xanthomonadaceae </it>revealed that <it>X. albilineans </it>and <it>X. fastidiosa </it>experienced a convergent reductive genome evolution during their descent from the progenitor of the <it>Xanthomonas </it>genus. Reductive genome evolutions of the two xylem-limited <it>Xanthomonadaceae </it>were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.</p> <p>Conclusion</p> <p>The two xylem-limited <it>Xanthomonadaceae</it>, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of <it>X. albilineans </it>differ from those of <it>X. fastidiosa </it>and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by <it>X. albilineans</it>, is discussed.</p

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

Sensing and adhesion are adaptive functions in the plant pathogenic xanthomonads

<p>Abstract</p> <p>Background</p> <p>Bacterial plant pathogens belonging to the <it>Xanthomonas </it>genus are tightly adapted to their host plants and are not known to colonise other environments. The host range of each strain is usually restricted to a few host plant species. Bacterial strains responsible for the same type of symptoms on the same host range cluster in a pathovar. The phyllosphere is a highly stressful environment, but it provides a selective habitat and a source of substrates for these bacteria. Xanthomonads colonise host phylloplane before entering leaf tissues and engaging in an invasive pathogenic phase. Hence, these bacteria are likely to have evolved strategies to adapt to life in this environment. We hypothesised that determinants responsible for bacterial host adaptation are expressed starting from the establishment of chemotactic attraction and adhesion on host tissue.</p> <p>Results</p> <p>We established the distribution of 70 genes coding sensors and adhesins in a large collection of xanthomonad strains. These 173 strains belong to different pathovars of <it>Xanthomonas </it>spp and display different host ranges. Candidate genes are involved in chemotactic attraction (25 genes), chemical environment sensing (35 genes), and adhesion (10 genes). Our study revealed that candidate gene repertoires comprised core and variable gene suites that likely have distinct roles in host adaptation. Most pathovars were characterized by unique repertoires of candidate genes, highlighting a correspondence between pathovar clustering and repertoires of sensors and adhesins. To further challenge our hypothesis, we tested for molecular signatures of selection on candidate genes extracted from sequenced genomes of strains belonging to different pathovars. We found strong evidence of adaptive divergence acting on most candidate genes.</p> <p>Conclusions</p> <p>These data provide insight into the potential role played by sensors and adhesins in the adaptation of xanthomonads to their host plants. The correspondence between repertoires of sensor and adhesin genes and pathovars and the rapid evolution of sensors and adhesins shows that, for plant pathogenic xanthomonads, events leading to host specificity may occur as early as chemotactic attraction by host and adhesion to tissues.</p

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

Detection of Xanthomonas axonopodis pv. phaseoli and Xanthomonas axonopodis pv. phaseoli var. fuscans on Phaseolus vulgaris (bean)

Article de revue (Article scientifique dans une revue à comité de lecture)International audienceThis method is derived from the validation studies carried out by ISTA in 2003, in collaborationwith the International Seed Health Initiative for Vegetables (ISHI-Veg) (Sheppard andRemeeus, 2005). For routine testing of bean seed a combination of two complementarysemi-selective media, MT and XCP1, is recommended with a pathogenicity test to confirmsuspect isolates. In 2010 in the USA and France conflicting data were obtained with the new ISTA method.Research in France (GEVES and INRA) and in the Netherlands (Naktuinbouw) showedthat some isolates that were responsible for positive results were causing symptoms in thepathogenicity assay but were not identified as Xap based on molecular methods (geneticbacterial fingerprinting in the Netherlands and pathogen specific PCR’s in France). Thereforeit was concluded that the pathogenicity assay used in the ISTA method, a crucial stepin the Xap test, is not reliable enough.A new pathogenicity assay was developed at INRA to allow a reliable characterizationof the aggressiveness of X. axonopodis pv. phaseoli wild type strains and mutants(Darsonval et al., 2009). A comparison study of the new pathogenicity test and primersspecific for X. axonopodis pv. phaseoli fuscans and non fuscans isolates (Audy et al.,1994;Boureau et al., 2012) was carried out as a collaboration between ISTA, ANSES, INRA andISHI-Veg. This study showed that the new pathogenicity test and Audy et al, (1994) primerswere good confirmation tools and that Diaggene (Boureau et al., 2012) primers gave goodresults but their use did not improve sensitivity of the method.</p

Transmission of Plant-Pathogenic Bacteria by Nonhost Seeds without Induction of an Associated Defense Reaction at Emergence▿ †

An understanding of the mechanisms involved in the different steps of bacterial disease epidemiology is essential to develop new control strategies. Seeds are the passive carriers of a diversified microbial cohort likely to affect seedling physiology. Among seed-borne plant-pathogenic bacteria, seed carriage in compatible situations is well evidenced. The aims of our work are to determine the efficiency of pathogen transmission to seeds of a nonhost plant and to evaluate bacterial and plant behaviors at emergence. Bacterial transmission from flowers to seeds and from seeds to seedlings was measured for Xanthomonas campestris pv. campestris in incompatible interactions with bean. Transmissions from seeds to seedlings were compared for X. campestris pv. campestris, for Xanthomonas citri pv. phaseoli var. fuscans in compatible interactions with bean, and for Escherichia coli, a human pathogen, in null interactions with bean. The induction of defense responses was monitored by using reverse transcription and quantitative PCR (RT-qPCR) of genes representing the main signaling pathways and assaying defense-related enzymatic activities. Flower inoculations resulted in a high level of bean seed contamination by X. campestris pv. campestris, which transmitted efficiently to seedlings. Whatever the type of interaction tested, dynamics of bacterial population sizes were similar on seedlings, and no defense responses were induced evidencing bacterial colonization of seedlings without any associated defense response induction. Bacteria associated with the spermosphere multiply in this rich environment, suggesting that the colonization of seedlings relies mostly on commensalism. The transmission of plant-pathogenic bacteria to and by nonhost seeds suggests a probable role of seeds of nonhost plants as an inoculum source