Variations in type III effector repertoires do not correlate with differences in pathological phenotypes and host range observed for Xanthomonas citri pv. citri pathotypes

Xanthomonas citri pv. citri (Xac) is a quarantine bacterium causing Asiatic citrus canker. Strains of Xac are classified as pathogenic variants i.e. pathotypes, according to their host range: strains of pathotype A infect a wide range of rutaceous species, whereas strains of pathotype A*/Aw infect a restricted host range consisting of Mexican lime (C. aurantifolia) and alemow (C. macrophylla). Based on a collection of 55 strains we investigated the role of type III effectors (T3E) in host specialization. By PCR we screened 56 Xanthomonas T3Es and showed that Xac possesses a repertoire of 28 effectors, 24 of which are shared by all strains, while 4 (xopAI, xopAD, xopAG and xopC1) are present only in some A*/ Aw strains. However, their distribution could not account for host specialization. XopAG is present in all Aw strains, but also in three A* strains genetically distant from Aw , and all xopAG-containing strains induced HR-like reactions on grapefruit and sweet orange. A strains are genetically less diverse, induce identical phenotypic responses, and share exactly the same T3Es. Conversely, A*/ Aw strains exhibited a wider genetic diversity in which clades correlated to geographical origin and T3Es repertoire but not to pathogenicity. A*/Aw strains showed a broad range of reactions on several Citrus, but genetically related strains did not share phenotypic responses. Our results showed that A*/Aw strains are more variable (genetically and pathogenetically) than initially expected and that this variability should not be ignored when trying to describe mechanisms involved in the pathogen evolution and host specialization. (Texte intégral

Behavior and Impact of Zirconium in the Soil–Plant System: Plant Uptake and Phytotoxicity

Because of the large number of sites they pollute, toxic metals that contaminate terrestrial ecosystems are increasingly of environmental and sanitary concern (Uzu et al. 2010, 2011; Shahid et al. 2011a, b, 2012a). Among such metals is zirconium (Zr), which has the atomic number 40 and is a transition metal that resembles titanium in physical and chemical properties (Zaccone et al. 2008). Zr is widely used in many chemical industry processes and in nuclear reactors (Sandoval et al. 2011; Kamal et al. 2011), owing to its useful properties like hardness, corrosion-resistance and permeable to neutrons (Mushtaq 2012). Hence, the recent increased use of Zr by industry, and the occurrence of the Chernobyl and Fukashima catastrophe have enhanced environmental levels in soil and waters (Yirchenko and Agapkina 1993; Mosulishvili et al. 1994 ; Kruglov et al. 1996)

Crispri as a tool for the functional study of gene families in Xanthomonas

The Xanthomonas genus includes several plant pathogens responsible for significant crop losses worldwide. Most of the functional studies of virulence in this genus have been carried out by directed mutagenesis through homologous recombination. However, this strategy is cumbersome for the study of gene families. CRISPR interference (CRISPRi) allows precise silencing of target genes by using a catalytically dead Cas9 (dCas9) which interferes with gene expression. Because of its RNA-directed nature, this technology can be used for silencing several genes in a single experiment in bacteria and other organisms. We implemented a CRISPRi strategy to silence several members of the Transcriptional activatorlike effectors (TALE) gene family at once in four different species of Xanthomonas. Our results underscore the importance of the activation of the SWEET gene family in cassava upon infection by Xanthomonas phaseoli pv. manihotis. Remarkably, we report the importance of this gene family in the infection of this host by the non-vascular pathogen X. cassavae. In addition, we successfully silenced several TALE genes in a total of five species, including X. oryzae pv. oryzae, X. citri pv. citri and X. campestris pv. campestris using CRISPRi, confirming the importance of this gene family in these pathosystems. The CRISPRi tool can be further modulated to silence sets of genes within a gene family for functional studies in Xanthomonas and other plant pathogenic bacteria

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

In-situ zircon U–Pb, oxygen and hafnium isotopic evidence for magma mixing and mantle metasomatism in the Tuscan Magmatic Province, Italy

In this study, we have used in-situ U–Pb, Hf and O isotopic analyses of zircon grains to gain insights into both magmatic processes and duration of magmatism in igneous rocks from the Tuscan Magmatic Province (0.1–9 Ma), Italy. Three plutonic centres have been investigated (Monte Capanne and Porto-Azzuro monzogranites in Elba and the Giglio monzogranite) as well as Capraia, the only volcanic centre in the Tuscan Archipelago. New ion microprobe zircon U–Pb data reveal a continuum of plutonic activity in Elba over 2 Ma (8.3–6.3 Ma), with coeval volcanic activity in Capraia (7.1–7.6 Ma), and plutonic activity resuming in Giglio (5.5 Ma) after a gap of 1 Ma. From these zircon data we also show that construction of the Monte Capanne pluton (Elba) may have occurred over a period of c. 0.5 Ma. A significant range of both 176Hf/177Hf (determined by LA–MC-ICPMS) and δ18O (determined by ion microprobe) in zircon (~ 7 epsilon Hf units and ~ 5‰, respectively) is present, which, together with zircon morphology and trace element data (Gagnevin et al., 2010), emphasises the importance of mixing and replenishment involving magma batches with both metaluminous and peraluminous affinities. Inherited and xenocrystic zircons also occur, but are scarce. These have a wide range of 176Hf/177Hf and δ18O values, further emphasising that a variety of crustal components has contributed to the genesis of the Tuscan magmas, either as contaminants or magma sources. While mixing undoubtedly occurred between mafic (metaluminous) and felsic (peraluminous) magmas, the range of Hf and O isotopic data suggests a diversity within the peraluminous component. The unradiogenic Hf composition (εHf(t) 6‰) of the inferred mantle-derived component (represented by Capraia volcanism, and at least in part, lamproitic in composition) strongly supports the idea that the mantle source involved in Tuscan magmatism was severely modified by subduction-related, crustal-derived metasomatic fluids

Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources

Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence. </jats:p