Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants

Background: The phenotypic consequences of large genomic architecture modifications within a clonal bacterial population are rarely evaluated because of the difficulties associated with using molecular approaches in a mixed population. Bacterial variants frequently arise among Photorhabdus luminescens, a nematode-symbiotic and insect-pathogenic bacterium. We therefore studied genome plasticity within Photorhabdus variants. Results: We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications. Conclusion: Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolutio

Optical mapping as a routine tool for bacterial genome sequence finishing

Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points

Entomopathogenic nematode/bacteria couples Steinernema sp. /Xenorhabdus bovienii: how can genomics help us to understand virulence variations?

Entomopathogenic nematode/bacteria couples Steinernema sp. /Xenorhabdus bovienii: how can genomics help us to understand virulence variations?. 5. Journée du réseau IM

A new formulation of EntomoPathogenic Nematodes (EPNs) vectorization of biological control agents

A new formulation of EntomoPathogenic Nematodes (EPNs) vectorization of biological control agents . Réunion du Consortium Biocontrôl

Milieu de culture sélectif pour la détection de Pseudomonas protegens

Le but de cette démarche était de détecter et d'isoler spécifiquement par une double approche moléculaire et culturale l’espèce Pseudomonas protegens, une bactérie de la rhizospère ayant un fort potentiel d’application agronomique avec des activités entomopathogènes et PGPR (1). Tout d'abord, nous avons développé une détection par PCR de P. protegens en ciblant un gène du locus fit impliqué dans la synthèse de la toxine entomopathogène FitD (2). Nous avons dessiné des amorces dans le gène fitF, qui code un senseur histidine-kinase. Au sein du genre Pseudomonas, ces amorces amplifient spécifiquement l’ADN génomique des deux espèces entomopathogènes, P. protegens et P. chlororaphis. Afin de distinguer les deux espèces, nous avons ensuite développé un milieu de culture minimum sélectif et spécifique de P. protegens, appelé milieu M9-PP-agar. La base, le milieu M9, est additionnée d'acide adipique comme unique source de carbone et d'un antimicrobien, l'irgasan. Contrairement à de nombreuses autres espèces de Pseudomonas dont P. chlororaphis, P. protegens est capable d’assimiler l'acide adipique. Parmi les antimicrobiens couramment utilisés pour sélectionner Pseudomonas aeruginosa (acide nalidixique, irgasan et cétrimide) (3), P. protegens est particulièrement résistant à l’irgasan. Sur M9-PP-agar, les colonies apparaissent brunes après 5 jours de culture. D'autres Pseudomonas (P. aeruginosa, P. putida) ou d’autres espèces bactériennes (Achromobacter, Agrobacterium, Serratia, Variovorax) sont capables de se multiplier plus ou moins tardivement sur M9-PP-agar mais en se différentiant par l’absence de couleur brune. Pour valider la sélectivité et la spécificité du milieu M9-PP-agar dans des matrices complexes, nous avons inoculé la souche de référence P. protegens CHAOT dans deux sols de bord de rivière argilo-limoneux (département Hérault), puis étalé des suspensions de ces sols sur le milieu sélectif. Par comparaison avec un milieu riche (gélose nutritive), une inhibition de croissance de la population bactérienne des sols et une croissance spécifique de P. protegens ont été observées. Ce nouveau milieu gélosé est donc un outil puissant pour l’isolement sélectif, rapide et efficace de P. protegens

Potential of the rpoB gene for metabarcoding of bacterial communities associated with entomopathogenic nematodes Steinernema

Potential of the rpoB gene for metabarcoding of bacterial communities associated with entomopathogenic nematodes [i]Steinernema[/i] . 8. Colloque de l'Association Francophone d'Ecologie Microbienne (AFEM