Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species

Homologous Recombination in Agrobacterium: Potential Implications for the Genomic Species Concept in Bacteria

International audienceAccording to current taxonomical rules, a bona fide bacterial species is a genomic species characterized by the genomic similarity of its members. It has been proposed that the genomic cohesion of such clusters may be related to sexual isolation, which limits gene flow between too divergent bacteria. Homologous recombination is one of the most studied mechanisms responsible for this genetic isolation. Previous studies on several bacterial models showed that recombination frequencies decreased exponentially with increasing DNA sequence divergence. In the present study, we investigated this relationship in the Agrobacterium tumefaciens species complex, which allowed us to focus on sequence divergence in the vicinity of the genetic boundaries of genomic species. We observed that the sensitivity of the recombination frequency to DNA divergence fitted a log-linear function until approximately 10% sequence divergence. The results clearly revealed that there was no sharp drop in recombination frequencies at the point where the sequence divergence distribution showed a ‘‘gap'' delineating genomic species. The ratio of the recombination frequency in homogamic conditions relative to this frequency in heterogamic conditions, that is, sexual isolation, was found to decrease from 8 between the most distant strains within a species to 9 between the most closely related species, for respective increases from 4.3% to 6.4% mismatches in the marker gene chvA. This means that there was only a 1.13-fold decrease in recombination frequencies for recombination events at both edges of the species border. Hence, from the findings of this investigation, we conclude that—at least in this taxon—sexual isolation based on homologous recombination is likely not high enough to strongly hamper gene flow between species as compared with gene flow between distantly related members of the same species. The 70% relative binding ratio cutoff used to define bacterial species is likely correlated to only minor declines in homologous recombination frequencies. Consequently, the sequence diversity, as a mechanistic factor for the efficiency of recombination (as assayed in the laboratory), appears to play little role in the genetic cohesion of bacterial species, and thus, the genomic species definition for prokaryotes is definitively not reconcilable with the biological species concept for eukaryotes

Contribution à la définition de l'espèce génomique chez les bactéries par MLSA et détermination du rôle de l'isolement sexuel dans la cohérence des espèces (exploration aux "bornes" de l'espèce dans le complexe d'espèces génomiques "Agrobacterium tumefaciens")

LYON1-BU.Sciences (692662101) / SudocSudocFranceF

Expression of Dickeya dadantii genes during infection of the pea aphid Acyrthosiphon pisum

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Virulence de la bactérie phytopathogène Dickeya dadantii contre le puceron du pois Acyrthosiphon pisum : analyse de l’expression des toxines insecticides Cyt et suivi histologique de l’infection bactérienne

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Virulence de la bactérie phytopathogène Dickeya dadantii contre le puceron du pois Acyrthosiphon pisum : analyse de l’expression des toxines insecticides Cyt et suivi histologique de l’infection bactérienne

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Phage-mediated biocontrol against plant pathogenic bacteria

International audiencePlant pathogenic bacteria can cause severe damaging diseases every year, ranging from spots, mosaic patterns or pustules on leaves and fruits, or smelly tuber rots to plant death, and collectively they cause losses of over $1 billion dollars worldwide to the food production chain. Antibiotics have been used against certain bacterial diseases with mixed results. To face dependence on the use of antibiotics and agrochemical products in agriculture, alternatives based on natural products are possible. Bacteriophages, also known informally as phages, have been used to treat infectious diseases since their discovery at the beginning of the 20th century. Phages can essentially propagate in two ways: the lytic cycle or the lysogenic pathway. Optimization of phage-based biocontrol requires a series of field and greenhouse experiments, since in vitro trials may not always fully reflect the harsh conditions of the real environment and of the different crops to cure

3D NMR structure of a new Cyt-like delta-endotoxins from Dickeya dadantii

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Transcriptome of Dickeya dadantii Infecting Acyrthosiphon pisum Reveals a Strong Defense against Antimicrobial Peptides

The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP) was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon) and phosphoethanolamine (pmrC, eptB) usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has bee

Pattern of aphid tissues infected with <i>D. dadantii</i>.

<p>Immunostaining with anti KdgM antibodies of aphids infected with the wild type <i>D. dadantii</i> strain. Anti KdgM antibodies were detected with anti IgG labeled with Alexa fluor 488 (green labeling) and DNA was stained with DAPI (blue labeling). <b>2A to 2D</b>: early infection stage: day 1 of infection (aphids collected on infected diet). <i>D. dadantii</i> is located mainly in the fat body (fb, 2A), within the gut lumen (gl, 2B), and can also be detected in some gut cells (gc, 2C) as well as in the embryonic fat body (efb, 2D). <b>2E to 1K</b>: early infection stage: day 2 post infection. <i>D. dadantii</i> is located as a general infection of the fat body (2E), as dense aggregates in the gut lumen (2F), in gut cells (2G) and, occasionnally, in all of the following tissues: brain (2H), cornicles (co, 2I) and in many embryos showing either embryonic fat body (efb, 1J) or embryonic gut infections (egc egl, 2K). <b>2L to 2O</b>: late infection stage: day 4 post-infection. A heavy infection of <i>D. dadantii</i> is seen in all the maternal and embryonic fat bodies (2L), the gut tissue and lumen (2M), and large parts of the embryonic fat body (2N) and embryo gut cells, but not in the embryonic bacteriocytes (egc, eba, 2O). Abbreviations - ba: bacteriocytes, brc: brain cells, co: cornicles, emb: embryo, eba: embryonic bacteriocyte; efb: embryonic fat body, egc: embryonic gut cells, egl: embryonic gut lumen, fb: fat body, gc: gut cells, gl: gut lumen, oe:eonocytes.</p