4-Hydroxy-2-alkylquinolines (HAQs), especially 3,4-dihydroxy-2-heptylquinoline (Pseudomonas quinolone signal) and its precursor, 4-hydroxy-2-heptylquinoline, are attracting much attention, mainly because of their role as signaling molecules in Pseudomonas aeruginosa. The pqsABCDE operon is centrally involved in their biosynthesis. The presence of a homologous operon in Burkholderia pseudomallei and B. thailandensis was recently reported. Thus, we have investigated the abilities of 11 Burkholderia species to produce HAQ-like molecules by liquid chromatography/mass spectrometry. We have identified 29 different HAQ derivatives produced by the only three Burkholderia species where a pqsABCDE homologue was found among available sequenced Burkholderia species genomes, including B. ambifaria, a member of the Burkholderia cepacia complex. In contrast with those of P. aeruginosa, Burkholderia HAQs typically bear a methyl group, hence their designation as 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs). We identified three families of HMAQs with a saturated or unsaturated alkyl chain at the 2 position, in contrast with the 1 position of P. aeruginosa, including one with an N-oxide group. Furthermore, the operon in these species contains two more genes downstream of the pqsE homologue, resulting in the hmqABCDEFG operon. While the inactivation of hmqA inhibits the production of HMAQs, the methylation of the quinoline ring requires a putative methyltransferase encoded by hmqG. Interestingly, hmqA or hmqG mutations increase the production of acyl homoserine lactones and, consequently, phenotypes under the control of quorum sensing in B. ambifaria: antifungal activity, siderophore production, and proteolytic activity. These results indicate that only HAQs bearing a methyl group (HMAQs) are involved in quorum-sensing regulation.

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.

SummaryThe Burkholderia cepacia complex (Bcc) is composed of 17 closely related species. These bacteria are widely but heterogeneously distributed in the natural environment, such as soil, water and rhizosphere. Bcc strains are able to colonize various ecological niches by adopting versatile lifestyles, including saprophytism and (positive or deleterious) association with eukaryotic cells. Bcc strains have proven to be very efficient in biocontrol, plant growth promotion and bioremediation. However, they also are important opportunistic pathogens that can cause severe respiratory infections among individuals suffering from cystic fibrosis or chronic granulomatous disease. Therefore, considering that the distinction between plant beneficial and clinical strains is not obvious, biotechnological applications of Bcc strains are currently not allowed. This minireview provides an overview of the wide range of lifestyles that Bcc bacteria can adopt, leading to glimpses into their tremendous adaptation potential and highlighting remaining questions concerning potential implicated mechanisms.

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Phase and antigenic variation is used by several bacterial species to generate intra-population diversity that increases bacterial fitness and is important in niche adaptation, or to escape host defences. By this adaptive process, bacteria undergo frequent and usually reversible phenotypic changes resulting from genetic or epigenetic alterations at specific genetic loci. Phase variation or phenotypic switch allows the expression of a given phenotype to be switched ON or OFF. Antigenic variation refers to the expression of a number of alternative forms of an antigen on the cell surface, and at a molecular level, shares common features with phase variation mechanisms. This review will focus on phase and antigenic variation mechanisms implying genome modifications, with an emphasis on the diversity of phenotypes regulated by these mechanisms, and the ecological relevance of variant appearance within a given population.

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.

Members of the Burkholderia cepacia complex (Bcc), such as B. ambifaria, are effective biocontrol strains, for instance, as plant growth-promoting bacteria; however, Bcc isolates can also cause severe respiratory infections in people suffering from cystic fibrosis (CF). No distinction is known between isolates from environmental and human origins, suggesting that the natural environment is a potential source of infectious Bcc species. While investigating the presence and role of phase variation in B. ambifaria HSJ1, an isolate recovered from a CF patient, we identified stable variants that arose spontaneously irrespective of the culture conditions. Phenotypic and proteomic approaches revealed that the transition from wild-type to variant types affects the expression of several putative virulence factors. By using four different infection models (Drosophila melanogaster, Galleria mellonella, macrophages and Dictyostelium discoideum), we showed that the wild-type was more virulent than the variant. It may be noted that the variant showed reduced replication in a human monocyte cell line when compared with the wild-type. On the other hand, the variant of isolate HSJ1 was more competitive in colonizing plant roots than the wild-type. Furthermore, we observed that only clinical B. ambifaria isolates generated phase variants, and that these variants showed the same phenotypes as observed with the HSJ1 variant. Finally, we determined that environmental B. ambifaria isolates showed traits that were characteristic of variants derived from clinical isolates. Our study therefore suggest that B. ambifaria uses phase variation to adapt to drastically different environments: the lung of patients with CF or the rhizosphere.

gThe soil-and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-␤-hydroxypropionyl-CoA, 4-hydroxy-3-methoxyphenyl-␤-ketopropionyl-CoA, vanillic acid, and protocatechuic acid. The genes atu1416, atu1417, and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-␤-ketopropionic acid (HMPKP)-CoA ␤-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent ␤-oxidative deacetylation that could also transform p-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.