Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in France: TABLE 1

International audienceStenotrophomonas maltophilia is a major opportunistic human pathogen responsible for nosocomial infections. Here, we report the draft genome sequences of Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France, which provide insights into the genetic determinism of intrinsic or acquired antibiotic resistance in this species. Citation Bodilis J, Youenou B, Briolay J, Brothier E, Favre-Bonté S, Nazaret S. 2016. Draft genome sequences of Stenotrophomonas maltophilia strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies

Comparative genomics of environmental and clinical burkholderia cenocepacia strains closely related to the highly transmissible epidemic ET12 lineage

The Burkholderia cenocepacia epidemic ET12 lineage belongs to the genomovar IIIA including the reference strain J2315, a highly transmissible epidemic B. cenocepacia lineage. Members of this lineage are able to cause lung infections in immunocompromised and cystic fibrosis patients. In this study, we describe the genome of F01, an environmental B. cenocepacia strain isolated from soil in Burkina Faso that is, to our knowledge, the most closely related strain to this epidemic lineage. A comparative genomic analysis was performed on this new isolate, in association with five clinical and one environmental B. cenocepacia strains whose genomes were previously sequenced. Antibiotic resistances, virulence phenotype, and genomic contents were compared and discussed with an emphasis on virulent and antibiotic determinants. Surprisingly, no significant differences in antibiotic resistance and virulence were found between clinical and environmental strains, while the most important genomic differences were related to the number of prophages identified in their genomes. The ET12 lineage strains showed a noticeable greater number of prophages (partial or full-length), especially compared to the phylogenetically related environmental F01 strain (i.e., 5-6 and 3 prophages, respectively). Data obtained suggest possible involvements of prophages in the clinical success of opportunistic pathogens

OprF polymorphism as a marker of ecological niche in Pseudomonas

OprF is the major outer-membrane protein of Pseudomonas sensu stricto (rRNA group I). In addition to playing a role as porin, membrane structural protein and root adhesion, this pleiotropic protein shows a length polymorphism corresponding to two types of OprF, termed OprF type 1 and OprF type 2. In a previous work, all the P. fluorescens isolated from bulk soil (non-rhizospheric) were shown to possess oprF type 1, while all the clinical P. fluorescens isolates and most rhizospheric strains corresponded to type 2. In this study, we further investigated the relation between the OprF polymorphism and the ecological niche by developing a culture-independent approach (a ratio polymerase chain reaction) to measure the percentage of each oprF type in environmental DNA samples, including two different soils and three different cultured plants (flax, wheat and grassland). Although the proportions of oprF type 2 between rhizospheric samples were quite variable, they were always very significantly higher (P95%) corresponded to type 1. We discuss the potential applications of this ecological fingerprint in an agronomic and taxonomic point of view

Alternative techniques to HPCD to evaluate the bioaccessible fraction of soil-associated PAHs and correlation to biodegradation efficiency

International audienceThe total amount of polycyclic aromatic hydrocarbons (PAHs) in soils, given by exhaustive chemical extractions, does not relate directly to environmental risk, since only a fraction may be accessible to soil organisms. The rapid PAH desorbing fraction (Frap), which is weakly and reversibly sorbed to soils, is called the bioaccessible fraction, and can be estimated by non-exhaustive aqueous extractions. In order to better estimate Frap, different mild-extractants were tested, such as various cyclodextrins, surfactants and butanol. Their extractability performances were correlated to the Kd partition coefficients of seven PAHs obtained through sorption isotherms from five soils, but also to the PAHs molecular size and to the amounts of organic matter and of some clays (smectites and kaolinites). If hydroxypropyl-β-cyclodextrin was actually a good extractant to assess PAH accessibility, the polymer of carboxymethyl-β-cyclodextrin (pCMCD) was better (with a lower cost) to estimate the rapid mass transfer between soil particles and the soil solution, depending also on soil ageing. But Frap, estimated through pCMCD extractions, did not reflect the biodegradation of the PAHs after three months in soil microcosms. The chemical method underestimated the dissipation of 3–4 ring PAHs and overestimated that of 5–6 ring PAHs. So biodegradation was not only limited by PAHs mass-transfer, but also by biological factors, favoring the access of microorganisms to residual strongly sorbed fractions of 3–4 ring PAHs, and inhibiting the degradation of accessible but highly toxic 5–6 ring PAHs

Cycloclasticus spp. but also Pseudomonas spp. as PAH degrading bacteria in the Seine estuary (France)

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Cycloclasticus spp. but also Pseudomonas spp. as PAH degrading bacteria in the Seine estuary (France)

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A long-branch attraction artifact reveals an adaptive radiation in Pseudomonas

A significant proportion of protein-encoding gene phylogenies in bacteria is inconsistent with the species phylogeny. It was usually argued that such inconsistencies resulted from lateral transfers. Here, by further studying the phylogeny of the oprF gene encoding the major surface protein in the bacterial Pseudomonas genus, we found that the incongruent tree topology observed results from a long-branch attraction (LBA) artifact and not from lateral transfers. LBA in the oprF phylogeny could be explained by the faster evolution in a lineage adapted to the rhizosphere, highlighting an unexpected adaptive radiation. We argue that analysis of such artifacts in other inconsistent bacterial phylogenies could be a valuable tool in molecular ecology to highlight cryptic adaptive radiations in microorganisms

Diversité contrastée des bactéries dégradant le phénanthrène dans le sol et faible impact de l’ajout de rhamnolipide

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