Niche Construction and Exploitation by Agrobacterium: How to Survive and Face Competition in Soil and Plant Habitats.

Agrobacterium populations live in different habitats (bare soil, rhizosphere, host plants), and hence face different environmental constraints. They have evolved the capacity to exploit diverse resources and to escape plant defense and competition from other microbiota. By modifying the genome of their host, Agrobacterium populations exhibit the remarkable ability to construct and exploit the ecological niche of the plant tumors that they incite. This niche is characterized by the accumulation of specific, low molecular weight compounds termed opines that play a critical role in Agrobacterium 's lifestyle. We present and discuss the functions, advantages, and costs associated with this niche construction and exploitation.

Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum.

Social bacteria use chemical communication to coordinate and synchronize gene expression via the quorum-sensing (QS) regulatory pathway. In Pectobacterium, a causative agent of the blackleg and soft-rot diseases on potato plants and tubers, expression of the virulence factors is collectively controlled by the QS-signals N-acylhomoserine lactones (NAHLs). Several soil bacteria, such as the actinobacterium Rhodococcus erythropolis, are able to degrade NAHLs, hence quench the chemical communication and virulence of Pectobacterium. Here, next-generation sequencing was used to investigate structural and functional genomics of the NAHL-degrading R. erythropolis strain R138. The R. erythropolis R138 genome (6.7 Mbp) contained a single circular chromosome, one linear (250 kbp) and one circular (84 kbp) plasmid. Growth of R. erythropolis and P. atrosepticum was not altered in mixed-cultures as compared with monocultures on potato tuber slices. HiSeq-transcriptomics revealed that no R. erythropolis genes were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the avirulent P. atrosepticum mutant expI, which is defective for QS-signal synthesis. By contrast 50 genes (<1% of the R. erythropolis genome) were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the NAHL-producing virulent P. atrosepticum. Among them, quantitative real-time reverse-transcriptase-PCR confirmed that the expression of some alkyl-sulfatase genes decreased in the presence of a virulent P. atrosepticum, as well as deprivation of organic sulfur such as methionine, which is a key precursor in the synthesis of NAHL by P. atrosepticum.

Growth biostimulation of quorum-quenching bacteria by gammagamma-heptalactone treatment in the hydroponic rhizosphere of Solanum tuberosum.

Several bacterial plant pathogens, including Pectobacterium, use a cell-to-cell communication system called quorum sensing (QS) to synchronize and regulate expression of the virulence factors. In this study, the biomolecule gamma-heptalactone (GHL) was introduced in hydroponic culture of Solanum tuberosum to stimulate growth of the native rhizospheric bacteria which are able to degrade the QS signal, hence potentially quench the QS-regulated virulence of Pectobacterium. During two annual campaigns, GHL-treatment efficiently stimulated the growth of QS-degrading bacterial population of Rhodococcus erythropolis in the rhizosphere of potato plants. Analytical chemistry showed that GHL rapidly disappeared because it could be assimilated as a carbon source by R. erythropolis. Moreover, pyrosequencing of the rrs-amplicons revealed a strong modification of the structure and diversity of bacterial populations, when GHL-treated and untreated conditions were compared. This work highlighted a potential innovative strategy for stimulating the growth and root colonization of QS-degrading bacteria, which would act as biocontrol agents against plant QS-pathogens.

Proline antagonizes GABA-induced quenching of quorum-sensing in Agrobacterium tumefaciens.

Plants accumulate free L-proline (Pro) in response to abiotic stresses (drought and salinity) and presence of bacterial pathogens, including the tumor-inducing bacterium Agrobacterium tumefaciens. However, the function of Pro accumulation in host-pathogen interaction is still unclear. Here, we demonstrated that Pro antagonizes plant GABA-defense in the A. tumefaciens C58-induced tumor by interfering with the import of GABA and consequently the GABA-induced degradation of the bacterial quorum-sensing signal, 3-oxo-octanoylhomoserine lactone. We identified a bacterial receptor Atu2422, which is implicated in the uptake of GABA and Pro, suggesting that Pro acts as a natural antagonist of GABA-signaling. The Atu2422 amino acid sequence contains a Venus flytrap domain that is required for trapping GABA in human GABA(B) receptors. A constructed atu2422 mutant was more virulent than the wild type bacterium; moreover, transgenic plants with a low level of Pro exhibited less severe tumor symptoms than did their wild-type parents, revealing a crucial role for Venus flytrap GABA-receptor and relative abundance of GABA and Pro in host-pathogen interaction.

[Diagnosis of thoracic outlet syndrome. Value of angiography in the sitting position]. / Diagnostic des syndromes du défilé cervico-thoraco-brachial: apport de l'artériographie réalisée en position assise.

PURPOSE: Thoracic outlet syndrome includes arterial, venous or neurological symptoms. Frequently difficult to diagnose clinically, confirmatory imaging studies are usually required. The purpose of this study is to review the diagnostic work-up during management of patients with thoracic outlet syndrome and demonstrate the value of angiography in the sitting position. MATERIALS AND METHODS: Retrospective study of 81 surgical procedures for thoracic outlet syndrome, between 1997 and 2005, in 56 patients aged 17-57 years. Surgery was bilateral in 26 cases, with bilateral surgery in a single setting for 1 patient. All patients presented clinical symptoms confirmed on US, angiography, venogram or EMG. Angiography, from a transfemoral approach, was initially performed in the supine position, without and with dynamic maneuver, and in the sitting position with dynamic maneuver when needed. RESULTS: In 48 patients, supine rest angiography showed stenosis in 6% of cases and supine dynamic angiography showed stenosis in 81% of cases, with severe stenosis in only 35% of cases (stenosis>80% or arterial occlusion). Angiography in the sitting position was performed in 33 patients, showing worsening of stenosis in 91% of cases, with severe stenosis in 87%. CONCLUSION: Angiography in the sitting position with dynamic maneuver improves the sensitivity for detection of thoraci coutlet syndrome. This procedure may be considered in addition to other imaging modalities routinely used including Doppler US, CT and MRI.

Metagenomics revealed a quorum quenching lactonase QlcA from yet unculturable soil bacteria.

Quorum sensing (QS) is a signal mediated cell-cell communication system that couples bacterial cell density to a synchronized gene expression (Fuqua et al., 1994). Mostly, in Gram negative bacteria QS signals are N-acylhomoserine lactones (NAHLs) that coordinate important functions such as virulence and pathogenicity. QS signals or the elements involved in their production or perception could be targeted to disrupt QS, a phenomenon called Quorum quenching (QQ). QQ properties (chemicals and enzymes) are naturally found in various Living organisms, like bacteria (Rhodococcus and Commamonas), plants (carrot, soybean, pea seedling, chilli, garlic etc), and animals (human sera, pork kidney tissues). Consequently, various bacterial genes encoding for NAHL degrading enzymes, like NAHL lactonases (AiiA in Bacillus, AiiB and AttM in Agrobacterium tumefaciens) and acylase/-amidohydrolase (AiiD in Ralstonia) were identified (Givskov et al., 2006). In Pectobacterium carotovorum (causal agent of soft rot diseases) production of various virulence factors and cell wall maceration enzymes is QS dependant, and relies upon successful production, stability, emission and perception of NAHLs (C-8, oxo-C8 and C-10). Disruption of QS signalling by NAHL degrading bacteria, modified bacteria or plants expressing NAHL lactonases resulted in the reduced virulence of the pathogen (Faure et al., 2007). Until recently, investigations on QQ enzymes were carried out mostly on cultivable bacteria, that represent a tiny fraction of soil and root-associated bacteria. In this study, a metagenomics approach (Handelsman, 2004) was employed to access the hidden diversity of uncultivable soil bacteria that revealed a QQ enzyme, an NAHL lactonase, in these bacteria (Riaz et al., 2008).

Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties.

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJN(T), was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJN(T) and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98.7 %) and Burkholderia phenazinium (98.5 %). Analysis of whole-cell protein profiles and DNA-DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJN(T) had a DNA G+C content of 61.0 mol%. Only low levels of DNA-DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJN(T) and closely related species were identified. The predominant fatty acids in strain PsJN(T) were 16 : 0, 18 : 1omega7c and summed feature 3 (comprising 16 : 1omega7c and/or iso-15 : 0 2-OH). Isolate PsJN(T) showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJN(T) and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJN(T) (=LMG 22146(T) = CCUG 49060(T)).

Radar-based alert system to operate a sewerage network: relevance and operational effectiveness after several years of use.

Since January 2000, the sewerage network of a very urbanised catchment area in the Greater Nancy Urban Community has been operated according to the alarms generated in real time by a storm alert system using weather radar data. This alert system is based on an automatic identification of intense rain cells in the radar images. This paper presents the characteristics of this alert system and synthesises the main results of two complementary studies realised in 2002 in order to estimate the relevance and the operational effectiveness of the alert system. The first study consisted in an off-line analysis of almost 50,000 intense rain cells detected in four years of historical radar data. The second study was an analysis of the experience feedback after two years of operational use of this alert system. The results of these studies are discussed in function of the initial operational objectives.

Genomic changes arising in long-term stab cultures of Escherichia coli.

Genomic scans of clones isolated from long-term stab cultures of Escherichia coli K-12 showed the loss of two large segments of the genome, with each lost segment being approximately 20 kb long. A detailed analysis of one of the deletions, located between 5.4 and 5.9 min, revealed that similar deletions had arisen in several other stab cultures. All deletions of this type exhibited a right terminus ending precisely at an IS5A element and a left terminus that varied over an approximately 5-kb range but was bordered in all but two cases by sequences belonging to the preferred consensus target sequence for IS5, YTAR. The ubiquity of such deletions in independent stab cultures and the increase in their frequency over time argue that they have a selective advantage. It is speculated that the loss of the crl locus is responsible for the selective advantage of the deletions.

[Violacein: a molecule of biological interest originating from the soil-borne bacterium Chromobacterium violaceum]. / La violacéine: une molécule d'intérêt biologique, issue de la bactérie tellurique Chromobacterium violaceum.

INTRODUCTION: Soil micro-organisms have evolved functions that allow them to withstand the strong competition for survival that characterizes most of their habitats. The production of antibiotic or antifungal compounds is one of these mechanisms. The relevant molecules often exhibit valuable therapeutic properties. EXEGESIS: Chromobacterium violaceum is a soil-borne bacterium producing a characteristic antibiotic termed violacein. It is part of a series of compounds released by C. violaceum to oppose competitors and predators in the soil and water environments. Violacein, and one of these compounds, i.e. structure FR901228, exhibit antiparasitic and antitumoral activities of potential medical interest. Genes involved in the synthesis of these compounds are available, the genome sequence of C. violaceum (strain ATCC 12472) being published. CONCLUSIONS: The above example, involving Chromobacterium, is not an exception: soil constitutes a reservoir of molecules, enzymatic activities and micro-organisms of biological interest, the study of which will undoubtedly lead to developments in fields as diverse as agronomy or animal and human therapeutics.

The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-Acyl homoserine lactonase activity.

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.

Purification and characterization of a membrane glycoprotein from the fish pathogen Flavobacterium psychrophilum.

AIMS: The cell envelope of the fish pathogen Flavobacterium psychrophilum contains more than 50 polypeptides resolved by sodium dodecyl sulphate-polyacrylaminde gel electrophoresis analysis including a major component named P60. Here, we have developed a simple and efficient procedure for the purification of P60 and therefore permitting its biochemical characterization. METHODS AND RESULTS: Membrane proteins were selectively extracted from isolated cell envelopes with the mild non-ionic detergent Triton X-100. About 10 polypeptides were identified from the detergent fraction, including P60. The P60-enriched fraction was thereafter subjected to an anion exchange chromatographic step in the presence of Triton X-100. The molecule was purified at the milligram level (yield, about 75%; purification factor, 6.2). Analyses performed by charge shift electrophoresis, Triton X-114 phase separation and by detection of sugar-modified components showed that P60 is a true amphiphilic membrane-associated glycoprotein. CONCLUSIONS: The method described in this paper provides pure and non-denaturated P60 and should prove to be easily scaled-up. As sugar-modified protein, P60 should be included in the growing list of glycosylated prokaryotic proteins. SIGNIFICANCE AND IMPACT OF THE STUDY: It offers the possibility of obtaining P60 in amounts allowing the testing of the potential of P60 as a candidate for anti-flavobacteria subunit vaccines, as P60 is one of the major antigens.

Radiation and functional specialization of the family-3 glycoside hydrolases.

A phylogenetic analysis of the glycoside hydrolases of family 3 (GH3s) was conducted in order to infer particular trends in its evolution: functional specialization, gene transfer events, gene duplications and paralogous evolution, and gene deletions. The phylogenetic analysis of GH3s revealed six clusters, i.e., A, B, C, D, E, and F that could fit the definition of 3 sub-families, i.e., AB, AB' and AB". While the sub-families AB' and AB" contain a single cluster, F and E, respectively, the AB sub-family is sub-divided into four clusters. Global analysis of the GH3 phylogenetic tree suggests a primary burst of amplification of the GH3s that might have led to these sub-families. Specializations, gene transfers, and gene duplications among each of these sub-families and phylogenetic clusters might then have occurred and have been inferred. The fine comparison of the enzyme properties and phylogenetic relationships of GH3s allowed to detect common functional groups that belong to the same cluster (D, E or F), or sub-cluster (A1, A2 or B2). The prokaryotic and eukaryotic beta-xylosidases and beta-glucosidases belong to the AB and AB' sub-families, and the N-acetylglucosaminidases are in sub-family AB" (in cluster E). In some instances (B1, B2, C1, C2, and C3), the lack of data and/or the high heterogeneity of the hydrolytic properties did not allow to infer a particular link between an enzyme functional group and a phylogenetic cluster, suggesting the emergence of some highly specialized GH3s.

Management of a detention-settling basin using radar data and risk notion.

This paper presents a practical application of sewage network management strategy using radar data to control a detention-settling basin. This practical application, used in operational mode since January 2000, is based on three main notions. Firstly, the use of radar data without rainfall estimation. Secondly, the definition of some gradual risk levels for the sewage network by a detailed modelling of the sewage system functioning. Thirdly the definition of relations between risk levels for the sewage network and types of rain events defined from radar data. The operational application produces gradual alarms for decision-making assistance: no risk, potential risk and confirmed risk.

Development and application of a nested PCR to monitor brood stock salmonid ovarian fluid and spleen for detection of the fish pathogen Flavobacterium psychrophilum.

AIMS: To develop a nested PCR to detect Flavobacterium psychrophilum based on the intergenic spacer region 16S-23S rRNA and in 16S rRNA for analysis of brood stock salmonid fish samples. METHODS AND RESULTS: The sensitivity and specificity of the test was evaluated using pure cultures, spiked and naturally contaminated samples. Samples were internal organs (spleen and kidney), eggs and ovarian fluid from rainbow trout and coho salmon from European fish farms (France, Spain). This nested PCR was more specific and sensitive that the nested PCR based on 16S rRNA sequences primers only. The detection limit of this PCR assay was one bacterium per PCR tube corresponding to 10 bacteria/mg of spleen and 5 bacteria/ml from ovarian fluid. Analysis of mixed ovarian fluid samples from reproductive salmonids in various French hatcheries demonstrated that 69% of hatcheries were contaminated with Fl. psychrophilum. The analysis of individual samples demonstrated that 39% of rainbow trout (Oncorhynchus mykiss) and 62.5% of coho salmon (O. kisutch) samples were contaminated. CONCLUSIONS: The results demonstrated a very sensitive and specific detection of this fish pathogen and that most of the female rainbow trout and coho salmon breeders analysed carry Fl. psychrophilum in the ovarian fluid. SIGNIFICANCE AND IMPACT OF THE STUDY: The understanding of Fl. psychrophilum dissemination and transmission and the detection of asymptomatic carriers is important for the development of free breeders stock and for significantly decreasing Flavobacteriose.

Use of real time control modelling on the urban sewage system of Nancy.

Since 1991, European Legislation on the urban treatment of wastewater requires local authorities to take into account the treatment of polluted water transported by the sewerage system and this during dry and wet weather conditions. In the seventies, the urban Community of Grand Nancy constructed storage tanks in its sewerage system in order to prevent flooding and wish today to use them to reduce and control the pollution discharges into the receiving water. This action is a part of a European LIFE project 1996-2000. The main aim of this project was to assess the effectiveness of reducing pollution of one particular retention basin, the 12,000 m3 Gentilly tank. This one has two operating modes: protection against floods during heavy rain and reduction of pollutant overflows during lighter rain. To assess its effect on the pollutant discharge, the HYDROWORKS DM software and its Real Time Control Module have been used, calibrated and validated. As this study is still in progress, this paper describes the studied site and the modelling results under different weather conditions and shows that the mathematical model can be used to simulate the operation of the catchment area and its associated sewerage system realistically.

An evolutionary alternative system for aryl beta-glucosides assimilation in bacteria.

Some bacteria of the soil microflora or of the digestive systems of mammals can grow on aryl beta-glucosides as sole carbon sources. The bgl operon of E. coli is the paradigm for such a catabolic pathway. In Azospirillum irakense, the two adjacent genes salAB encode beta-glucosidases which are required for salicin assimilation. In this report, we analyse the sequence of salC, the last gene to be identified in the salCAB operon and investigate the phylogenetic origins of the sal and bgl genes. The results suggest an alternative model for the assimilation of aryl beta-glucosides in bacteria.

The celA gene, encoding a glycosyl hydrolase family 3 beta-glucosidase in Azospirillum irakense, is required for optimal growth on cellobiosides.

The CelA beta-glucosidase of Azospirillum irakense, belonging to glycosyl hydrolase family 3 (GHF3), preferentially hydrolyzes cellobiose and releases glucose units from the C(3), C(4), and C(5) oligosaccharides. The growth of a DeltacelA mutant on these cellobiosides was affected. In A. irakense, the GHF3 beta-glucosidases appear to be functional alternatives for the GHF1 beta-glucosidases in the assimilation of beta-glucosides by other bacteria.