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Benmalek Y.,University of Science and Technology Houari Boumediene | Cayol J.-L.,Universites Of Provence Et Of La Mediterranee | Bouanane N.A.,University of Science and Technology Houari Boumediene | Hacene H.,University of Science and Technology Houari Boumediene | And 2 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2010

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterium, designated strain 1YB-R12T, was isolated from a soil sample in western Algeria. The novel isolate was heterotrophic, chemoorganotrophic, halotolerant and psychrotolerant. The temperature and pH optima for growth were 28-30°C and pH 7.3-8. The bacterium tolerated up to 6% (w/v) NaCl. Cells were non-motile, non-gliding and non-spore-forming, and were characterized by a variable morphological cycle. Flexirubin-type pigments were not detected. 16S rRNA gene sequence analysis showed that strain 1YB-R12T occupied a distinct lineage within the genus Chryseobacterium and shared highest sequence similarity with Chryseobacterium haifense LMG 24029T (96.5 %). The DNA G+C content of strain 1YB-R12T was 40.9 mol%. The predominant cellular fatty acids were anteiso-C15 : 0 (41.4 %) and iso-C 15 : 0 (14.4 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain 1YB-R12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium solincola sp. nov. is proposed. The type strain is 1YB-R12 T (=DSM 22468T=CCUG 55604T). © 2010 IUMS.


Mnif S.,University of Sfax | Chamkha M.,University of Sfax | Labat M.,Universites Of Provence Et Of La Mediterranee | Sayadi S.,University of Sfax
Journal of Applied Microbiology | Year: 2011

Aims: To study the bacterial diversity associated with hydrocarbon biodegradation potentiality and biosurfactant production of Tunisian oilfields bacteria. Methods and Results: Eight Tunisian hydrocarbonoclastic oilfields bacteria have been isolated and selected for further characterization studies. Phylogenetic analysis revealed that three thermophilic strains belonged to the genera Geobacillus, Bacillus and Brevibacillus, and that five mesophilic strains belonged to the genera Pseudomonas, Lysinibacillus, Achromobacter and Halomonas. The bacterial strains were cultivated on crude oil as sole carbon and energy sources, in the presence of different NaCl concentrations (1, 5 and 10%, w/v), and at 37 or 55°C. The hydrocarbon biodegradation potential of each strain was quantified by GC-MS. Strain C450R, phylogenetically related to the species Pseudomonas aeruginosa, showed the maximum crude oil degradation potentiality. During the growth of strain C450R on crude oil (2%, v/v), the emulsifying activity (E24) and glycoside content increased and reached values of 77 and 1.33gl -1, respectively. In addition, the surface tension (ST) decreased from 68 to 35.1mNm -1, suggesting the production of a rhamnolipid biosurfactant. Crude biosurfactant had been partially purified and characterized. It showed interest stability against temperature and salinity increasing and important emulsifying activity against oils and hydrocarbons. Conclusions: The results of this study showed the presence of diverse aerobic bacteria in Tunisian oilfields including mesophilic, thermophilic and halotolerant strains with interesting aliphatic hydrocarbon degradation potentiality, mainly for the most biosurfactant produced strains. Significance and Impact of the Study: It may be suggested that the bacterial isolates are suitable candidates for practical field application for effective in situ bioremediation of hydrocarbon-contaminated sites. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.


Aguilera M.,CNRS Institute of Molecular Sciences of Marseilles | Aguilera M.,University of Granada | Rakotoarivonina H.,CNRS Institute of Molecular Sciences of Marseilles | Rakotoarivonina H.,University of Reims Champagne Ardenne | And 6 more authors.
Research in Microbiology | Year: 2012

Differential gene expression analysis was performed in monoxenic mice colonized with Ruminococcus gnavus strain E1, a major endogenous member of the gut microbiota. RNA arbitrarily primed-PCR fingerprinting assays allowed to specifically detect the invivo expression of the aga1 gene, which was further confirmed by RT-PCR. The aga1 gene encoded a protein of 744 residues with calculated molecular mass of 85,207Da. Aga1 exhibited significant similarity with previously characterized α-Galactosidases of the GH 36 family. Purified recombinant protein demonstrated high catalytic activity (104±7Umg -1) and efficient p-nitrophenyl-α-d-galactopyranoside hydrolysis [k cat/K m=35.115±8.82s -1mM -1 at 55°C and k cat/K m=17.48±4.25s -1mM -1 at 37°C]. © 2011 Institut Pasteur.


Grossi V.,University Claude Bernard Lyon 1 | Cravo-Laureau C.,University of Pau and Pays de l'Adour | Rontani J.-F.,French National Center for Scientific Research | Cros M.,University Claude Bernard Lyon 1 | Hirschler-Rea A.,Universites Of Provence Et Of La Mediterranee
Research in Microbiology | Year: 2011

Two alkene-degrading sulphate-reducing bacteria from the genus Desulfatiferula (Desulfatiferula olefinivorans strain LM2801T and Desulfatiferula sp. strain BE2801) were investigated for their 1-alkene metabolism. Their total cellular fatty acids were predominantly C-even when they were grown on C-even 1-alkene (1-hexadecene), whereas a mixture of fatty acids with C-odd or C-even carbon chains predominated when cells were grown on C-odd 1-alkene (1-pentadecene). This is consistent with the fatty acid composition of other sulphate-reducing strains previously reported to grow on n-alkenes. Linear and 3-OH-fatty acids appear to be the main fatty acids produced by the two Desulfatiferula strains. The analysis of their neutral lipids led to identifying several n-alkanols and n-ketones with the same number of carbon atoms as the alkene growth substrate and with functionality located between C-1 and C-5. Growth of strains LM2801T and BE2801 on (per) deuterated 1-alkenes provided direct evidence of their anaerobic transformation to corresponding 1-alkanols, n-ketones and linear (3-OH-) fatty acids. These results demonstrate that Desulfatiferula strains oxidize a 1-alkene by oxidation of the double bond at C-1, but also at C-2 to C-5 (after eventual isomerization of the double bond) yielding the corresponding C-2 to C-5 n-ketones (via the corresponding n-alkanols). The formation of specific 3-OH-fatty acids by elongation of shorter chain fatty acids was also demonstrated. Based on our observations, pathways for anaerobic 1-alkene metabolism in sulphate-reducing bacteria from the genus Desulfatiferula are proposed. They indicate that n-ketones can constitute new metabolites of the biodegradation of n-alkenes in anaerobic environments. © 2011 Institut Pasteur.


Khelaifia S.,Universites Of Provence Et Of La Mediterranee | Fardeau M.-L.,Universites Of Provence Et Of La Mediterranee | Pradel N.,Universites Of Provence Et Of La Mediterranee | Aussignargues C.,Universites Of Provence Et Of La Mediterranee | And 6 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

A novel sulfate-reducing bacterium, designated C1TLV30T, was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2-4×0.5 μm). Strain C1TLV30 T grew at temperatures between 15 and 45°C (optimum 30°C) and at pH 5.4-8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl 1 -1) and tolerated up to 80 g NaCl 1 -1. Strain C1TLV30 T used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H 2S and CO 2 in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30T possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6% and the genome size was estimated at 3.5±0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30 T was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4%). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30 T (=DSM 21447 T =JCM 1548 T) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov. © 2011 IUMS.


Lieutaud A.,CNRS Optic of Semiconductor nanoStructures Group | Van Lis R.,CNRS Optic of Semiconductor nanoStructures Group | Duval S.,CNRS Optic of Semiconductor nanoStructures Group | Capowiez L.,CNRS Optic of Semiconductor nanoStructures Group | And 8 more authors.
Journal of Biological Chemistry | Year: 2010

We characterized the aro arsenite oxidation system in the novel strain Ralstonia sp. 22, a β-proteobacterium isolated from soil samples of the Salsigne mine in southern France. The inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c554. Our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. Analysis of the phylogeny of the aro gene cluster revealed that it results from a lateral gene transfer from a species closely related to Achromobacter sp. SY8. This constitutes the first clear cut case of such a transfer in the Aro phylogeny. The biochemical study of the enzyme demonstrates that it can accommodate in vitro various cytochromes, two of which, c 552 and c554, are from the parent species. Cytochrome c552 belongs to the sox and not the aro system. Kinetic studies furthermore established that sulfite and sulfide, substrates of the sox system, are both inhibitors of Aro activity. These results reinforce the idea that sulfur and arsenic metabolism are linked. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.


Gregoire P.,Universites Of Provence Et Of La Mediterranee | Gregoire P.,University of Bordeaux Segalen | Fardeau M.-L.,Universites Of Provence Et Of La Mediterranee | Guasco S.,Aix - Marseille University | And 5 more authors.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2012

A novel strictly anaerobic bacterium designated SPDX02-08 T was isolated from a deep terrestrial geothermal spring located in southwest France. Cells (1-2 × 2-6 μm) were non-motile, non sporulating and stained Gram negative. Strain SPDX02-08 T grew at a temperature between 40 and 60°C (optimum 55°C), pH between 6.3 and 7.3 (optimum 7.2) and a NaCl concentration between 0 and 5 g/l (optimum 2 g/l). Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate, nitrite, Fe (III) or fumarate. In the presence of sulfate, strain SPDX02-08 T completely oxidized pyruvate, propionate, butyrate, isobutyrate, valerate, isovalerate and hexadecanoate. Stoichiometric measurements revealed a complete oxidation of part of lactate (0.125 mol of acetate produced per mole lactate oxidized). Strain SPDX02-08 T required yeast extract to oxidize formate and H 2 but did not grow autotrophically on H 2. Among the substrates tested, only pyruvate was fermented. The G+C content of the genomic DNA was 57.6 mol%. Major cellular fatty acids of strain SPDX02-08 T were iso-C 15:0, C 15:0, and C 16:0. Phylogenetic analysis of the 16S small-subunit (SSU) ribosomal RNA gene sequence indicated that strain SPDX02-08 T belongs to the genus Desulfosoma, family Syntrophobacteraceae, having Desulfosoma caldarium as its closest phylogenetic relative (97.6% similarity). The mean DNA/DNA reassociation value between strain SPDX02-08 T and Desulfosoma caldarium was 16.9 ± 2.7%. Based on the polyphasic differences, strain SPDX02-08 T is proposed to be assigned as a new species of the genus Desulfosoma, Desulfosoma profundi sp. nov. (DSM 22937 T = JCM 16410 T). GenBank accession number for the 16S rRNA gene sequence of strain SPDX02-08 T is HM056226. © 2011 Springer Science+Business Media B.V.


Lepoivre C.,French Institute of Health and Medical Research | Lepoivre C.,Aix - Marseille University | Bergon A.,French Institute of Health and Medical Research | Bergon A.,Aix - Marseille University | And 9 more authors.
BMC Bioinformatics | Year: 2012

Background: Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph.Results: We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation.Conclusions: The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis. © 2012 Lepoivre et al; licensee BioMed Central Ltd.


PubMed | Universites Of Provence Et Of La Mediterranee
Type: Journal Article | Journal: Current microbiology | Year: 2011

This article reports on a new culture system designed for studying the effects of nutritional factors on the growth of hyperthermophilic and chemolithotrophic microorganisms. The system comprises 5-l stainless steel jars, an automatic gas dispenser, propylene microplates, and a robotic platform. The culture system was validated using Aquifex aeolicus, a hyperthermophilic, chemolithotrophic, and microaerophilic bacterium, which requires hydrogen, oxygen, CO, and minerals for growth. We demonstrated that the cell densities measured on 147 cultures of A. aeolicus microplated in jar at 80C under partial pressures (in kPa) of water vapor (47), H (117.7), O (28.1), CO (31.4), and N (3.9), followed a normal distribution, with a mean of 0.72 and a standard deviation of 0.04 (variation coefficient: 5.7%). In addition, cross-comparison of the growth kinetics of A. aeolicus in serum bottles and in a jar system highlighted similar kinetics patterns (both mean growth rates were 0.18 and 0.17 h-1, respectively), whereas the maximum cell densities reached were slightly lower in jar than in bottle (0.73 vs. 0.88 OD units, respectively). Furthermore, these results showed that, contrary to bottles, the total pressure of gas in jars remained constant throughout the biotic experiments, even with seven microplates completely filled with grown cultures. In addition, this system has been validated also for hyperthermophilic strictly anaerobes such as Thermotoga maritima or aerobes such as Sulfolobus solfataricus. This new culture system offers an interesting alternative for cultivating hyperthermophiles, using gas as substrate under constant pressure, thus making it possible to miniaturize experiments and study a large number of nutritional factors in one experimental run.


PubMed | Universites Of Provence Et Of La Mediterranee
Type: Comparative Study | Journal: Antonie van Leeuwenhoek | Year: 2012

A novel strictly anaerobic bacterium designated SPDX02-08(T) was isolated from a deep terrestrial geothermal spring located in southwest France. Cells (1-22-6m) were non-motile, non sporulating and stained Gram negative. Strain SPDX02-08(T) grew at a temperature between 40 and 60C (optimum 55C), pH between 6.3 and 7.3 (optimum 7.2) and a NaCl concentration between 0 and 5g/l (optimum 2g/l). Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate, nitrite, Fe (III) or fumarate. In the presence of sulfate, strain SPDX02-08(T) completely oxidized pyruvate, propionate, butyrate, isobutyrate, valerate, isovalerate and hexadecanoate. Stoichiometric measurements revealed a complete oxidation of part of lactate (0.125mol of acetate produced per mole lactate oxidized). Strain SPDX02-08(T) required yeast extract to oxidize formate and H(2) but did not grow autotrophically on H(2). Among the substrates tested, only pyruvate was fermented. The G+C content of the genomic DNA was 57.6mol%. Major cellular fatty acids of strain SPDX02-08(T) were iso-C(15:0), C(15:0), and C(16:0). Phylogenetic analysis of the 16S small-subunit (SSU) ribosomal RNA gene sequence indicated that strain SPDX02-08(T) belongs to the genus Desulfosoma, family Syntrophobacteraceae, having Desulfosoma caldarium as its closest phylogenetic relative (97.6% similarity). The mean DNA/DNA reassociation value between strain SPDX02-08(T) and Desulfosoma caldarium was 16.92.7%. Based on the polyphasic differences, strain SPDX02-08(T) is proposed to be assigned as a new species of the genus Desulfosoma, Desulfosoma profundi sp. nov. (DSM 22937(T)=JCM 16410(T)). GenBank accession number for the 16S rRNA gene sequence of strain SPDX02-08(T) is HM056226.

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