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Publications (64)

  • [Show abstract] [Hide abstract] ABSTRACT: Desulfovibrio piezophilus strain C1TLV30(T) is a mesophilic piezophilic sulfate-reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep-sea living bacterium at the physiologic and transcriptomic levels. Our results showed that lactate oxidation and energy metabolism were affected by the hydrostatic pressure. Especially, acetyl-CoA oxidation pathway and energy conservation through hydrogen and formate recycling would be more important when the hydrostatic pressure is above (26 MPa) than below (0.1 MPa) the optimal one (10 MPa). This work underlines also the role of the amino acid glutamate as a piezolyte for the Desulfovibrio genus. The transcriptomic analysis revealed 146 differentially expressed genes emphasizing energy production and conversion, amino acid transport and metabolism and cell motility and signal transduction mechanisms as hydrostatic pressure responding processes. This dataset allowed us to identify a sequence motif upstream of a subset of differentially expressed genes as putative pressure-dependent regulatory element.
    Article · Jun 2016 · Environmental Microbiology Reports
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    [Show abstract] [Hide abstract] ABSTRACT: Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth.
    Full-text Article · Apr 2016 · Extremophiles
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    [Show abstract] [Hide abstract] ABSTRACT: Multicellular magnetotactic prokaryotes (MMPs) are a peculiar group of magnetotactic bacteria, each comprising approximately 10-100 cells of the same phylotype. Two morphotypes of MMP have been identified, including several species of globally distributed spherical mulberry-like MMPs (s-MMPs), and two species of ellipsoidal pineapple-like MMPs (e-MMPs) from China (Qingdao and Rongcheng cities). We recently collected e-MMPs from Mediterranean Sea sediments (Six-Fours-les-Plages) and Drummond Island, in the South China Sea. Phylogenetic analysis revealed that the MMPs from Six-Fours-les-Plages and the previously reported e-MMP Candidatus Magnetananas rongchenensis have 98.5% sequence similarity and are the same species, while the MMPs from Drummond Island appear to be a novel species, having > 7.1% sequence divergence from the most closely related e-MMP, Candidatus Magnetananas tsingtaoensis. Identification of the novel species expands the distribution of e-MMPs to Tropical Zone. Comparison of nine physical and chemical parameters revealed that sand grain size and the content of inorganic nitrogen (nitrate, ammonium and nitrite) in the sediments from Rongcheng City and Six-Fours-les-Plages were similar, and lower than found for sediments from the other two sampling sites. The results of the study reveal broad diversity and wide distribution of e-MMPs.
    Full-text Article · Dec 2015 · Environmental Microbiology Reports
  • Nathalie Pradel · Maxime Fuduche · Bernard Ollivier
    [Show abstract] [Hide abstract] ABSTRACT: In this study, we report for the first time the presence of magnetotactic bacteria (MTB) on the Northeastern Atlantic coast. Microscopy observations indicated a heterogeneous population of MTB morphotypes. The analysis of the 16S rDNA by pyrosequencing technology revealed four operational taxonomic sequence units affiliated within the Magnetococcales order, class Alphaproteobacteria. One of them was closely related to sequences of MTB from the Tunisian coast, central Mediterranean Sea. This work offers information on anew environmental context and on biogeography of MTB, highlights the putative impact that marine currents may have on MTB distribution on Earth, and underlines the role that pristine or polluted areas may play on the structure of the MTB communites.
    Article · Sep 2015 · Environmental Science and Pollution Research
  • Raja Lakhal · Anne Postec · Nathalie Pradel · [...] · Anne Godfroy
    [Show abstract] [Hide abstract] ABSTRACT: A novel, anaerobic, chemoorganotrophic bacterium, designated strain Ra1766HT, was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) at 2002 m depth. Cells were thin, motile, Gram-positive flexible rods forming terminal endospores. Strain Ra1766HT grew at temperatures between 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and salinity between 5-60 g/L (optimum 30 g/L). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate, succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end-products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14:0 C16:1 ω7, C16:1 ω7 DMA and C16: The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and phospholipids. The G + C % content of the genomic DNA was 33.7 %. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766HT was affiliated to the bacterial cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766HT was Geosporobacter subterraneus (94.2 % similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766HT (= DSM 27501T = JCM 19377T) is proposed as the type strain of a novel species of a novel genus, Crassaminicella profunda.
    Article · Jun 2015 · International Journal of Systematic and Evolutionary Microbiology
  • Nathalie Pradel · Jean-Luc Cayol · Marie-Laure Fardeau · [...] · Bernard Ollivier
    [Show abstract] [Hide abstract] ABSTRACT: The occurrence of magnetotactic bacteria (MTB) on a Tunisian marine coast exposed to heavy metals pollution (Sfax, Gulf of Gabès, Mediterranean Sea) was investigated. The MTB population of this Southern Mediterranean coast was compared to the MTB populations previously investigated on the French Northern Mediterranean coast. A dominant MTB coccus morphotype was observed by microscopy analysis. By pyrosequencing technology, the analysis of the 16S ribosomal RNA (rDNA) revealed as much as 33 operational taxonomic sequence units (OTUs) close to sequences of MTB accessible in the databases. The majority were close to MTB sequences of the "Med group" of α-Proteobacteria. Among them, a dominant OTU_001 (99 % of the MTB sequences) affiliated within the Magnetococcales order was highlighted. Investigating the capacities of this novel bacterium to be used in bioremediation and/or depollution processes could be envisaged.
    Article · Mar 2015 · Environmental Science and Pollution Research
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    Nathalie Pradel · Lucie Etienne-Mesmin · Jonathan Thévenot · [...] · Valérie Livrelli
    [Show abstract] [Hide abstract] ABSTRACT: Shiga toxin-producing Escherichia coli (STEC) are able to cause serious illnesses ranging from diarrhea to hemorrhagic colitis and hemolytic-uremic syndrome (HUS). These bacteria colonize the digestive tract of humans and produce Shiga-toxins, which are considered to be essential for virulence and are crucial in lethal infection. Colon colonization is supposed to be a determinant step in the development of the infection, but the virulence traits that mediate this step are unclear. We analyzed the ability of 256 STEC strains belonging to seropathotype A (the most virulent O157:H7 serotype) to seropathotype E (not involved in human disease) to adhere to HEp-2, HCT-8, and T84 cell lines. Of the 256 STEC tested most (82%) were non-adherent in our assays. The adhesion levels were globally low and were not related to pathogenicity, although the highest levels were associated to O26:H11 and O103:H2 strains of seropathotype B (associated with HUS but less commonly than serotype O157:H7), possessing both the eae and toxB genes.
    Full-text Article · Feb 2015 · Frontiers in Microbiology
  • Maxime Fuduche · Anne Postec · Sylvain Davidson · [...] · Nathalie Pradel
    [Show abstract] [Hide abstract] ABSTRACT: Magnetotactic bacteria synthesize intracellular magnetite and/or greigite magnetosome crystals. They play a significant role in both iron and sulfur cycles in sedimentary aquatic environments. To get insight into the bio-geochemical contribution of MTB, more studies concerning their ecology and their distribution in diverse habitats are necessary. The MTB community of an oil-industry polluted area of the French Mediterranean coast has been previously investigated. Here, we investigate the MTB community from coastal sediments of a Mediterranean pristine area using optical and transmission electron microscopy and phylogenetic analysis based on 16S rRNA gene sequences. A particularly high diversity of MTB was observed, with cocci phylogenetically distributed across the order Magnetococcales, including a novel cluster with sequences from the Mediterranean Sea designated as “Med group”, and novel morphotypes.
    Article · Dec 2014 · Current Microbiology
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    Amira Amrani · Aurélie Bergon · Hélène Holota · [...] · Nathalie Pradel
    [Show abstract] [Hide abstract] ABSTRACT: RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.
    Full-text Article · Sep 2014 · PLoS ONE
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    [Show abstract] [Hide abstract] ABSTRACT: Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantially varied lifestyles, including free-living, commensal, pathogenic, symbiotic, and piezophilic. Here, we present the genome sequence of a luminous, piezophilic Photobacterium phosphoreum strain, ANT-2200, isolated from a water column at 2,200 m depth in the Mediterranean Sea. It is the first genomic sequence of the P. phosphoreum group. An analysis of the sequence provides insight into the adaptation of bacteria to the deep-sea habitat.
    Full-text Article · Mar 2014 · Genome Announcements
  • Article · Feb 2014 · Environmental Microbiology
  • Raja Lakhal · Nathalie Pradel · Anne Postec · [...] · Marie-Laure Fardeaul
    [Show abstract] [Hide abstract] ABSTRACT: A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic, halophilic, Gram-stain-negative bacterium, was isolated from sediments of Guaymas Basin. The strain, designated Ra1766G1(T), grew at 20-40 degrees C (optimum, 30-35 degrees C) and at pH 6.0-8.0 (optimum, pH 6.5-7.5). It required 0.5-7.5 % NaCl (optimum, 2-3 %) for growth. Sulfate, thiosulfate, elemental sulfur, sulfite, fumarate, nitrate and nitrite were not used as terminal electron acceptors. Strain Ra1766G1(T) used cellobiose, glucose, mannose, maltose, arabinose, raffinose, galactose, ribose, sucrose, pyruvate and xylose as electron donors. The main fermentation product from glucose metabolism was acetate. The predominant cellular fatty acids were anteiso-C-15:0, iso-C-15:0, anteiso DMA-C-15:0 and C-16:0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, iso-DMA-C-15:0 glycolipids and phospholipids. The G+C content of the genomic DNA was 31.2 mol%. The closest phylogenetic relatives of strain Ra1766G1(T) were Natranaerovirga pectinivora AP3(T) (92.4 % 16S rRNA gene sequence similarity), Natranaerovirga hydrolytica APP2(T)(90.2 %) and Defluviitalea saccharophila 6LT2(T) (88.9 %). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766G1(T) represents a novel species of a new genus for which the name Vallitalea guaymasensis is proposed. The type strain of the type species is Ra1766G1(T) (=DSM 24848(T)=JCM17997(T)).
    Article · Aug 2013
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    [Show abstract] [Hide abstract] ABSTRACT: Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.
    Full-text Article · Jun 2013 · Environmental Microbiology
  • Nathalie Pradel · Manon Bartoli · Alain Bernadac · [...] · Marie-Laure Fardeau
    [Show abstract] [Hide abstract] ABSTRACT: An anaerobic thermophilic bacterium designated CA9F1 was isolated from a thermal spring in France. Strain CA9F1 was observed to grow at temperatures between 55 and 70 °C (optimum 65 °C) and at pH between 6.8 and 9.5 (optimum pH 7.4). Strain CA9F1 does not require salt for growth (0-10 g l(-1) NaCl), with an optimum at 1 g l(-1). The DNA G+C content was determined to be 38.5 mol% (Tm). The major cellular fatty acids identified were C15:0, C16:0, C17:0 iso. Based on phenotypic, chemotaxonomic and genotypic properties, strain CA9F1 was identified as Thermovenabulum gondwanense and this species was studied in more detail. Strain CA9F1 is a Gram-positive bacterium which forms a complex and regular multilayered cell wall structure, here characterised as being due to the presence of an S-layer. The network covers the entire cell surface and forms a hexagonal structure resembling that observed for Deinococcus radiodurans. The main protein component of the S-layer possesses domains comparable to that of the S-layer protein of Halothermothrix orenii. The characteristics of the strain were compared to that of T. gondwanese R270(T) isolated from microbial mats thriving in the thermal waters of a Great Artesian Basin bore runoff channel at 66 °C, in Australia. Significant differences were observed between CA9F1 and the type strain. One of the major physiological differences is the inability of CA9F1 to reduce Fe(III). An emended description of T. gondwanense is given.
    Article · Jun 2013 · Antonie van Leeuwenhoek
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    Raja Lakhal · Nathalie Pradel · Anne Postec · [...] · Marie-Laure Fardeau
    [Show abstract] [Hide abstract] ABSTRACT: A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic, halophilic bacterium staining Gram-negative, was isolated from sediments of Guaymas basin. The strain, designated Ra1766G1T, grew at 20-40 °C (optimum 30-35 °C) and at pH 6.0-8.0 (optimum pH 6.5-7.5). It required 0.5%-7.5% NaCl (optimum 2%-3%) for growth. Sulfate, thiosulfate, elemental sulfur, sulfite, fumarate, nitrate and nitrite were not used as terminal electron acceptors. Strain Ra1766G1T used cellobiose, glucose, mannose, maltose, arabinose, raffinose, galactose, ribose, saccharose, pyruvate and xylose as electron donors. The main fermentation product from glucose metabolism was acetate. The predominant cellular fatty acids were anteiso-C15:0, iso-C15:0, anteiso DMA-C15:0 and C16:0. The main polar lipids consisted of diphosphatiglycerol, phosphatidylglycerol, glycolipids and phospholipids.The G+C content of the genomic DNA was 31.2 mol%. The closest phylogenetic relatives of Ra1766G1T were Natranaerovirga pectinivoraT (92.4% similarity), Natranaerovirga hydrolytica (90.2% similarity) and Defluviitalea saccharophilaT (88.9% similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766G1T (= DSM 24848T = JCMT= 16313) is proposed as the type strain of a novel species of a novel genus, Vallitalea guaymasensis gen. nov., sp. nov.
    Full-text Article · Feb 2013 · International Journal of Systematic and Evolutionary Microbiology
  • Dataset: Table S7
    Nathalie Pradel · Boyang Ji · Grégory Gimenez · [...] · Alain Dolla
    [Show abstract] [Hide abstract] ABSTRACT: List of oligonucleotide primers used. (PDF)
    Dataset · Jan 2013
  • Dataset: Table S3
    Nathalie Pradel · Boyang Ji · Grégory Gimenez · [...] · Alain Dolla
    [Show abstract] [Hide abstract] ABSTRACT: Gene expression levels by qRT-PCR. (PDF)
    Dataset · Jan 2013
  • Dataset: Text S1
    Nathalie Pradel · Boyang Ji · Grégory Gimenez · [...] · Alain Dolla
    [Show abstract] [Hide abstract] ABSTRACT: Supplemental information on Materials and Methods. (DOC)
    Dataset · Jan 2013
  • Dataset: Figure S2
    Nathalie Pradel · Boyang Ji · Grégory Gimenez · [...] · Alain Dolla
    [Show abstract] [Hide abstract] ABSTRACT: Phylogenetic analysis of genes DESPIv2_11220 (A), DESPIv2_11837 (B). The 20 best BLAST hit proteins versus nr were retrieved from Genbank. The phylogenetic reconstruction was achieved on the trimmed alignment using PhyML with a WAG matrix. Branch support estimated using a bootstrap of 100. (TIF)
    Dataset · Jan 2013
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    Nathalie Pradel · Boyang Ji · Grégory Gimenez · [...] · Alain Dolla
    [Show abstract] [Hide abstract] ABSTRACT: Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
    Full-text Article · Jan 2013 · PLoS ONE