Bernard Ollivier's research while affiliated with Aix-Marseille Université and other places

Publications (406)

Article
Full-text available
Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ra...
Article
This is the first report on obligate sugar oxidation by members of the phylum Thermotogae (e.g. Mesotoga spp.). Other members of this phylum are recognized as hydrogen-producing fermentative bacteria which do not require electron acceptors for growing. Obligate sugar oxidation has been documented only twice by the past in Bacteria (Krumholz and Bry...
Article
This work assessed the role of the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus in anaerobic iron corrosion, at 70 °C, in the presence and the absence of lactate as energy source. Experiments performed with A. fulgidus planktonic cells, displayed their capacity to form a biofilm on an iron coupon and exhibited their biocorros...
Article
Hot oil reservoirs harbor diverse microbial communities, with many of them inhabiting thermophilic or hyperthermophilic fermentative Thermotogae species. A new Thermotoga sp. strain TFO was isolated from an Californian offshore oil reservoir which is phylogenetically related to thermophilic species T. petrophila RKU-1T and T. naphthophila RKU-10T,...
Article
Full-text available
Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Mo...
Article
Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Mo...
Article
A novel Gram-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacterium, designated strain PAR22NT, was isolated from sediment samples collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR22NT grew at temperatures between 15 and 37 °C (optimum, 32 °C), at pH between pH 8.3 and 10.1 (optimum, pH...
Chapter
Pa.lu.di.fi'lum L. fem. n. palus, ‐dis a marsh; L. neut. n. filum a thread; N.L. neut. n. Paludifilum a thread from a marsh. Firmicutes / Bacilli / Bacillales / Thermoactinomycetaceae / Paludifilum The genus Paludifilum comprises one species with a validly published name, Paludifilum halophilum, which was isolated from superficial sediment of a sol...
Chapter
Fon.ti.cel'la. L. masc. n. fons, fontis a spring, fountain; L. fem. n. cella a storeroom, in biology a cell; N.L. fem. n. Fonticella a cell (bacterium) isolated from a spring. Firmicutes / Clostridia / Clostridiales / Clostridiaceae / Fonticella The genus Fonticella, at the time of writing, comprised of only one species, for which the name has been...
Chapter
An.a.e.ro.sa.li.bac'ter. Gr. pref. an not; Gr. n. aer, aeros, air; L. neut. n. sal, salis, salt; N.L. masc. n. bacter, a rod; N.L. masc. n. Anaerosalibacter, an anaerobic halotolerant rod. Firmicutes / Clostridia / Clostridiales / Tissierellaceae / Anaerosalibacter The genus Anaerosalibacter comprises two species with validly published names, Anaer...
Article
Full-text available
Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the...
Chapter
Me.tha.no.cal'cu.lus. N.L. neut. n. methanum methane; N.L. masc. n. calculus pebble; gravel; N.L. masc. n. Methanocalculus a methane‐producing pebble‐shaped bacterium. Euryarchaeota / Methanomicrobiales / Methanomicrobiales / Methanocalculaceae / Methanocalculus The genus Methanocalculus comprises six species with validly published names: Methanoca...
Article
Full-text available
In 2008, as part of a feasibility study for radioactive waste disposal in deep geological formations, the French National Radioactive Waste Management Agency (ANDRA) drilled several boreholes in the transposition zone in order to define the potential variations in the properties of the Callovo–Oxfordian claystone formation. This consisted of a rare...
Chapter
Spo.ro.sa.li.bac.te'ri.um. Gr. n. spora a seed and, in bacteriology, a spore; L. n. sal, salis salt; L. neut. n. bacterium a rod; N.L. neut. n. Sporosalibacterium a moderately halophilic sporulated rod. Firmicutes / Clostridia / Clostridiales / Clostridiaceae / Sporosalibacterium The genus Sporosalibacterium, at the time of writing, comprised two v...
Article
Full-text available
The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universa...
Article
Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants...
Article
Full-text available
The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively in...
Book
How can the evolutionary success of prokaryotes be explained ? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years ? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemi...
Chapter
In natural world, no organism exists in absolute isolation, and thus every organism must interact with the environment and other organisms. Next-generation sequencing technologies are increasingly revealing that most of the cells in the environment resist cultivation in the laboratory and several prokaryotic divisions have no known cultivated repre...
Article
How can the evolutionary success of prokaryotes be explained ? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years ? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemi...
Chapter
How can the evolutionary success of prokaryotes be explained? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemica...
Book
The purpose of this book is to show the essential and indispensable role of prokaryotes in the evolution of a living world. The evolutionary success of prokaryotes is explained together with their role in the evolution of the geosphere, the biosphere and its functioning, as well as their ability to colonize all biotopes, including the most extreme...
Chapter
The various schemes proposed to classify microorganisms in the living world have long been subject of heated debates. The classical dichotomic distinction between Prokaryotae (cells without nucleus) and Eukaryotae (cells with nucleus) functional and phenotypic categories was deeply changed by rRNA gene-based analysis that divided the living world i...
Book
The various schemes proposed to classify microorganisms in the living world have long been subject of heated debates. The classical dichotomic distinction between Prokaryotae (cells without nucleus) and Eukaryotae (cells with nucleus) functional and phenotypic categories was deeply changed by rRNA gene-based analysis that divided the living world i...
Article
In natural world, no organism exists in absolute isolation, and thus every organism must interact with the environment and other organisms. Next-generation sequencing technologies are increasingly revealing that most of the cells in the environment resist cultivation in the laboratory and several prokaryotic divisions have no known cultivated repre...
Article
The various schemes proposed to classify microorganisms in the living world have long been subject of heated debates. The classical dichotomic distinction between Prokaryotae (cells without nucleus) and Eukaryotae (cells with nucleus) functional and phenotypic categories was deeply changed by rRNA gene-based analysis that divided the living world i...
Book
In natural world, no organism exists in absolute isolation, and thus every organism must interact with the environment and other organisms. Next-generation sequencing technologies are increasingly revealing that most of the cells in the environment resist cultivation in the laboratory and several prokaryotic divisions have no known cultivated repre...
Article
On a volcanic and anaerobic planet characterized by abundant hydrothermal activity, physicochemical gradients and disequilibria at the local scale would have been fundamental for the emergence of life on Earth. Unfortunately, the early rock record pertaining to this existential process no longer exists, and, while chemists attempt to recreate life...
Chapter
On a volcanic and anaerobic planet characterized by abundant hydrothermal activity, physicochemical gradients and disequilibria at the local scale would have been fundamental for the emergence of life on Earth. Unfortunately, the early rock record pertaining to this existential process no longer exists, and, while chemists attempt to recreate life...
Article
Full-text available
Piezophilic Desulfovibrio profundus strain 500-1 was isolated in the Japan Sea from a sediment layer at 500-m depth under a water column of 1,000 m. Here, we report the genome sequence of this strain, which includes a 4,168,905-bp circular chromosome and two plasmids of 42,836 bp and 6,167 bp.
Article
Full-text available
Mesotoga prima strain PhosAc3 is a mesophilic representative of the phylum Thermotogae comprising only fermentative bacteria so far. We show that while unable to ferment glucose, this bacterium is able to couple its oxidation to reduction of elemental sulfur. We demonstrate furthermore that M. prima strain PhosAc3 as well as M. prima strain MesG1 a...
Article
Full-text available
Novel Gram-stain-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacteria, designated strains PAR180(T) and PAR190, were isolated from sediments collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR180(T) grew at temperatures between 15 and 40 °C (optimum 35 °C), and at pH between 8.3 and 10.4...
Article
Full-text available
Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of...
Article
In humans, sleeping sickness (i.e. Human African Trypanosomiasis) is caused by the protozoan parasites Trypanosoma brucei gambiense (Tbg) in West and Central Africa, and T. b. rhodesiense in East Africa. We previously showed in vitro that Tbg is able to excrete/secrete a large number of proteins, including Translationally Controlled Tumour Protein...
Chapter
De.flu.vi.i.ta'le.a. L. neut. n. defluvium sewage, wastewater; L. fem. n. talea a rod; N.L. fem. n. Defluviitalea a rod isolated from wastewater. Firmicutes / Clostridia / Clostridiales / Defluviitaleaceae / Defluviitalea The genus Defluviitalea, at the time of writing, comprises two validly published species, D. saccharophila which was isolated fr...
Chapter
De.flu.vi.i.ta.le.a.ce'a.e. N.L. n. Defluviitalea, type genus of the family; suff. -aceae, ending to denote a family; N.L. fem. pl. n. Defluviitaleaceae, the Defluviitalea family. Firmicutes / Clostridia / Clostridiales / Defluviitaleaceae The family Defluviitaleaceae belongs to the order Clostridiales. To date, it is currently represented by only...
Article
In humans, sleeping sickness (i.e. Human African Trypanosomiasis) is caused by the protozoan parasites Trypanosoma brucei gambiense (Tbg) in West and Central Africa, and T. b. rhodesiense in East Africa. We previously showed in vitro that Tbg is able to excrete/secrete a large number of proteins, including Translationally Controlled Tumor Protein (...
Article
Full-text available
Two novel strictly anaerobic bacteria, strains Bs105T and Bs107T, were isolated from a deep aquifer-derived hydrocarbonoclastic community. The cells were rod-shaped, not motile and had terminal spores. Phylogenetic affiliation and physiological properties revealed that these isolates belong to two novel species of the genus Desulfotomaculum . Optim...
Article
Full-text available
A novel filamentous, halophilic, thermotolerant bacterium, strain SMBg3T was isolated from superficial sediment of a solar saltern in Sfax, Tunisia. The isolate is Gram-staining-positive, aerobic, catalase- and oxidase-positive. Optimum growth occurred at 40–45°C, with 10% (w/v) NaCl and at pH 8.0–9.0. Long and well developed aerial and substrate m...
Article
Full-text available
A mesophilic anaerobic bacterium, designated KHALHBD91T was isolated from the moderately hot spring of Hamman Biadha, Tunisia. The strain was Gram staining negative, non sporulating, non motile and rod shaped, appearing singly (0.5-2.0µm x 0.5-1µm).It grew anaerobically at temperatures between 20 and 50°C (optimum 37°C) and at pH between 5.5-7.8 (o...
Article
Full-text available
A novel anaerobic, alkaliphilic, Gram-positive, spore-forming bacterium was isolated from a carbonaceous hydrothermal chimney in the Prony Bay, New Caledonia. This bacterium designated strain 3bT grew at temperatures from 30 to 43 °C (optimum 37°C) and at pH between 7.8 and 10.1 (optimum 9.5). Added NaCl was not required for growth (optimum 0-0.2%)...
Article
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 ene...
Poster
The genus Fusibacter belongs to the phylum Firmicutes, class Clostridia, order Clostridiales. Only three species pertaining to this genus have been reported so far. These Fusibacter species were recognized as slightly halophilic fermentative anaerobes with the ability to use thiosulfate and elemental sulfur as terminal electron acceptors producing...
Article
Full-text available
Microbiology of a hypersaline oil reservoir located in Central Africa was investigated with molecular and culture methods applied to preserved core samples. Here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16S rRNA gene sequences retrieved from the extracted DNA are phylogenetically related...
Article
The current paper reports on the purification of an extracellular thermostable keratinase (KERCA) produced from C. algeriensis strain TH7C1T, a thermophilic, anaerobic bacterium isolated from a hydrothermal hot spring in Algeria. The maximum keratinase activity recorded after 24-h of incubation at 50 °C was 21000 U/ml. The enzyme was purified by am...
Article
Taking into account their 16S rRNA gene sequences, it appears that Acetomicrobium flavidum and the three Anaerobaculum species described so far belong to the same phylogenetic clade with high levels (>95 %) of similarity. In this respect, these three Anaerobaculum species should be reclassified within the genus Acetomicrobium which has priority ove...
Article
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 Magnetococcal...
Article
A mesophilic anaerobic bacterium, designated KHALHBd91(T) was isolated from the moderately hot spring of Hammam Biadha, Tunisia. The strain was Gram-staining-negative, non-sporulating, non-motile and rod-shaped, appearing singly (0.5-2.0 x 0.5-1 mu m). It grew anaerobically at temperatures between 20 and 50 degrees C (optimum 37 degrees C) and at p...
Article
The present study investigates the purification and biochemical characterization of an extracellular thermostable xylanase (called XYN35) from Caldicoprobacter algeriensis sp. nov., strain TH7C1T, a thermophilic, anaerobic strain isolated from the hydrothermal hot spring of Guelma (Algeria). The maximum xylanase activity recorded after 24 h of incu...
Article
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 Magnetococcal...
Chapter
Ther.mo.ha.lo.bac'ter. Gr. adj. thermos hot; Gr. n. hals salt; N.L. n. bacter masc. equiv. of Gr. neut. dim. n. bakterion small rod; N.L. masc. n. Thermohalobacter a thermophilic fermentative halophile. Firmicutes / ?Clostridia? / Clostridiales / Clostridiaceae / Thermohalobacter Rod-shaped cells, generally occurring singly or in pairs, about 0.5 ?...
Chapter
Ther.mo.de.sul.fo.bac.te' ri.a. M.L. fem. pl. n. Thermodesulfobacteriales type order of the class; dropping the ending to denote an class; M.L. fem. pl. n. Thermodesulfobacteria the class of Thermodesulfobacteriales. Thermodesulfobacteria / Thermodesulfobacteria
Chapter
Cald.an.ae.ro.bac'ter. L. adj. caldus hot; Gr. pref. an not; Gr. n. aer air; N.L. masc. n. bacter equivalent of Gr. neut. dim. n. bakterion rod, staff; N.L. masc. n. Caldanaerobacter a rod that grows in the absence of air at high temperatures.
Chapter
Ther.mo.de.sul.fo.bac.te.ri.a' les. M.L. neut. n. Thermodesulfobacterium type genus of the order; -ales ending to denote an order; M.L. fem. pl. n. Thermodesulfobacteriales the order of Thermodesulfobacterium. Thermodesulfobacteria / Thermodesulfobacteria / Thermodesulfobacteriales
Chapter
Spo.ro.bac'ter. Gr. n. spora a spore; N.L. n. bacter masc. equivalent of Gr. neut. dim. n. bakterion rod; N.L. masc. n. Sporobacter a spore-forming rod. Firmicutes / ?Clostridia? / Clostridiales / ?Ruminococcaceae? / Sporobacter Slightly curved rods that are 0.2?0.4 ? 1?2 ?m and occur singly or in pairs. Motile by peritrichous flagella. Gram-stain-...
Chapter
Fu.si.bac'ter. L. n. fusus a spindle; N.L. n. bacter masc. equivalent of Gr. neut. dim. n. bakterion rod; N.L. masc. n. Fusibacter a small spindle-shaped rod. Firmicutes / “Clostridia” / Clostridiales / incertae Sedis - Family II / Fusibacter Spindle-shaped rods with cells that are 1 × 2–5 µm, and occurring singly or in pairs. Motile by one to four...
Chapter
A.min.o.bac'te.ri.um. N.L. n. aminum amine; Gr. dim. n. bakterion a small rod; N.L. neut. n. Aminobacterium the amino acid rod. Synergistetes / Incertae Sedis / Incertae Sedis / Incertae Sedis / Aminobacterium Cells are strictly anaerobic, nonsporeforming, nonmotile or motile by means of one or two lateral flagella, slightly curved rods, occurring...
Chapter
De.sul.fo.hal.o' bium. L. pref. de from; L. n. sulfur sulfur; Gr. n. hals the sea, salt; Gr. n. bios life; M.L. adj. halobius living on salt; M.L. masc. n. Desulfohalobium a sulfate-reducing, salt-requiring, rod-shaped bacterium. Proteobacteria / Deltaproteobacteria / Desulfovibrionales / Desulfohalobiaceae / Desulfohalobium Rod-shaped cells, 0.7–0...
Chapter
Mah.el'la. L. dim. ending -ella; N.L. fem. n. Mahella named in honor of the American microbiologist Robert A. Mah for his important contribution to the taxonomy of anaerobes. Firmicutes / “Clostridia” / Thermoanaerobacterales / incertae Sedis - Family IV / Mahella Cells are straight rods, about 3–20 µm × 0.5 µm, occurring singly or in pairs. The ro...
Article
Full-text available
Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coe...
Chapter
Spor.an.a.e.ro.bac'ter. Gr. fem. n. spora spore; Gr. pref. an not; Gr. n. aer air; anaero not (living) in air; N.L. n. bacter masc. equivalent of Gr. neut. dim. n. bakterion rod, staff; N.L. masc. n. Sporanaerobacter a sporeforming anaerobic rod. Firmicutes / “Clostridia” / Clostridiales / incertae Sedis - Family I / Sporanaerobacter Cells are stri...
Chapter