[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.
Environmental Science and Pollution Research 09/2015; DOI:10.1007/s11356-015-5322-9 · 2.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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 coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems.
Frontiers in Microbiology 09/2015; 1(6). DOI:10.3389/fmicb.2015.00857 · 3.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes. At the steady state, a very efficient removal of protein (92 %) was observed. Our results demonstrate a decrease of archaeal and bacterial abundance over time. Members of the phylum Synergistetes, with a peculiar emphasis for those pertaining to families Dethiosulfovibrionaceae and Aminiphilaceae, are of major ecological significance regarding the treatment of this industrial wastewater. The prominent role to be played by members of the phylum Synergistetes regarding protein and/or amino acid degradation is discussed.
Environmental Science and Pollution Research 07/2015; DOI:10.1007/s11356-015-4973-x · 2.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Strain KhalAKB1T, a novel mesophilic, anaerobic rod-shaped bacterium was isolated from waters collected from a mesothermic tunisian spring. Cells are Gram-positive staining rods, occurring singly or in pairs and motile by one lateral flagellum. Strain KhalAKB1T grows at temperatures between 15° C and 45° C (optimum 30°C), pH between 5.5 and 8.5 (optimum 7.0) and NaCl concentration between 0 and 35 g l-1 (optimum 1 g l-1). It ferments yeast extract and a wide range of carbohydrates as electron donors including cellobiose, D-glucose, D-ribose, D-sucrose, D-xylose, D-maltose, D-galactose, and starch. Acetate, ethanol, CO2, and H2, are end products from glucose metabolism. It reduces elemental sulfur, but not sulfate, thiosulfate or sulfite, into sulfide The DNA G+C content is 37.6 mol %. The predominant cellular fatty acids are C14:0 and C16:0. Phylogenetic analysis of the 16S rRNA gene sequence suggests Fusibacter bizertensis as being the closest relative of this isolate (identity of 97.2 %). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain KhalAKB1T is proposed to be assigned to a novel species within the genus Fusibacter, order Clostridiales, Fusibacter fontis sp. nov. The type strain is KhalAKB1T (= DSM 28450 = JCM 19912).
International Journal of Systematic and Evolutionary Microbiology 07/2015; DOI:10.1099/ijsem.0.000445 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Taking into account its phenotypical and genetic characteristics, Acetomicrobium faecale was first recognized as a member of the genus Acetomicrobium, family Bacteroidaceae, order Bacteroidales, phylum Bacteroidetes, with Acetomicrobium flavidum being the type species of the genus. However, it was found that Acetomicrobium faecale presented 95.8 %, 97.6 % and 98.4 % similarity, respectively, with Caldicoprobacter guelmensis, Caldicoprobacter algeriensis and Caldicoprobacter oshimai and only 82 % similarity with Acetomicrobium flavidum. The DNA G+C content of A. faecale is 45 mol%, which is the same order than the DNA G+C content of the three Caldicoprobacter strains and its main fatty acids is C16:0; iso-C17:0 is its second major fatty acid, common too with the Caldicoprobacter strains. Based on further phylogenetic, genetic, and chemotaxonomic studies, we propose Acetomicrobium faecale (=DSM 20678T = JCM 30420T) to be reclassified as Caldicoprobacter faecalis comb. nov.
International Journal of Systematic and Evolutionary Microbiology 07/2015; DOI:10.1099/ijsem.0.000409 · 2.51 Impact Factor
[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.
International Journal of Systematic and Evolutionary Microbiology 06/2015; 65(9). DOI:10.1099/ijsem.0.000386 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A novel anaerobic bacterium, strain ST07-YET, was isolated from a carbonate chimney of the Prony Hydrothermal Field (PHF) in New Caledonia. Cells were Gram-positive-staining, straight rods (0.7-0.8 x 3.0-5.0 µm). They were motile by the means of lateral flagella. Strain ST07-YET was mesophilic (optimum 35°C), moderately alkaliphilic and halotolerant (optimum pH 8.7 and 5 g l-1 NaCl). Elemental sulfur, sulfate, thiosulfate, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Yeast extract, peptone, tryptone, casamino-acids, crotonate, pyruvate, galactose, maltose, sucrose, ribose, trehalose and glucose were used as carbon sources. Glucose fermentation led to acetate, H2 and CO2 formation. Arginine, serine, histidine, lysine, methionine and cysteine improved growth, but the Stickland reaction was negative for the combinations of amino acids tested. The major metabolic products from yeast extract fermentation were H2, acetate, butyrate, isobutyrate, isovalerate and propionate. The predominant cellular fatty acids were C16:0, C16:1 cis9, C14:0 and C16:1 cis7 (>5% of total fatty acids). The G+C content of the genomic DNA was 32.9 mol %. Phylogenetic analysis revealed that strain ST07-YET was most closely related to Clostridium sticklandii DSM 159T and Acetoanaerobium noterae NOT-3T (96.7% and 96.8% 16S rRNA gene sequence identity). On the basis of phylogenetic, chemotaxonomic and physiological properties, strain ST07-YET (= DSM 27512 = JCM 19400) is proposed as a novel species of the genus Acetoanaerobium, order Clostridiales, phylum Firmicutes, as Acetoanaerobium pronyense sp. nov..
International Journal of Systematic and Evolutionary Microbiology 05/2015; 65(8). DOI:10.1099/ijs.0.000307 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mesotoga strain PhosAc3 was the first mesophilic cultivated member of the order Thermotogales. This genus currently contain two described species, M. prima and M. infera. Strain PhosAc3, isolated from a Tunisian digestor treating phosphogypsum, is phylogenetically closely related to M. prima strain MesG1.Ag.4.2 T. Strain PhosAc3 has a genome of 3.1 Mb with a G + C content of 45.2%. It contains 3,051 protein-coding genes of which 74.6% have their best reciprocal BLAST hit in the genome of the type species, strain MesG1.Ag.4.2 T. For this reason we propose to assign strain PhosAc3 as a novel ecotype of the Mesotoga prima species. However, in contrast with the M. prima type strain, (i) it does not ferment sugars but uses them only in the presence of elemental sulfur as terminal electron acceptor, (ii) it produces only acetate and CO 2 from sugars, whereas strain MesG1.Ag.4.2 T produces acetate, butyrate, isobutyrate, isovalerate, 2-methyl-butyrate and (iii) sulfides are also end products of the elemental sulfur reduction in theses growth conditions.
[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.
Environmental Science and Pollution Research 03/2015; DOI:10.1007/s11356-015-4314-0 · 2.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A novel anaerobic, mesophilic, slightly halophilic sulfate-reducing bacterium designated strain Khaled BD4T was isolated from waters from a Tunisian thermal spring. The cells were vibrio-shaped or sigmoids (5-7 x 1-1.5 µm) and occurred singly or in pairs. Strain Khaled BD4T was Gram-staining-negative, motile, non-sporulated. It grew at temperature between 25 and 45°C (optimum 37 °C), at pH between 5.5 and 8.3 (optimum pH 7.0) and with NaCl between 0.5-8% (optimum 3%). It required vitamins or yeast extract for growth. Sulfate, thiosulfate, sulfite and elemental sulfur served as terminal electron acceptors, but not fumarate, nitrate or nitrite. Strain Khaled BD4T utilized H2 in the presence of 2 mM acetate (carbon source), but also lactate, formate, pyruvate and fumarate in the presence of sulfate. Lactate was incompletely oxidized to acetate. Amongst substrates used, only pyruvate was fermented. Desulfoviridin and c-type cytochrome were present. The G + C content of the DNA was 54.6 mol%. The main fatty acids were anteiso-C15:0, iso-C18:0, iso-C17:0 and iso-C14:0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Khaled BD4T had Desulfovibrio giganteus (96.7% similarity) as its closest phylogenetic relative. On the basis of the 16S rRNA gene sequence comparisons together with genetic and physiological characteristics, strain Khaled BD4T is proposed to be assigned to a new bacterial species, for which the name Desulfovibrio biadhensis is proposed. The type strain is Khaled BD4T (= DSM 28904T = JCM 30146T).
International Journal of Systematic and Evolutionary Microbiology 01/2015; 65(Pt 4). DOI:10.1099/ijs.0.000088 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2 % of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.
Environmental Science and Pollution Research 01/2015; 22(18). DOI:10.1007/s11356-015-4113-7 · 2.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Extreme physicochemical conditions (low and high temperatures, high salinity, low and high pH, high hydrostatic pressure, etc.) existing on Earth are compatible with the occurrence of microbial life. The diversity and metabolic features of microbial trophic groups inhabiting extreme environments (cold, hot, saline, acidic, alkaline, and deep marine) are described. They include hydrothermal vents, acid springs, hypersaline and/or alkaline lakes, permafrost, and deep-sea environments, etc. To live or survive under such drastic conditions, prokaryotes (Bacteria or Archaea) have developed a variety of physiological and metabolic strategies allowing them to adapt to in situ extreme conditions. Many of these extremophiles are recognized to be of industrial interest or to be potential candidates for future biotechnological applications. Clearly, the discovery of extremophiles living in terrestrial, subterrestrial, and deep marine environments has changed our perception of microbial life. One or a combination of extreme physicochemical conditions that they have to face may have prevailed in the primitive atmosphere and favored early extremophilic life not only on Earth but perhaps also on other planets.
[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.
Current Microbiology 12/2014; 70(4). DOI:10.1007/s00284-014-0745-y · 1.42 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The hydrogen-producing strain PROH2 pertaining to the genus Clostridium was successfully isolated from a shallow submarine hydrothermal chimney (Prony Bay, New Caledonia) driven by serpentinization processes. Cell biomass and hydrogen production performances during fermentation by strain PROH2 were studied in a series of batch experiments under various conditions of pH, temperature, NaCl and glucose concentrations. The highest hydrogen yield, 2.71 mol H-2/mol glucose, was observed at initial pH 9.5, 37 degrees C, and glucose concentration 2 g/L, and was comparable to that reported for neutrophilic clostridial species. Hydrogen production by strain PROH2 reached the maximum production rate (0.55 mM-H-2/h) at the late exponential phase. Yeast extract was required for growth of strain PROH2 and improved significantly its hydrogen production performances. The isolate could utilize various energy sources including cellobiose, galactose, glucose, Maltose, sucrose and trehalose to produce hydrogen. The pattern of end-products of metabolism was also affected by the type of energy sources and culture conditions used. These results indicate that Clostridium sp. strain PROH2 is a good candidate for producing hydrogen under alkaline and mesothermic conditions.
International Journal of Hydrogen Energy 11/2014; 39(34). DOI:10.1016/j.ijhydene.2014.09.111 · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A novel anaerobic, alkaliphilic, Gram-positive staining bacterium was isolated from a hydrothermal chimney in the Prony Bay, New Caledonia. This strain designated FatMR1(T) grew at temperatures from 20 to 55 °C (optimum 37 °C) and at pH between 7.5 and 10.5 (optimum 8.8-9). NaCl is not required for growth (optimum 0.2-0.5 %), but is tolerated up to 3 %. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite are not used as terminal electron acceptors. Strain FatMR1(T) fermented pyruvate, yeast extract, peptone and biotrypcase and used fructose as the only sugar. The main fermentation products from fructose and proteinaceous compounds (e.g. peptone and biotrypcase) were acetate, H2 and CO2. Crotonate was disproportionated to acetate and butyrate. The predominant cellular fatty acids were C14:0 and C16:0. The G + C content of the genomic DNA was 37.1 mol %. On the basis of phylogenetic, genetic, and physiological properties, strain FatMR1(T) (=DSM 25890(T), =JCM 18390(T)) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as a novel species of the genus Alkaliphilus, A. hydrothermalis sp. nov.
[Show abstract][Hide abstract] ABSTRACT: Strain LTF Kr01, a novel mesophilic, anaerobic, halotolerant, rod-shaped bacterium was isolated from a drain at the bottom of a corroded kerosene storage tank of the Société Tunisienne des Industries de Raffinage (STIR), Bizerte, North Tunisia. Cells are Gram- positive rods, and occur singly or in pairs, motile by one lateral flagellum. Strain LTF Kr01 grows at temperatures between 15°C and 40°C (optimum 30°C), pH between 5.5 and 8.1 (optimum 7.2) and NaCl concentration between 0 and 50 g l-1 (optimum 5 g l-1). It reduces thiosulfate and elemental sulfur into sulfide, but not sulfate and or sulfite. It utilizes a large number wide range of carbohydrates (cellobiose, D-glucose, D-fructose, D-mannitol,D-ribose, D-sucrose, D-xylose, D-maltose, D-galactose, starch, and trehalose), and produces acetate, CO2, and H2, as end products from glucose fermentation. The DNA G+C content is 37.4 mol %. The predominant cellular fatty acids are C14:0 and C16:0. Phylogenetic analysis of the 16SrRNA gene sequence suggests that Fusibacter tunisiensis is its closest relative (identity of 94.6%). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain LTF Kr01T is proposed described as a novel species of the genus Fusibacter, order Clostridiales for which the name F. bizertensis sp. nov. is proposed. The type strain is LTF Kr01T (= DSM 28034 =JCM 19376).
International Journal of Systematic and Evolutionary Microbiology 10/2014; 65(Pt 1). DOI:10.1099/ijs.0.066183-0 · 2.51 Impact Factor