Continuous enrichment cultures : insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys

The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulftitator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO2 and H-2 produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments

Halanaerobacter jeridensis sp. nov., isolated from a hypersaline lake

An obligatory anaerobic, moderately halophilic bacterium, designated strain CEJFG43(T), was isolated from a sample of sediment collected below the salt crust on the hypersaline El Jerid lake, in southern Tunisia. The cells of this novel strain were Gram-staining-negative, non-sporulating, motile, short rods. They grew in media with 6-30% (w/v) NaCl (optimum 15%), at 20-60 °C (optimum 45 °C) and at pH 5.5-9.5 (optimum pH 8.3). The micro-organism fermented glucose, fructose, ribose, raffinose, galactose, mannose, sucrose, maltose, xylose, mannitol, pyruvate and glycerol. The products of glucose fermentation were lactate, ethanol, acetate, H(2) and CO(2). The genomic G+C DNA content of strain CEJFG43(T) was 33.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFG43(T) belonged in the genus Halanaerobacter and was most closely related to Halanaerobacter lacunarum DSM 6640(T) (95.3% gene sequence similarity) and Halanaerobacter chitinivorans DSM 9569(T) (95.3%). The predominant cellular fatty acids were non-branched (C(16:0) and C(16:1)). Based on the phylogenetic and phenotypic evidence, strain CEJFG43(T) represents a novel species in the genus Halanaerobacter for which the name Halanaerobacter jeridensis sp. nov. is proposed. The type strain is CEJFG43(T) ( = DSM 23230(T) = JCM 16696(T))

Vallitalea pronyensis sp nova, isolated from a marine alkaline hydrothermal chimney

A novel thermotolerant, anaerobic, Gram-stain-positive, spore-forming bacterium was isolated from a hydrothermal chimney in Prony Bay, New Caledonia. This strain, designated FatNl3(T), grew at 15-55 degrees C (optimum 30 degrees C) and at pH 5.8-8.9 (optimum 7.7). It was slightly halophilic, requiring at least 0.5% NaCl for growth (optimum 2.5-3.0 %), and was able to grow at up to 6% NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Growth of strain FatNl3(T) was inhibited in the presence of sulfite (2 mM) or nitrite (2 mM). Strain FatNl3(T) fermented cellobiose, glucose, mannose, maltose, sucrose, galactose, lactose, ribose, fructose, rhannnose, raffinose, xylose, yeast extract, peptone and biotrypticase. The main fermentation products from glucose metabolism were acetate, ethanol, H-2 and CO2. The predominant cellular fatty acids were iso-C-15:0 and anteiso-C-15:0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, and unknown glycolipids and phospholipids. The G+C content of the genomic DNA was 36.6 mol%. On the basis of phylogenetic and physiological properties, strain FatNl3(T) (=DSM 25904=JCM 18391) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as the type strain of a novel species of the genus Vallitalea, for which the name Vallitalea pronyensis sp. nov. is proposed

Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia,

International audienceA novel anaerobic, alkaliphilic, Gram-positive staining bacterium was isolated from a hydrothermal chimney in the Prony Bay, New Caledonia. This strain designated FatMR1T 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 FatMR1T 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 FatMR1T (=DSM 25890T, =JCM 18390T) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as a novel species of the genus Alkaliphilus, A. hydrothermalis sp. nov

Characterization of Halanaerocella petrolearia gen. nov., sp nov., a new anaerobic moderately halophilic fermentative bacterium isolated from a deep subsurface hypersaline oil reservoir New taxa : Firmicutes (Class Clostridia, Order Halanaerobiales, Halobacteroidaceae, Halobacteroides)

An anaerobic, halophilic, and fermentative bacterium, strain S200(T), was isolated from a core sample of a deep hypersaline oil reservoir. Cells were rod-shaped, non-motile, and stained Gram-positive. It grew at NaCl concentrations ranging from 6 to 26% (w/v), with optimal growth at 15% (w/v) NaCl, and at temperatures between 25 and 47A degrees C with an optimum at 40-45A degrees C. The optimum pH was 7.3 (range 6.2-8.8; no growth at pH 5.8 and pH 9). The doubling time in optimized growth conditions was 3.5 h. Strain S200(T) used exclusively carbohydrates as carbon and energy sources. The end products of glucose degradation were lactate, formate, ethanol, acetate, H-2, and CO2. The predominant cellular fatty acids were non-branched fatty acids C-16:1, C-16:0, and C-14:0. The G + C mole% of the DNA was 32.7%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain S200(T) formed a distinct lineage within the family Halobacteroidaceae, order Halanaerobiales, and was most closely related to Halanaerobaculum tunisiense DSM 19997(T) and Halobacteroides halobius DSM 5150(T), with sequence similarity of 92.3 and 91.9%, respectively. On the basis of its physiological and genotypic properties, strain S200(T) is proposed to be assigned to a novel species of a novel genus, for which the name Halanaerocella petrolearia is proposed. The type strain of Halanaerocella petrolearia is strain S200(T) (=DSM 22693(T) = JCM 16358(T))

Interest of Human Papillomavirus DNA quantification and genotyping in paired cervical and urine samples to detect cervical lesions

International audienceBackgroundCervical cancer is caused by persistent infection with high-risk human papillomavirus (HR-HPV). Conventional human papillomavirus (HPV) testing requires cervical sampling. However, vaginal and urine self-sampling methods are more acceptable for patients and result in increased participation when they are available in screening programs. In this context, we have developed a non-invasive screening method via the detection of HPV DNA in urine samples.PurposeTo compare HPV viral loads and genotypes in paired cervical and urine samples, and to assess correlation between virological and cytological results in women seeking gynecological consultation.MethodsPaired urine and cervical specimens were collected and analyzed from 230 of 245 women participating in the previously described prospective PapU study. HPV DNA detection and quantification were performed using a real-time PCR method with short fragment PCR primers. Genotyping was carried out using the INNO-LiPA HPV genotyping assay.ResultsThe prevalence of HPV in the 230 paired urine and cervical smear samples was 42 and 49&nbsp;%, respectively. Overall agreement for HPV positivity and negativity between the paired samples was 90&nbsp;% (κ&nbsp;=&nbsp;0.80). High HPV viral load in both cervical and urine samples was associated with cytological abnormalities. HPV-positive women were mostly infected with HR-HPV types. The agreement between high- and low-risk HPV (LR-HPV) detection in both samples was 97&nbsp;% (κ&nbsp;=&nbsp;0.95 for HR-HPV and κ&nbsp;=&nbsp;0.97 for LR-HPV).ConclusionsHigh concordance rates for HPV-DNA quantification and high/low-risk HPV genotyping in paired urine/cervical samples suggest that urinary HPV DNA testing could be useful for cervical lesion screening.</p