A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

BACKGROUND: In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential. RESULTS: We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this. CONCLUSION: Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.

Persephonella atlantica sp. nov.: How to adapt to physico-chemical gradients in high temperature hydrothermal habitats.

A novel thermophilic, microaerophilic and anaerobic, hydrogen- sulphur- and thiosulphate-oxidising bacterium, designated MO1340T, was isolated from a deep-sea hydrothermal chimney collected from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge. Cells were short, motile rods of 1.4-2.2µm length and 0.5-0.8µm width. Optimal growth was observed for a NaCl concentration of 2.5 % (w/v) at pH 6.5. As for other members of the genus Persephonella, strain MO1340T was strictly chemolithoautotrophic and could oxidise hydrogen, elemental sulphur or thiosulphate using oxygen as electron acceptor. Anaerobic nitrate reduction using hydrogen could also be performed. Each catabolic reaction had a different optimal growth temperature (65 to 75°C) and an optimal dissolved oxygen concentration (11.4 to 119.7 µM at 70°C for aerobic reactions) that varied according to the electron donors utilised. These experimental results are consistent with the distribution of these catabolic substrates along the temperature gradient observed in active hydrothermal systems. They strongly suggest that this adaptive strategy could confer a selective advantage for strain MO1340T in the dynamic part of the ecosystem where hot, reduced hydrothermal fluid mixes with cold, oxygenated seawater. Phylogenetic analysis indicated that strain MO1340T was a member of the genus Persephonella within the order Hydrogenothermales as it shared a 16S rRNA gene sequence similarity <95.5 % and ANI respectively 75.66 % with closest described Persephonella (P. hydrogeniphila 29WT). On the basis of the physiological and genomic properties of the new isolate, the name Persephonella atlantica sp. nov. is proposed. The type strain is MO1340T (=UBOCC-M-3359T =JCM 34026T).

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan.

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

Pyrococcus kukulkanii sp. nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent.

A novel hyperthermophilic, piezophilic, anaerobic archaeon, designated NCB100T, was isolated from a hydrothermal vent flange fragment collected in the Guaymas basin at the hydrothermal vent site named 'Rebecca's Roost' at a depth of 1997 m. Enrichment and isolation were performed at 100 °C under atmospheric pressure. Cells of strain NCB100T were highly motile, irregular cocci with a diameter of ~1 µm. Growth was recorded at temperatures between 70 and 112 °C (optimum 105 °C) and hydrostatic pressures of 0.1-80 MPa (optimum 40-50 MPa). Growth was observed at pH 3.5-8.5 (optimum pH 7) and with 1.5-7 % NaCl (optimum at 2.5-3 %). Strain NCB100T was a strictly anaerobic chemo-organoheterotroph and grew on complex proteinaceous substrates such as yeast extract, peptone and tryptone, as well as on glycogen and starch. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The fermentation products from complex proteinaceous substrates were CO2 and H2. The G+C content of the genomic DNA was 41.3 %. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NCB100T belongs to the genus Pyrococcus, showing 99 % similarity with the other described species of the genus Pyrococcus. On the basis of physiological characteristics, DNA G+C content, similarity level between ribosomal proteins and an average nucleotide identity value of 79 %, strain NCB100T represents a novel species for which the name Pyrococcus kukulkanii sp. nov. is proposed. The type strain is NCB100T (=DSM 101590T=Souchothèque de Bretagne BG1337T).

Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture.

Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge.

To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 µm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.

Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin.

Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS ("Autonomous in situ Instrumented Colonization System") were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions.

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field.

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge) were investigated using molecular approaches. DNA and RNA were extracted from mat samples overlaying hydrothermal deposits and Bathymodiolus azoricus mussel assemblages. We constructed and analyzed libraries of 16S rRNA gene sequences and sequences of functional genes involved in autotrophic carbon fixation [forms I and II RuBisCO (cbbL/M), ATP-citrate lyase B (aclB)]; methane oxidation [particulate methane monooxygenase (pmoA)] and sulfur oxidation [adenosine-5'-phosphosulfate reductase (aprA) and soxB]. To gain new insights into the relationships between mats and mussels, we also used new domain-specific 16S rRNA gene primers targeting Bathymodiolus sp. symbionts. All identified archaeal sequences were affiliated with a single group: the marine group 1 Thaumarchaeota. In contrast, analyses of bacterial sequences revealed much higher diversity, although two phyla Proteobacteria and Bacteroidetes were largely dominant. The 16S rRNA gene sequence library revealed that species affiliated to Beggiatoa Gammaproteobacteria were the dominant active population. Analyses of DNA and RNA functional gene libraries revealed a diverse and active chemolithoautotrophic population. Most of these sequences were affiliated with Gammaproteobacteria, including hydrothermal fauna symbionts, Thiotrichales and Methylococcales. PCR and reverse transcription-PCR using 16S rRNA gene primers targeted to Bathymodiolus sp. symbionts revealed sequences affiliated with both methanotrophic and thiotrophic endosymbionts.

Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

A novel aerobic, gram-negative bacterial strain, designated 17X/A02/237(T), was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237(T) contained ubiquinone Q-8 and its major fatty acids were C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)ω7c, C(16 : 0), C(18 : 0) and C(10 : 0) 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237(T) ( = DSM 19752(T) = CIP 109759(T) = MOLA 288(T)).

Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum.

A novel Gram-negative bacteria, named CZ41_10a(T), was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 mum long and 0.7 mum wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58(T), its closest relative, strain CZ41_10a(T) was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA-DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10a(T) (=DSM 19539(T)=CIP 109604(T)=MOLA [corrected] 84(T)). An emended description of the genus Thalassobaculum is also given.

Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

A novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain AT1325(T), was isolated from a deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge. This strain was subjected to a polyphasic taxonomic analysis. Cells were Gram-negative motile rods (approximately 2.4 x 0.6 microm) with a single polar flagellum. Strain AT1325(T) grew at 55-75 degrees C (optimum, 65-70 degrees C), at pH 5.5-8.0 (optimum, 6.5-7.5) and in the presence of 1.5-4.5 % (w/v) NaCl (optimum, 2.5 %). Cells grew chemolithoautotrophically with H2 as an energy source and SO4(2-) as an electron acceptor. Alternatively, the novel isolate was able to use methylamine, peptone or yeast extract as carbon sources. The dominant fatty acids (>5 % of the total) were C(16 : 0), C(18 : 1)omega7c, C(18 : 0) and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA of strain AT1325(T) was 45.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain AT1325(T) within the family Thermodesulfobacteriaceae, in the bacterial domain. Comparative 16S rRNA gene sequence analysis indicated that strain AT1325(T) belonged to the genus Thermodesulfatator, sharing 97.8 % similarity with the type strain of Thermodesulfatator indicus, the unique representative species of this genus. On the basis of the data presented, it is suggested that strain AT1325(T) represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator atlanticus sp. nov. is proposed. The type strain is AT1325(T) (=DSM 21156(T)=JCM 15391(T)).

Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent.

A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T)).

Haliea rubra sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated strain CM41_15a(T), was isolated from the surface of coastal waters of the north-western Mediterranean Sea. Cells were non-motile straight rods that formed red colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the genus Haliea within the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain CM41_15a(T) represents a novel species, for which the name Haliea rubra sp. nov. is proposed. The type strain is CM41_15a(T) (=DSM 19751(T)=CIP 109758(T)=MOLA 104(T)).

Effect of variation of environmental conditions on the microbial communities of deep-sea vent chimneys, cultured in a bioreactor.

Both cultivation and molecular techniques were used to investigate the microbial diversity and dynamic of a deep-sea vent chimney. The enrichment cultures performed in a gas-lift bioreactor were inoculated with a black smoker chimney sample collected on TAG site on the mid-Atlantic ridge. To mimic as close as possible environmental conditions, the cultures were performed in oligotrophic medium with nitrogen, hydrogen and carbon dioxide (N(2)/H(2)/CO(2)) gas sweeping. Also, the temperature was first settled at a temperature of 85 degrees C and colloidal sulphur was added. Then, the temperature was lowered to 60 degrees C and sulphur was omitted. Archaeal and bacterial diversity was studied in both culture and natural samples. Through 16S rRNA gene sequences analysis of the enrichment cultures microorganisms affiliated to Archeoglobales, Thermococcales were detected in both conditions while, Deferribacterales and Thermales were detected only at 65 degrees C in the absence of sulphur. Single-stranded conformational polymorphism and quantitative PCR permit to study the microbial community dynamic during the two enrichment cultures. The effect of environmental changes (modification of culture conditions), i.e. temperature, medium composition, electron donors and acceptors availability were shown to affect the microbial community in culture, as this would happen in their environment. The effect of environmental changes, i.e. temperature and medium composition was shown to affect the microbial community in culture, as this could happen in their environment. The modification of culture conditions, such as temperature, organic matter concentration, electron donors and acceptors availability allowed to enrich different population of prokaryotes inhabiting hydrothermal chimneys.

Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents.

Recent studies indicate that ammonia is an important electron donor for the oxidation of fixed nitrogen, both in the marine water column and sediments. This process, known as anammox, has so far only been observed in a large range of temperature habitats. The present study investigated the role of anammox in hydrothermal settings. During three oceanographic expeditions to the Mid-Atlantic Ridge, hydrothermal samples were collected from five vent sites, at depths ranging from 750 to 3650 m from cold to hot habitats. Evidence for the occurrence of anammox in these particular habitats was demonstrated by concurrent surveys, including the amplification of 16S rRNA gene sequences related to known anammox bacteria, ladderanes lipids analysis and measurement of a (14)N(15)N dinitrogen production in isotope-pairing experiments at 60 and 85 degrees C. Together these results indicate that new deep-branching anammox bacteria may be active in these hot habitats.

Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131(T), was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/131(T) represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131(T) (=DSM 19753(T) =CIP 109757(T) =MOLA 225(T)).

Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea.

Two novel Gram-negative bacteria, designated strains DR41_21(T) and DR41_18(T), were isolated from coastal, surface waters of the north-western Mediterranean Sea. The cells were motile, pleomorphic rods, 2.9 microm long and 0.9 microm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 60 mol%. Phylogenetic analysis of 16S rRNA gene sequences positioned the isolates in the class Alphaproteobacteria within the family Rhodospirillaceae. The 16S rRNA gene sequence similarity of the two strains was 98.8 % but DNA-DNA hybridization indicated only 55 % relatedness. Strain DR41_21(T) was able to denitrify and possessed nirK and nosZ genes, unlike strain DR41_18(T), which possessed only nirK. These isolates represent two novel species of a new genus, Nisaea gen. nov., for which the names Nisaea denitrificans sp. nov. and Nisaea nitritireducens sp. nov. are proposed. The type strain of Nisaea denitrificans is DR41_21(T) (=DSM 18348(T)=CIP 109265(T)=OOB 129(T)) and the type strain of Nisaea nitritireducens is DR41_18(T) (=DSM 19540(T)=CIP 109601(T)=OOB 128(T)).

Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14b(T) (=DSM 19538(T)=CIP 109603(T)=OOB 103(T)).

Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T).

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 Thermodesulfatator 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, CO(2) 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.