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A taxonomic study was carried out on strain L6M1-5T, which was isolated from deep-sea sediment collected from the South Atlantic Ocean. The isolate was Gram-reaction-negative, oxidase-negative and catalase-weakly positive. Growth was observed in the presence of 0.5–15 % (w/v) NaCl (optimum 3–5 %), at 10–41 °C (optimum 28–30 °C), and pH 5.0–10.5 (optimum pH 7.0). The principal fatty acids were summed feature8 (C18 : 1ω7c/ω6c) (84.2 %), C18 : 0 (6.3 %), C12 : 1 3-OH (3.2 %) and C16 : 0 (2.7 %). The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unknown phospholipids and one unknown lipid. Ubiquinone-10 was the major quinone. The G+C content of the genomic DNA was 66.0 mol %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain L6M1-5T belonged to the genus Mameliella and shared 95.8 % sequence similarity with Mameliella alba JLT354-WT. The combined genotypic and phenotypic data show that strain L6M1-5T represents a novel species of the genus Mameliella, for which the name Mameliella. atlantica sp. nov. is proposed. The type strain is L6M1-5T ( = MCCC 1A07531T = JCM 30230T).

A short-rod shaped, non-motile and Gram-negative strain, designated as DT23-4(T), was isolated from a dotriacontane-degrading bacterial consortium, enriched in the surface seawater of the Indian Ocean. To delineate its taxonomic position, strain DT23-4(T) was subjected to polyphasic characterization. Strain DT23-4(T) can grow at temperatures from 10 to 41 °C, in the range of pH 6-10 and at salinities from 0 to 18 % (w/v). It is positive for denitrification, oxidase and catalase, but negative for gelatin hydrolysis and indole production. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DT23-4(T) affiliates to the genus Thioclava, sharing high sequence similarity to Thioclava dalianensis DLFJ1-1(T) (98.2 %), Thioclava atlantica 13D2W-2(T) (96.8 %), Thioclava pacifica TL 2(T) (95.9 %) and less than 95.7 % with other species of the family Rhodobacteraceae. The digital DNA:DNA hybridization (dDDH) pairwise values between strain DT23-4(T) and T. dalianensis DLFJ1-1(T), T. atlantica 13D2W-2(T) and T. pacifica TL 2(T) were 21.5 ± 2.3, 20.6 ± 2.3 and 20.9 ± 2.3 %, respectively. Similarly, the average nucleotide identity values between strain DT23-4(T) and these three type strains were 78.0, 77.1 and 77.3 %, respectively. The principal fatty acid was identified as Summed Feature 8 (C18:1 ω7c/ω6c) (81.9 %). The quinone of strain DT23-4(T) was identified as Q10 (100 %). The polar lipids of strain DT23-4(T) were found to contain phosphatidylethanolamine, phosphatidylglycerol, two glycolipids and four phospholipids. The genomic DNA G+C content was determined to be 60.3 mol%. On the basis of genotypic, phenotypic and chemotaxonomic analyses, strain DT23-4(T) can be concluded to represent a novel species of the genus Thioclava, for which the name Thioclava indica sp. nov. is proposed, with the type strain DT23-4(T) (= MCCC 1A00513(T) = LMG 27698(T) = KCTC 33533(T)).

A unique thermophilic fermentative hydrogen-producing strain H53214 was isolated from a deep-sea hydrothermal vent environment, and identified as Caloranaerobacter azorensis based on bacterial 16S rRNA gene analysis. The optimum culture condition for hydrogen production by the bacterium, designated C. azorensis H53214, was investigated by the response surface methodology (RSM). Eight variables including the concentration of NaCl, glucose, yeast, tryptone, FeSO 4 and MgSO 4 , initial pH and incubation temperature were screened based on the Plackett–Burman design. The results showed that initial pH, tryptone and yeast were significant variables, which were further optimized using the steepest ascent method and Box–Behnken design. The optimal culture conditions for hydrogen production were an initial pH of 7.7, 8.3 g L −1 tryptone and 7.9 g L −1 yeast. Under these conditions, the maximum cumulative hydrogen volume, hydrogen yield and maximum H 2 production rate were 1.58 L H 2 L −1 medium, 1.46 mol H 2 mol −1 glucose and 25.7 mmol H 2 g −1 cell dry weight (CDW) h −1 , respectively. By comparison analysis, strain H53214 was superior to the most thermophilic hydrogen producers because of the high hydrogen production rate. In addition, the isolation of C. azorensis H53214 indicated the deep-sea hydrothermal environment might be a potential source for fermentative hydrogen-producing thermophiles.

A Gram-stain-negative, strictly aerobic, chemoheterotrophic marine bacterium, designated 20V17T, was isolated from a deep-sea hydrothermal vent chimney collected from the South-west Indian Ridge. Cells of strain 20V17T were motile, short rods, 1.2–1.8 µm in length and 0.5–0.7 µm in width. Growth was observed at between 20 and 37 °C (optimum 25 °C–28 °C), pH 5.0 and 8.0 (optimum pH 7.0) and 0.5 and 8 % (w/v) NaCl (optimum 1.5–2.0 % NaCl). The major fatty acids were C18 : 1ω7c (74.4 %), C19 : 0 cyclo ω8c (11 %), C18 : 0 (5.1 %) and C18 : 0 3-OH (2.8 %), and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and four unidentified phospholipids. Ubiquinone 10 was the major quinone. The G+C content of genomic DNA was 66.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 20V17T belonged to the genus Defluviimonas and shared 96.5 and 96.1 % sequence similarity with Defluviimonas denitrificans D9-3T and Defluviimonas aestuarii BS14T, respectively. On the basis of the taxonomic data obtained in this study, strain 20V17T represents a novel species of the genus Defluviimonas , for which the name Defluviimonas indica sp. nov. is proposed. The type strain is 20V17T (CGMCC 1.10859T = JCM 17871T = MCCC 1A01802T).

Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K. olearia 7.02% and K. shengliensis 7.83%), with dissimilarity percentages close to the threshold generally described for genus delineation. Nevertheless, the percentage of conserved proteins (POCP), which is much higher than 50% (around 70%), together with phenotypic features of the isolates, confirm the affiliation all Kosmotoga species described so far to the same genus. Electronic supplementary material The online version of this article (doi:10.1186/s40793-016-0214-2) contains supplementary material, which is available to authorized users.

Differential characteristics of eight genera of Thermotogae, with genome sequences. Data were taken from Defluviitoga [2], Fervidobacterium [3, 39], Kosmotoga [5, 15, 16], Marinitoga [6, 40], Mesotoga [8], Petrotoga [4, 41], Thermosipho [10, 42], and Thermotoga [12, 43]. ND, No data available; +, positive; -, negative; ±, positive for some species, but not all. (DOCX 18 kb)

Comparison of POCP value and 16S rRNA gene identity for pairs of genomes from different genera of Thermotogae. (DOCX 21Â kb)

Phylogenetic tree based on 16S rRNA gene sequences showing the position of K. pacifica strain SLHLJ1T within the phylum Thermotogae. The alignment was performed with 16S rDNA sequences of related species and environmental sequences. The topology shown was obtained with the neighbor-joining algorithm. Bootstrap values (from 1000 replicates) are indicated at the branch nodes. The scale bar represents 2% sequence divergence. (PDF 462Â kb)

To investigate the diversity of culturable sulfur-oxidizing bacteria in hydrothermal vent environments of the South Atlantic, and analyze their characteristics of sulfur oxidation.We enriched and isolated sulfur-oxidizing bacteria from hydrothermal vent samples collected from the South Atlantic. The microbial diversity in enrichment cultures was analyzed using the Denatural Gradient Gel Electrophoresis method. Sulfur-oxidizing characteristics of the isolates was further studied by using ion chromatography.A total of 48 isolates were obtained from the deep-sea hydrothermal vent samples, which belonged to 23 genera and mainly grouped into alpha-Proteobacteria (58.3%), Actinobacteria (22.9%) and gama-Proteobacteria (18.8%). Among them, the genus Thalassospira, Martelella and Microbacterium were dominant. About 60% of the isolates exibited sulfur-oxidizing ability and strain L6M1-5 had a higher sulfur oxidation rate by comparison analysis.The diversity of sulfur-oxidizing bacteria in hydrothermal environments of the South Atlantic was reported for the first time based on culture-dependent methods. The result will help understand the biogechemical process of sulfur compounds in the deep-sea hydrothermal environments.

Clara cell secretory protein (CC10) is an important anti-inflammatory mediator in the adult lung, but its role in newborn pulmonary protection is uncertain. We examined the early postnatal behavior of CC10 in newborn serum and tracheal fluid and hypothesized that CC10 production is positively influenced by gestation. Blood from 165 infants from the first, third/fourth, and seventh days of life (gestational ages: 23-29 wk, 30-36 wk, >36 wk) and tracheal fluid (TF) from the first day of life from 32 ventilated infants were analyzed for CC10. Surfactant proteins A (SPA) and B (SPB) were also analyzed from the blood of a subgroup of infants. Serum CC10 on day 1 was highest in term infants (69.4 ng/mL), followed by moderately preterm (55.8 ng/mL), and then extremely preterm infants (median 42.1 ng/mL). Term infants also had higher tracheal fluid CC10 than preterm infants. (20.152 ng/mL versus 882 ng/mL). Mechanical ventilation increased serum CC10 only in moderately preterm infants, and only on d 1 [68.4 ng/mL versus 42.1 ng/mL (nonventilated moderately preterm infants)]. Serum CC10 decreased progressively by the end of the first week in all infants, in contrast to SPA and SPB, which increased. Our results show that CC10 is detectable in the blood of newborn infants and that a production surge occurs at birth. This surge is more pronounced in term infants and may confer them with superior extrauterine pulmonary protection compared with preterm infants.

Hydrogen is an important energy source for deep-sea hydrothermal vent ecosystems. However, little is known about microbes and their role in hydrogen turnover in the environment. In this study, the diversity and physiological characteristics of fermentative hydrogen-producing microbes from deep-sea hydrothermal vent fields were described for the first time. Seven enrichments were obtained from hydrothermal vent sulfides collected from the Southwest Indian Ocean, East Pacific and South Atlantic. 16S rRNA gene analysis revealed that members of the Caloranaerobacter genus were the dominant component in these enrichments. Subsequently, three thermophilic hydrogen producers, strains H363, H53214 and DY22619, were isolated. They were phylogenetically related to species of the genus Caloranaerobacter. The H2 yields of strains H363, H53214, DY22619 and MV107, which was the type species of genus Caloranaerobacter, were 0.11, 1.21, 3.13 and 2.85 mol H2/mol glucose, respectively. Determination of the main soluble metabolites revealed that strains H363, H53214 and MV107 performed heterolactic fermentations, while strain DY22619 performed butyric acid fermentation, indicating distinct fermentation patterns among members of the genus. Finally, a diversity of forms of [FeFe]-hydrogenase with different modular structures was revealed based on draft genomic data of Caloranaerobacter strains. This highlights the complexity of hydrogen metabolism in Caloranaerobacter, reflecting adaptations to environmental conditions in hydrothermal vent systems. Collectively, results suggested that Caloranaerobacter species might be ubiquitous and play a role in biological hydrogen generation in deep-sea hydrothermal vent fields.

A taxonomic study was carried out on strain 13D2W-2(T), which was isolated from a sulphur-oxidizing bacterial consortium, enriched by the deep-sea sediment of the Atlantic Ocean. The isolate was observed to be Gram-negative, oxidase- and catalase-positive, short rod-shaped and motile by means of a flagellum. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 4 to 41 °C, and the strain found to be able to reduce nitrate but not degrade gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 13D2W-2(T) belongs to the genus Thioclava, with highest sequence similarity of 97.8 % to Thioclava dalianensis DLFJ1-1(T), followed by Thioclava pacifica TL 2(T) (97.7 %), while the sequence similarities to other members of the genus were all below 97.0 %. The digital DNA:DNA hybridization estimated values between strain 13D2W-2(T) and, respectively, T. dalianensis DLFJ1-1(T) and T. pacifica TL 2(T) were 22.6 ± 2.4 and 25.6 ± 2.4 %. The ANI values between strain 13D2W-2(T) and T. dalianensis DLFJ1-1(T) and T. pacifica TL 2(T) were 78.49 and 81.91 % respectively. The principal fatty acid identified was Summed Feature 8 (C18:1 ω7c/ω6c) (74.38 %). The isoprenoid quinone of strain 13D2W-2(T) was identified as Q10 (100 %). The major polar lipids of strain 13D2W-2(T) were found to be comprised of phosphatidylethanolamine, phosphatidylglycerol, an aminophospholipid, a glycolipid and three unknown phospholipids. The G+C content of the chromosomal DNA was determined to be 65.3 mol%. The combined genotypic and phenotypic data show that strain 13D2W-2(T) represents a novel species of the genus Thioclava, for which the name Thioclava atlantica sp. nov. is proposed, with the type strain 13D2W-2(T) ( = MCCC 1A02612(T) = LMG 27145(T)).

International audience; A novel strictly anaerobic thermophilic heterotrophic bacterium, strain SLHLJ1(T), was isolated from a Pacific hydrothermal sediment. Cells were Gram-negative coccobacilli (approximately 1.0 × 0.6 μm) with a toga. It grew at temperatures between 33 and 78 °C (optimum 70 °C). Elemental sulphur and L-cystine stimulated its growth. It contained C16:0, C16:1 ω11c, C18:0 and C18:1 ω9c as major fatty acids (>5%), 3 phospholipids and 2 glycolipids as polar lipids. Its DNA G+C content was 43.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLHLJ1(T) within the family Thermotogaceae. The novel isolate was most closely related to Kosmotoga arenicorallina (97.93 % 16S rRNA gene sequence similarity), K. olearia (92.43%) and K. shengliensis (92.17 %). On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with its closest relatives, we propose its assignment to a novel species of the genus Kosmotoga. The name Kosmotoga pacifica sp. nov. is proposed with strain SLHLJ1(T) (=DSM 26965(T) = JCM 19180(T) = UBOCC 3254(T)) as the type species.