Lipid composition of the liver oil of deep-sea sharks from the Chatham Rise, New Zealand

Deep-sea sharks approach neutral buoyancy by means of a large liver that contains large amounts of low-density lipids, primarily squalene and diacyl glyceryl ether (DAGE). As an animal increases in size and matures sexually, many biochemical changes take place within the animal. It was hypothesized that maintenance of neutral buoyancy in deep-sea sharks involves fine-scale changes in the chemical composition of the liver oil as individual sharks grow and develop. To test this hypothesis, the lipid composition of liver oil for individuals of different size and sex of deep-sea sharks from the Chatham Rise, New Zealand was compared. The composition of liver oil varied within and among species. Several species contained large amounts of squalene and DAGE, whereas only traces of these lipids were present in other species. The amounts of squalene and DAGE in liver oil were inversely related, and squalene content tended to decrease as sharks increased in size. Species with high squalene levels (>80%) in liver oil were not abundant on the Chatham Rise, although levels of DAGE (a lipid of increasing commercial interest) were elevated in many species. Maintenance of neutral buoyancy in deep-sea sharks appears to involve changes in the composition of low-density liver lipids as the sharks increase in size and mature.     

Marinitoga lauensis sp. nov., a novel deep-sea hydrothermal vent thermophilic anaerobic heterotroph with a prophage

A novel moderately thermophilic, heterotrophic anaerobe, designated strain LG1^T, was isolated from the Mariner deep-sea hydrothermal vent field along the Eastern Lau Spreading Center and Valu Fa Ridge. Cells of strain LG1^T were motile rods, occurring singly or in pairs, 0.6 μm in width and 1.2 μm in length. The strain LG1^T grew between 40 and 70 °C (optimum 50–55 °C), at a pH between 5 and 8 (optimum pH 6.5) and with 7.5–50 g L⁻¹ NaCl (optimum 30 g L⁻¹). Sulfur, cystine and thiosulfate were reduced to sulfide, and cell yield was improved in the presence of cystine. Strain LG1^T was an organotroph able to use a variety of organic compounds. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain LG1^T was affiliated to the genus Marinitoga within the order Petrotogales. It shared 95.34–96.31% 16S rRNA gene sequence similarity with strains of other Marinitoga species, and is most closely related to Marinitoga okinawensis. Genome analysis revealed the presence of a prophage sharing high sequence homology with the viruses MPV1, MCV1 and MCV2 hosted by Marinitoga strains. Based on the data from the phylogenetic analyses and the physiological properties of the novel isolate, we propose that strain LG1^T is a representative of a novel species, for which the name Marinitoga lauensis sp. nov. is proposed; the type strain is LG1^T (=DSM 106824 = JCM 32613).     

Culture dependent and independent analyses of 16S rRNA and ATP citrate lyase genes: a comparison of microbial communities from different black smoker chimneys on the Mid-Atlantic Ridge

The bacterial and archaeal communities of three deep-sea hydrothermal vent systems located on the Mid-Atlantic Ridge (MAR; Rainbow, Logatchev and Broken Spur) were investigated using an integrated culture-dependent and independent approach. Comparative molecular phylogenetic analyses, using the 16S rRNA gene and the deduced amino acid sequences of the alpha and beta subunits of the ATP citrate lyase encoding genes were carried out on natural microbial communities, on an enrichment culture obtained from the Broken Spur chimney, and on novel chemolithoautotrophic bacteria and reference strains originally isolated from several different deep-sea vents. Our data showed that the three MAR hydrothermal vent chimneys investigated in this study host very different microbial assemblages. The microbial community of the Rainbow chimney was dominated by thermophilic, autotrophic, hydrogen-oxidizing, sulfur- and nitrate-reducing Epsilonproteobacteria related to the genus Caminibacter. The detection of sequences related to sulfur-reducing bacteria and archaea (Archaeoglobus) indicated that thermophilic sulfate reduction might also be occurring at this site. The Logatchev bacterial community included several sequences related to mesophilic sulfur-oxidizing bacteria, while the archaeal component of this chimney was dominated by sequences related to the ANME-2 lineage, suggesting that anaerobic oxidation of methane may be occurring at this site. Comparative analyses of the ATP citrate lyase encoding genes from natural microbial communities suggested that Epsilonproteobacteria were the dominant primary producers using the reverse TCA cycle (rTCA) at Rainbow, while Aquificales of the genera Desulfurobacterium and Persephonella were prevalent in the Broken Spur chimney.     

南海深海新颖低温脂肪酶的克隆、表达及酶学性质鉴定

从南海深海放线菌Pseudonocardia antitumoralis SCSIO 01299中克隆一个脂肪酶基因 lipaseB5。lipaseB5 基因片段大小为972bp,编码的蛋白质具有323个氨基酸残基并与Pseudonocardia sp. HH130629-09中假定脂肪酶有98%的同源性。以pET28a(+)为载体,将重组质粒转化到E. coli BL21(DE3)中,实现lipaseB5高效表达,并利用Ni-NTA 亲和层析纯化lipaseB5。LipaseB5最适反应底物为对硝基苯酚癸酸酯(p-NPD),最适温度为30℃,最适反应pH为7.5。LipaseB5催化p-NPD水解反应的活性达到140.14U/mg,V_max和K_m分别为109.8μmol/min、0.976mmol/L,催化橄榄油的活力为32.019 7U/mg。LipaseB5在pH7.5~8.5保持良好的pH稳定性;在10~20℃低温下保持较高的酶活力,在10~40℃内具有温度稳定性。LipaseB5对大部分金属离子有很好的耐受性,低浓度的Li⁺、Mg²⁺对该酶活性有促进作用。LipaseB5对高浓度的NaCl有很好的耐受性,在100mmol/L的NaCl存在下,酶活性大约保持在103%。LipaseB5对多种短链醇类有机溶剂和表面活性剂有很好的耐受性,TritonX-100、Tween-80和Tween-20对lipaseB5酶有激活作用。     

Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial community composition in deep-sea sediments of the South China Sea

The South China Sea, which is one of the largest marginal seas in the world, is predicted to have suitable accumulation conditions and exporting prospects for natural gas hydrate. The aim of this study was to explore the bacterial community composition of deep-sea sediments from such an ecosystem. DNA was extracted by five different methods and used as templates for PCR amplification of the V3 regions of the 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) was used to separate the amplified products and analyse the 16S rRNA gene diversity of sediment samples. The results of DGGE indicated that the bacterial community composition is influenced by DNA extraction methods. Sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belong to Proteobacteria, Bacteroidetes, gram-positive bacteria and Archaea. Integrating different DNA extraction procedures are needed to analyse the actual bacterial diversity from environment when the amplification of 16S rRNA gene and construction of representative clone library were adopted.     

Geochemical and microbiological evidence for a hydrogen-based,hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field

Subsurface microbial communities supported by geologically and abiologically derived hydrogen and carbon dioxide from the Earths interior are of great interest, not only with regard to the nature of primitive life on Earth, but as potential analogs for extraterrestrial life. Here, for the first time, we present geochemical and microbiological evidence pointing to the existence of hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) dominated by hyperthermophilic methanogens beneath an active deep-sea hydrothermal field in the Central Indian Ridge. Geochemical and isotopic analyses of gaseous components in the hydrothermal fluids revealed heterogeneity of both concentration and carbon isotopic compositions of methane between the main hydrothermal vent (0.08 mM and –13.8 PDB, respectively) and the adjacent divergent vent site (0.2 mM and –18.5 PDB, respectively), representing potential subsurface microbial methanogenesis, at least in the divergent vent emitting more ¹³C-depleted methane. Extremely high abundance of magmatic energy sources such as hydrogen (2.5 mM) in the fluids also encourages a hydrogen-based, lithoautotrophic microbial activity. Both cultivation and cultivation-independent molecular analyses suggested the predominance of Methanococcales members in the superheated hydrothermal emissions and chimney interiors along with the other major microbial components of Thermococcales members. These results imply that a HyperSLiME, consisting of methanogens and fermenters, occurs in this tectonically active subsurface zone, strongly supporting the existence of hydrogen-driven subsurface microbial communities.     

Characterization of a Deep-Sea Sediment Metagenomic Clone that Produces Water-Soluble Melanin in Escherichia coli

To access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment DNA was extracted and cloned into fosmid vector (pCC1FOS) generating a library of 39,600 clones with inserts of 24–45 kb. The clone fss6 producing red-brown pigment was isolated and characterized. The pigment was identified as melanin according to its physico-chemical characteristics. Subcloning and sequences analyses of fss6 demonstrated that one open reading frame (ORF2) was responsible for the pigment production. The deduced protein from ORF2 revealed significant amino acid similarity to the 4-hydroxyphenylpyruvate dioxygenase (HPPD) from deep-sea bacteria Idiomarina loihiensis. Further study demonstrated that the production of melanin was correlated with homogentistic acid (HGA). The p-hydroxyphenylpyruvate produced by the Escherichia coli host was converted to HGA through the oxidation reaction of introduced HPPD. The results demonstrate that expression of DNA extracted directly from the environment might generate applicable microbial gene products. The construction and analysis of the metagenomic library from deep-sea sediment contributed to our understanding for the reservoir of unexploited deep-sea microorganisms.     

A new species of Liropus (Crustacea, Amphipoda, Caprellidae) from Le Danois bank (southern Bay of Biscay)

A new species of the genus Liropus (Crustacea, Amphipoda, Caprellidae) is described based on specimens collected from Le Danois bank (‘El Cachucho’ fishing grounds), Bay of Biscay. Liropus cachuchoensis n. sp. can be distinguished from all its congeners mainly by the absence of eyes and by the presence of a dorsal projection proximally on pereonites 3, 4 and 5 in males, on 3 and 5 in females. The new species has been found living on muddy bottoms on the southern flank of the bank and adjacent continental slope, between 619 and 1062 m depth, with a maximum abundance (56.1 ind./100 m²) recorded at 1044–1062 m. Morphological comparisons among the world's members of Liropus, a key to species, and data on their distribution are presented.     

Isolation of extremophiles with the detection and retrieval of<Emphasis Type="Italic"> Shewanella</Emphasis> strains in deep-sea sediments from the west Pacific

Tests to detect the presence of piezophilic Shewanella strains in the deep-sea sediments of the west, mid- and east Pacific at different depths were done by amplification of previously identified pressure-regulated operons (ORF1,2 and ORF3). The operon fragments were detected in all the deep-sea sediment samples, indicating the broad presence of piezophilic deep-sea Shewanella species or related species in the deep-sea sediments across the Pacific. Extremophiles were isolated from the deep-sea sediment of the west Pacific under atmospheric pressure. Two psychrophilic/psychrotrophic strains, WP2 and WP3, were assigned to the Shewanella genus as determined by their 16S rDNA sequences. WP2 and WP3 were both capable of amplifying pressure-regulated operons; the sequences of the pressure-regulated operons of WP2 and WP3 share high identity between each other, but have more differences from those of S. benthica and S. violacea. The major fatty acids of WP2 and WP3 are 3OH-i-13:0, 14:0, i-15:0, 16:0, 16:1, 18:1, and 20:5. Combined phenotypic analysis, 16S rDNA sequences, and DNA–DNA hybridization results suggest that WP2 and WP3 are two new deep-sea Shewanella species.Communicated by K. Horikoshi