Deep Seawater Samples Research Articles

Draft genome sequence of Pseudomonas sp. GOM6, a lipolytic strain isolated from seawater of the Gulf of Mexico.

We report here the draft genome sequence of a marine Pseudomonas sp. novel species with lipase activity isolated from a deep-sea water sample of the Gulf of Mexico. The genome consists of 4.3 Mbp in 48 contigs.

Direct Production of Bio-Recalcitrant Carboxyl-Rich Alicyclic Molecules Evidenced in a Bacterium-Induced Steroid Degradation Experiment.

Carboxyl-rich alicyclic molecules (CRAM) are highly unsaturated compounds extensively distributed throughout aquatic environments and sediments. This molecular group is widely referred to as a major proxy of recalcitrant organic materials, but its direct biosynthesis remains unclear. Steroids are a typical anthropogenic contaminant and have been previously suggested to be precursors of CRAM; however, experimental evidence to support this hypothesis is lacking. Here, a steroid-degrading bacterium, Comamonas testosteroni ATCC 11996, was incubated in a liquid medium supplemented with testosterone (a typical steroid) as the sole carbon source for 90 days. Testosterone-induced metabolites (TIM) were extracted for molecular characterization and to examine the bioavailability during an additional 90-day incubation after inoculation with a natural coastal microbial assemblage. The results showed that 1,775 molecular formulas (MFs) were assigned to TIM using ultrahigh-resolution mass spectrometry, with 66.99% categorized as CRAM-like constituents. A large fraction of TIM was respired or transformed during the additional 90-day seawater incubation; nevertheless, 638 MFs of the TIM persisted or increased during incubation. Among the 638 MFs, 394 were commonly assigned in natural deep seawater samples (depths of 500 to 2,000 m) from the South China Sea. Compared to the catabolites of the well-established testosterone degradation pathway, we compiled a list of bio-refractory MFs and potential chemical structures, some of which shared structural homology with CRAM. These results demonstrated direct microbial production of bio-refractory CRAM from steroid hormones and indicated that some of the biogenic CRAM resisted microbial decomposition, potentially contributing to the aquatic refractory dissolved organic matter (DOM) pool. IMPORTANCE CRAM are an operationally defined DOM group comprising a complex mixture of carboxylated and fused alicyclic structures. This DOM group is majorly characterized as refractory DOM in the marine environment. However, the origins of the complex CRAM remain unclear. In this study, we demonstrated that testosterone (a typical steroid) could be transformed into bio-refractory CRAM by a single bacterial strain and observed that some of the CRAM highly resisted microbial degradation. Through molecular comparison and screening, potential chemical structures of steroid-induced CRAM were suggested. This study established the biological connection between steroids and bio-refractory CRAM, and it provides a novel perspective explaining the fate of terrestrial contaminants in aquatic environments.

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Deep-sea ecosystems present difficulties in surveying and continuous monitoring of the biodiversity of deep-sea ecosystems because of the logistical constraints, high cost, and limited opportunities for sampling. Environmental DNA (eDNA) metabarcoding analysis provides a useful method for estimating the biodiversity in aquatic ecosystems but has rarely been applied to the study of deep-sea fish communities. In this study, we utilized pumped deep-sea water for the continuous monitoring of deep-sea fish communities by eDNA metabarcoding. In order to develop an optimum method for continuous monitoring of deep-sea fish biodiversity by eDNA metabarcoding, we determined the appropriate amount of pumped deep-sea water to be filtered and the practical number of filtered sample replicates required for biodiversity monitoring of deep-sea fish communities. Pumped deep-sea water samples were filtered in various volumes (5–53 L) at two sites (Akazawa: pumping depth 800 m, and Yaizu: pumping depth 400 m, Shizuoka, Japan) of deep-sea water pumping facilities. Based on the result of evaluations of filtration time, efficiency of PCR amplification, and number of detected fish reads, the filtration of 20 L of pumped deep-sea water from Akazawa and filtration of 10 L from Yaizu were demonstrated to be suitable filtration volumes for the present study. Fish biodiversity obtained by the eDNA metabarcoding analyses showed a clear difference between the Akazawa and Yaizu samples. We also evaluated the effect of the number of filter replicates on the species richness detected by eDNA metabarcoding from the pumped deep-sea water. At both sites, more than 10 sample replicates were required for the detection of commonly occurring fish species. Our optimized method using pumped deep-sea water and eDNA metabarcoding can be applied to eDNA-based continuous biodiversity monitoring of deep-sea fish to better understand the effects of climate change on deep-sea ecosystems.

Experimental Insight into the Enigmatic Persistence of Marine Refractory Dissolved Organic Matter.

More than 90% of marine dissolved organic matter (DOM) is biologically recalcitrant. This recalcitrance has been attributed to intrinsically refractory molecules or to low concentrations of molecules, but their relative contributions are a long-standing debate. Characterizing the molecular composition of marine DOM and its bioavailability is critical for understanding this uncertainty. Here, using different sorbents, DOM was solid-phase extracted from coastal, epipelagic, and deep-sea water samples for molecular characterization and was subjected to a 180-day incubation. 1H nuclear magnetic resonance spectroscopy and ultra-high-resolution mass spectrometry (UHRMS) analyses revealed that all of the DOM extracts contained refractory carboxyl-rich alicyclic molecules, accompanied with minor bio-labile components, for example, carbohydrates. Furthermore, dissolved organic carbon concentration analysis showed that a considerable fraction of the extracted DOM (86-95%) amended in the three seawater samples resisted microbial decomposition throughout the 180-day heterotrophic incubation, even when concentrated threefold. UHRMS analysis revealed that DOM composition remained mostly invariant in the 180-day deep-sea incubations. These results underlined that the dilution and intrinsic recalcitrance hypotheses are not mutually exclusive in explaining the recalcitrance of oceanic DOM, and that the intrinsically refractory DOM likely has a relatively high contribution to the solid-phase extractable DOM in the ocean.

Effect of Mineral-Balanced Deep-Sea Water on Kidney Function and Renal Oxidative Stress Markers in Rats Fed a High-Salt Diet.

This study investigated the effect of mineral-balanced deep-sea water (DSW) on kidney health using an animal model of kidney injury due to a high-sodium diet. High magnesium/low sodium (HMLS) and high magnesium/high calcium (HMHC) DSW samples with different mineral contents were prepared. Sprague–Dawley rats were fed an 8% sodium chloride (NaCl) diet for four weeks to induce kidney injury, and each group was supplied with purified water or mineral water. Kidney injury was observed in the NaCl group according to increased kidney injury markers and malondialdehydes, providing evidence of oxidative stress. However, the kidney injury was repaired by the intake of mineral-balanced DSW. It was confirmed that the HMLS and HMHC groups showed improved Na+ excretion through the urine. Kidney injury markers in urine decreased and upregulation of low-density lipoprotein receptor-related protein2 mRNA expression was observed in the HMLS and HMHC groups. In addition, superoxide dismutase activity was increased in the HMHC groups. The gene expression patterns of the RNA sequencing were similar between the CON and HMLS groups. These results suggest that DSW has beneficial effects on kidney health due to the balanced magnesium and calcium levels in models of kidney injury caused by excessive sodium intake.

Aliidiomarina indica sp. nov., isolated from deep seawater.

A Gram-stain-negative, rod-shaped bacterial strain, designated SW123T, was isolated from a deep-sea water sample collected from the Indian Ocean. Strain SW123T was strictly aerobic, catalase- and oxidase-positive. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and summed feature 9 (comprising C16 : 0-methyl or iso-C17 : 1 ω9c). Ubiquinone-8 was the sole respiratory quinone. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content was 49.4 mol%. 16S rRNA gene sequence analysis showed that strain SW123T was closely related to Aliidiomarina shirensis AIST (96.7 % sequence similarity), Aliidiomarina iranensis GBPy7T (96.3%), Aliidiomarina haloalkalitolerans AK5T (96.0%) and Aliidiomarina celeris F3105T (95.9%). Phylogenetic trees based on 16S rRNA gene sequences showed that strain SW123T represented a novel member of the genus Aliidiomarina, forming a distinct cluster with A. celeris F3105T. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW123T represents a novel species of the genus Aliidiomarina, with the name Aliidiomarina indica sp. nov. The type strain is SW123T (=CGMCC1.16169T=KCTC 82234T).

Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench.

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6T, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0 % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6T was affiliated with the genus Marinomonas, sharing 93.1-97.0 % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0, C10 : 0 3-OH and C18 : 0. The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6T was considered to represent a novel species within the genus Marinomonas, for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6T (=KCTC 72501T=MCCC 1K03890T).

Gimesia benthica sp. nov., a planctomycete isolated from a deep-sea water sample of the Northwest Indian Ocean.

A Gram-stain-negative, stalked, oval-shaped and budding bacterial strain, designated E7T, was isolated from a deep-sea water sample collected from the Northwest Indian Ocean. The novel strain was strictly aerobic, and catalase- and oxidase-positive. It grew at 6-40 °C (optimum 30 °C) and pH 5.5-8.0 (optimum pH 7.0-7.5). The strain required 0.5-9.0 % (w/v) NaCl (optimum 3.0-5.0 %) for growth. Aesculin, starch, pectin and Tween 20 were hydrolysed. Based on 16S rRNA gene sequence analysis, strain E7T showed the highest similarity with Gimesia maris DSM 8797T (97.5 %). The average nucleotide identity and in silico DNA-DNA hybridization values between strain E7T and G. maris DSM 8797T were 78.0 and 19.3 %, respectively. The predominant cellular fatty acids of strain E7T were C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), phosphatidyldimethylethanolamine (PDME), phosphatidylcholine (PC) and diphosphatidylglycerol (DPG). The genomic DNA G+C content of strain E7T was 52.8 mol%. On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain E7T represents a novel species of the genus Gimesia, for which the name Gimesia benthica sp. nov. is proposed. The type strain is E7T (=CGMCC 1.16119T=KCTC 72737T).

Halovulum marinum sp. nov., isolated from deep-sea water of the Indian Ocean, and emended description of the genus Halovulum.

A novel Gram-stain-negative, aerobic, motile by peritrichous flagella, oval to rod-shaped bacterium, designated strain 2CG4T, was isolated from a deep-sea water sample collected from the Northwest Indian Ocean. The results of phylogenetic analysis of both 16S rRNA gene and RpoC protein sequences indicated that this strain was affiliated with the genus Halovulum in the Amaricoccus clade of the family Rhodobacteraceae of the class Alphaproteobacteria, sharing 95.3 % similarity at the 16S rRNA gene sequence level with the type strain of Halovulum dunhuangense YYQ-30T, the only species in the genus Halovulum. The predominant fatty acids (>10 %) of 2CG4T were summed feature 8 (C18 : 1ω7c and/ or C18 : 1ω6c; 61.1 %) and cyclo-C19 : 0ω8c (15.6 %). The polar lipids of 2CG4T were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sulfoquinovosyldiacylglycerol. The only isoprenoid quinone of 2CG4T was ubiquinone-10. The DNA G+C content of 2CG4T was determined to be 69.4 %. The central gene pufLM for the photosynthetic reaction was not detected. No growth occurred for 2CG4T in the absence of NaCl. On the basis of these data, it is concluded that the 2CG4T represents a novel species of the genus Halovulum, for which the name Halovulum marinum sp. nov. is proposed. The type strain is 2CG4T (=CGMCC 1.16468T=JCM 32611T).

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms

BackgroundMarine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.ResultsIn this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.ConclusionsOur study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling.En6fqpb_2L47ybAR2Rb-e_Video

Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench.

A novel Rhodobacteraceae bacterium, strain W43T, was isolated from a deep-sea water sample from the New Britain Trench. Strain W43T exhibited the highest 16S rRNA gene sequence similarity of 96.5% to Sedimentitalea nanhaiensis DSM 24252T, Phaeobacter gallaeciensis DSM 26640T, Phaeobacter inhibens DSM 16374T, and Phaeobacter porticola P97T. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of the genome showed that strain W43T formed an independent monophyletic branch within the family Rhodobacteraceae. Strain W43T was Gram-stain-negative, rod-shaped, and grew optimally at 16-20°C, pH 6.5-7.0 and 2% (w/v) NaCl. The principal fatty acids were C18:1ω7c/C18:1ω6c, major respiratory quinone was ubiquinone-10 and predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The 5 080 916bp long genome, comprising a circular chromosome and four plasmids, exhibits a G+C content of 55.9 mol%. The combined phenotypic, chemotaxonomic and molecular data show that strain W43T represents a novel species of a novel genus, for which the name Parasedimentitalea marina gen. nov. sp. nov. is proposed (type strain W43T=MCCC 1K03532T=KCTC 62635T).

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea.

A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July–August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.

An international intercomparison of stable carbon isotope composition measurements of dissolved inorganic carbon in seawater

AbstractWe report results of an intercomparison of stable carbon isotope ratio measurements in seawater dissolved inorganic carbon (δ13C‐DIC) which involved 16 participating laboratories from various parts of the world. The intercomparison involved distribution of samples of a Certified Reference Material for seawater DIC concentration and alkalinity and a preserved sample of deep seawater collected at 4000 m in the northeastern Atlantic Ocean. The between‐lab standard deviation of reported uncorrected values measured with diverse analytical, detection, and calibration methods was 0.11‰ (1σ). The multi‐lab average δ13C‐DIC value reported for the deep seawater sample was consistent within 0.1‰ with historical measured values for the same water mass. Application of a correction procedure based on a consensus value for the distributed reference material, improved the between‐lab standard deviation to 0.06‰. The magnitude of the corrections were similar to those used to correct independent data sets using crossover comparisons, where deep water analyses from different cruises are compared at nearby locations. Our results demonstrate that the accuracy/uncertainty target proposed by the Global Ocean Observing System (±0.05‰) is attainable, but only if an aqueous phase reference material for δ13C‐DIC is made available and used by the measurement community. Our results imply that existing Certified Reference Materials used for seawater DIC and alkalinity quality control are suitable for this purpose, if a “Certified” or internally consistent “consensus” value for δ13C‐DIC can be assigned to various batches.

Meridianimarinicoccus roseus gen. nov., sp. nov., a novel genus of the family Rhodobacteraceae isolated from seawater.

A Gram-stain negative, pink-pigmented, strictly aerobic, non-motile and coccoid-shaped bacterial strain, designated TG-679T, was isolated from a deep-sea water sample collected from the South China Sea. Cells of strain TG-679T were catalase- and oxidase-positive, lacked bacteriochlorophyll a and carotenoid. Strain TG-679T was found to grow at 10-40 °C (optimum, 28 °C), pH 5.5-10.0 (optimum, pH 7.5) and with 0.5-2.0 % (w/v) NaCl (optimum, 1.5 %). Chemotaxonomic analysis of strain TG-679T indicated that the sole respiratory quinone was Q-10, the predominant cellular fatty acid was C18 : 1ω7c, and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid and two unidentified glycolipids. The genomic DNA G+C content of strain TG-679T was 65.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TG-679T constituted a separated branch in the family Rhodobacteraceae. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain TG-679T is clearly distinct from any validly published genus. Based on polyphasic taxonomic characterization, strain TG-679T is considered to represent a novel species of a novel genus, for which the name Meridianimarinicoccus roseus gen. nov., sp. nov. is proposed. The type strain of the species is TG-679T (=KCTC 62454T=MCCC 1K03496T).

Alcanivorax profundi sp. nov., isolated from deep seawater of the Mariana Trench.

A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strain, designated as MTEO17T, was isolated from a 1000 m deep seawater sample of the Mariana Trench. Growth was observed at 10-45 °C (optimum, 37 °C), in the presence of 0.0-12.0 % NaCl (w/v; optimum, 3.0 %) and at pH 6.0-10.0 (optimum, pH 7.0-8.0). Phylogenetic analysis, based on the 16S rRNA gene sequence, revealed that strain MTEO17T belonged to the genus Alcanivorax and showed the highest sequence similarity of 97.9 % to Alcanivorax nanhaiticus MCCC 1A05629T. The estimated average nucleotide identity and DNA-DNA hybridization values between strain MTEO17T and A. nanhaiticus MCCC 1A05629T were 78.98 and 23.80 %, respectively. The significant dominant fatty acids were C16 : 0, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids comprised two phosphatidylethanolamines, one phosphatidylglycerol, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content of strain MTEO17T was 57.5 %. On the basis of the polyphasic evidence, strain MTEO17T is proposed to represent a novel species of the genus Alcanivorax, for which the name Alcanivorax profundi sp. nov. is proposed. The type strain is MTEO17T (=KCTC 52694T=MCCC 1K03252T).

Hyphobacterium indicum sp. nov., isolated from deep seawater, and emended description of the genus Hyphobacterium.

A novel aerobic, Gram-stain-negative bacterium, designated strain 2ED5T, was isolated from a deep seawater sample in the north-west Indian Ocean. Cells of the strain were oval- to rod-shaped, and motile by a polar flagellum or sessile by a prostheca. The strain formed creamy white colonies on 2216E marine agar plates. It grew at 10-40 °C (optimum 28 °C) and pH 5.0-8.0 (optimum pH 6.0-7.0). The strain required 1-6 % (w/v) NaCl for growth and grew optimally in the presence of 2-3 % NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 2ED5T was affiliated with the genus Hyphobacterium in the family Hyphomonadaceae of the class Alphaproteobacteria, sharing 95.1 % similarity at the 16S rRNA gene sequence level with the type strain of Hyphobacterium vulgare, the only species in the genus Hyphobacterium. The major fatty acids of the strain were C18 : 1ω7c and iso-C17 : 1ω9c, and the polar lipids included monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol, glucuronopyranosyl diglyceride, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unidentified glycolipid. The strain contained ubiquinone Q-10 as the predominant respiratory quinone. The G+C content of the genomic DNA of the strain was 60.9 mol%. Based on the results of this polyphasic analysis, strain 2ED5T represents a novel species in the genus Hyphobacterium, for which the name Hyphobacterium indicum sp. nov. is proposed. The type strain is 2ED5T (=CGMCC 1.16466T=JCM 32612T).

Rubritalea profundi sp. nov., isolated from deep-seawater and emended description of the genus Rubritalea in the phylum Verrucomicrobia.

A Gram-stain-negative, short-rod, facultatively anaerobic, non-motile and red-pigmented bacterium, designated SAORIC-165T, was isolated from a deep-seawater sample collected from the Pacific Ocean. The 16S rRNA gene sequence analysis showed that strain SAORIC-165T was most closely related to Rubritalea marina Pol012T (95.7 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Rubritalea in the phylum Verrucomicrobia. Optimal growth of strain SAORIC-165T was observed at 10 °C, pH 7.0 and in the presence of 2.0-3.5 % (w/v) NaCl. The DNA G+C content of strain SAORIC-165T was 50.7 mol% and MK-9 was the predominant isoprenoid quinone. The major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and C14 : 0. The major polar lipids constituted phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids and aminolipids. On the basis of the taxonomic data obtained in this study, it was concluded that strain SAORIC-165T represented a novel species of the genus Rubritalea, for which the name Rubritalea profundi sp. nov. is proposed. The type strain of Rubritalea profundi is SAORIC-165T (=NBRC 110691T=KCTC 52460T).

Hyphococcus flavus gen. nov., sp. nov., a novel alphaproteobacterium isolated from deep seawater.

A Gram-staining-negative, aerobic, non-spore-forming, coccoid to rod shaped bacteria with prosthecate and flagellum, designated as HSF6T, was isolated from deep seawater samples collected from the South China Sea at depth of 2.5 km and subjected to a polyphasic taxonomic investigation. Colonies of strain HSF6T were 1-2 mm in diameter, smooth, circular, convex and yellow. Strain HSF6T was found to grow at 15-37 °C (optimum, 25-35 °C), pH 5.0-9.5 (optimum, pH 7.0-7.5) and with 0-8 % (w/v) NaCl (optimum, 2 %). Chemotaxonomic analysis showed the predominant respiratory quinone of strains HSF6T were ubiquinone-10, and the major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. The polar lipids were monoglycosyldiglyceride (MGDG), sulfo-quinovosyl diacylglycerol (SQDG), three unknown glycolipids (GL1-3) and five unknown lipids (L1-5). The DNA G+C content of strain HSF6T was determined to be 51.0 mol% with HPLC. The comparison of 16S rRNA gene sequence similarities show that strain HSF6T was related most closely to genus Parvularcula with similarity ranging from 91.0 to 91.8 %. The phylogenetic trees, using the 16S rRNA gene sequence, reconstructed with neighbour-joining, maximum-parsimony and maximum-likelihood methods showed that strain HSF6T constituted a separated branch in the family 'Parvularculaceae'. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain HSF6T is clearly distinct from validly published genera. On the basis of these features, we propose strain HSF6T (=MCCC 1K03223T=KCTC 52486T) represents a novel species of a novel genus with the name Hyphococcus flavus gen. nov., sp. nov.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation.

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Activity Concentrations of <sup>137</sup>Cs and <sup>90</sup>Sr in Seawaters of East Sea, Korea

Background: This study was a long-term evaluation of 137Cs and 90Sr activity concentrations in seawater samples from the East Sea, Korea, in order to establish current activity levels. Results and long-term monitoring trends will be useful in the future monitoring of environmental radioactivity. Materials and Methods: Surface seawater samples were collected quarterly from Guryongpo and Jangho in the East Coast between 1998 and 2010 and the quarterly deep seawater samples were collected from three sites in the sea adjacent to Ulleung-do between 2012 and 2015. The activity concentrations of 137Cs were measured using a gamma-spectrometer. The activity concentrations of 90Sr and 90Y in a radioactive equilibrium state were measured using a gas flow proportional counter. Results and Discussion: We found the annual average activity concentrations of 137Cs in the surface seawater was 1.66-2.89 mBq∙kg-1 in Guryongpo and 1.68-2.43 mBq∙kg-1 in Jangho. The annual average activity concentrations of 90Sr in the surface seawater was 0.83- 1.98 mBq∙kg-1 in Guryongpo and 0.82-1.57 mBq∙kg-1 in Jangho. The annual average activity concentrations of 137Cs in the deep seawater sites were 1.51-1.73 mBq∙kg-1, 1.19-1.60 mBq∙kg-1 and 0.87-1.15 mBq∙kg-1 in TH, JD, and HP. The annual average activity concentrations of 90Sr in the same deep seawater sites were 1.00-1.94 mBq∙kg-1, 0.82-1.26 mBq∙kg-1, and 0.79-1.32 mBq∙kg-1. The effective half-life was calculated by analyzing change over time in the activity concentration in the surface seawater. The effective half-life of 137Cs was 15.3 ± 0.1 years in Guryongpo and 102 ± 3 years in Jangho. The effective half-life of 90Sr was 28.3 ± 4.3 years in Guryongpo and 16.6 ± 0.1 years in Jangho. The ratio of the average activity concentration (137Cs/90Sr) was 1.72 in the surface seawater, which is similar to the reported ratio of the global radioactive fallout. The ratio in the deep seawater was 1.24, which is somewhat low compared to the global ratio (1.6, 1.8). Conclusion: Activity concentrations of 137Cs and 90Sr in the seawaters of the East Sea were similar to the previously reported activity levels in the East Sea and northwestern Pacific as a result of global radioactive fallout following atmospheric nuclear weapon tests.