Seawater In Japan Research Articles

Rhabdamoeba marina is a heterotrophic relative of chlorarachnid algae.

Rhabdamoeba marina is a unique and poorly reported amoeba with an uncertain phylogenetic position. We successfully cultured R. marina from coastal seawater in Japan and performed a molecular phylogenetic analysis using the small subunit ribosomal RNA (SSU rRNA) gene sequence. Our phylogenetic analysis showed that R. marina branched as a basal lineage of Chlorarachnea, a group of marine photosynthetic algae belonging to the phylum Cercozoa within the supergroup Rhizaria. By comparing the ecological and morphological characteristics of R. marina with those of photosynthetic chlorarachneans and other cercozoans, we gained insight into the evolution and acquisition of plastids in Chlorarachnida.

Assessment of the risk posed by three antifouling biocides to Pacific oyster embryos and larvae in Hiroshima Bay, Japan.

The Pacific oyster (Crassostrea gigas) is an important species in oyster farming worldwide, including in Japan. Hiroshima Bay is one of the most important oyster farming areas in Japan. We investigated the occurrence of antifouling biocides used worldwide including diuron, Irgarol 1051 (Irgarol), and 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT), which have been detected at sub-ppb levels in seawater in Japan, and estimated their no observed effect concentrations (NOECs). In recent years, the spat settlement of Pacific oysters has become poor, which presents a challenge for oyster aquaculture in Hiroshima Bay; hence, we conducted embryotoxicity and larva settlement tests using Pacific oysters. Compared to diuron and Irgarol, DCOIT exhibited a higher toxicity toward oyster embryos, and the minimum 24-h NOEC toxicity value for the oyster embryos was <3 ng/L. The highest concentrations of diuron, Irgarol, and DCOIT in the environmental seawater in the Seto Inland Sea were 27.6, 3.2, and 24 ng/L, respectively. Considering the NOECs, the environmental concentrations of these biocides suggest that the ecological risks posed by diuron and Irgarol are low, whereas those posed by DCOIT are high. However, the rate of detection of DCOIT was low because it degraded rapidly in the seawater before treatment for chemical analysis, except in the case of the treatment on the research vessel.

Bacterial community structure analysis of deep-sea water and surface seawater in Japan by pyrosequencing

Bacterial community structure analysis of deep-sea water and surface seawater in Japan by pyrosequencing

CURRENT DATA ON COMPOSITION AND DISTRIBUTION OF TRAWL MACROZOOBENTHOS IN THE RUSSIAN WATERS OF THE JAPAN SEA

The bottom trawl survey (430 stations) was conducted over the shelf and continental slope in the Russian sector of the Japan Sea (total depth range 10–750 m) on April 1 — July 8, 2015. In total, 211 taxa of invertebrates were recorded in the trawl catches. Most of them belonged to sea stars (36), shrimps (32), gastropods (27), bivalves (23), crabs and craboids (11), polychaetes (11), coral polyps (10), and sponges (10). The total biomass of macrozoobenthos in the surveyed area was assessed as 1572.5 . 103 t (136.6 . 103 t in Peter the Great Bay, 341.5 . 103 t at southern Primorye, 686.0 . 103 t at northern Primorye, and 408.4 . 103 t at western Sakhalin) that was higher than the mean long-term level. The total stock of commercial invertebrates was assessed as 630.0 . 103 t. Its highest portion (265.2 . 103 t or 42.1 %) was concentrated in the western Tatar Strait. The average biomass of macrozoobenthos was 13.5 ± 1.1 g/m2 , including 6.3 ± 0.5 g/m2 of commercial species. The most abundant groups were basket stars (372.2 . 103 t), crabs (231.6 . 103 t), shrimp (226.9 . 103 t), sponges (182.9 . 103 t), sea lilies (167.5 . 103 t), sea stars (77.2 . 103 t), sea urchins (59.0 . 103 t), craboids (48.7 . 103 t), and bivalves (49.5 . 103 t). Vertical distribution of both total and commercial benthos was distinguished by peaks on the upper shelf (10–50 m) and upper slope (300–400 m). Over the surveyed northern Japan Sea waters, 18 biocoenotic complexes of trawl macrozoobenthos were identified. The largest area was occupied by the complex of immobile sestonophagous sea lily Heliometra glacialis (131 stations in the depth range of 104–692 m with average biomass 5.5 g/m2 ), other wide-spread complexes were those of polyphagous snow crab Chionoecetes opilio (71 stations, 27–552 m, 4.4 g/m2 ), mobile sestonophagous basket star Gorgonocephalus eucnemis (40 stations, 58–372 m, 6.6 g/m2 ), and polyphagous fawn sea urchin Strongylocentrotus pallidus (40 stations, 17–351 m, 4.7 g/m2 ).

The novel mef(C)-mph(G) macrolide resistance genes are conveyed in the environment on various vectors.

The novel tandem genes mef(C) and mph(G) have been reported in marine bacteria in Japan. This paper aimed to characterise the extent of environmental distribution of mef(C) and mph(G) as well as their dissemination and persistence in aquatic bacterial communities. Erythromycin-resistant bacteria were isolated from Japan, Taiwan and Thailand aquaculture sites. The mef(C)-mph(G) genes were detected by PCR. The size of mobile genetic elements conveying mef(C) and mph(G) was examined by Southern blotting. The conjugation rate was assessed by filter mating. The mef(C)-mph(G) tandem genes were distributed in erythromycin-resistant isolates from aquaculture seawater in Japan and northern Taiwan and in animal farm wastewater in Thailand. A total of 29 bacterial isolates were positive for mef(C)-mph(G). The genes were found on vectors of various sizes. Partial sequencing of the traI relaxase gene revealed homology with a pAQU1-like plasmid, an IncA/C-type plasmid and an SXT/R391 family integrative conjugative element (SRI) as vectors. Thirteen isolates (45%) were positive for traI(pAQU-IncA/C-SRI), whereas the others were negative. The traI(pAQU-IncA/C-SRI)-positive isolates exhibited a higher transfer frequency (10-4-10-5 transconjugants/donor) than traI(pAQU-IncA/C-SRI)-negative isolates (<10-9). These results suggest that mef(C)-mph(G) are coded on various vectors and are distributed among marine and wastewater bacteria in Asian countries. Vectors with traI(pAQU-IncA/C-SRI) play a role in the spread of mef(C)-mph(G).

Long‐term decrease in phosphate concentrations in the surface layer of the southern Japan Sea

AbstractTo identify possible causes for the long‐term trends in nutrient concentrations in the southern Japan Sea (JS), we studied nutrient concentrations that were obtained by the Japan Meteorological Agency. Our evaluation shows that phosphate concentrations declined in the surface layers in summer (0–20 and 21–50 m depth) and winter (0–20, 21–50, and 51–100 m depth) over the last 40 years, while no significant linear trend was observed for nitrate concentrations. The declining trend in the phosphate concentration was quantified as 1.8–3.3 nM yr−1. The increase in atmospheric nutrient deposition to the JS could not explain the decline in phosphate concentration. In addition, the mixed‐layer depth during winter did not demonstrate any significant trend, and an increase in phosphate concentrations was not observed in any layers; therefore, the decrease in nutrient supply from deep JS water was not considered a major possible cause for the decline in the phosphate concentration. In contrast, the phosphate concentration in the surface of the southern JS during winter showed a significant positive correlation with the concentration in the 21–50 m depth layer of the saline East China Sea (ECS) water in the preceding summer, and the surface water of the southern JS was almost entirely replaced by water originating from the ECS during May–October. Therefore, it is concluded that the declining trend in the phosphate concentrations in the southern JS is caused by horizontal advection of ECS water.

Identification of a poly(3-hydroxybutyrate)-degrading bacterium isolated from coastal seawater in Japan as Shewanella sp.

A poly[(R)-3-hydroxybutyrate] [P(3HB)]-degrading bacterium (strain JKCM-AJ-6,1α) was isolated from coastal seawater near the port of Yaizu, Suruga Bay, Japan. The strain grew well in a marine mineral medium supplemented with P(3HB) powder as the sole carbon source. Phylogenetic analysis revealed that the strain JKCM-AJ-6,1α belonged to the genus Shewanella. The isolate was unable to grow at temperatures above 50 °C, and the optimum range of growth temperatures was 30 °C–37 °C; however, the optimum temperature for degradation of P(3HB) was 15 °C. The maximum specific growth rate (μ = 1.0 h−1) was attained at a NaCl concentration of 0.2 M, but the strain was able to grow even in the presence of 0.8 M NaCl. This suggests that the strain is a typical marine bacterium. This is the first report showing P(3HB) depolymerase activity in a member of the genus Shewanella. It is concluded that the genus Shewanella may be one of the key bacterial groups involved in the P(3HB) cycle in marine environments.

Salinity minimum in the subsurface layers of the Japan Sea

Seasonal variability of vertical salinity distribution in the Japan Sea is considered. On the base of high accuracy data from the databases WODC-2013 (USA), JODC (Japan), and the databases of Far-Eastern State Hydrometeorological Institute and Pacific Oceanological Institute (Russia), several cases of salinity minimums are analyzed and interpreted taking into account seasonal variability of salinity profiles. High vertical homogeneity by salinity is noted for the Japan Sea waters, and the subsurface salinity minimum can be considered as a result of continuous changes of freshwater balance. It could be formed in the layers from the sea surface to 150-250 m as a temporary local extreme caused by prevalence of evaporation over precipitation on the sea surface in some seasons - that’s why it is observed seasonally. There is concluded that such conservative patterns as water masses are absent in the sea, at least in its active upper layers, but vertical salinity profiles are changing permanently under influence of changing freshwater fluxes, and their extremes appear or disappear in compliance with the dialectic laws.

Wenyingzhuangia heitensis sp. nov., a new species of the family Flavobacteriaceae within the phylum Bacteroidetes isolated from seawater.

A Gram-negative, strictly aerobic, beige-pigmented, non-motile, rod-shaped strain designated H-MN17(T) was isolated from seawater in Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flavobacteriaceae within the phylum Bacteroidetes and that it showed highest sequence similarity (97.5%) to Wenyingzhuangia marina D1(T). The hybridization values for DNA-DNA relatedness between the strains of H-MN17(T) and W. marina D1(T) were lower than 70%, which is accepted as the phylogenetic definition of a novel species. The DNA G+C content of strain H-MN17(T) was 31.8mol%; MK-6 was the major menaquinone; and anteiso-C15:0, anteiso-C17:0 and anteiso-C19:0 were identified as the major (>10%) cellular fatty acids. A complex polar lipid profile was present consisting of phosphatidylethanolamine, three unidentified lipids, three unidentified glycolipids and three unidentified aminolipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Wenyingzhuangia for which the name Wenyingzhuangia heitensis sp. nov. is proposed. The type strain of W. heitensis sp. nov. is H-MN17(T) (=KCTC 42245(T)=NBRC 110601(T)).

Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098.

Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is able to degrade various types of n-alkanes. Here, we report the complete genome of strain NBRC 101098.

Identification of Novel Non-Metal Haloperoxidases from the Marine Metagenome

Haloperoxidase (HPO, E.C.1.11.1.7) is a metal-containing enzyme oxidizing halonium species, which can be used in the synthesis of halogenated organic compounds, for instance in the production of antimicrobial agents, cosmetics, etc., in the presence of halides and H2O2. To isolate and evaluate a novel non-metal HPO using a culture-independent method, a cassette PCR library was constructed from marine seawater in Japan. We first isolated a novel HPO gene from Pseudomonas putida ATCC11172 by PCR for constructing the chimeric HPO library (HPO11172). HPO11172 showed each single open-reading frame of 828 base pairs coding for 276 amino acids, respectively, and showed 87% similarity with P. putida IF-3 sequences. Approximately 600 transformants screened for chimeric genes between P. putida ATCC11173 and HPO central fragments were able to identify 113 active clones. Among them, we finally isolated 20 novel HPO genes. Sequence analyses of the obtained 20 clones showed higher homology genes with P. putida or Sinorhizobium or Streptomyces strains. Although the HPO A9 clone showed the lowest homology with HPO11172, clones in group B, including CS19, showed a relatively higher homology of 80%, with 70% identy. E. coli cells expressing these HPO chimeric genes were able to successfully bioconvert chlorodimedone with KBr or KCl as substrate.

Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

Two halophilic moderately acidophilic archaeal strains, MH1-136-2(T) and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2(T) was pink pigmented, while MH1-370-1 was orange-red pigmented. Strain MH1-136-2(T) was able to grow at 9-30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5-6.2 (optimum, pH 5.2-5.5) and at 18-55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12-30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2-6.0 (optimum, pH 5.2-5.5) and 20-50 °C (optimum, 45 °C). Strain MH1-136-2(T) required at least 1 mM Mg(2+), while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2(T) and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3(T) with 98.3 % similarity. The level of DNA-DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2(T) and Halarchaeum acidiphilum MH1-52-1(T), Halarchaeum salinum MH1-34-1(T) and Halarchaeum rubridurum MH1-16-3(T) was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum, for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2(T) ( = JCM 16331(T) = CECT 7573(T)) isolated from solar salt produced in Japan.

A Study on the Industrialization of Deep Seawater in Japan and Korea, and its Implications on the Utilization of Jeju Magma Seawater

A Study on the Industrialization of Deep Seawater in Japan and Korea, and its Implications on the Utilization of Jeju Magma Seawater

Seasonal Hypoxia of Amursky Bay in the Japan Sea: Formation and Destruction

Based on detailed hydrological and hydrochemical surveys carried out in each of the four seasons of 2008, Amursky Bay in the north west quadrant of the Japan Sea was found to experience seasonal hypoxia. The primary process of hypoxia formation is a microbiological degradation of the ”excess” amount of diatoms under rather low photosynthetic active radiation in bottom layer and weak water dynamics. The microbiological decay of dead diatoms under light deficient conditions intensively consumes dissolved oxygen and produces phosphates, ammonium, silicates, and dissolved inorganic carbon. Existence of a phytoplankton ”excess” is caused by phytoplankton bloom resulting from nutrient pulses into Amursky Bay. There are two main sources of these nutrients: the waste waters of Vladivostok city and discharge from Razdolnaya River. The river delivers more than two times the amount of nutrients than the waste waters of Vladivostok. It is suggested that the phytoplankton ”excess” might be caused by an enhanced supply of nutrients delivered into the surface layer resulting from the increased discharge of the river on a short time scale. Our data suggest that hypoxia is seasonal, with a peak at the end of summer. The upwelling of the Japan Sea water in the beginning of the fall season and its advection across the shelf is the primary process by which the hypoxia is destroyed. During the winter, strong vertical mixing due to termohaline convection makes the water column uniform and brings more oxygen into the water along with high primary production under the ice. Thus, during the winter season, the ecosystem of Amursky Bay recovers completely.

Origin of deep water in the Japan Sea over the last 145 kyr

We examined the paleoceanographic origin of the deep water in the Japan Sea over the last 145kyr by using stable isotope data from foraminifera and paleontological data related to diatoms and planktonic foraminiferal coiling direction from core KT05-9p2 recovered from the Yamato Rise in the center of the Japan Sea. Carbon and oxygen isotope records of benthic and planktonic foraminiferal tests reveal that not only the Tsushima Current but also the Oyashio Current have been the major sources of Japan Sea water during the past 145kyr and that changes in deep water properties correspond with eustatic sea-level fluctuations. Seasonal cooling of surface water mainly derived from the Tsushima Current is known to have produced deep water during high sea-level stands. Baroclinic forcing that prevailed during surface-water freshening resulted in the inflow of the Oyashio Current through the Tsugaru Strait at the northeast end of the Japan Sea. After entering the Japan Sea, the Oyashio water sank to the bottom and contributed to deep water formation. Oxygen isotope values of benthic foraminiferal tests from the horizons corresponding to MIS 3 and 4 are similar to the calculated values for Oyashio Current water from periods during which sea level was ~80m lower than at present. The occurrence of authigenic branching pyrite from weakly disturbed layers indicates the onset of oxygen deficiency immediately below the sediment–water interface during stages of low sea-level stands, suggesting the prevalence of deep water stagnation from the weakening of overturning circulation during Japan Sea isolation. Glacio-eustatic sea-level changes have greatly influenced the oceanic regime of the Japan Sea.

Isotopic determination of U, Pu and Cs in environmental waters following the Fukushima Daiichi Nuclear Power Plant accident

Concentrations of the radionuclides, U, Pu, and Cs were measured in water samples (10-20 L) to study analyte dispersion and migration following the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. A total of 8 water samples including oceanic water and paddy-field water were collected in the vicinity of the plant. Determinations of U, Pu and Cs isotopes were performed by accelerator mass spectrometry (AMS), inductively coupled plasma mass spectrometry (ICP-MS), and γ-ray spectrometry. The 236U/238U atom ratio was in the range 1.83-8.20 × 10-9 for fresh water and around 0.57 × 10-9 for seawater while the concentration of 236U was about 104-105 and 106 atoms/kg, respectively. Plutonium (239,240Pu) was detected in one riverine sample and the marine samples at very low levels and with large uncertainty. The concentrations of 137Cs in fresh riverine samples were 0.02-0.46 Bq/kg which are more than three orders of magnitude larger than the global fallout level. As for seawater samples within 80 km offshore of the FDNPP, the concentrations of 137Cs were 10-20 times higher than that of the Japan Sea water. Also 134Cs and 137Cs were of similar concentrations in all samples. The results show that volatile and refractory nuclides such as Cs, U and Pu exist in the dissolved phase, which can be readily assimilated by plants/humans. However the environmental impact of Pu and U in the vicinity of the FDNPP is considered to be low in comparison to that of the volatile radionuclide Cs.

Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia

The taxonomic position of bacterial strain AM11-6(T), isolated from seawater in Japan, was determined by using a polyphasic taxonomic approach. The strain was a strictly aerobic and Gram-staining-negative slender rod, motile by gliding. The major respiratory quinone was menaquinone-6 and the predominant cellular fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH, C(14 : 0) and iso-C(15 : 1) G. The polar lipid pattern indicated the presence of an unidentified phospholipid, several glycolipids and an unidentified polar lipid. The G+C content of the genomic DNA was 36.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AM11-6(T) clustered with members of the genera Wandonia and Fluviicola in the family Cryomorphaceae of the phylum Bacteroidetes. The strain required NaCl and MgCl(2) for growth and could be differentiated from members of other genera in the family Cryomorphaceae by fatty acid composition and other phenotypic characters. On the basis of these results, we describe the novel genus and species, Salinirepens amamiensis gen. nov., sp. nov. The type strain of Salinirepens amamiensis is AM11-6(T) (= NBRC 101268(T) = NCIMB 14607(T)). Emended descriptions of the genera Fluviicola and Wandonia are also proposed.

Loktanella atrilutea sp. nov., isolated from seawater in Japan

A Gram-negative, rod-shaped bacterium, IG8(T), was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8(T) represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA-DNA hybridization values between strain IG8(T) and the type strains of L. salsilacus (27.9-36.1 %) and L. fryxellensis (11.3-31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8(T) was 66.3 mol%. On the basis of DNA-DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8(T) (=IAM 15450(T)=NCIMB 14280(T)).

Pseudovibrio japonicus sp. nov., isolated from coastal seawater in Japan

A Gram-negative, motile, rod-shaped bacterium (WSF2(T)) was isolated from coastal seawater of the Boso Peninsula in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WSF2(T) represented a separate lineage within the genus Pseudovibrio. The DNA G+C content of strain WSF2(T) was 51.7 mol%. DNA-DNA hybridization values between strain WSF2(T) and the type strains of Pseudovibrio species were significantly lower than those accepted as the phylogenetic definition of a species. Furthermore, some biochemical characteristics indicated that strain WSF2(T) differed from other Pseudovibrio species. Based on these characteristics, it is proposed that the isolate represents a novel species, Pseudovibrio japonicus sp. nov. The type strain is WSF2(T) (=IAM 15442(T)=NCIMB 14279(T)=KCTC 12861(T)).

Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan

Two strains of gliding, agarolytic bacteria, strains YS10(T) and YML5, were isolated from coastal seawater off Kamogawa, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolates represent a separate lineage within the genus Flammeovirga. DNA-DNA hybridization values between these isolates and the type strains of species of the genus Flammeovirga were significantly lower than those accepted as threshold values for the phylogenetic definition of a species. Furthermore, some of the phenotypic characteristics indicate that the isolates differ from other Flammeovirga species. Based on these differences, it is suggested that the isolates represent a novel species, for which the name Flammeovirga kamogawensis sp. nov. is proposed. The type strain is YS10(T) (=IAM 15451(T)=NCIMB 14281(T)).