Search

The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities., Competing Interests: The authors have declared that no competing interests exist.

The spatial variations of low-level 134 Cs concentrations (activities) in seawater off the Japanese Archipelago, particularly in the eastern East China Sea (ECS), in 2018 and 2019 were examined. The 134 Cs concentrations, decay-corrected to the date of the Fukushima Dai-ichi Nuclear Power Plant accident, in seawaters were 0.5-2.0 mBq/L. High 134 Cs concentrations (1.1-2.0 mBq/L) of the Kuroshio Current subsurface water (densities of 25-26σ θ ) in the eastern ECS could indicated the contribution of the subtropical mode water from the Pacific Ocean side, and total column inventories were 330-426 Bq/m 2 . In contrast, as indicated by the same 134 Cs concentration level at the surface of the eastern ECS and Sea of Japan, larger portions of the subsurface waters remained in the ECS and Yellow Sea side in response to the existence of the shallow Tsushima Strait., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Pen shell (Atrina cf. japonica) resources have been devastated in Ariake Bay, Japan, and to facilitate the recovery of this species, there is an urgent need to fully understand the factors contributing to its high levels of mortality. Pen shells living in natural waters grow through successive life stages, and environmental factors may affect these bivalves differently at different stages. Accordingly, to elucidate the causes of mortality in natural waters, it is necessary to gain an understanding of the quantitative effects of environmental factors on bivalves at each life stage. In this study, we sought to determine the differential effects of hypoxic conditions on 1-year-old (average shell length: 93.9 mm) and 2-year-old (146.5 mm) pen shells bred under artificial conditions. We exposed shells of each age group to six different dissolved oxygen (DO) concentrations for 96 h and monitored their behavior and survival rate. Based on the survival status, we estimated the lethal DO concentrations that induced 50%, 95%, and 5% mortality (LC 50 , LC 95 , and LC 5 , respectively) at each age. We found that for 1-year-old shells, the LC 50 values at 48, 72, and 96 h were 0.51, 0.74, and 0.84 mg/L, respectively, whereas the corresponding values for 2-year-old shells were 0.74, 1.27, and 1.80 mg/L. Furthermore, we found that for 1- and 2-year-old shells, the estimated ranges from LC 95 to LC 5 at 48, 72, and 96 h were 0.39-0.68, 0.62-0.88, and 0.64-1.12 mg/L, and 0.31-1.75, 0.77-2.09, and 1.29-2.53 mg/L, respectively. Under low DO concentrations (0.47 to 1.93 mg/L and 0.49 to 3.30 mg/L for 1- and 2-year-old shells, respectively), we observed pen shells with more than half of their shell length protruding above the substrate. In addition to age and body size, the 1- and 2-year-old pen shells used in the present study also differed with respect to reproductive status, with 7.6% of 1-year-old and 96.7% of 2-year-old shells considered to be fully ripe. Collectively, our observations indicate that 2-year-old pen shells are less tolerant to hypoxic conditions than are 1-year-old pen shells, and we suspect that the differences in hypoxic tolerance could be attributable to differences in the physiological status of the pen shells during gonadal development. We believe the findings of this study will make an important contribution to enhancing our understanding of the effects of hypoxia on the viability of A. cf. japonica in natural waters., (Copyright © 2020. Published by Elsevier B.V.)

We investigated two sediment cores to understand whether a tsunami in Onagawa Bay, Japan caused environmental changes. The value of δ 13 C ranged from -21.9‰ to -24.3‰ and of δ 15 N ranged from 5.1 to 5.9‰. We conclude that the source of the sediment in the present study area was mainly oceanic and not terrestrial. The chlorophyll concentration ranged from 1.8 to 4.0 μg/g ww, and did not vary greatly between surface and bottom layers. We inferred that all layers were deposited after the tsunami. The major phytoplankton taxa in sediments were diatoms from DNA sequencing. The presence of harmful dinoflagellates was minor. The concentrations of several heavy metals decreased slightly after the tsunami. We inferred that heavy metals in sediments were diluted by the tsunami disturbance. The land in Onagawa suffered serious damage, but disturbance of the seabed was much less evident., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Mass mortality due to necrosis signs occurred in hatchery-reared zoea stage larvae of the mud crab Scylla serrata in Okinawa, Japan, and a causative bacterium was isolated. In this study, we identified and characterized the bacterium by genome analysis, biochemical properties and pathogenicity. The bacterium was a Gram-negative, non-motile, long rod, forming yellow colonies on a marine agar plate. It grew at 20-33°C (not at 37°C) and degraded chitin and gelatin. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Aquimarina hainanensis. Genome sequence data obtained from Illumina MiSeq generated 29 contigs with 3.56 Mbp in total length and a G + C content of 32.5%. The predicted 16 chitinase genes, as putative virulence factors, had certain homologies with those of genus Aquimarina. Experimental infection with the bacterium conducted on larvae of four crustacean species, brine shrimp Artemia franciscana, freshwater shrimp Caridina multidentata, swimming crab Portunus trituberculatus and mud crab S. serrata, revealed that this bacterium was highly virulent to these species. The present study suggests that the bacterium caused mass mortality in mud crab seed production was A. hainanensis and can be widely pathogenic to crustaceans., (© 2020 John Wiley & Sons Ltd.)

Natal origin of subadult (age-1) Pacific bluefin tuna (PBT, Thunnus orientalis ) from the California Current Large Marine Ecosystem (CCLME) was determined using natural tracers in ear stones (otoliths). Age-0 PBT collected from the two known spawning areas in the western Pacific Ocean (East China Sea, Sea of Japan) were used to establish baseline signatures from otolith cores over 4 years (2014-2017) based on a suite of trace elements (Li, Mg, Mn, Sr, Zn and Ba). Distinct chemical signatures existed in the otolith cores of age-0 PBT collected from the two spawning areas, with overall classification accuracy ranging 73-93% by year. Subadult PBT collected in the CCLME over the following 4 years (2015-2018) were then age-class matched to baselines using mixed-stock analysis. Natal origin of trans-Pacific migrants in the CCLME ranged 43-78% from the East China Sea and 22-57% from the Sea of Japan, highlighting the importance of both spawning areas for PBT in the CCLME. This study provides the first estimates on the natal origin of subadult PBT in this ecosystem using otolith chemistry and expands upon the application of these natural tracers for population connectivity studies for this species.

Pituitary gonadotropins, follicle-stimulating hormone (Fsh) and luteinizing hormone (Lh), play central roles in the control of gonadal development of vertebrates. In mammals, Fsh and Lh exclusively activate their respective cognate receptors: Fsh receptor (Fshr) in the Sertoli cell and Lh/choriogonadotropin receptor (Lhcgr) in the Leydig cell. In teleosts, the distinct functions of Fsh and Lh and information on cellular localization of their receptors are still poorly understood. Recently we established FreeStyle 293-F cell lines producing recombinant Japanese eel Fsh and Lh (reFsh and reLh), which form a single chain consisting of a common α-subunit and β-subunits. In this study, we conducted functional analyses of reFsh and reLh, focusing on the binding specificities to their receptors and effects on testicular steroidogenesis in vitro. Assays with gonadotropin receptors-expressing COS-7 cells indicated reFsh stimulated its cognate receptor, meanwhile reLh activated both receptors. Although results of in vitro incubations showed that reFsh and reLh induced testicular 11-ketotestosterone production in a dose and time-dependent manner by upregulating expression of steroidogenic enzymes, the effective doses of reLh were apparently lower and the effects of reLh emerged faster in comparison with reFsh. Results of quantitative real-time PCR using testicular cell fractions showed that fshr and lhcgr1 mRNA were detected both in Sertoli and Leydig cells. These analyses revealed that reFsh and reLh were biologically active and hence will be useful for future studies. Moreover, our data showed that both eel Fsh and Lh acted as steroidogenic hormones through their receptors in testicular somatic cells; however, Lh was more potent on androgen production, implying differential functions on spermatogenesis., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Lipid and fatty acid composition of female Pacific bluefin tuna (PBF, Thunnus orientalis) reproductive and somatic tissues in southwestern North Pacific and Sea of Japan spawning grounds are compared. Total lipid (TL) levels are higher in liver than white muscle tissues. An increased gonadosomatic index (GSI) during the early spawning season coincided with decreased TL. Levels of triacylglycerols (TAG) in PBF liver tissues from the Nansei Islands and Sea of Japan, and white muscle in fishes from the Sea of Japan, decreased during the spawning season, while TAG in ovary tissues did not. Concurrent reductions in TL and increases in GSI early in the spawning season suggest TAG depletion was caused by allocation from liver and white muscle tissues to oocytes, that the liver is one of the important lipid-storage organs in PBF, and this species mostly reliant on capital deposits as a mixed capital-income breeder. Differences of docosahexaenoic acid (DHA) levels between spawning grounds were lower in ovary than in muscle and liver tissues. However, eicosapentaenoic (EPA) and arachidonic acid (ARA) levels that influence egg development and embryo and larval growth are significantly higher in PBF tissues from the Sea of Japan than Nansei Islands, which coincided with larval quality. These suggest a maternal effect exists, with egg quality influencing offspring survival, and that the reproductive strategy of PBF varies according to local variation at each spawning ground., Competing Interests: JAPAN NUS Co. Ltd provided support in the form of salary for Yumi Okochi. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

In recent years, blooms of toxic Alexandrium ostenfeldii strains have been reported from around the world. In 2013, the species formed a red tide in a shallow lagoon in western Japan, which was the first report of the species in the area. To investigate the genetic relatedness of Japanese A. ostenfeldii and global isolates, the full-length SSU, ITS and LSU sequences were determined, and phylogenetic analyses were conducted for isolates from western and northern Japan and from the Baltic Sea. Genotyping and microsatellite sequence comparison were performed to estimate the divergence and connectivity between the populations from western Japan and the Baltic Sea. In all phylogenetic analyses, the isolates from western Japan grouped together with global isolates from shallow and low saline areas, such as the Baltic Sea, estuaries on the east coast of U.S.A. and from the Bohai Sea, China. In contrast, the isolates from northern Japan formed a well-supported separate group in the ITS and LSU phylogenies, indicating differentiation between the Japanese populations. This was further supported by the notable differentiation between the sequences of western and northern Japanese isolates, whereas the lowest differentiation was found between the western Japanese and Chinese isolates. Microsatellite genotyping revealed low genetic diversity in the western Japanese population, possibly explained by a recent introduction to the lagoon from where it was detected. The red tide recorded in the shallow lagoon followed notable changes in the salinity of the waterbody and phytoplankton composition, potentially facilitating the bloom of A. ostenfeldii., (Copyright © 2019 Elsevier B.V. All rights reserved.)

In northern Japan, juvenile chum salmon Oncorhynchus keta (Walbaum) are released from hatcheries to enhance the fishery resource. Infections with ectoparasitic protozoans, particularly the flagellate Ichthyobodo salmonis and the ciliate Trichodina truttae, occasionally cause severe mortality among hatchery-reared juveniles. This study examined the susceptibility of the two parasites to wide-ranging UV irradiation (experiment 1) and then investigated whether UV disinfection of the rearing water using a commercial device was useful for preventing infections among juveniles in a small-scale rearing system over a 28-day period (experiment 2). In experiment 1, parasite mortality reached 100% with UV irradiation doses of ≥9.60 × 10 5  μW s/cm 2 for I. salmonis and ≥8.40 × 10 5  μW s/cm 2 for T. truttae. In experiment 2, disinfection of the rearing water at a UV irradiation dose of 2.2 × 10 6  μW s/cm 2 succeeded in complete prevention of both parasites in the juvenile salmon. These results elucidate the minimum dose of UV irradiation for inactivation of I. salmonis and T. truttae, and demonstrate the usefulness of water disinfection using a commercial UV irradiation device to prevent infections by these parasites in hatchery-reared juvenile chum salmon., (© 2018 John Wiley & Sons Ltd.)

The identification and quantification of okadaic acid (OA)/dinophysistoxin (DTX) analogues and pectenotoxins (PTXs) in Dinophysis samples collected from coastal locations around Japan were evaluated by liquid chromatography mass spectrometry. The species identified and analyzed included Dinophysis fortii , D. acuminata , D. mitra ( Phalacroma mitra ), D. norvegica , D. infundibulus , D. tripos , D. caudata , D. rotundata ( Phalacroma rotundatum ), and D. rudgei . The dominant toxin found in D. acuminata was PTX2 although some samples contained DTX1 as a minor toxin. D. acuminata specimens isolated from the southwestern regions (Takada and Hiroshima) showed characteristic toxin profiles, with only OA detected in samples collected from Takada. In contrast, both OA and DTX1, in addition to a larger proportion of PTX2, were detected in D. acuminata from Hiroshima. D. fortii showed a toxin profile dominated by PTX2 although this species had higher levels of DTX1 than D. acuminata . OA was detected as a minor toxin in some D. fortii samples collected from Yakumo, Noheji, and Hakata. PTX2 was also the dominant toxin found among other Dinophysis species analyzed, such as D. norvegica , D. tripos , and D. caudata , although some pooled picked cells of these species contained trace levels of OA or DTX1. The results obtained in this study re-confirm that cellular toxin content and profiles are different even among strains of the same species.

Extremophilic microalgae are primary producers in acidic habitats, such as volcanic sites and acid mine drainages, and play a central role in biogeochemical cycles. Yet, basic knowledge about their species composition and community assembly is lacking. Here, we begin to fill this knowledge gap by performing the first large-scale survey of microalgal diversity in acidic geothermal sites across the West Pacific Island Chain. We collected 72 environmental samples in 12 geothermal sites, measured temperature and pH, and performed rbcL amplicon-based 454 pyrosequencing. Using these data, we estimated the diversity of microalgal species, and then examined the relative contribution of contemporary selection (i.e., local environmental variables) and dispersal limitation on the assembly of these communities. A species delimitation analysis uncovered seven major microalgae (four red, two green, and one diatom) and higher species diversity than previously appreciated. A distance-based redundancy analysis with variation partitioning revealed that dispersal limitation has a greater influence on the community assembly of microalgae than contemporary selection. Consistent with this finding, community similarity among the sampled sites decayed more quickly over geographical distance than differences in environmental factors. Our work paves the way for future studies to understand the ecology and biogeography of microalgae in extreme habitats., (© 2018 Phycological Society of America.)

The degree of iteroparity in stream-resident forms of masu salmon Oncorhynchus masou was examined using mark-recapture studies in natural streams. In a partially migratory population, at least 10% of resident males survived after maturation and repeatedly matured for up to 5 years. In the landlocked amago salmon subspecies, the post-maturation survival rate was at least 7% and repeat maturation was observed for up to 3 years for both males and females., (© 2018 The Fisheries Society of the British Isles.)

A method for the direct preparation of fatty-acid methyl esters (FAME) was simplified for fatty-acid analysis of a single fish larva using gas chromatography (GC). The method included the isolation of a larval trunk and drying in a glass vial, followed by saponification of all the contents without prior lipid extraction. Thereafter, the fatty acids released were methylated by trimethylsilyldiazomethane. This method has advantages over another method, direct acid-catalyzed transesterification, because both the saponification and methylation at room temperature can reduce loss of unsaturated fatty acids and formation of artifacts unavoidable in acidic reaction at high temperature. GC of the products showed that the simplified method can yield methyl esters without artifacts interfering analysis. More than 50 fatty acids were determined, which are twice as many as those previously analyzed using high-performance liquid chromatography. Observation of consistent small impurities in GC of blank tests allowed the accurate determination of fatty acids by correcting the peak areas. Dry matter weights (<3 mg) and the total fatty-acid contents displayed a linear relationship. Fatty-acid analysis of wild larvae of bluefin tuna, yellowfin tuna, and skipjack tuna collected from the waters around Japan (n = 100) revealed that the eicosapentaenoic acid (EPA) level in bluefin tuna collected from the Japan Sea was significantly higher than that in the three species collected from Nansei Islands. The simplified direct saponification/methylation method will be a powerful tool for investigating growth and survival of individual larval tuna and other fish species., (© 2018 AOCS.)

Objective: Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity within these populations remains unknown. In this study, we estimated the genetic diversity and key quantitative genetic parameters such as heritability and genomic breeding value for body size traits by means of genomic best linear unbiased prediction to assess the genetic health of these populations., Results: Ninety-nine and 83 females from the selective and random groups, respectively, were genotyped at 2350 putative SNPs by means of double digest restriction associated DNA sequencing. The genetic diversity in the selectively bred group was low, as were the estimated heritability and prediction accuracy for length and weight (h 2  = 0.26-0.28; accuracy = 0.34), compared to the randomly bred group (h 2  = 0.50-0.60; accuracy = 0.51-0.54). Although the tested sample size was small, these results suggest that further selection is difficult for the selectively bred population, while there is some potential for the randomly bred group, especially with the aid of genomic information.

In order to characterize how bacterial communities are propagated over spatial scales in a coastal area, the bacterial community composition was examined along with a transect line set in a bay at an expiry of spring phytoplankton bloom. Four distinctive bacterial communities were found within the bay by a fingerprinting method of 16S rRNA gene amplicons. The most widely distributed one was distributed in the surface and middle layers at whole area of the bay. The water was characterized by low inorganic nutrients concentration and high bacterial abundance, suggesting that the bacterial community had been developed in the bloom. Pyrosequencing analyses of the gene amplicons indicated that Rhodobacteriaceae and Flavobacteriaceae were abundant in the bacterial community, though the most abundant bacterial taxon was SAR11. The second group was distributed in the bottom water at the coastal side of the bay where considerably high Chl. a concentration was observed, probably because of the sedimentation of phytoplankton bloom. The community diversity was high and Alteromonadaceae, Saprospiraceae, and some families of Actinobacter existed more in this community than the others. The third group was distributed in the deep water near the border with the outside of the bay. The ratio of SAR11 was the highest in this community; besides, Burkholderianceae and Rhodospilliraceae existed in relatively high abundances. Another bacterial community having intermediate characters was observed in the middle to bottom layers around a central part of the bay where vertical water mixing was observed. These findings suggest that spatially different bacterial communities were formed under the influences of phytoplankton bloom and/or hydrographic events such as oceanic seawater intrusion of the bay., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)

In this study, we compared the eukaryote biodiversity between Hiroshima Bay and Ishigaki Island in Japanese coastal waters by using the massively parallel sequencing (MPS)-based technique to collect preliminary data. The relative abundance of Alveolata was highest in both localities, and the second highest groups were Stramenopiles, Opisthokonta, or Hacrobia, which varied depending on the samples considered. For microalgal phyla, the relative abundance of operational taxonomic units (OTUs) and the number of MPS were highest for Dinophyceae in both localities, followed by Bacillariophyceae in Hiroshima Bay, and by Bacillariophyceae or Chlorophyceae in Ishigaki Island. The number of detected OTUs in Hiroshima Bay and Ishigaki Island was 645 and 791, respectively, and 15.3% and 12.5% of the OTUs were common between the two localities. In the non-metric multidimensional scaling analysis, the samples from the two localities were plotted in different positions. In the dendrogram developed using similarity indices, the samples were clustered into different nodes based on localities with high multiscale bootstrap values, reflecting geographic differences in biodiversity. Thus, we succeeded in demonstrating biodiversity differences between the two localities, although the read numbers of the MPSs were not high enough. The corresponding analysis showed a clear seasonal change in the biodiversity of Hiroshima Bay but it was not clear in Ishigaki Island. Thus, the MPS-based technique shows a great advantage of high performance by detecting several hundreds of OTUs from a single sample, strongly suggesting the effectiveness to apply this technique to routine monitoring programs., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The ecological impacts of the 2011 Great East Japan Earthquake and tsunami and the following recolonization of the subtidal benthic polychaete community were examined by monthly pre- and post-quake field surveys that were conducted in Onagawa Bay from 2007 to 2013. Before the tsunami, the species composition in this benthic community was constant and was dominated by cirratulid and magelonid polychaetes. The density and biomass of benthic polychaetes drastically decreased after the tsunami, and the polychaete community fluctuated during the 2 years after the natural disaster. Spionid and capitellid polychaetes were dominant at this period. In June 2013, the community entered a new constant stage dominated by maldanids, which is different from the pre-quake community. Ecological impacts due to chemical pollution were suggested in addition to the tsunami disturbance. These overlapping effects and physical, chemical and biological factors affected the recovery and recolonization of the polychaete community after the natural disaster., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Evolutionary ecologists often expect that natural and sexual selection result in systematic co-occurrence patterns of sex-biased mortality and sexual size dimorphism (SSD) within animal species. However, whether such patterns actually occur in wild animals is poorly examined. The following expectation, the larger sex suffers higher mortality, was primarily tested here for apparently native sea-run masu salmon (Oncorhynchus masou) in three populations in Hokkaido, Japan. Field surveys on sex ratios, body sizes, and ages of smolts and returning adults revealed that two of the three populations exhibited an expected pattern, a female-biased marine mortality and SSD, but one population demonstrated an unexpected co-occurrence of male-biased marine mortality and female-biased SSD. These female-biased SSDs were attributed to faster marine growth of females because of no sex difference in smolt body size. It has been previously suggested that breeding selection favoring large size generally act more strongly in females than in males in Japanese anadromous masu, as there is a weak sexual selection on adult males but universally intensive natural selection on adult females. Thus, this hypothesis explains female-biased SSDs well in all study populations. Interpopulation variation in sex-biased mortality found here might result from differences in marine predation and/or fishing pressures, given that selection driving female-biased SSD makes females forage more aggressively than males during the marine phase. Taken together, these results raise the possibility that evolutionary forces have shaped adaptive sex-specific foraging strategies under relationships between growth and mortality, resulting in co-occurrence patterns of sex-biased mortality and SSD within animal species.

We conducted a one-year survey of macrozoobenthic community structure at 5 stations in a eutrophic canal in inner Tokyo Bay, focusing on the impacts of hypoxia, sediment H2S, and species interaction in the littoral soft-bottom habitats. Complete defaunation or decreasing density of less-tolerant taxa occurred under hypoxia during warmer months, especially at subtidal or sulfidic stations; this was followed by rapid recolonization by opportunistic polychaetes in fall-winter. Sedimentary H2S increased the mortality of macroinvertebrates under hypoxia or delayed population recovery during recolonization. The density of several polychaetes (e.g., Pseudopolydora reticulata) declined in winter, coincident with immigration of the predator Armandia lanceolata. This suggests that absence of A. lanceolata under moderate hypoxia enabled the proliferation of prey taxa. We conclude that oxygen concentration, sediment H2S, and hypoxia-induced changes in species interactions are potential drivers for spatiotemporal changes in macrozoobenthic assemblage structure in hypoxia-prone soft-bottom communities., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

Ayu Plecoglossus altivelis, a herbivorous fish, is an important fishery resource and key component of the foodweb in many Japanese streams. Radionuclide contamination of this species is likely transferred to higher trophic levels, include humans, in the food chain. After the Fukushima accident in March 2011, ayu were exposed to highly contaminated silt while feeding on algae attached to the riverbed stones. To understand the route by which herbivorous fish are exposed to radionuclides, the activity concentrations of sum of (134)Cs and (137)Cs (radiocesium) were analyzed in riverbed samples (algae and silt) and in the internal organs and the muscle of ayu in five river systems in the Fukushima Prefecture between summer 2011 and autumn 2013. Although there was a positive correlation between the radiocesium activity concentrations in the muscle and the internal organs of ayu, the median activity concentration in the muscle was much lower than those in the internal organs. The activity concentrations of radiocesium in the riverbed samples and the internal organs and the muscle of ayu were correlated with contamination levels in soil samples taken from the watershed upstream of the sample sites. The results of the generalized linear mixed models suggest that the activity concentrations in both the internal organs and the muscle of ayu declined over time. Additionally, the activity concentrations in the internal organs were correlated with those in the riverbed samples that were collected around the same time as the ayu. The activity concentrations in the muscle were correlated with ayu body size. Our results suggest that ayu ingest (134)Cs and (137)Cs while grazing silt and algae from the riverbed, and a part of the (134)Cs and (137)Cs is assimilated into the muscle of the fish., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Air-breathing divers are assumed to have evolved to apportion their time between surface and underwater periods to maximize the benefit gained from diving activities. However, whether they change their time allocation depending on the aim of the dive is still unknown. This may be particularly crucial for 'surfacers' because they dive for various purposes in addition to foraging. In this study, we counted breath events at the surface and estimated oxygen consumption during resting, foraging and other dives in 11 green turtles (Chelonia mydas) in the wild. Breath events were counted by a head-mounted acceleration logger or direct observation based on an animal-borne video logger, and oxygen consumption was estimated by measuring overall dynamic body acceleration. Our results indicate that green turtles maximized their submerged time, following this with five to seven breaths to replenish oxygen for resting dives. However, they changed their dive tactic during foraging and other dives; they surfaced without depleting their estimated stores of oxygen, followed by only a few breaths for effective foraging and locomotion. These dichotomous surfacing tactics would be the result of behavioural modifications by turtles depending on the aim of each dive., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

Temperature-driven life-history modifications by adaptation occur in ectotherms, and therefore, life-history modifications by adaptation need to be taken into consideration when predicting population responses to the climate change. Partial migration is a common form of life-history diversity in which a population contains both migratory and resident behaviours. Salmonid fish exhibit a wide range of life-history diversity and, in particular, partial migration. We evaluated the effect of temperature-driven life-history modifications on population dynamics in partially migratory masu salmon (Oncorhynchus masou) by field observations and theoretical models. Field observations revealed that spatial patterns of alternative migratory tactics were associated with temperature gradients. The occurrence of resident males increased, whereas the proportion of migrant males and the proportion of delayed migrants including both sexes decreased with increasing temperature and, thereby, with improved early growth conditions. The expected fitness for each migratory tactic was computed in a life-history model with early growth conditions as a function. Individual fitness was maximized by adopting resident tactics under favourable early growth conditions, early migrant tactics under intermediate early growth conditions and delayed migrant tactics under unfavourable early growth conditions. The results suggest that individuals exhibited a status-dependent conditional strategy, that is, the adoption of alternative migratory tactics is influenced by the status of individuals to make the best of a situation. A simulation model suggests that increased residency by males to increased temperature leads to a substantial decrease in the number of migrants. Moreover, the decrease in the number of delayed (older) migrants with increasing temperature magnified fluctuations in abundance. Our findings indicate the importance of temperature-driven life-history modifications for predicting dynamics of natural populations under climate warming., (© 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.)

Four long-spined sea urchin species in the genus Diadema are known to occur around the Japanese Archipelago. Three species (D. savignyi, D. setosum, and D. paucispinum) are widely distributed in the Indo-Pacific Ocean. The fourth species was detected by DNA analysis among samples originally collected as D. savignyi or D. setosum in Japan and the Marshall Islands and tentatively designated as Diadema-sp, remaining an undescribed species. We analyzed nucleotide sequences of the cytochrome oxidase I (COI) gene in the "D. savignyi-like" samples, and found all 17 individuals collected in the mainland of Japan (Sagami Bay and Kyushu) to be Diadema-sp, but all nine in the Ryukyu Archipelago (Okinawa and Ishigaki Islands) to be D. savignyi, with large nucleotide sequence difference between them (11.0%±1.7 SE). Diadema-sp and D. savignyi shared Y-shaped blue lines of iridophores along the interambulacrals, but individuals of Diadema-sp typically exhibited a conspicuous white streak at the fork of the Y-shaped blue iridophore lines, while this feature was absent in D. savignyi. Also, the central axis of the Y-shaped blue lines of iridophores was approximately twice as long as the V-component in D. savignyi whereas it was of similar length in Diadema-sp. Two parallel lines were observed to constitute the central axis of the Y-shaped blue lines in both species, but these were considerably narrower in Diadema-sp. Despite marked morphological and genetic differences, it appears that Diadema-sp has been mis-identified as D. savignyi for more than half a century.

The concentrations of PCB congeners in the blubber and liver of mother Steller sea lions (Eumetopias jubatus; SSLs) and their fetuses from the coast of Hokkaido, Japan in 2008, 2010 and 2012 were analyzed by HRGC-HRMS, in order to elucidate PCB congener profiles and maternal-to-fetal transfer of PCBs in SSLs. ΣPCBs in the fetuses were 1400 ± 660 (the mean ± SD) ng/g-fat in the blubber and 570 ± 320 ng/g-fat in the liver, respectively. There was a concern that SSLs had been contaminated by PCBs during the fetal period. The concentrations of the major congeners in the blubber and liver were a correlation between the fetus and mother (blubber: r=0.9934, liver: r=0.9160; P ≦ 0.05). The results indicated that PCBs in the fetuses came from the mothers. #177 and #199 showed no correlations between the fetus and the mother in the blubber and liver. This indicated a selective capture by some natural protector such as the placenta., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Three Gram-negative, non-motile, strictly aerobic strains, designated LNM-20(T), LCM-1 and LAM-13, were isolated from thalli of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates were associated with the genus Polaribacter in the family Flavobacteriaceae and were most closely related to Polaribacter dokdonensis DSW-5(T) (96.2 % 16S rRNA gene sequence similarity) and Polaribacter gangjinensis K17-16(T) (95.0 %). The DNA G+C content of the isolates was 28.6-29.2 mol%. DNA-DNA hybridization analysis showed that the isolates belonged to a single species distinct from both of their closest relatives. The only isoprenoid quinone detected was menaquinone-6. The main polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1ω10c and iso-C15 : 0 3-OH. The phenotypic features of strain LNM-20(T) differed from those of their closest relatives in several regards (colony colour, growth with 1 % NaCl and on TSA plus 2.5 % NaCl, hydrolysis of Tweens 40 and 80, and oxidization of five carbon compounds). On the basis of phylogenetic, chemotaxonomic and phenotypic analysis, the isolates represent a novel species in the genus Polaribacter, for which the name Polaribacter porphyrae sp. nov. is proposed. The type strain is LNM-20(T) ( = LMG 26671(T)  = NBRC 108759(T)). Emended descriptions of the genus Polaribacter and P. dokdonensis and P. gangjinensis are also proposed.

Ammonia oxidization is the first and a rate-limiting step of nitrification, which is often a critical process in nitrogen removal from estuarine and coastal environments. To clarify the correlation of environmental conditions with the distribution of ammonia oxidizers in organic matter-rich coastal sediments, ammonia-oxidizing archaea (AOA) and bacteria (AOB) ammonia monooxygenase alpha subunit gene (amoA) abundance was determined in sediments of Matsushima Bay located in northeast Japan. The AOA and AOB amoA copy numbers ranged from 1.1×10(6) to 1.7×10(7) and from 7.1×10(5) to 7.6×10(6) copies g(-1) sediment, respectively. AOA and AOB amoA abundance was negatively correlated with dissolved oxygen levels in the bottom water. AOA amoA abundance was also correlated with total phosphorus levels in the sediments. On the other hand, no significant relationship was observed between the amoA abundance and ammonium, organic matter (ignition loss), or acid volatile sulfide-sulfur levels in the sediments. These results show the heterogeneous distribution of ammonia oxidizers by the difference in environmental conditions within the bay. Moreover, AOA amoA diversity was relatively low in the area of high AOA amoA abundance, suggesting the variability of AOA community composition.

The initial factors that cause a decline in the survival of in situ settled corals remain poorly understood. In this study, we demonstrated through field experiments that the design of artificial grid plates may influence the initial survival of Acropora corals, with narrower grids being the most effective. In fact, grid plates with a 2.5-cm mesh presented the highest recorded survival rate (14%) at 6 months after settlement (representing approximately 50 corals per 0.25 m(2) of plate). This is the first study where such high survival rates, matching those of cultures under aquarium conditions, were obtained in the field without using additional protective measures, such as guard nets against fish grazing after seeding. Therefore, our results provide a foundation for establishing new and effective coral restoration techniques for larval seeding, in parallel to clarifying the details of the early life stages of reef-building corals., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Seasonal variation in body size and nutritional condition of juvenile walleye pollock Theragra chalcogramma was examined to elucidate the mechanism underlying their first-winter survival on the continental shelf of the Doto area, northern Japan, based on monthly samples collected over 2 years. Stored lipid mass was highest during autumn, but 93% (2004) and 80% (2005) of lipids were exhausted by the onset of winter. Lipid levels in the winter of 2004 remained low (7-14% of the autumnal maximum), and there was reduced growth rate until the spring, whereas in 2005 lipid levels were higher and more variable (10-46% of the maximum) and some growth occurred. An analysis of the allometric relationships between body size and stored energy showed that larger individuals accumulated disproportionately more energy in the autumn, but the advantage disappeared prior to the winter. In January 2004, stored lipid energy was low throughout the Doto continental shelf relative to the continental slope area. These results suggest that winter feeding opportunities on the shelf are severely limited but not completely absent. Previous studies have shown that winter temperatures on the shelf are lower than those in the slope area. It is possible that juvenile T. chalcogramma survive winter on the shelf without a high level of pre-winter lipid storage because the occasional feeding in the cold shelf water benefits energy conservation.

Considerable interannual variation in the abundance of larval and juvenile Pacific herring Clupea pallasii was detected in Miyako Bay, on the Pacific coast of northern Japan; abundances were high in 2001 and 2003 and low in 2000 and 2002. Hatch dates and growth rates for larval and juvenile survivors were estimated through otolith analysis. Water temperature and food availability were monitored on the spawning and nursery grounds in the inner part of the bay. The number of spawning females caught in nets set around the spawning ground was recorded during each spawning season (January to May) in 2000-2003. No correlation was found between the number of spawning females and the abundance of larvae and juveniles on the spawning and nursery grounds. The hatch dates of surviving larvae and juveniles were concentrated at the end of the spawning season in 2001 and in the middle of the season in 2003. The larvae experienced relatively high prey concentrations during the first-feeding period in 2001 but low concentrations in 2003. Survival of larvae during the first-feeding period may be a function of prey concentration as well as water temperature. In 2003, low water temperature would reduce starvation mortality during the first-feeding period. In contrast, unfavourable feeding conditions with higher temperatures during the first-feeding period seemed to result in low larval survival in 2000 and 2002. The 2001 larvae grew faster than those in 2003 because of the late hatch dates and the higher ambient temperatures that resulted. Temperature might be a major factor controlling growth rates of C. pallasii larvae in Miyako Bay.

Latitudinal variation in egg size and number in anadromous masu salmon Oncorhynchus masou was examined. Relatively greater variation in egg size occurred among rivers than among females within rivers or within females. Egg size was generally greater and egg number generally lower at more northerly latitudes.

To clarify the natural diet of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus, the sources of 18S rDNA clones obtained from the hepatopancreas were investigated. Of a total of 1537 clones examined, 160 had different restriction profiles from the host larvae, in which 21 restriction types were observed. Nucleotide sequences of 16 of 21 restriction types were successfully determined and their assignments were investigated by homology search and phylogenetic analysis. From seven late-stage larvae collected in spring to early summer, eukaryote DNA molecules of Teleostei, Oomycetes, Mycetozoa, and Fungi were identified. Exogenous DNA from four younger phyllosoma larvae collected in late autumn could not be recovered. A previous study identified DNAs of cnidarians and urochordates in late-stage phyllosoma larvae of a closely related species collected in winter. This indicates that the phyllosoma larvae are opportunistic carnivores, whose diets correlate with the relative abundance of prey organisms in the ambient water.

Several strains of Protoceratium reticulatum, one of the dinoflagellates producing yessotoxins (YTXs), were collected from various shellfish producing areas in Japan. YTXs in the cultured strains were analyzed by liquid chromatography-mass spectrometry (LC-MS). Neutral loss scan monitoring, multiple reaction monitoring (MRM) for more than 20 YTX analogues, and full-scan MS/MS spectra obtained with a hybrid triple quadrupole/linear ion trap mass spectrometer showed that yessotoxin (YTX), 45,46,47-trinoryessotoxin (trinorYTX), 1-homoyessotoxin (homoYTX), and 45,46,47-trinor-1-homoyessotoxin (trinor-1-homoYTX) were the dominant toxins in these strains of P. reticulatum. Enone isomer of 42,43,44,45,46,47,55-heptanor-41-oxoyessotoxin (noroxoYTX enone) was also detected in some strains. Toxin profiles and contents were different among the strains. Some strains produced YTX, trinorYTX, 1-homoYTX, trinor-1-homoYTX, and noroxoYTX enone, whereas other strains produced only YTX or 1-homoYTX. This is the first identification of 1-homoYTX and noroxoYTX enone in P. reticulutum in Japan. Some strains did not produce any detectable YTX analogues.

In many benthic organisms with a planktonic larval stage, local populations have different morphology. Such difference may arise from some of the following proximate mechanisms. "Local recruitment (LR)": no larvae move between local populations, and segregated populations possess alleles coding for locally adaptive morphology. "Intragenerational selection (IS)": larvae move between local populations, and individuals with alleles for locally adaptive morphology survive after recruitment. "Phenotypic plasticity (PP)": larvae move between local populations and show phenotypic plasticity to adapt to a locality after recruitment. We examined which mechanism explains our finding that a planktonic developer Turbo coronatus coronatus (Gastropoda) had significantly longer spines on its shell on more exposed shores at scales of < 2 km. Experiments at Ishigaki Island, Okinawa, Japan, showed the following results. (a) Shorter- and longer-spined populations occurring within 2 km showed non-significant low psi(ST) values (-0.0040 to 0.00095) for the mitochondrial DNA COI region. This suggests no segregation of the local populations, supporting the mechanisms IS and PP. (b) T. c. coronatus generated significantly longer spines 70 days after being transplanted to the habitat of a longer-spined population, supporting IS and PP. (c) Individuals caged in the sea for 79 days generated longer spines than individuals in the laboratory, supporting PP. In conclusion, shore-specific morphology of T. c. coronatus arises most likely from phenotypic plasticity and possibly from intragenerational selection.

We present novel microsatellite markers of the Japanese abalone (Haliotis discus hannai) for general mapping studies in this species. A total of 75 microsatellite markers were developed, and the allele-transmission patterns of these markers were studied in three families generated by pair crosses. For allele scoring, we employed the 5'-tailed primer polymerase chain reaction (PCR) technique, which substantially reduces the cost for fluorescent labeling of primers. Of the 225 possible marker-family combinations (75 markers x 3 families), 18 cases of informative null-allele segregation were inferred. When such null-allele segregations were allowed, more than 70% of the 75 markers in the families turned out to be markers with an expected segregation ratio of 1:1:1:1, allowing maximal exploitation of the codominant nature of microsatellite markers. There were 16 instances of segregation distortion at the 5% significance level. The test for independence of segregation assigned the 75 markers into 17 linkage groups, which is in close agreement with the haploid chromosome number of H. discus hannai (n = 18). Six markers could not be placed into any linkage group. We suggest that these markers could help construct a H. discus hannai linkage map.

Mass mortalities of the pen shell Atrina pectinata occurred in the fishing grounds of Ariake Bay, in southwestern Japan, during late spring and summer in 2003 and 2004. Histological examination revealed extensive necrosis in the epithelial cells of the kidney and gill, and impairment of the endothelial cells of the mantle arteria. Although cestode larvae belonging to the genus Tylocephalum were found in the mantle, adductor muscle, kidney, and digestive gland, their prevalence and the intensity of infection were low. Examinations of moribund pen shells for Haplosporidium spp. infection using PCR analysis and for Perkinsus spp. infection using Ray's fluid thioglycollate medium were negative. Unenveloped virus-like particles were detected by transmission electron microscopy in the cytoplasm of affected kidney and gill cells of moribund pen shells. They were icosahedral spherical and 50 to 55 nm in diameter. These virus-like particles found in moribund pen shells are different from those described in other marine mollusks, and may be the causative agent of the mass mortalities of pen shells.

We document the potential of novel microsatellites as a genetic tool in furthering our understanding of the Crassostrea gigas genetic structure. From the microsatellite-enriched libraries we constructed, 123 repeat regions that had sufficient sequence information to design polymerase chain reaction primer sets were isolated. From these, 9 primer pairs were screened in a C. gigas population of 67 individuals to evaluate the genetic variability. All but 1 of the 9 loci showed allelic variation (number of alleles, 2-20; observed heterozygosity, 0.119-0.925; unbiased expected heterozygosity, 0.139-0.914). Considerable discrepancy of genotypic proportions from the Hardy-Weinberg equilibrium was observed at 1 locus with an apparent heterozygote deficiency. Several loci were successfully amplified in 3 other related species with the appropriate allele size: 6 loci in C. sikamea, 4 loci in C. ariakensis, and 5 loci in C. nippona.

We cloned and sequenced the complete mitochondrial genome of Japanese flounder (Paralichthys olivaceus). A circular 17,090 bp mitochondrial genome from the flounder contains 37 structural genes as in other vertebrates so far reported. This is the first report of the complete mitochondrial sequence from a higher teleostean fish (Acanthopterygii). The organization including gene order is quite similar to that of other teleostean fishes as well as placental mammals. The putative control region of the Japanese flounder mitochondrial genome contains a length variable region of about a 74 bp tandem repeat cluster. As a preliminary study we adopted the maximum likelihood and neighbor-joining inference methods to examine phylogenetic relationships among teleostean and related fishes. Comparisons of amino acid sequences of protein-coding genes and nucleotide sequences of tRNA genes resolved some middle to deep branches among some teleostean fishes. The flounder mitochondrial genome does not show an indication of evolutionary rate difference among teleosts leading to difficulty in phylogenetic analyses, and our data is useful for future evolutionary studies dealing with higher teleostean fishes.