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Aquaculture contributes to the sustainable development of food security, marine resource conservation, and economy. Shifting aquaculture feed from fish meal and oil to terrestrial plant derivatives may result in cost savings. However, many carnivorous fish cannot be sustained on plant-derived materials, necessitating the need for the identification of important factors for farmed fish growth and the identification of whether components derived from terrestrial plants can be used in feed. Herein, we focused on the carnivorous fish leopard coral grouper ( P. leopardus ) to identify the essential growth factors and clarify their intake timing from feeds. Furthermore, we evaluated the functionality of starch, which are easily produced by terrestrial plants. Results reveal that carbohydrates, which are not considered essential for carnivorous fish, can be introduced as a major part of an artificial diet. The development of artificial feed using starch offers the possibility of increasing the growth of carnivorous fish in aquaculture.

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.

Eel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

With the worldwide demand for tropical penaeid prawn increasing in recent decades, more research on shrimp culture methods is needed to enhance efficiency and profitability for shrimp farmers. The objective of this study was to develop a technique to boost the productivity, feed efficiency, and profitability of the giant tiger prawn (Penaeus monodon). To accomplish this, a novel culture setup was established in which two benthic organisms, a filamentous green alga (Chaetomorpha sp.) and a microsnail (Stenothyra sp.), were propagated together with P. monodon post-larvae during an early culture stage and then offered to shrimp as supplementary live feeds in intensive aquaculture ponds. For the experiment, shrimp post-larvae (density: approximately 33 individuals m-2) were cultured in outdoor concrete ponds (9 × 9 × 1.2 m) under either control (fed only artificial feed, n = 3) or experimental (fed artificial feed and benthic organisms, n = 3) conditions until they reached marketable size (15 weeks). Apparent green algae consumption was 6.81 kg (8.4% green alga to total feed consumption), whereas microsnail consumption was 1.96 kg (2.4% microsnail to total feed consumption). Compared with the control group of giant tiger prawn, the experimental group showed significantly higher productivity (total number of shrimp produced: 118%; total shrimp production: 133%), feed efficiency (feed conversion ratio of artificial shrimp feed: 89%), and profitability (shrimp sales: 139%; balance between shrimp sales and costs: 146%), while labor and financial costs were kept minimal. These results can be explained by the enhanced growth of shrimp at the early stages of culture. The techniques developed in this study will help to advance the efficiency of intensive aquaculture operations for giant tiger prawn and also improve profitability for shrimp farmers., 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.)

A new snailfish, Paraliparis flammeus , is described on the basis of 18 specimens collected off the Pacific coast of Tohoku District, northern Japan at depths of 422-890 m. The new species is distinguished from 28 species of Paraliparis described from the North Pacific by the following combination of characters: mouth oblique; uppermost pectoral-fin base below horizontal through posterior margin of maxillary; 60-63 vertebrae, 54-58 dorsal-fin rays, 50 or 51 anal-fin rays, six principal caudal-fin rays, and 17-20 pectoral-fin rays. A maximum likelihood tree based on 106 COI gene sequences (492 bp) of Paraliparis recovered a monophyletic group comprising P. flammeus , Paraliparis cephalus , and Paraliparis dipterus . Paraliparis cephalus is similar to P. flammeus in having an oblique mouth, but it has four caudal-fin rays (vs six rays) and the uppermost pectoral-fin base above a horizontal through the maxillary posterior margin. Paraliparis dipterus differs from P. flammeus in having a horizontal mouth, 12-14 pectoral-fin rays, and lacking pyloric caeca (present in P. flammeus ). Paraliparis flammeus is most similar to the eastern North Pacific Paraliparis mento in having an oblique mouth and the uppermost pectoral-fin base below a horizontal through the posterior margin of the maxillary. However, P. flammeus differs from P. mento in having six caudal-fin rays (vs five rays) and greater preanal length (29.9-35.3% SL vs 26.7-28.5% SL). A poorly known species, Paraliparis mandibularis , previously known from only two specimens collected from Tosa Bay, southern Japan, is redescribed based on the holotype and seven newly collected specimens. It is also similar to the new species but has 27-30 pectoral-fin rays and a shorter pectoral-fin lower lobe (13.8-15.9% SL in P. mandibularis vs 16.7-23.4% SL in P. flammeus )., (Yoshiaki Kai, Kenta Murasaki, Ryo Misawa, Atsushi Fukui, Eisuke Morikawa, Yoji Narimatsu.)

We present the first draft whole-genome sequence for the Parmales (Bolidophyceae, Heterokonta), a picoplanktonic sister group of diatoms, using a Triparma laevis f. inornata strain that was isolated from the Oyashio region in the western North Pacific Ocean., (Copyright © 2020 Kuwata et al.)

Coral reefs support diverse communities, and relationships among organisms within these communities are quite complex. Among the relationships, clarifying the habitat association and foraging substrate selection relative to habitat characteristics is of central importance to ecology since these two aspects are the fundamentals for survival and growth of organisms. The aims of the present study were to investigate the spatial distribution and feeding substrate selection of 14 species of butterflyfishes on an Okinawan coral reef in Japan. Species-specific spatial distributions varied with habitat characteristics (e.g., encrusting corals, massive corals, branching Acropora and rock). For feeding substrates, seven species of obligate coral polyp feeders exhibited significant positive selectivity for tabular Acropora , corymbose Acropora , encrusting corals and massive corals but significant negative selectivity for dead corals, coral rubble and rock. Among six species of facultative coral polyp feeders, two species exhibited significant positive selectivity for encrusting corals and massive corals, and one species showed significant positive selectivity for dead corals as feeding substrates. In contrast, three species exhibited no significant positive selectivity for any feeding substrates. A similar result was observed for one non-coralline invertebrate feeder. Among the 14 species, 12 species showed a relatively close relationship between spatial distribution and feeding substrates but the remaining two species did not. The present study is the first study to elucidate species-specific spatial distributions and feeding substrate selection of butterflyfishes on an Okinawan coral reef. The results of the present study suggest that diverse substrates, including various types of living corals (especially encrusting corals, massive corals, tabular Acropora , corymbose Acropora and branching Acropora ) and non-coralline substrates (rock) are the primary determinants of spatial distributions and feeding sites. Thus, diverse substrates are important for maintaining high species diversity of butterflyfishes and changes of the substrates would likely change the spatial patterns and foraging behavior, although species-specific responses may be found, depending on their species-specific dependence on vulnerable substrates., Competing Interests: The authors declare there are no competing interests., (©2020 Nanami.)

There is accumulating evidence that insulin-like growth factors (IGFs), primary mediators of somatic growth, play an important role in fish reproduction. Previously, we showed that IGF-1 and IGF-2 are expressed in the ovarian follicle cells of the yellowtail ( Seriola quinqueradiata ) during the vitellogenic phase, suggesting that IGFs may be involved in ovarian steroidogenesis. In this study, we examined the effects of IGF-1 and IGF-2 on gene expression and activity of steroidogenic enzymes in yellowtail ovary in vitro . IGF-1 and IGF-2 had no effect on mRNA levels of several steroidogenesis-related genes ( star , cyp11a1 , hsd3b , cyp17a2 , and cyp19a1 ). However, both IGFs enhanced the transcription of cyp17a1 in vitellogenic ovaries, although such up-regulation was not found in the ovary at the pre-vitellogenic stage. The stage-dependent effects of IGFs were correlated with changes in ovarian cyp17a1 mRNA levels during the reproductive cycle: transcript abundances increased in conjunction with ovarian development. In addition, IGF-induced cyp17a1 gene expression was significantly inhibited by wortmannin, suggesting that PI3 kinase plays an essential role in IGF-mediated ovarian steroidogenesis. Furthermore, IGF-1 and IGF-2 promoted the conversion of both progesterone and 17α-hydroxyprogesterone to androstenedione in vitellogenic ovaries, suggesting that both IGFs stimulated 17α-hydroxylase and C 17-20 lyase activities. Taken together, these findings suggest that IGF-1 and IGF-2 act directly on follicle cells to stimulate steroid production through an increase in gene expression and enzymatic activity of cyp17a1 via induction of PI3 kinase., (© 2020 The Authors.)

Metacercarial cysts of the parasite Scaphanocephalus (Platyhelminthes: Trematoda: Heterophyidae) are frequently found on the pectoral fins and skin of parrotfishes (Labridae: Scarini) inhabiting Okinawan coral reefs in southern Japan. The prevalence of metacercarial cysts in 30 parrotfish species was investigated and compared through a market survey. Although parasite prevalence differed between parrotfishes, all species examined are considered to be suitable hosts. Prevalence was high in Scarus chameleon (38.5%, n = 13), S. rubroviolaceus (33.4%, 2797), S. ghobban (26.6%, 6441), and several other species that share, in part, common feeding habits. Conversely, prevalence was low in S. prasiognathos (0.4%, 1842), Bolbometopon muricatum (0.4%, 270), and Hipposcarus longiceps (0.1%, 8512) which have different feeding habits. Despite a few exceptions, feeding ecology and other indirect behaviors are considered to affect the prevalence of metacercarial cysts in parrotfishes. Taxonomic affiliation and nocturnal mucous cocoon usage are not considered to affect parasite prevalence., Competing Interests: On behalf of all authors, the corresponding author states that there is no conflict of interest., (© 2020 The Authors.)

Background: Aggregation affects the fertilization rate of species that utilize external fertilization. However, the process of aggregation has not been studied in detail, using either theoretical models or real world observations. We used the Ezo abalone Haliotis discus hannai as a model animal species to evaluate whether mucus trail following (MTF) facilitates aggregation by reducing the distance between members of opposite sexes. We also examined whether the fertilization rate increase with mucus-trail-following is an evolutionary driving force in mucus following behavior., Methods: We used a y-maze to test whether H. discus hannai follows the mucus trails of other individuals. Distances between members of the opposite sex of MTF individuals were compared to non-MTF individuals using an individual-based model (IBM) consistent with the behavior of H. discus hannai . To examine whether MTF behavior evolved to reduce distances between members of the opposite sex, we constructed simple population genetic models of a diploid population with nonoverlapping, discrete generations., Results: Haliotis discus hannai chose the y-maze arm with the mucus trail more frequently than the one without, regardless of the sex of the abalone that secreted the mucus or the reproductive season. In the IBM the distance between opposite sexes was significantly reduced by MTF behavior; however, the difference in distances between opposite sex compared to same sex individuals was only several centimeters. Simple population genetic models indicated that the aggregating effect of MTF between the opposite sex members could be an evolutionary driving force., Conclusions: These results suggest that observed MTF behavior might have evolved as a mechanism to increase the fertilization rates although other factors could also be involved., Competing Interests: The author declares there are no competing interests., (©2020 Matsumoto.)

In chelonids, oxygen is primarily stored in the lungs during a dive. Therefore, management of blood oxygen transportation to peripheral tissues by cardiovascular adjustments during submergence is crucial to maximize their dive duration, and consequently, the time spent for ecological activities such as foraging. However, the cardiac response to exercise has rarely been examined in sea turtles. In this study, heart rate and its relationship with exercise during voluntary dives were determined in six captive green turtles (19.4±1.5 kg) by simultaneously recording depth, acceleration and electrocardiogram. Our results demonstrated that the heart rate of green turtles was generally low (11.1±0.4 bpm) during resting dives, but they often exhibited instantaneously extreme tachycardia (up to 78.4 bpm). Green turtles elevated their heart rate up to 39.8±1.5 bpm during ventilation after resting dives, while up to 33.1±1.4 bpm after active dives. The heart rate immediately elevated with onset of exercise, and increased linearly with exercise. This result may indicate that turtles immediately need to transport oxygen from the lungs to peripheral tissues by pulmonary and systemic circulations to meet the metabolic demands of exercise because they mainly store oxygen in their lungs., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists 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.

Marine fish stocks are an important part of the world food system and are particularly important for many of the poorest people of the world. Most existing analyses suggest overfishing is increasing, and there is widespread concern that fish stocks are decreasing throughout most of the world. We assembled trends in abundance and harvest rate of stocks that are scientifically assessed, constituting half of the reported global marine fish catch. For these stocks, on average, abundance is increasing and is at proposed target levels. Compared with regions that are intensively managed, regions with less-developed fisheries management have, on average, 3-fold greater harvest rates and half the abundance as assessed stocks. Available evidence suggests that the regions without assessments of abundance have little fisheries management, and stocks are in poor shape. Increased application of area-appropriate fisheries science recommendations and management tools are still needed for sustaining fisheries in places where they are lacking., Competing Interests: Competing interest statement: All authors are involved in fisheries management or provide fisheries advice in ways that can be viewed as competing interests. Many are employed by national fisheries agencies or nongovernmental organizations that advocate for specific fisheries policies. The academic scientists have received funding from sources that include government fisheries agencies, fishing companies, and environmental nongovernmental organizations., (Copyright © 2020 the Author(s). Published by PNAS.)

Giant clams have evolved to maximize sunlight utilization by their photosymbiotic partners, while affording them protection from harmful ultraviolet (UV) light. The presence of UV absorbing substances in the mantle is thought to be critical for light protection; however, the exact localization of such compounds remains unknown. Here, we applied a combination of UV liquid chromatography (LC), LC-mass spectrometry (MS), MS imaging, and UV micrography to localize UV absorbing substances in the giant clam Tridacna crocea. LC-MS analysis revealed that the animal contained three classes of mycosporines: progenitor, primary, and secondary mycosporines. MS imaging revealed that primary and secondary mycosporines were localized in the outermost layer of the mantle; whereas progenitor mycosporines were distributed throughout the mantle tissue. These findings were consistent with the results of UV micrography, which revealed that the surface layer of the mantle absorbed UV light at 320 ± 10 nm. This is the first report indicating that progenitor and primary mycosporines are metabolized to secondary mycosporines by the giant clam and that they are differentially localized in the surface layer of the mantle to protect the animal from UV light.

The spawning behavior of a Japanese flying squid (Todarodes pacificus) is described based on up-close observation of a captive female. The squid was first transferred from a 10-ton tank to a polystyrene plastic box containing 45 liters of seawater. About one hour later, the mantle-contraction rate increased rapidly, followed by a brief convulsion of the mantle and arms and a whitening of the body. The mantle contractions become shallow and rapid, and several seconds later, semitransparent jelly presumably from the nidamental glands emerged from the funnel and passed between the ventral pair of arms. Approximately 90 seconds after the egg mass first emerged, the female began ejecting oocytes through the funnel into the egg mass using rapid, powerful mantle contractions. Soon after the oocytes were ejected, translucent strands (presumably sperm) emanated from the buccal membrane. The female continued to eject oocytes for approximately two minutes, after which the mantle convulsed, and the mantle-contraction rate decreased slowly for about one minute until the contractions stopped. The squid died soon afterwards.

Natural diets of leptocephalus larvae have been enigmatic. In this study, we collected DNA samples from the gut contents and body surface of leptocephali belonging to the five Anguilliform families (Anguillidae, Chlopsidae, Congridae, Muraenidae, and Serrivomeridae) from the northwest Pacific and performed next-generation 18S rDNA sequencing. Wide variety of eukaryotes was detected in both samples, from which eight eukaryotic groups (jellyfish, conoid parasite, tunicate, copepod, krill, segmented worm, fungi, and dinoflagellate) were selected on the basis of abundance. All groups except conoid parasites were common in both the samples. Cnidarian 18S rDNA reads were the most abundant in both the samples; however, the number of samples having cnidarian reads and the read counts were significantly higher in the body surface scraping samples than in the gut content samples, regardless of careful rinsing of the body surface. These results indicate that the cnidarian DNAs are most likely found because of cross contamination from the body surface and/or environment. 18S rDNA read counts of copepod and tunicate in the gut contents were greater than or comparable with those in the body surface scraping samples, which may correspond to the previous observations of fecal pellets and larvacean houses in the leptocephali gut. Thus, the present study supports previous implications that leptocephali utilize detritus materials, so called marine snow., Competing Interests: The authors have declared that no competing interests exist.

Larval descriptions of tropical marine and coastal fishes are very few, and this taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification in ecological and early life history studies of larval fishes is crucial for fishery management and habitat protection. The present study aimed to evaluate the usefulness of DNA barcodes to support larval fish identification since conventional dichotomous keys based on morphological traits are not efficient due to the lack of larval traits and the rapid morphological changes during ontogeny. Our molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from the Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were identified at the species level, two taxa (4%) at the genus level, and 14 taxa (29%) at family level. The relatively low rate of species-level identification is not necessarily due to the DNA barcoding method per se , but a general lack of reference sequences for speciose and non- commercial fish families such as Gobiidae, Blenniidae, and Callionymidae. Larval morphology remains important in species diagnoses when molecular matches are ambiguous. A lower ethanol percentage (50%) for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analyses. The 10% Chelex resin used to extract DNA is also cost- effective for long term monitoring of larval fishes. Hence, the DNA barcoding method is an effective and easy way to aid the identification of estuarine larval fishes at the species level.

Diatoms play important roles in primary production and carbon transportation in various environments. Large-scale diatom bloom occurs worldwide; however, metabolic responses of diatoms to environmental conditions have been little studied. Here, we targeted the Oyashio region of the western subarctic Pacific where diatoms bloom every spring and investigated metabolic response of major diatoms to bloom formation by comparing metatranscriptomes between two depths corresponding to different bloom phases. Thalassiosira nordenskioeldii and Chaetoceros debilis are two commonly occurring species at the study site. The gene expression profile was drastically different between the surface (late decline phase of the bloom; 10 m depth) and the subsurface chlorophyll maximum (SCM, initial decline phase of the bloom; 30 m depth); in particular, both species had high expression of genes for nitrate uptake at the surface, but for ammonia uptake at the SCM. Our culture experiments using T. nordenskioeldii imitating the environmental conditions showed that gene expression for nitrate and ammonia transporters was induced by nitrate addition and active cell division, respectively. These results indicate that the requirement for different nitrogen compounds is a major determinant of diatom species responses during bloom maturing.

Calibration of the molecular rate is one of the major challenges in marine population genetics. Although the use of an appropriate evolutionary rate is crucial in exploring population histories, calibration of the rate is always difficult because fossil records and geological events are rarely applicable for rate calibration. The acceleration of the evolutionary rate for recent coalescent events (or more simply, the time dependency of the molecular clock) is also a problem that can lead to overestimation of population parameters. Calibration of demographic transition (CDT) is a rate calibration technique that assumes a post-glacial demographic expansion, representing one of the most promising approaches for dealing with these potential problems in the rate calibration. Here, we demonstrate the importance of using an appropriate evolutionary rate, and the power of CDT, by using populations of the sandy beach amphipod Haustorioides japonicus along the Japanese coast of the northwestern Pacific Ocean. Analysis of mitochondrial sequences found that the most peripheral population in the Pacific coast of northeastern Honshu Island (Tohoku region) is genetically distinct from the other northwestern Pacific populations. By using the two-epoch demographic model and rate of temperature change, the evolutionary rate was modeled as a log-normal distribution with a median rate of 2.2%/My. The split-time of the Tohoku population was subsequently estimated to be during the previous interglacial period by using the rate distribution, which enables us to infer potential causes of the divergence between local populations along the continuous Pacific coast of Japan., Competing Interests: The authors have declared that no competing interests exist.

Saxitoxin (STX) and its analogues produced by toxic dinoflagellates accumulate in bivalves, and routine monitoring of bivalves is important to prevent cases of human poisoning. In this study, we describe a rapid detection method for the analysis of STXs using ultra-performance liquid chromatography with post-column fluorescent detection and to investigate water depths and sampling points optimal for shellfish toxin monitoring. Cultured scallops ( Mizuhopecten yessoensis ) and mussels ( Mytilus galloprovincialis ) were collected from various water depths and sampling points were used in this study. Irrespective of bivalve species, toxin concentrations in bivalves were lower at deeper water depths. The toxin concentrations of bivalves did not differ greatly when bivalves were collected from the same bay. Although the levels of contamination of bivalves with STXs can depend on various environmental and geographical factors, our findings are useful for formulating a sampling protocol for the prevention of harvesting contaminated shellfish., Competing Interests: The authors declare no conflict of interest.

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 bluefin tuna aquaculture, high mortalities of hatchery-reared juveniles occur in sea cages owing to wall collisions that are caused by high-speed swimming in panic due to changes in illuminance. Here, we report that targeted gene mutagenesis of the ryanodine receptor (RyR1b), which allows the sarcoplasmic reticulum to release Ca 2+ in fast skeletal muscle, using highly active Platinum TALENs caused slow swimming behaviour in response to external stimuli in Pacific bluefin tuna (PBT) larvae. This characteristic would be a useful trait to prevent wall collisions in aquaculture production. A pair of Platinum TALENs targeting exons 2 and 43 of the PBT ryr1b gene induced deletions in each TALEN target site of the injected embryos with extremely high efficiency. In addition, ryr1b expression was significantly decreased in the mutated G0 larvae at 7 days after hatching (DAH). A touch-evoked escape behaviour assay revealed that the ryr1b-mutated PBT larvae swam away much less efficiently in response to mechanosensory stimulation at 7 DAH than did the wild-type larvae. Our results demonstrate that genome editing technologies are effective tools for determining the functional characterization of genes in a comparatively short period, and create avenues for facilitating genetic studies and breeding of bluefin tuna species.

The present study aimed to elucidate the population dynamics of land hermit crabs on the coast of the Boso Peninsula, Chiba Prefecture, Japan, which is the northern limit of their geographical distribution. We conducted monthly field surveys at four sites from April 2012 to December 2014 and visually searched for crabs. Laboratory experiments were also conducted to evaluate the overwintering ability of two species, Coenobita purpureus and C . rugosus , which were detected during the field surveys; adult crabs and laboratory-raised juveniles were exposed to low-temperature conditions that simulated the in situ temperatures during the early overwintering period. Newly landed juveniles first appeared in August. They were identified as either C . purpureus or C . rugosus , with C . purpureus being the dominant species. Early juveniles grew until October. The abundance of early juveniles decreased with decreasing air temperatures, and dead individuals were found during the overwintering period. The low-temperature tolerance ability of C . purpureus was stronger than that of C . rugosus . Some crabs successfully overwintered, and all were identified as C . purpureus . The growth and overwintering success of juveniles varied among the survey sites depending on the local temperature regime. Our results highlight the frontier for expanding the northern geographical distribution of land hermit crab populations by the colonization and overwintering success of C . purpureus .

Surface ocean phosphate is commonly below the standard analytical detection limits, leading to an incomplete picture of the global variation and biogeochemical role of phosphate. A global compilation of phosphate measured using high-sensitivity methods revealed several previously unrecognized low-phosphate areas and clear regional differences. Both observational climatologies and Earth system models (ESMs) systematically overestimated surface phosphate. Furthermore, ESMs misrepresented the relationships between phosphate, phytoplankton biomass, and primary productivity. Atmospheric iron input and nitrogen fixation are known important controls on surface phosphate, but model simulations showed that differences in the iron-to-macronutrient ratio in the vertical nutrient supply and surface lateral transport are additional drivers of phosphate concentrations. Our study demonstrates the importance of accurately quantifying nutrients for understanding the regulation of ocean ecosystems and biogeochemistry now and under future climate conditions.

Unlike most bivalve shellfishes, giant clams (tridacnines) harbor symbiotic microalgae (zooxanthellae) in their fleshy bodies. Zooxanthellae are not maternally inherited by tridacnine offspring, hence, the larvae must acquire zooxanthellae from external sources, although such algal populations or sources in the environment are currently unknown. It is well known that giant clams expel fecal pellets that contain viable zooxanthellae cells, but whether these cells are infectious or just an expelled overpopulation from the giant clams has not been investigated. In this study, we observed the ultrastructural and photosynthetic competencies of zooxanthellae in the fecal pellets of Tridacna crocea and further tested the ability of these cells to infect T. squamosa juveniles. The ultrastructure of the zooxanthellae cells showed that the cells were intact and had not undergone digestion. Additionally, these zooxanthellae cells showed a maximum quantum yield of photosystem II (Fv/Fm) as high as those retained in the mantle of the giant clam. Under the assumption that feces might provide symbionts to the larvae of other giant clams, fecal pellets from Tridacna squamosa and T. crocea were given to artificially hatched 1-day-old T. squamosa larvae. On the 9th day, 15-34% of the larvae provided with the fecal pellets took up zooxanthellae in their stomach, and on the 14th day, zooxanthellae cells reached the larval margin, indicating the establishment of symbiosis. The rate reaching this stage was highest, ca. 5.3%, in the larvae given whole (nonhomogenized) pellets from T. crocea. The composition of zooxanthellae genera contained in the larvae were similar to those in the fecal pellets, although the abundance ratios were significantly different. This study is the first to demonstrate the potential of giant clam fecal pellets as symbiont vectors to giant clam larvae. These results also demonstrate the possibility that fecal pellets are a source of zooxanthellae in coral reefs., Competing Interests: The authors have declared that no competing interests exist.

Trophic positions (TPs) are key parameters for determining trophic magnification factors (TMFs) of environmental pollutants. We used compound-specific nitrogen isotope analysis of amino acids (CSIA-AA), with which we expected to obtain precise TPs, to estimate the TMFs of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in the pelagic and benthic food webs of Tokyo Bay. The objective of the present study was to evaluate the difference between TMFs derived from TPs estimated by CSIA-AA (TP Glu/Phe ) and TMFs derived from TPs estimated by bulk stable isotope analysis (TP bulk ). TP Glu/Phe tended to be lower than TP bulk for many pelagic and benthic fishes. In the pelagic food web, the slopes for the relationships between PCB concentrations and TP Glu/Phe exceeded those between PCB concentrations and TP bulk for many congeners in samples from December 2014, and TMF Glu/Phe values (0.89-6.9) were higher than TMF bulk values (0.92-3.8). However, there were no statistically significant differences between the slopes of the relationships between PCB and PBDE concentrations and TP bulk or TP Glu/Phe for any of the congeners (analysis of covariance, P ≥ 0.08). In the benthic food web, PCB concentrations correlated with TP Glu/Phe for 9 PCB congeners in the samples collected during December 2014, although the concentrations of none of the PCB congeners correlated with TP bulk . A decrease of TMF Glu/Phe and TMF bulk values from December 2014 to May 2015 suggested that variation of PCB and PBDE concentrations in the organisms had more effect than TPs on the TMFs., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions.

Clarifying the underlying mechanisms that enable closely related species to coexist in a particular environment is a fundamental aspect of ecology. Coral reefs support a high diversity of marine organisms, among which rabbitfishes (family Siganidae) are a major component The present study aimed to reveal the mechanism that allows rabbitfishes to coexist on coral reefs in Okinawa, Japan, by investigating the spatial distributions, feeding ecologies, and behavioral interactions of four species: Siganus unimaculatus, S. virgatus, S. corallinus , and S. puellus . All four species had a size-specific spatial distribution, whereby small individuals were found in sheltered areas that were covered by branching and bottlebrush Acropora spp. and large individuals were found in both sheltered and exposed rocky areas. However, no clear species-specific spatial distribution was observed. There was some variation in the food items taken, with S. unimaculatus primarily feeding on brown foliose algae, red foliose algae, and red styloid algae, and S. virgatus and S. puellus preferring brown foliose algae and sponges, respectively. However, S. corallinus did not show any clear differences in food preferences from S. virgatus or S. unimaculatus , mainly feeding on brown foliose algae and red styloid algae. The four species exhibited differences in foraging substrate use, which was probably related to differences in their body shape characteristics: S. unimaculatus has a slender body with a remarkably protruding snout and mainly used concave substrates for feeding, whereas S. virgatus has a deeper body with a low degree of snout protrusion and mainly used convex substrates. The other two species have a low degree of snout protrusion combined with a deeper body in the case of S. corallinus and a slender body in the case of S. puellus and used concave, flat, and convex substrates to an equal degree for feeding. Behavioral interactions were categorized into "agonistic behaviors" (attack and agonistic displays) and "no interactions." For all four species, a greater frequency of agonistic behaviors was observed when two conspecific pairs approached each other than when two heterospecific individuals encountered each other. Together, these results suggest that food item partitioning is one of the main factors enabling the coexistence of these four syntopic rabbitfish species, which is enhanced by species-specific differences in feeding substrates as a result of their different body shape and behavioral characteristics., Competing Interests: The author declares there are no competing interests.