Search

Abstract The 2011 off the Pacific coast of Tohoku Earthquake occurred off southern Sanriku, Japan, on March 11 and generated strong shaking and huge tsunami along the entire eastern coast of Tohoku. The mainshock and numerous large aftershocks caused mass-wasting sedimentation events on the continental shelf, slope, and trench bottom. To investigate the impacts of the 2011 Tohoku Earthquake on the deep-sea bottom-water environment off Sanriku, we conducted shipboard surveys up to ~ 2000 dbar during 2011–2018 and long-term monitoring of the seafloor on the continental slope using a deep-sea station (~ 1000 dbar) off Otsuchi Bay during 2012–2018. The high turbidity (maximum ~ 6%) was observed for the bottom water deeper than 500 dbar on the continental slope of the entire area off Sanriku during 2012–2018. This high turbidity was caused by sporadic sediment resuspension induced by frequent large aftershocks. Furthermore, dissolved oxygen concentrations in the bottom layer from 1000 to 1500 dbar dropped significantly by about 10% after the earthquake, while nutrients and dissolved inorganic carbon showed no significant changes but exhibited wide variations. The high turbidity was associated with the increase in the concentrations of phosphate, dissolved inorganic carbon, and methane, as well as the decrease in those of dissolved oxygen and nitrate. This suggests that remineralization of suspended organic matter resulting from the respiration and denitrification of microbial communities after the earthquake caused the chemical properties of the deep-sea bottom-water. The deep-sea bottom-water environment change was maintained by sporadic sediment resuspension due to continued large aftershocks and was likely caused by variations in dissolved inorganic carbon and phosphate. There are two peaks in the concentration and carbon isotope ratio of methane on the deeper slope from 1000 to 2000 dbar near the hypocenter, which were advected along isopycnal surfaces of 27.38σθ (1000 dbar) and 27.56σθ (1500 dbar). The source of the shallower peak of chemical input is considered to be the sediment resuspension from the shallow sediment on the continental slope induced by the mainshock and large aftershocks. Graphical abstract

Hyperspectral data in the near infrared range were examined for nine common types of plastic particles of 1 mm and 100-500 μm sizes on dry and wet glass fiber filters. Weaker peak intensities were detected for small particles compared to large particles, and the reflectances were weaker at longer wavelengths when the particles were measured on a wet filter. These phenomena are explainable due to the effect of the correlation between the particle size and the absorption of infrared light by water. We constructed robust classification models that are capable of classifying polymer types, regardless of particle size or filter conditions (wet vs. dry), based on hyperspectral data for small particles measured on wet filters. Using the models, we also successfully classified the polymer type of polystyrene beads covered with microalgae, which simulates the natural conditions of microplastics in the ocean. This study suggests that hyperspectral imaging techniques with appropriate classification models allow the identification of microplastics without the time- and labor-consuming procedures of drying samples and removing biofilms, thus enabling more rapid analyses.

The 2011 off the Pacific coast of Tohoku Earthquake occurred off southern Sanriku, Japan, on 11 March and generated strong shaking and a huge tsunami along the entire eastern coast of Tohoku. The mainshock and numerous aftershocks caused mass-wasting sedimentation events on the continental shelf, slope, and trench bottom. To investigate the impacts of the 2011 Tohoku Earthquake on the deep-sea environment off Sanriku, we conducted shipboard surveys up to ~2000 dbar during 2011–2018 and long-term monitoring of the seafloor on the continental slope using a deep-sea station (~1000 dbar) off Otsuchi Bay during 2014–2018. The turbidity calculated from light transmissometer anomaly data for the bottom layer deeper than 500 dbar on the continental slope was ~6% and higher than the values usually observed there. This high turbidity during 2011–2018 was caused by sporadic sediment resuspension induced by frequent aftershocks in the area off Sanriku. We found that dissolved oxygen concentrations between 1000 dbar and 1500 dbar dropped significantly by about 10% after the earthquake, whereas nutrients and dissolved inorganic carbon showed no significant difference and displayed a wide variation. The correlation between light transmissometer anomaly values and chemical parameters at 1000–1500 dbar suggests that turbidity increased the concentrations of phosphate, silicate, dissolved inorganic carbon, and methane, and decreased dissolved oxygen and nitrate. The deep-sea chemical environment was changed by remineralization resulting from the respiration and denitrification of microbial communities after the earthquake. The environmental change in the deep sea was maintained by sediment resuspension caused by continued aftershocks and was likely caused by variations in dissolved inorganic carbon and nutrients on the slope after the mainshock and aftershocks. The concentration and carbon isotope ratio of methane between 1000 and 2000 dbar near the hypocenter shows two peaks with high light transmissometer anomaly values near the isopycnal surfaces of 27.38σθ (1000 dbar) and 27.56σθ (1500 dbar). These sources of chemical input contributed by sediment resuspension induced by the mainshock and aftershocks might have been derived from shallow sediment on the continental slope and deep sub-seafloor reservoirs.

In this study, sediments from whale-fall chemosynthetic ecosystems (two different sites, one naturally occurring at 4200 m water depth in South Atlantic Ocean and one artificially immersed at 100 m water depth in Kagoshima Bay, Japan) were investigated by Ion Torrent PGM sequencing of the ITS region of ribosomal RNA to reveal fungal communities in these unique marine environments. As a result, a total of 107 (897 including singletons) Operational Taxonomic Units (OTUs) were obtained from the samples explored. Composition of the 107 OTUs at the phylum level among the five samples from two different whale-fall sites was assigned to Ascomycota (46%), Basidiomycota (7%), unidentified fungi (21%), non-fungi (10%), and sequences with no affiliation to any organisms in the public database (No-match) (16%). The high detection of the unidentified fungi and unassigned fungi was revealed in the whale-fall environments in this study. Some of these unidentified fungi are allied to early diverging fungi and they were more abundant in the sediments not directly in contact with whalebone. This study suggests that a cryptic fungal community exists in unique whale-fall ecosystems.

Few studies have investigated the prevalence of polybrominated diphenyl ethers (PBDEs) in deep-sea sharks. In this study, the levels and profiles of PBDEs were determined in liver samples of eight different species of deep-sea sharks collected in Suruga Bay, Japan. Widespread contamination of PBDEs in the deep-sea environment was reconfirmed in this study as these persistent organic pollutants (POPs) were detected in all specimens analyzed. Mean ΣPBDE levels in the deep-sea sharks ranged from 7 to 517 ng/g of lipid weight. The distribution patterns of BDE homologues were similar in all species where tetra-BDEs provided the dominant contribution to total PBDEs (46%). PBDEs levels were similar to, or higher than, those seen in other deep-sea sharks from different regions. The levels of PBDEs were likely to reflect their feeding preferences as higher PBDE levels were seen in species with higher trophic positions.

Oomycete infection of various freshwater animals, including salmonid eggs, causes significant economic damage to aquaculture worldwide. In this study, we detected oomycetes in infected chum salmon Oncorhynchus keta eggs at two hatcheries in northern Japan, in the source water used for egg incubation, and in the air at the hatcheries to clarify the source(s) of oomycete transmission using a DNA molecular marker. Seven oomycete taxa, belonging to Saprolegniaceae and Pythiaceae, were detected from the infected eggs. From the source water used for egg incubation and the air at the hatcheries, nine oomycete taxa, including those found on infected eggs, were detected, suggesting that both water and air are potential sources of oomycete transmission. There is no report of airborne transmission of these oomycetes detected in this study so far. Regarding protection and sterilization against oomycete infection in aquaculture hatcheries, not only water used at hatcheries but also the air in hatcheries may need to be considered hereafter.

We report the discovery of the deep-sea fungus, Alisea longicolla on a wood log artificially immersed at 495 m depths in deep sea, off the Nansei Islands, Japan. Three different species of wood logs, whale bones and coconuts were deployed at approximate depths of 250, 500, 1000, 2000, 3000 and 5000 m. Densely colonised A. longicolla was found on the Ubame oak (Quercus phillyraeoides) wood log from the 500 m deployment site, which was collected 1302 d (about 3 y and 7 mo) after the deployment. Alisea longicolla was originally described as a new genus of deep-sea ascomycete within the family Halosphaeriaceae, associated with sunken wood collected in 630–791 m water depths off the Vanuatu Islands. Our results provide further evidence to support that A. longicolla may be an endemic deep-sea fungus, and it grows slowly but is active and reproductive in deep-sea environments. The occurrence of obligate deep-sea fungi appears to be very rare in the environments and few data is available. Further investigation on A. longicolla will extend our understanding of the ecology, physiology and evolution of deep-sea fungi.

The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (Sao Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.

Graphical abstract, Microplastics are abundant even on the deep-sea floor far from land and the ocean surface where human activities take place. To obtain samples of microplastics from the deep-sea floor, a research vessel and suitable sampling equipment, such as a multiple corer, a box corer, or a push corer manipulated by a remotely operated (ROV) or human occupied vehicle (HOV) are needed. Most such corers use sampling tubes made of plastic, such as polycarbonate, acrylic, or polyvinyl chloride. These plastic tubes are easily scratched by sediment particles, in particular during collection of coarse sandy sediments, and, consequently, the samples may become contaminated with plastic from the tube. Here, we report on the use of aluminum tubes with both a multiple corer and a push corer to prevent such plastic contamination. When compared with plastic tubes, aluminum tubes have the disadvantages of heavier weight and non-transparency. We suggest ways to overcome these problems, and we also present an onboard processing protocol to prevent plastic contamination during sediment core sampling when plastic tubes are used. • Use of a sediment corer with aluminum tubes reduces the risk of plastic contamination in the sediment samples • The proposed method allows undisturbed sediment cores to be retrieved with comparable efficiency to conventional transparent core tubes

Graphical abstract, Removing non-plastic materials is a mandatory process for studying microplastics in environmental samples, and non-plastic materials, both inorganic and organic matter, are often removed chemically through sequential processes. In the multiple chemical treatment processes, the samples need to be collected and the reagent removed at the end of each chemical treatment before the samples are again exposed to a different reagent in a separate container. This leads to a loss of microplastics to some extent. Here, we developed a new, yet simple, small sieve made of stainless-steel that can fit in a laboratory beaker (e.g. 200 ml volume), allowing it to be transferred as-is between chemical treatments of environmental samples, even being soakable in a beaker of acid solution. The collection rates of microplastics were significantly higher in the small stainless-steel sieve than the commonly used filter method for different size of microplastic particles. The use of the new sieve means the processes of rinsing off and filtering samples can be abbreviated throughout the entire process of non-plastic matter removal from environmental samples, contributing to a lower chance of microplastic loss. The time consumed in the sieve method was also significantly lower than for the filtering method due to the elimination of the collection and rinsing steps, thus the use of this sieve can reduce processing time for the samples. The new method is innovative in terms of reducing both the microplastic loss and processing time during chemical treatment processes. • The method developed allows the lower chance of microplastic loss during chemical digestion process • The method reduces the time of sequential processes during chemical digestion

To study the influence of different ocean currents on the trophic spectra found in a sympatric fish community, we analyzed the radiocarbon contents (Δ14C) and stable carbon (δ13C) and nitrogen (δ15N) isotopic compositions in their bulk muscle tissues and the δ15N of individual amino acids in 26 species of demersal fish collected from off Tohoku (Pacific coast), northeastern Japan. The Δ14C values of the fish varied from –42 to +41‰, consistent with the Δ14C of the dissolved inorganic carbon in the cold Oyashio Current (typically about –50‰) and the warm Kuroshio Current (typically about +50‰). The trophic positions (TPs) of the fish estimated from the δ15N values of amino acids increased from 3.1 to 4.5 with increasing snout length. A negative correlation was observed between Δ14C and TP in gadiform fish and flatfish, suggesting that the Oyashio Current delivers a high TP diet to these fish groups. These results suggest that the trophic ecology of marine fish in the coastal western North Pacific is primarily controlled by the two major surface water currents, but is also significantly influenced by a combination of species-specific feeding and migration strategies.

Symbiotic associations with beneficial microorganisms endow a variety of host animals with adaptability to the environment. Stable transmission of symbionts across host generations is a key event in the maintenance of symbiotic associations through evolutionary time. However, our understanding of the mechanisms of symbiont transmission remains fragmentary. The deep-sea clam Phreagena okutanii harbors chemoautotrophic intracellular symbiotic bacteria in gill epithelial cells, and depends on these symbionts for nutrition. In this study, we focused on the association of these maternally transmitted symbionts with ovarian germ cells in juvenile female clams. First, we established a sex identification method for small P. okutanii individuals, and morphologically classified female germ cells observed in the ovary. Then, we investigated the association of the endosymbiotic bacteria with germ cells. We found that the symbionts were localized on the outer surface of the cell membrane of primary oocytes and not within the cluster of oogonia. Based on our findings, we discuss the processes and mechanisms of symbiont vertical transmission in P. okutanii.

The deep-sea is considered to be an ultimate sink for marine plastic debris. The abyssal (3500-6500 m) covers the bulk of the deep ocean floor yet little is known about the extent of plastic debris on the abyssal seafloor. We undertook a quantitative assessment of debris presents on the abyssal seafloor (5700-5800 m depth) beneath the Kuroshio Extension current system in the Northwest Pacific, which is one of the major transit points for massive amounts of debris sourced from Asia that are entering the North Pacific Ocean. The dominant type of debris was single-use plastics-mainly bags and food packaging. The density of plastic debris (average 4561 items km−2) in the abyssal zone was the highest recorded for an abyssal plain, suggesting that the deep-sea basin of the Northwest Pacific is a significant reservoir of plastic debris.

Plastic pollution has become one of the most emergent issues threating aquatic and terrestrial ecosystems. However, it is still challenging to rapidly detect small microplastics. Here, we present a method to rapidly detect microplastics using hyperspectral imaging in which we optimized a commercially available hyperspectral imaging system (Pika NIR-640, Resonon Inc., USA). The optimizations included: (1) changing the four-lamp assembly to a symmetrical set of converged-light near-infrared lamps that are placed sideways instead of above the sample stage; (2) adopting a macro-photography technique by applying an extension tube between the camera and the lens, and moving the lens of the hyperspectral camera to the imaging target (working distance of ~3 cm); (3) adjusting the exposure and aspect ratio by tuning the frame rate and scan speed of the imaging system. After optimization, the detection resolution of each pixel improved from 250 µm to 14.8 µm. With the optimized system, microplastics down to 100 µm in size were rapidly detected. This result is promising for the application of our new method in the accelerated detection of microplastics and will contribute to a better understanding of the microplastic pollution situation., Graphical abstract Image, graphical abstract

To elucidate the localization of oomycetes (water molds) and bacteria in a single egg of chum salmon, Oncorhynchus keta, eggs infected with oomycetes were examined by bright-field microscopy, scanning electron microscopy (SEM), and fluorescent in situ hybridization (FISH) using oomycete universal and bacterial species-specific probes. Furthermore, DNA barcoding for oomycetes and bacteria was performed on the chorion and cytoplasm of the eggs using genomic DNA extracted from the sections of eggs used for FISH analyses. Using bright-field microscopy and SEM, it was shown that oomycete hyphae penetrated the chorion and invaded the cytoplasm of the eggs. Based on DNA barcoding, two oomycetes (Pythium monospermum and Pythium sp. SE-OP1), and three bacterial species (Flavobacterium plurextorum, Flavobacterium sp. SE-BF1 and Undibacterium pigrum) were predominantly detected in the infected eggs. FISH analyses indicated that localization of the oomycetes was not noticeable different between the chorion and cytoplasm of the eggs. In contrast, FISH analyses using bacterial species-specific probes demonstrated clear differences in their localization. Flavobacterium sp. SE-BF1 and U. pigrum were predominantly found inside the chorion and around the oomycete hyphae invading the cytoplasm, respectively. These results are the first to indicate the possibility that U. pigrum has a specific relationship with oomycetes and coordinately invades eggs with oomycetes. However, it seems that Flavobacterium sp. SE-BF1 invades by a mechanism different from that of U. pigrum. Although this study is preliminary and the interaction between oomycetes and U. pigrum associated with chum salmon egg infection needs to be elucidated in detail, this finding may provide new insights into the infection mechanism of bacteria in salmon eggs, which is a longstanding problem in salmon hatcheries.

This study reports plastic debris pollution in the deep-sea based on the information from a recently developed database. The Global Oceanographic Data Center (GODAC) of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) launched the Deep-sea Debris Database for public use in March 2017. The database archives photographs and videos of debris that have been collected since 1983 by deep-sea submersibles and remotely operated vehicles. From the 5010 dives in the database, 3425 man-made debris items were counted. More than 33% of the debris was macro-plastic, of which 89% was single-use products, and these ratios increased to 52% and 92%, respectively, in areas deeper than 6000 m. The deepest record was a plastic bag at 10898 m in the Mariana Trench. Deep-sea organisms were observed in the 17% of plastic debris images, which include entanglement of plastic bags on chemosynthetic cold seep communities. Quantitative density analysis for the subset data in the western North Pacific showed plastic density ranging from 17 to 335 items km−2 at depths of 1092–5977 m. The data show that, in addition to resource exploitation and industrial development, the influence of land-based human activities has reached the deepest parts of the ocean in areas more than 1000 km from the mainland. Establishment of international frameworks on monitoring of deep-sea plastic pollution as an Essential Ocean Variable and a data sharing protocol are the keys to delivering scientific outcomes that are useful for the effective management of plastic pollution and the conservation of deep-sea ecosystems.

Diplonemids were recently found to be the most species-rich group of marine planktonic protists. Based on phylogenetic analysis of 18S rRNA gene sequences and morphological observations, we report the description of new members of the genus Rhynchopus - R. humris sp. n. and R. serpens sp. n., and the establishment of two new genera - Lacrimia gen. n. and Sulcionema gen. n., represented by L. lanifica sp. n. and S. specki sp. n., respectively. In addition, we describe the organism formerly designated as Diplonema sp. 2 (ATCC 50224) as Flectonema neradi gen. n., sp. n. The newly described diplonemids share a common set of traits. Cells are sac-like but variable in shape and size, highly metabolic, and surrounded by a naked cell membrane, which is supported by a tightly packed corset of microtubules. They carry a single highly reticulated peripheral mitochondrion containing a large amount of mitochondrial DNA, with lamellar cristae. The cytopharyngeal complex and flagellar pocket are contiguous and have separate openings. Two parallel flagella are inserted sub-apically into a pronounced flagellar pocket. Rhynchopus species have their flagella concealed in trophic stages and fully developed in swimming stages, while they permanently protrude in all other known diplonemid species.

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Deep-sea vesicomyid clams, including the genus Phreagena, harbor obligate sulfur-oxidizing symbiotic bacteria in gill epithelial cells. Difficulty in maintaining Phreagena clams in rearing tanks has been a major obstacle to achieving a better understanding of their unique biology. To improve the method of rearing Phreagena clams, here we reared them in an artificial chemosynthetic aquarium and evaluated the effects of the aquarium system on long-term clam rearing. We compared the survival of clams reared in the artificial chemosynthetic tank with the survival of those in the normal tank, and analyzed the symbiont abundance using semi-quantification of fluorescent in situ hybridization signals. Our results indicate that the artificial chemosynthetic aquarium system had specific effects on symbiont abundance and possibly on host survival. Furthermore, transmission electron microscopic observations of sulfur globules in the symbiont cells and expression analyses of the dsrA gene of the symbiont indicated that stocked elemental sulfur could be consumed as an energy source to reduce sulfide shortages. We discuss the importance of higher and more stable sulfide concentrations and the proportions of available O2 and CO2 in driving appropriate metabolic functions of the symbiont and improving the survival of the clams.

In an effort to broaden our understanding of the biodiversity and distribution of gregarines infecting crustaceans, this study describes two new species of gregarines, Thiriotia hyperdolphinae n. sp. and Cephaloidophora oradareae n. sp., parasitizing a deep sea amphipod (Oradarea sp.). Amphipods were collected using the ROV Hyper-Dolphin at a depth of 855 m while on a cruise in Sagami Bay, Japan. Gregarine trophozoites and gamonts were isolated from the gut of the amphipod and studied with light and scanning electron microscopy, and phylogenetic analysis of 18S rDNA. T. hyperdolphinae n. sp. was distinguished from existing species based on morphology, phylogenetic position, as well as host niche and geographic locality. While Cephaloidophora oradareae n. sp. distinguished itself from existing Cephaloidophora, based on a difference in host (Oradarea sp.), geographic location, and to a certain extent morphology. We established this new species with the understanding that a more comprehensive examination of diversity at the molecular level is necessary within Cephaloidophora. Results from the 18S rDNA molecular phylogeny showed that T. hyperdolphinae n. sp. was positioned within a clade consisting of Thiriotia spp., while C. oradareae n. sp. grouped within the Cephaloidophoridae. Still, supplemental genetic information from gregarines infecting crustaceans will be needed to better understand relationships within this group of apicomplexans. This article is protected by copyright. All rights reserved.

In a previous report, we analyzed the stomach contents of juvenile chum salmon Oncorhynchus keta by morphological observation and also by molecular identification using the mitochondrial cytochrome c oxidase subunit I (COI) region. However, one of the most frequently detected COI sequences could not be assigned to any specific taxon, even at the phylum level. In the present study, we conducted in situ hybridization (ISH) on the stomach contents of juvenile chum salmon using the COI sequence and polymerase chain reaction amplification of a 18S ribosomal RNA gene from the tissue sections where ISH signals were detected. As a result, the organism that was enigmatic at the phylum level was found to be an appendicularian. Moreover, Oikopleura longicauda collected from the bay where the juvenile chum salmon samples were obtained was shown to have the same COI sequences as this taxonomic “orphan” COI sequence from the stomach contents. The present results suggest that the COI sequences previously deposited in public databases for “Oikopleura” are actually derived from taxonomic groups other than appendicularians, and that this may have hampered our understanding of prey richness in the stomach or gut of certain marine animals based on DNA barcoding.

It is widely held that sterols are key cyclic triterpenoid lipids in eukaryotic cell membranes and are synthesized through oxygen-dependent multi-enzyme pathways. However, there are known exceptions―ciliated protozoans, such as Tetrahymena, along with diverse low-oxygen adapted eukaryotes produce, instead of sterols, the cyclic triterpenoid lipid tetrahymanol that does not require molecular oxygen for its biosynthesis. Here, we report that a number of anaerobic microbial eukaryotes (protists) utilize neither sterols nor tetrahymanol in their membranes. The lack of detectable sterol-like compounds in their membranes may provide an opportunity to reconsider the physiological function of sterols and sterol-like lipids in eukaryotes. This article is protected by copyright. All rights reserved.

Microplastic pollution has become an urgent issue because it adversely affects ecosystems. However, efficient methods to detect and characterize microplastic particles are still in development. By conducting a series of laboratory assessments based on near-infrared hyperspectral imaging in the wavelength range of 900–1700 nm, we report the fundamental spectral features of (i) 11 authentic plastics and (ii) 11 filter substrate materials. We found that different plastic polymers showed distinct spectral features at 1150–1250 nm, 1350–1450 nm and 1600–1700 nm, enabling their automatic recognition and identification with spectral separation algorithms. Using an improved hyperspectral imaging system, we demonstrated the detection of three types of microplastic particles, polyethylene, polypropylene and polystyrene, down to 100 μm in diameter. As a filter substrate, a gold-coated polycarbonate filter (GPC0847-BA) showed constant reflectance over 900–1700 nm and a large radiative contrast against loaded plastic particles. Glass fiber filters (GF10 and GF/F) would also be suitable substrates due to their low cost and easy commercial availability. This study provides key parameters for applying hyperspectral imaging techniques for the detection of microplastics.

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

In symbiotic systems in which symbionts are transmitted horizontally, hosts must accept symbionts from the environment while defending themselves against invading pathogenic microorganisms. How they distinguish pathogens from symbionts and how the latter evade host immune defences are not clearly understood. Recognition of foreign materials is one of the most critical steps in stimulating immune responses, and pattern recognition receptors (PRRs) play vital roles in this process. In this study, we focused on a group of highly conserved PRRs, peptidoglycan recognition proteins (PGRPs), in the deep-sea mussel, Bathymodiolus septemdierum, which harbours chemosynthetic bacteria in their gill epithelial cells. We isolated B. septemdierum PGRP genes BsPGRP-S and BsPGRP-L, which encode a short- and a long-type PGRP, respectively. The short-type PGRP has a signal peptide and was expressed in the asymbiotic goblet mucous cells in the gill epithelium, whereas the long-type PGRP was predicted to include a transmembrane domain and was expressed in gill bacteriocytes. Based on these findings, we hypothesize that the secreted and transmembrane PGRPs are engaged in host defence against pathogenic bacteria and/or in the regulation of symbiosis via different cellular localizations and mechanisms.

Cabled seafloor platforms can overcome many constraints of stand-alone systems and archived long-term seafloor monitoring, and their advantages include unlimited power, real-time communication, a synchronized clock, and virtually unlimited data storage. Using monthly images from a fixed camera on a cabled deep-sea observatory in the Off Hatsushima seep site in Sagami Bay, Japan, fluctuations in clam density (Phreagena soyoae and P. okutanii) were observed over 5 years, March 1994–July 1999. Eight disturbances were seen, including five phytodetritus deposition events associated with seasonal blooms, two earthquake-associated turbid flows, and one caused by a maintenance visit by a remotely operated vehicle. Overall, these observations indicate that the vesicomyids experienced an ongoing decline throughout the observation series, and strong disturbance events such as earthquakes appeared to be too severe for the clams to survive. As such, vesicomyid clams are unlikely to survive the foreseeable impacts of deep-sea mining. These results show that long-term observations of deep-sea chemosynthetic communities are useful for understanding their resilience and for making an environmental impact assessment.

To identify the stomach contents of marine organisms, morphological observations are commonly conducted. However, the results obtained by this traditional method are frequently biased, as it is difficult to detect partially digested, soft-bodied organisms. To resolve this, recent studies have used DNA-based (DNA barcoding) analyses to examine the diet breadth of marine organisms. Here, we compared the prey richness of juvenile fishes using morphological observations and DNA-based analyses, with a focus on juvenile chum salmon Oncorhynchus keta. A higher number of prey taxa were successfully identified using DNA-based analyses than morphological observations. However, we also noticed several shortcomings of the DNA-based analyses, as reported in other diet-analysis studies that used molecular techniques. For example, the degree of digestion among prey taxa might have resulted in differential sensitivity to DNA detection. Additionally, several prey taxa could not be precisely identified, as the sequence data for some of the targeted organismal groups are unavailable in public gene databases. Remarkably, it is also possible that DNA-based analyses detected secondary prey, and therefore, the richness of prey taxa was likely overestimated. Thus, dietary analyses of juvenile fishes need to be carefully conducted, considering the respective advantages and disadvantages of DNA-based and morphological techniques.

Temperature is an important factor affecting the distributions and life-history traits of marine animals. Deep-sea hydrothermal vents are suitable environments to examine ecologic differences related to temperature, due to the steep temperature gradients around the vents. Rearing experiments under various temperature conditions (5–30 °C) at atmospheric pressure demonstrated a difference in thermal effects on egg hatching and larva in two co-occurring, vent-associated alvinocaridid shrimps – the peripherally distributed Alvinocaris longirostris and the centrally distributed Shinkaicaris leurokolos. The duration before hatching became shorter as temperature increased, while the maximum hatching rate occurred at higher temperatures in S. leurokolos (10–20 °C) than in A. longirostris (10 °C). Hatched larvae of both species were negatively buoyant, and larva with normal abdominal length could actively swim and stay suspended in the mid- or surface water layers of the culture plates under our experimental conditions. However, no larvae settled or metamorphosed into juveniles under the rearing conditions used in this study. Larvae with shortened abdomens occurred under most of the experimental conditions, although they were less frequent at 10 °C in A. longirostris and 20 °C in S. leurokolos. The maximum survival periods at these temperatures were 88 days in A. longirostris and 30 days in S. leurokolos. These characteristics may cause differences in the distributional ranges of the two species. The present results indicate that temperature is an important factor controlling life-history traits of vent shrimps.

To estimate polychlorinated biphenyls (PCBs) pollution by the 2011 earthquake and tsunami off the Pacific coast of Tohoku, we report monitoring results of their concentration in deep-sea fish, benthic invertebrates, and sediments collected off Tohoku in 2012–014. Total concentration of PCBs in the deep-sea organisms ranges from 0.12 to 51 ng g−1 dry weight (8.7–374 ng g−1 lipid), whereas that of sediments ranges from 0.086 to 4.0 ng g−1 dry sediment. These ranges are well below the regulatory standards determined by the Ministry of the Environment in Japan (pelagic fish: 500 ng g−1 dry weight, pelagic sediment: 10 μg g−1 dry sediment). With the reported data before the 2011 tsunami event, we did not find any significant increase in PCBs concentration off Tohoku during 2012–2014. For the biological samples, we also measured the nitrogen isotopic composition of individual amino acids for determining the precise trophic position to examine possible biomagnification through the food web. We did not find any significant correlation between the trophic position and PCB concentration.

A large amount of tsunami debris from the Great East Japan Earthquake in 2011 was sunk on the seafloor and threatened the marine ecosystem and local communities' economy, especially in fisheries. However, few studies estimated spatial accumulations of tsunami benthic debris, comparing to their flows on the ocean surface. Here, a spatially varying coefficient model was used to estimate tsunami debris accumulation considering the spatial structure of the data off the Tohoku region. Our model revealed the number of vessels nearest the coast at the tsunami event had the highest positive impact, whereas the distance from the coast and kinetic energy influenced negatively. However, the effect of the proximity to the coast wasn't detected in the Sendai bay, indicating spatial dependency of these effects. Our model estimation provides the fundamental information of tsunami debris accumulation on the seafloor, supporting early reconstruction and risk reduction in marine ecosystems and local communities.

The impact of the 2011 Tohoku-oki earthquake and subsequent turbidites on the deep-sea environment was investigated by conducting sedimentological, radionuclide, and benthic foraminiferal analyses of core sediments collected from water depths of 3230 and ~3570 m, 5 and 17 months after the earthquake. Sedimentological profiles and patterns of excess 210Pb, 134Cs, and 137Cs indicate that the analyzed sediment core records deposits before the earthquake, turbidite deposits just after the earthquake, and deposits after the Fukushima Daiichi Nuclear Power Plant (FNPP1) accident, which caused the release of a large amount of radioactive material four days after the earthquake. Core 4W-2012 F-RN was collected at 3585 m water depth 17 months after the earthquake. Within this core, an event deposit layer (6.5 cm thick) consisting of turbidites contains highly diverse and possibly reworked foraminiferal assemblages. Overlying these turbidites are sediments with high 134Cs concentrations that were deposited after the FNPP1 accident. Overall foraminiferal and species abundances show a marked decrease in the sediments above the deposited turbidites. The abundance of opportunistic and competitive species shows a gradual upward increase in the uppermost sediment layers, and these species are dominant in the top 1 cm of the core. Our findings demonstrate that although foraminiferal assemblages in the sediment overlying the turbidites related to the 2011 earthquake might include allochthonous assemblages, turbidites deposited after the earthquake caused a marked decrease in benthic foraminiferal diversity and allowed opportunistic species to colonize in a low-diversity assemblage within 17 months. These foraminiferal faunal changes, together with analysis of sedimentological structure, provide valuable information for identifying these types of sedimentation events in core sediments from the deep-sea floor.

Toxic dinoflagellates belonging to the genus Dinophysis acquire plastids indirectly from cryptophytes through the consumption of the ciliate Mesodinium rubrum. Dinophysis acuminata harbours three genes encoding plastid-related proteins, which are thought to have originated from fucoxanthin dinoflagellates, haptophytes and cryptophytes via lateral gene transfer (LGT). Here, we investigate the origin of these plastid proteins via RNA sequencing of species related to D. fortii. We identified 58 gene products involved in porphyrin, chlorophyll, isoprenoid and carotenoid biosyntheses as well as in photosynthesis. Phylogenetic analysis revealed that the genes associated with chlorophyll and carotenoid biosyntheses and photosynthesis originated from fucoxanthin dinoflagellates, haptophytes, chlorarachniophytes, cyanobacteria and cryptophytes. Furthermore, nine genes were laterally transferred from fucoxanthin dinoflagellates, whose plastids were derived from haptophytes. Notably, transcription levels of different plastid protein isoforms varied significantly. Based on these findings, we put forth a novel hypothesis regarding the evolution of Dinophysis plastids that ancestral Dinophysis species acquired plastids from haptophytes or fucoxanthin dinoflagellates, whereas LGT from cryptophytes occurred more recently. Therefore, the evolutionary convergence of genes following LGT may be unlikely in most cases.

Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.

Fungal strain FKJ-0025 was isolated from deep-sea sediment collected at the Wakamiko Caldera in Kagoshima Bay (water depth: 200 m). The fungal strain FKJ-0025 was identified as the genus Sarcopodium based on its morphology and internal transcribed spacer (ITS) sequence. Two new compounds, designated sarcopodinols A (1) and B (2), were isolated together with the known compound SF-227 (3).

Functionally and morphologically degenerate mitochondria, so-called mitochondrion-related organelles (MROs), are frequently found in eukaryotes inhabiting hypoxic or anoxic environments. In the last decade, MROs have been discovered from a phylogenetically broad range of eukaryotic lineages and these organelles have been revealed to possess diverse metabolic capacities. In this study, the biochemical characteristics of an MRO in the free-living anaerobic protist Cantina marsupialis, which represents an independent lineage in stramenopiles, were inferred based on RNA-seq data. We found transcripts for proteins known to function in one form of MROs, the hydrogenosome, such as pyruvate:ferredoxin oxidoreductase, iron-hydrogenase, acetate:succinate CoA-transferase, and succinyl-CoA synthase, along with transcripts for acetyl-CoA synthetase (ADP-forming). These proteins possess putative mitochondrial targeting signals at their N-termini, suggesting dual ATP generation systems through anaerobic pyruvate metabolism in Cantina MROs. In addition, MROs in Cantina were also shown to share several features with canonical mitochondria, including amino acid metabolism and an "incomplete" tricarboxylic acid cycle. Transcripts for all four subunits of complex II (CII) of the electron transport chain were detected, while there was no evidence for the presence of complexes I, III, IV, or F1Fo ATPase. Cantina MRO biochemistry challenges the categories of mitochondrial organelles recently proposed.

Long-term monitoring of the seafloor environment off Otsuchi Bay, northeastern Japan, was carried out to investigate environmental changes of the deep-sea floor after the 2011 off the Pacific coast of the Tohoku Earthquake. We deployed two deep-sea stations, one on an upper continental slope site (around 300 m water depth) and the other on a bathyal (998 m) site, to measure current intensity and direction, water temperature, salinity, dissolved oxygen, and turbidity, and to obtain seafloor images. The monitoring period on the upper slope was 9 months (March–September 2013), and 14 months (August 2012–October 2013) at the bathyal site. The oceanographic data from the upper slope site recorded the seasonal exchange of water masses and dense marine snowfall from April to May 2013. On 7 December 2012, a large aftershock of the 2011 earthquake caused increased turbidity at the bathyal site, and seafloor photographs and videos recorded the disturbance and recovery of benthic habitats. The data from these deployments show that long-term monitoring can provide important oceanographic, biological, and sedimentological data from deep-sea sites. Together with shipboard and deep-tow observations and data collected by remotely operated vehicles, long-term monitoring can be a valuable tool for understanding deep-sea environments and their variability.

Hydrothermal vent organisms undergo extreme environments that may require unique innovations. The present study reports a distinct case of cellular supportive systems in the nervous systems of a scale-worm, Branchinotogluma japonica, endemic to deep-sea hydrothermal vents. We found two organizations in the tissues of these animals. First, multi-layers of glia ensheath the ventral cell bodies of the brain and ventral nerve cord, in a manner similar to that of myelin or lamellar ensheathments. Second, matrices of numerous penetrative fibers, or tonofilaments, composed of bundles of ca. 20-nm fibers, are directly connected with the basal parts of epidermal cuticles and run into the diffuse intercellular spaces of the brain neuropils and peripheral nerves. Both types of tissue might be mechanical supportive structures for the neuronal cell bodies. In addition, as a glial function, the multi-layer membranes and the epithelial support cells may be required for physicochemical homeostatic regulation to filter toxic heavy metals and for inhibiting breakdown of glial membrane integrity under strong oxidative stress imposed by hypoxia in the hydrothermal vent environment. Similar functions are known in the well-studied cases of the blood-brain barrier in mammalian brains, including in human stroke.

We examined the effects of mass sedimentation events caused by the 2011 off the Pacific coast of Tohoku Earthquake on abundances and vertical distributions of prokaryotes and metazoan meiofauna in sediments, using sediment cores collected from eight bathyal stations off Tohoku 1 year after the M9.0 earthquake. Event deposits 1–7 cm thick were observed at the topmost part of the sediment cores at all sampling stations. At some stations, prokaryotic cell abundances were lower in the surface event-deposit layers compared to those in deeper sediments. These variations were explained by environmental parameters such as a dimensionless sorting factor and mean grain size, suggesting that turbidite sedimentation affected prokaryotic cell abundances. Nematodes had anomalously higher subsurface abundances at the stations where subsurface peak prokaryotic cell numbers were observed, whereas copepods always showed peak densities in the sediment surface layer. Although there are no available data for prokaryotic cell abundances and meiofaunal densities before the earthquake from the same sites, it is likely that the subsurface peaks in prokaryotic cell numbers and nematode densities resulted from the sedimentation events. The effects of sedimentation events on the organisms were observed 1 year after the earthquake, indicating that episodic sedimentation events on scales of several centimeters have a large effect on small organisms inhabiting sediments.

After the adoption of the Aichi Target, data accumulation and evaluation regarding biodiversity have progressed rapidly. The use of ecologically and biologically significant areas (EBSAs) criteria to evaluate important areas enables the identification of effective and prioritized areas for ecosystem management. This includes strategic environmental assessment and discussions aimed at establishing protected marine areas based on scientific data. This paper reviews previous and current ideas as well as the methods used, for the identification of EBSAs. In particular, the following issues are addressed: problems associated with different types of marine ecosystems in the Japanese Archipelago, such as seagrass and seaweed beds, coral reefs, offshore pelagic plankton, and deep-sea benthic ecosystems; and problems associated with the integration of multiple criteria that are not totally exclusive. Several candidate variables accounting for each of the 7 criteria used to identify ecologically important areas are presented. Data availability is the most important criterion that allowed for the comprehensive evaluation of different types of ecosystems in the same localities. In particular, for coastal ecosystems such as seagrass, seaweed beds, and coral reefs, it is possible to carry out broad spatial comparisons using variables representing most of these 7 criteria. Regarding methods for the quantitative evaluation of each criterion and their integration, application of these methods to kelp forest ecosystems in Hokkaido, Northern Japan is presented as a case study.

Saprolegnia parasitica, belonging to oomycetes, is one of virulent pathogen of fishes such as salmon and trout, and causes tremendous damage and losses in commercial aquacultures by saprolegniasis. Previously, malachite green, an effective medicine, had been used to control saprolegniasis. However, this drug has been banned around the world due to its mutagenicity. Therefore, novel anti-saprolegniasis compounds are urgently needed. As a new frontier to discover bioactive compounds, we focused on the deep-sea fungi for the isolation of anti-saprolegniasis compounds. In this paper, on the course of anti-saprolegniasis agents from 546 cultured broths of 91 deep-sea fungal strains, we report a new compound, named quellenin (1) together with three known compounds, diorcinol (2), violaceol-I (3) and violaceol-II (4), from deep-sea fungus Aspergillus sp. YK-76. This strain was isolated from an Osedax sp. annelid, commonly called bone-eating worm, collected at the Sao Paulo Ridge in off Brazil. Compounds 2, 3 and 4 showed anti-S. parasitica activity. Our results suggest that diorcinol and violaceol analogs and could be good lead candidates for the development of novel agents to prevent saprolegniasis.

The environments around deep-sea hydrothermal vents are very harsh conditions for organisms due to the possibility of exposure to highly toxic compounds and extremely hot venting there. Despite such extreme environments, some indigenous species have thrived there. Alvinellid worms (Annelida) are among the organisms best adapted to high-temperature and oxidatively stressful venting regions. Although intensive studies of the adaptation of these worms to the environments of hydrothermal vents have been made, little is known about the worms' sensory adaptation to the severe chemical conditions there. To examine the sensitivity of the vent-endemic worm Paralvinella hessleri to low pH and oxidative stress, we determined the concentration of acetic acid and hydrogen peroxide that induced avoidance behavior of this worm, and compared these concentrations to those obtained for related species inhabiting intertidal zones, Thelepus sp. The concentrations of the chemicals that induced avoidance behavior of P. hessleri were 10-100 times lower than those for Thelepus sp. To identify the receptors for these chemicals, chemical avoidance tests were performed with the addition of ruthenium red, a blocker of transient receptor potential (TRP) channels. This treatment suppressed the chemical avoidance behavior of P. hessleri, which suggests that TRP channels are involved in the chemical avoidance behavior of this species. Our results revealed for the first time hypersensitive detection systems for acid and for oxidative stress in the vent-endemic worm P. hessleri, possibly mediated by TRP channels, suggesting that such sensory systems may have facilitated the adaptation of this organism to harsh vent environments.

Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets. Many clades in the phylogenetic trees of 13 host species (Abyssogena mariana, Ab. phaseoliformis, Akebiconcha kawamurai, Calyptogena fausta, C. laubieri, C. magnifica, C. nautilei, C. pacifica, Isorropodon fossajaponicum, Phreagena kilmeri, Ph. okutanii, Ph. soyoae, and Pliocardia stearnsii) and their symbionts were well resolved. Six of the 13 host-symbiont pairs (C. fausta, C. magnifica, C. pacifica, Ph. kilmeri, Ph. okutanii, and Ph. soyoae, and their respective symbionts) showed topological congruence. However, the remaining seven pairs (Ak. kawamurai, Ab mariana, Ab. phaseoliformis, C. laubieri, C. nautilei, I. fossajaponicum, and Pl. stearnsii and their corresponding symbionts) showed incongruent topologies, which were supported by the approximately unbiased and Bayes factor tests. Coevolution analyses indicated that six pairs cospeciated, whereas host switching events occurred in the remaining seven pairs. Markedly, multiple host switching events may have occurred in the lineages from the common ancestral symbiont of C. pacifica and C. fausta. Our phylogenetic and coevolution analyses provide additional evidence for host switching during the evolution of vesicomyids.