Ryota Nakajima

• PhD
• Senior Researcher at Japan Agency for Marine-Earth Science and Technology

The influx of microplastics (MPs) into the Arctic Ocean poses a collective risk, particularly with pronounced sea ice depletion due to global warming. A total of 73 replicate sediment samples were collected at different depths (38 to 79 m) from Chukchi and the Beaufort Seas at 8 stations in the Arctic region during the R/V Mirai cruise (MR22-06C) f...

A new deep-sea fungus, Oceanitis abyssalis sp. nov. was described based on analyses of the LSU rDNA sequences and morphological characteristics. The new species was found on a branch of Prunus sp. collected at 5707 m depth of the abyssal plain in the Northwest Pacific Ocean, east off the Japan Islands. To the best of our knowledge, our discovery is...

Mesoscale eddies – ocean vortices with spatial scales of tens to hundreds of kilometers and time scales of months to years – are among the most energetic forms of flow in the ocean, and may act as significant transporters of floating microplastics. Yet, shipboard observation has thus far not clarified the abundance and transport of microplastics in...

Polychlorinated biphenyls (PCBs) persistently pollute marine ecosystems even though their production has been discontinued decades ago. Deep-sea organisms have been shown to accumulate PCBs and other persistent organic compounds; however, the extent of contamination and its effects remain poorly understood. Here, we measured PCB concentrations in s...

Microbes can decompose biodegradable plastics on land, rivers and seashore. However, it is unclear whether deep-sea microbes can degrade biodegradable plastics in the extreme environmental conditions of the seafloor. Here, we report microbial decomposition of representative biodegradable plastics (polyhydroxyalkanoates, biodegradable polyesters, an...

With the high number of microplastic-like particles captured by net hauls including manta or neuston nets, it is often required to subsample in order to decrease sample volume for microplastic enumeration and analysis. Plankton splitter is commonly used to divide microplastic samples. However, current devices such as Folsom plankton splitter and Mo...

The microplastics inflow into the Arctic Ocean may increase environmental stress on the Arctic marine ecosystem on the Pacific side, where sea ice has been significantly reduced because of global warming. However, quantitative data on microplastics are very limited in the Beaufort Sea, which is covered by sea ice for most of the year, even in summe...

The accumulation of polybrominated diphenyl ethers (PBDEs) and benzotriazole UV stabilizers (BZT-UVs) were examined in the hadal amphipod Hirondellea gigas caught from a near-land trench off the Japan island (9200 m). H. gigas were collected from two distinct sites: one is located at the outlet of submarine canyons directly connected to land and th...

Millions of tons of riverine plastic waste enter the ocean via estuaries annually. The plastics accumulate, fragment, mix and interact with organisms in these dynamic systems, but such processes have received limited attention relative to open-ocean sites. In this Perspective, we discuss the occurrence and convergence of microplastics at estuarine...

The recent influx of microplastics into the Arctic Ocean may increase environmental stress on the western Arctic marine ecosystem, which is experiencing significant sea-ice loss due to global warming. Quantitative data on microplastics in the western Arctic Ocean are very limited, and the microplastic budget of the water column is completely unknow...

It is becoming obvious that the abundance of microplastics is increasing in worldwide oceans, raising concerns about their impact on marine ecosystems. Tiny plastic particles enter the body of marine organisms not only via oral ingestion but also through the body surface (e.g., gills or epidermis), but the mechanism of internalization into cells is...

Chitin is a key component of hard parts in many organisms, but the biosynthesis of the two distinctive chitin allomorphs, α- and β-chitin, is not well understood. The accurate determination of chitin allomorphs in natural biomaterials is vital. Many chitin-secreting living organisms, however, produce poorly crystalline chitin. This leads to spectru...

Chitin is a key component of hard parts in many organisms, but the biosynthesis of the two distinctive chitin allomorphs, α- and β-chitin, is not well-understood. The accurate determination of chitin allomorphs in natural biomaterials is vital. Many chitin-secreting living organisms, however, produce poorly crystalline chitin which leads to spectru...

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 thi...

Extreme storms, such as tropical cyclones, are responsible for a significant portion of the plastic debris transported from land to sea yet little is known about the storm response of microplastics and other debris in offshore and open waters. To investigate this, we conducted floating plastic surveys in the center of Sagami Bay, Japan approximatel...

Marine ecosystems are continuously subjected to anthropogenic environmental pollution. Understanding the spread of pollution and the potential risks it poses to deep-sea ecosystems is important for developing better conservation measures. Here, we identified non-negligible levels of persistent organic pollutants in deep-sea chemosynthetic bivalves...

Community-based diversity analyses, such as metabarcoding, are increasingly popular in the field of metazoan zooplankton community ecology. However, some of the methodological uncertainties remain, such as the potential inflation of diversity estimates resulting from contamination by pseudogene sequences. Furthermore, primer affinity to specific ta...

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 we...

The abyss (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. Using video imagery we undertook a quantitative assessment of the debris present on the abyssal seafloor (5700–5800 m depth) beneath the Kuroshio Extension current system in the Northwest Pacific. This body...

Plastic waste has become a growing concern in terms of marine pollution, but little information is available on plastic debris and its possible risks of chemical additives exposure in the deep-sea. This study focused on identification of polymer type and additive concentrations in 21 plastic debris collected from deep-sea of Sagami Bay, Japan and W...

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...

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 Exte...

Microplastic pollution in marine environments is an emerging global issue revealing the importance of microplastic monitoring. Although numerous papers have been published in recent years in relation to microplastics, the methods and techniques for identifying and quantifying them remain underdeveloped, and many researchers are working to develop o...

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 fundamen...

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...

Separating microplastics from marine and freshwater sediments is challenging, but necessary to determine their distribution, mass, and ecological impacts in benthic environments. Density separation is commonly used to extract microplastics from sediments by using heavy salt solutions, such as zinc chloride and sodium iodide. However, current device...

The optimal spatial resolution for analysis of the spatial distribution of organisms is determined by the scale of their ecological processes (e.g., mobility of target species). This study examined the spatial extent of habitats of five megafaunal species with different levels of mobility [(1) the shrimp, Nematocarcinus sp. (benthic, comparatively...

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...

Egg surface ornamentation, egg production rates, and hatching success of two calanoid copepod species (Acartia pacifica and Acartia cf. erythraea) were examined in a tropical coral reef of Tioman Island, Malaysia, near the equator (2°N). All observed females of A. pacifica and A. cf. erythraea produced eggs with spines on the surface, either short...

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...

Dissolved organic matter (DOM) constitutes the largest organic matter pool in coral reef waters and is released and utilized by various coral reef organisms. In this chapter, we review the distribution and fluctuation of DOM concentrations in coral reefs around the world, with a special focus on Shiraho Reef, Ishigaki Island, Okinawa, Japan, where...

Exudates derived from hermatypic corals were incubated with <2 µm filtered seawater containing heterotrophic bacteria and <10 µm filtered seawater containing bacteria and nanoflagellates (HNF) under dark conditions for 96 h to quantify the growth of both bacteria and HNF in response to coral-derived dissolved organic matter (DOM). The addition of c...

3D visual mapping of the seafloor has found applications ranging from environment monitoring and survey of marine minerals to underwater archaeology and inspection of modern articial structures. However, the attenuation of light is signicantly more pronounced in water than in air or in space, and so in order to obtain underwater images in colour, i...

The relative contributions of grazing versus microbial food webs to the production of mesozooplankton communities in coral reef ecosystems remains an important and understudied field of inquiry. Here, we investigated the biomass and production of component organisms within these two food webs, and compared them to those of mesozooplankton on a cora...

The boundary zone between two different hydrological regimes is often a biologically enriched environment with distinct planktonic communities. In the center of the Amazon River basin, muddy white water of the Amazon River meets with black water of the Negro River, creating a conspicuous visible boundary spanning over 10 km along the Amazon River....

Average (mean ± SD) density (inds m−3) and relative density (%RA) of various cladoceran species at the Amazon (Solimões) and the Negro Rivers at the center of the Amazon basin

Average (mean ± SD) density (inds m−3) and relative density (%RA) of various copepod species at the Amazon (Solimões) and the Negro Rivers at the center of the Amazon basin

Average (mean ± SD) density (inds m−3) and relative density (%RA) of various insect larvae at the Amazon (Solimões) and the Negro Rivers at the center of the Amazon basin

Biological and environmental raw data Biological data includes density of cladocerans, copepods, insect larvae and fish larvae. Environmental data includes water temperature, Secchi depth, and the concentrations of chlorophyll-a (chl-a) and particulate organic carbon (POC) and nitrogen (PON).

Daily field surveys were conducted at a coastal-shelf station in Sagami Bay, Japan after the passage of typhoon Malou in 2010 to evaluate the after-effect of a typhoon passage on the physical-chemical environment, phytoplankton bloom formation and microbial processes within and below the euphotic layer. The passage of Malou induced an abrupt decrea...

The boundary zone between two different hydrological regimes is often a biologically enriched environment with distinct planktonic communities. In the center of the Amazon River basin, muddy white water of the Amazon River meets with black water of the Negro River, creating a conspicuous visible boundary spanning over 10 km along the Amazon River....

The boundary zone between two different hydrological regimes is often a biologically enriched environment with distinct planktonic communities. In the center of the Amazon River basin, muddy white water of the Amazon River meets with black water of the Negro River, creating a conspicuous visible boundary spanning over 10 km along the Amazon River....

The boundary zone between two different hydrological regimes is often a biologically enriched environment with distinct planktonic communities. In the center of the Amazon River basin, muddy white water of the Amazon River meets with black water of the Negro River, creating a conspicuous visible boundary spanning over 10 km along the Amazon River....

Previous studies have suggested that Crown-of-Thorns starfish (COTS) larvae may be able to survive in the absence of abundant phytoplankton resources suggesting that they may be able to utilize alternative food sources. Here, we tested the hypothesis that COTS larvae are able to feed on coral-derived organic matter using labeled stable isotope trac...

This paper describes a method to survey the distribution of megabenthos over multi-hectare regions of the seafloor. Quantitative biomass estimates are made by combining high-resolution 3D image reconstructions, used to model spatial relationships between representative taxa, with lower-resolution reconstructions taken over a wider area in which the...

Deep-sea hydrothermal systems often support large and diverse populations of vent-associated organisms. While these organisms are well adapted to surviving in dynamic and unstable environmental conditions, the interest in deep-sea mining raises concerns about the potential impacts of human activities on the health of these ecosystems. In this work,...

After the passage of typhoon Malou in 2010, daily field samplings were conducted at both inshore (Sta. A) and offshore (Sta. M) stations in Sagami Bay, Japan, to evaluate responses of bacteria and phytoplankton to variations of physical-chemical environments induced by typhoon passage. Malou passage caused an abrupt decline of salinity and a large...

In order to test the hypothesis that species composition of planktonic copepods varies with seasonal monsoons in tropical coral reef waters of South East Asia, we investigated the copepod community structure in a coral reef of Malaysia over different monsoonal periods (the southwest, the northeast and inter-monsoons). Small copepods such as Paracal...

There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and...

There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and...

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...

In order to extract quantitative information on deep-sea benthic animals (no. individuals or biomass in an area) using oblique video/photo images taken by deep-sea submersible survey platforms, a new method was established to estimate the imaged area of the seafloor from the oblique images. The trapezoidal area appearing on the lower half of the sc...

Aim To characterize the species richness, endemism and community structure of benthic macro-/megafauna in the deep-sea chemosynthetic ecosystems around the Japanese archipelago and determine the conservation priority for deep-sea chemosynthetic habitats. Location Twenty-seven methane seeps from the Kuril–Japan Trench, Nankai Trough, Ryukyu Trench...

Quantitative research on composition, biomass and production rates of zoo- plankton community is crucial to understand the trophic structure in coral reef pelagic ecosystems. In the present study, micro- (35–100 lm) and net- (>100 lm) metazooplankton were investigated in a fringing coral reef at Tioman Island of Malaysia. Sampling was done during t...

It is well known that corals release transparent and mucoid organic matter (coral mucus) to the ambient seawater. This mucus release is important for various physiological functions of corals such as defense against stress, particle trap and cellular metabolic regulation. Coral mucus is mainly composed of carbohydrates, proteins and lipids, of whic...

Gelatinous zooplankton abundance and species composition were investigated at 3-h intervals for a 48-h period at a fringing reef in Malaysia. A total of 20 gelatinous zooplankton species were observed; the community was dominated by the calycophoran siphonophore Diphyes chamissonis (79.9%), followed by the trachymedusdae Aglaura hemistoma (5.6%) an...

In order to examine small invertebrate scavenging fauna of tropical coral reef waters, baited traps were deployed in a coral reef of Bidong Island, Malaysia. The samples taken by the traps constituted only a single species of isopods (Cirolana sp.) and ostracods from three families (Cypridinidae, Cylindroleberididae, and Paradoxostomatidae). Cirola...

Analyses of past typhoons, tropical cyclones and hurricanes have suggested that global warming may lead to increasing intensities of these episodic events and that the impacts of typhoons on oceanic biogeochemistry will also be augmented. In the present study, daily variations of the physical–chemical environment and phytoplankton community success...

[1] The Integrated Ocean Drilling Program (IODP) Expedition 331 investigated the Iheya North hydrothermal field in the Okinawa Trough. Several post-drilling underwater vehicle investigations were conducted over 2 years to identify post-drilling changes in fluid discharge pattern, mineral deposition, and fluid chemistry. Drilling-induced high-temper...

[1] The Integrated Ocean Drilling Program (IODP) Expedition 331 investigated the Iheya North hydrothermal field in the Okinawa Trough. Several post-drilling underwater vehicle investigations were conducted over 2 years to identify post-drilling changes in fluid discharge pattern, mineral deposition, and fluid chemistry. Drilling-induced high-temper...

3D visual mapping of the seafloor has found ap-plications ranging from environment monitoring and survey of marine minerals to underwater archeology and inspection of modern man-made structures. However, the attenuation of light is significantly more pronounced in water than in air or in space, and so in order to obtain underwater images in colour,...

In order to test the hypothesis that the microbial enrichment in the sea-surface micro- layer (SML) over coral reefs is significant, we investigated the abundance and production of the microbial community in the SML and sub-surface water (SSW) at a fringing coral reef of Malaysia. Samples were taken at 2 coral sites with different live coral covera...

Little is known about blue copepods in ma­ rine habitats. To date, a few copepod species from the family Pontellidae including Pontella fera, Labido cera glauca and Labido cera acutifrons and a few species from the family Corycaeidae such as Corycaeus amazonicus have been recorded to be blue-pigmented. Here we report, for the first time, a blue-col...

The rates of sedimentation and growth of the branching coral Acropora formosa at Marine Park, Tulai and Renggis reefs in Tioman Island, Malaysia were surveyed between November 2000 and October 2001. The sedimentation rates were measured using sediment traps and the coral growth rates were measured using digital photography and computer image analys...

Climate change has the potential for intensification of typhoons, which will cause stronger effects on aquatic ecosystems in the future. The effect of typhoon Mawar (T0511), passing Manazuru Port located in the west- ern part of Sagami Bay, Japan, was investigated from August to September 2005. Immediately after the passage of Mawar, photosynthetic...

Inorganic nutrient contents of mucus released by Acropora corals and its utilization by heterotrophic bacteria at several hour intervals in the coral mucus were investigated at a coral reef in Malaysia. The dissolved inorganic phosphate (DIP) concentration was 135-fold higher compared to the ambient seawater, probably due to inorganic P release fro...

The quality and quantity of particulate organic carbon (POC) were investigated in a fringing coral reef of Tioman Island, Malaysia to better understand the food sources for reef meso-zooplankton. Phytoplankton biomass in the water column was on average 0.22 (± 0.07) mg Chl-a m -3 , of which picophytoplankton was the most important (size <3 µm, 50-7...

Measurements of both particulate and dissolved organic carbon (POC and DOC) release by corals are important in understanding the organic carbon cycle in reef systems. In this study, branches of Acropora formosa (Dana, 1846) were incubated for 5 hrs and the release of POC and DOC into the ambient water was simultaneously measured. POC release rate (...

Biologically diverse coral-reef ecosystems are both directly and indirectly susceptible to changes in the spectral ultraviolet radiation (UVR) distribution. The purpose of this study was to (1) measure the variability of UVR and photosynthetically active radiation (PAR) penetration in the water above coral reefs around the Malaysian peninsula, (2)...

The use of line-intercept transect (LIT) method combined with image analysis, i.e. photo line intercept transect (PLIT) method, where digital photos of corals along a transect line are taken and the length of corals intercepting the transect line are measured, was evaluated for coral reef monitoring. Coral coverage (%) and generic diversity were ex...

We examined the bias in the estimation of zooplankton biomass in net-samples in coral reef waters by measuring seston weight, which contains non-living matter (or detritus) and net-phytoplankton in addition to zooplankton. Net-samples were collected at a coral reef at Tioman Island, Malaysia, and divided them into two aliquots to be used for both m...

The use of line-intercept transect (LIT) method combined with image analysis, ie photo line intercept transect (PLIT) method, where digital photos of corals along a transect line are taken and the length of corals intercepting the transect line are measured, was evaluated for coral reef monitoring. Coral coverage (%) and generic diversity were exam...

Zooplankton was sampled at 3-h intervals for a 48-h period from a coral reef of Tioman Island, Malaysia. It was size-fractionated into three size classes: 100–200, 200–335, and >335μm using different sieves with different mesh sizes. Total zooplankton (>100μm) abundance and biomass in the water column were high later at night (0300h), not just afte...

Insitu mucus release by Acropora nobilis and degradation of mucus from A. nobilis and Acropora formosa, by heterotrophic bacteria were investigated at Bidong and Tioman Island, Malaysia. Mucus release rate for A. nobilis was on average 38.7±35.2mg C m−2 h−1, of which ca. 70% consisted of dissolved organic carbon (DOC) and 30% particulate organic ca...

To understand coral-reef zooplankton ecology on a diel basis, zooplankton abundance, biomass and size composition from a fringing coral-reef of Redang Island, Malaysia, were investigated at three-hour intervals for a 48 hour period. Zooplankton was collected vertically and size-fractionated into three size-classes; 100–200mm, 200–335 m m, and 􏰣335...

Coral community structures at eleven fringing reef sites were investigated along the coast of Peninsular Malaysia. Estimated coverage of coral communities is examined by applying quantitative digital image analysis to the line transect method. Four coral community types were characterized by dominant genera and lifeforms: Acropora branching communi...

Biomass in zooplankton (>100μm) and particulate organic matter (POM) (0.7-100μm) was investigated every 3 hours for two days at the fringing reef of Redang and Tioman Island, the east coast of Peninsular Malaysia. The zooplankton was size-fractionated into three fractions (100-200μm, 200-335μm, and >335μm) and POM was divided into two size-fraction...