Dr. Ryota Nakajima

A biological oceanographer

High fish abundance in the confluence of two large rivers in the Amazon

Ryota and his team report a high fish larvae abundance in the confluence zone between black and white water rivers in the Amazon River system.
In the center of the Amazon River basin, 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, which can even be seen from space. Local fishermen acknowledge the confluence of black and white water rivers is rich in fish abundance, and indeed there are many freshwater dolphins there. So Ryota was wondering what’s going on in the confluence and suspecting there were many prey zooplankton here.
His study found that the confluence boundary offers benefits of both high prey concentration (zooplankton) from the black water river and low predation risk from the white water river for fish larvae, explaining the high abundance of fish larvae in the confluence zone. That’s why the dolphins like the confluence zone!

Zooplankton community changes over monsoons

Ryota and his colleagues investigated zooplankton community in a coral reef of Malaysia .

The research team collected copepods with a plankton net over different monsoonal periods.

They found that more than 70% of the community was dominated by small copepods throughout the year, and the species composition varied with seasonal monsoons.

The research team considers that differences in water source and food availability shape the distinct structure of the copepod assemblages in tropical coral reef waters of South East Asia.


Nakajima R, Yoshida T, Othman BHR, Toda T (2015) Monsoonal changes in the planktonic copepod community structure in a tropical coral reef at Tioman Island, Malaysia. Regional Studies in Marine Science 2: 9-26.

Sea-surface microlayer is rich in microbes over coral reefs

Do you know the sea-surface microlayer?

The sea-surface microlayer is the thin boundary layer between the atomosphere and ocean, with a typical thickness of 10-250 µm.

It is also called ‘surface film’ or ‘surface skin’. The sea-surface micolayer is generally enriched in both dissolved and particulate organic matters and microbes.

The sea-surface microlayer can be sampled with a metal mesh screen with a mesh width of 1mm (this is one of the methods to collect sea-surface microlayer).

First you immerse the metal screen in the water at an angle and return to the horizontal position underwater, then slowly pulled up.

The metal screen is subsequently drained at an angle to collect the surface samples.

Ryota and his team collected microbial samples from the sea-surface microlayer at three sites with different coral coverage, high coral coverage, low coral coverage, and offshore site with no corals.

The research team found that the abundance of bacteria and bacterivorous protists were higher in the sea-surface microlayer than the subsurface water, and those in the microlayer increased with increasing coral coverage.

They consider the higher amount of organic matter or mucus released by corals enhanced the number of bacteria and bacterivorous protists.

Because coral mucus often includes air bubbles that provide buoyancy, which slowly ascent to the sea-surface and accumulate.

Passing through the water column, its sticky surface traps various organic particles such as bacteria.

Therefore coral mucus can contribute to the formation of enrichment of organic matter and microbes in the air-sea interface.

A higher coral coverage in an area can mean a higher organic matter or coral mucus input, which may have resulted in a more stimulated microbial community at the air-sea interface compared to areas with lower coral coverage.


Nakajima R, Tsuchiya K, Nakatomi N, Yoshida T, Tada Y, Konno F, Toda T, Kuwahara VS, Hamasaki K, Othman BHR, Segaran TC, Effendy AWM (2013) Enrichment of microbial abundance in the sea-surface microlayer over a coral reef: implications for biogeochemical cycles in reef ecosystems. Marine Ecology Progress Series 490: 11-22.

What happens after drilling the deep-sea floor?

Ryota and his team monitored the benthic ecosystem at 1,060 m depth of hydrothermally active areas in the Okinawa Trough, off Japan, where a scientific drilling by the Deep Sea Scientific Drilling Vessel Chikyu was performed on September 2010.

This monitoring was started before the drilling operation and lasted 40 months thereafter.

As a result, it led to elucidate impacts of variation in deep-sea habitats on hydrothermal vent communities.

Prior to drilling, the seabed was covered by soft silty sediment, where Calyptogena clam colonies dominated.

After the drilling operation, the clam colonies were completely buried under the drilling deposits.

Then, at 11 months after the drilling, drilling-induced hydrothermal fluid discharges and numerous tiny chimneys were observed on the seafloor.

In addition, benthos communities on the artificial hydrothermal vent fields occupied by Shinkaia crosnieri galatheid crabs were also found.

It is presumed that they have been migrated from the nearby habitats.

The previously soft sediment had hardened probably due to chemical reaction of fluid composition, becoming rough and undulated with many fissures after 25 months of the drilling operation.

The image shows how a new ecosystem is formed around the hydrothermal vent areas.


Nakajima R, Yamamoto H, Kawagucci S, Takaya Y, Nozaki T, Chen C, Fujikura K, Miwa T, Takai K (2015) Post-drilling change in seabed landscape and megabenthos in a deep-sea hydrothermal system, the Iheya North field, Okinawa Trough. PLoS ONE 10: e0123095.

Typhoon enhances the production of bacteria and phytoplankton

Kenji Tsuchiya and his colleagues investigated responses of bacteria and phytoplankton to physical-chemical environments induced by typhoon passages.

The study showed that the passage of typhoon Malou in a coastal water of Japan in 2010 caused an abrupt decline of salinity and a large increase in the amount of nutrients, immediately enhancing bacterial production.

The study also sowed that phytoplankton production exceeded bacterial production two days after Malou passage, and then reached a maximum five days later.

The study team considers that sediment resuspension induced by typhoon passage enhanced bacterial productivity abruptly just after the passage at an inshore station.

The bacterial response could be regulated by difference in relative contribution of nutrient sources after the passage of typhoon.


Tsuchiya T, Kuwahara VS, Hamasaki K, Tada Y, Ichikawa T, Yoshiki T,  Nakajima R, Imai A, Shimode S, Toda T (2015) Typhoon-induced response of phytoplankton and bacteria in temperate coastal waters. Estuarine, Coastal and Shelf Science 167: 458-465.

The first multi-hectare scale 3D survey of a deep-sea vent community

Blair Thornton and his colleagues investigated the distribution of megabenthos over multi-hectare regions (2.5 ha) of the seafloor of a deep-sea hydrothermal vent site off Japan for the first time.

The study region was the target of scientific drilling during the IODP Expedition 331 in 2010.

The research team surveyed biomass of megabenthos using high- and low-resolution 3D image reconstructions (it goes with Blair Scan) 3 years and 4 months after the site was drilled.

They found more than 100,000 organisms from 6 taxa. The study showed the biomass of the drilled site was lower than observed in nearby naturally discharging areas.


Thornton B, Bodenmann A, Pizarro O, Williams SB, Friedman A,  Nakajima R, Takai K, Motoki K, Watsuji T, Hirayama H, Matsui Y, Watanabe H, Ura T (2016) Biometric assessment of deep-sea vent megabenthic communities using multi-resolution 3D image reconstructions. Deep Sea Research I 116: 200-219.

Crown of Thorns starfish (COTS) larvae can take up organic matter derived from corals

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.


In this study, Ryota and his colleagues tested the hypothesis that COTS larvae are able to feed on coral-derived organic matter using labeled stable isotope tracers.

The results show that coral-derived organic matter such as coral mucus can be taken up by COTS larvae and may be an important alternative or additional food resource for COTS larvae through periods of low phytoplankton biomass.

The research team says that this additional food resource could potentially facilitate COTS outbreaks by reducing resource limitation.


Nakajima R, Nakatomi N, Kurihara H, Fox M, Smith J, Okaji K (2016) Crown-of-thorns starfish larvae can feed on organic matter released from coralsDiversity 8: 18.