Shinji Shimode

Yokohama National University · Manazuru Marine Center, Graduate School of Environment and Information Sciences

To better understand the life history and ontogenetic vertical migration of Neocalanus gracilis (Dana), geographical and seasonal change in the copepodid population structure was investigated in the western North Pacific. Multi-layered zooplankton samples were collected from 1000 m depth to the surface at 21 stations (ca. 15 to 48 degrees N, 127 de...

To clarify the life histories of two tropical–subtropical Eucalanidae species, Rhincalanus nasutus and Rhincalanus rostrifrons, we investigated the geographical and vertical distributions of their copepodid populations in the northwestern (NW) Pacific Ocean. Zooplankton samples were collected between 15°N and 49°N in the NW Pacific. Rhincalanus nas...

We investigated the geographical and vertical distribution of the copepodid stages of Eucalanus californicus in the northwestern (NW) Pacific Ocean, and compared life history characteristics against the northeastern (NE) population of the species and the neighboring subarctic sister species, Eucalanus bungii. In the NW Pacific, multi-layered zoopla...

Unique architectures of microbial skeletons are viewed as a model for the architectural design of artificial structural materials. In particular, the specific geometric arrangement of a spherical skeleton 0.5–1.5 mm in diameter of shell-bearing protists, Phaeodaria (Aulosphaera sp.), is remarkably interesting because of its similarity to a geodesic...

Feeding rates of adult copepods is an important parameter that determines their productivity and population growth. Feeding is influenced by several factors including food quantity and copepod density. The marine harpacticoid copepod, Tigriopus japonicus , is used in the testing of contaminants in marine ecosystems and is also a promising candidate...

DNA metabarcoding on a single organism is a promising approach to clarify the biological interactions (e.g., predator-prey relationships and symbiosis, including parasitism) of difficult-to-culture protists. To evaluate the effectiveness of this method, Radiolaria and Phaeodaria, which are ecologically important protistan groups, were chosen as tar...

Calanus sinicus is one of the most dominant planktonic copepods and plays a key role as a secondary producer in the mid-latitude coastal shelf areas of the Northwestern Pacific. In this study, we investigated seasonal changes in in situ egg production rate (EPR) of C. sinicus collected from March 2014 to February 2015 in Sagami Bay, Japan. Simultan...

Considerable skill is required to identify copepods at the species level based on their morphological characteristics. However, DNA analysis does not require advanced microscopy techniques and provides objective data on the phylogenetic relationships between samples. Therefore, DNA analysis is useful as an alternative method for taxonomic studies o...

Silica frustules of most planktonic diatoms have many shallow holes in which the length (L) is smaller than the width (W). The present study focuses on a silica ultrastructure of setae of a planktonic diatom having deep (L/W > 1) holes. Here, we characterized microscopically patterned nanoholes on the silica walls of thick, robust, and hollow setae...

Sagami Bay, Japan is influenced by both the warm Kuroshio Current and the cold Oyashio Current and rich nutrients are supplied from multiple river sources and the deep-sea, forming a dynamic ecosystem. The aim of the present study was to investigate eukaryotic and bacterial communities in the coastal waters of Sagami Bay, using 16S rRNA and 18S rRN...

We clarified the specific micrometric arrangement and nanometric structure of the radiolarian crystalline spines that are not a simple single crystal. A body of the celestite (SrSO 4 ) skeleton of acantharian Acanthometra cf. multispina (Acanthometridae) composed of 20 radial spines having four blades was characterized using microfocus X-ray comput...

Calcitic spines ∼1 μm in diameter are projecting from a trochospiral test of a spinose planktonic foraminifer. According to electron diffraction, Raman spectra, and detailed electron microscope observation, the spines...

Silica frustules of most planktonic diatoms have many shallow holes in which the length (L) is smaller than the width (W). The present study focuses on a silicic ultrastructure of the setae of a planktonic diatom having deep (L/W > 1) holes. Here, we characterized nanoholes on the silica walls of hollow setae of a colony of Chaetoceros coarctatus ....

We studied the micrometric morphology and nanometric structure of the celestite (SrSO 4 ) skeleton of acantharian family Acanthometridae. A body of the skeleton composed of 20 radial spines with four blades was characterized using microfocus X-ray computed tomography. The regular arrangement of three types of spines was clarified with the connectio...

Chaetognaths are ubiquitous in the marine environment and are among the most abundant carnivorous plankton. Nevertheless, characterization of physiological parameters remains limited largely due to the difficulty in obtaining the data from pelagic chaetognaths in laboratory studies. This study therefore aimed to determine the feeding and growth rat...

The sea surface microlayer (SML), less than 1,000‐μm uppermost layer of the ocean water column, is located at the air‐sea interface and plays critical roles in global biogeochemical cycles and climate change through air‐sea gas exchange. To clarify the significance of the dynamics of carbon monoxide (CO) in the SML, where active photochemical and b...

Bacterial production has been often estimated from DNA synthesis rates by using tritium-labeled thymidine. Some bacteria species cannot incorporate extracellular thymidine into their DNA, suggesting their biomass production might be overlooked when using the conventional method. In the present study, to evaluate appropriateness of deoxyribonucleosi...

Sapphirinid copepods, which are marine zooplankton, exhibit tunable structural colors originating from a layered structure of guanine crystal plates. In the present study, the coloring portion of adult male of a sapphirinid copepod, Sapphirina nigromaculata, under the dorsal body surface was characterized to clarify the regulation and actuation mec...

Understanding global warming effects on marine zooplankton is key to proper management of marine resources and fisheries. This is particularly urgent for Japan where the coastal water temperature has been increasing faster than the global average over the past decade. Conventional sampling and monitoring programmes, by ignoring the in situ vital st...

Ammonium excretion by planktonic copepods is an important process supplying nitrogen to primary producers and other microbial activity in pelagic ecosystems. Because of methodological constraints, conventional analyses using sealed chamber methods have required the adoption of unnatural experimental settings, such as a small container, high density...

Evaluation of the physiological states of copepods can improve current understanding of the dynamics of zooplankton population and contribute to assessments of the health of trophic linkages in marine ecosystems. However, assessing the starvation status of copepods in situ using conventional methods is difficult because of spatial and temporal chan...

Digestion time and feeding of the pelagic chaetognath Zonosagitta nagae, which occurs predominantly in warm waters around Japan, were investigated in the laboratory. Young individuals of Z. nagae ranging from 4.1–7.6 mm in body length were used for the experiments with adult females of the copepod Acartia steueri as prey. The mean digestion time of...

The occurrence of the calanoid copepod Acartia japonica Mori, 1940 is reported for the first time from the Pacific coastal waters of Honshu, Japan. The species was first found in 2013, and subsequently in 2014, 2015 and 2016, at Manazuru Port in Sa-gami Bay. The seasonal appearance of the species was limited to the period from summer to autumn. The...

The sea surface microlayer (SML) is defined as the less than 1 mm uppermost layer of the ocean water column, and it plays critical roles in global biogeochemical cycles and climate change. In the SML, organic matter and microorganisms are usually enriched compared to the subsurface water (SSW). To describe seasonality in the enrichment of microorga...

The occurrence of the calanoid copepod Acartia japonica Mori, 1940 is reported for the first time from the Pacific coastal waters of Honshu, Japan. The species was first found in 2013, and subsequently in 2014, 2015 and 2016, at Manazuru Port in Sa-gami Bay. The seasonal appearance of the species was limited to the period from summer to autumn. The...

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 nitrogen (δ¹⁵N) and carbon stable isotope (δ¹³C) values of six species of euphausiids predominant in the northwestern (NW) Pacific Ocean were investigated to elucidate species-specific feeding habits and seasonal and regional differences. The order of annual mean δ¹⁵N values was: Tessarabrachion oculatumHansen, 1911 (11.2 ± 0.8‰) > Thysanoessa...

This study aimed to clarify the vertical differences in bacterial growth and grazing pressure on bacteria by heterotrophic nanoflagellates (HNF) and to identify the controlling factors of bacterial growth in temperate coastal waters of Sagami Bay, Japan. In addition to environmental factors, the annual monthly variations in bacterial growth rate (B...

We studied seasonal and regional change in vertical distribution and DVM patterns of four euphausiid species (Euphausia pacifica, Thysanoessa inspinata, Thysanoessa longipes, and Tessarabrachion oculatum) from two years of surveys using MOCNESS above 1500 m depth across a transect in 3 regions of the northwestern (NW) Pacific, off east of Japan; Oy...

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...

This study proposed a non-radioactive quantitative measurement of bacterial production using stable isotope nitrogen-15-labeled deoxyadenosine ([15N5]-2′-deoxyadenosine; 15N-dA) by liquid chromatography mass spectrometry (LC–MS). The method of preparing 15N-dA described in this study included incubation of seawater or lake water with 15N-dA for 5–2...

Short-term variation in the ammonium excretion rate by Calanus sinicus during the post-capture period was evaluated in 1-h incubations. Incubation water volume (13 mL vs. 100 mL) did not significantly affect the excretion rate, and the overall mean excretion rate of C. sinicus was similar to reported values from congeneric species. However, the 24-...

We evaluated the internal transcribed spacer 2 and large subunit ribosomal DNA (ITS2-28S) region as a molecular marker for identifying calanoid copepods in the subtropical western North Pacific. The ITS2-28S sequence was successfully amplified in 232/244 individuals, a much higher rate of success than for cytochrome oxidase I amplification (77/244...

The relationship between euphausiid community structure and water region was studied during a 2-year seasonal survey in the northwestern (NW) Pacific Ocean. The euphausiid community structure and its associated species were analyzed from 38 micronekton samples collected during eight cruises. The euphausiid community structure and its distribution p...

To cope with the problems in the marine ecosystem caused by the ballast water from ships, the IMO adopted the International Convention for the Control and Management of Ships' Ballast Water and Sediments in 2004. In response to this legislation, ballast water treatment systems are being developed worldwide. The ballast-free ship concept proposed by...

The rhythmic migration pattern of the dinoflagellate Ceratium furca is a result of ecological adaptation to avoid high irradiance. The high proportions of dividing cells at deeper depths are likely to be an ecological response to maintain their population away from the turbulence in the near-surface layer.

A mesoscale iron fertilization experiment was carried out in the western subarctic Pacific during summer 2004. The iron-patch was traced for 26 days after the enrichment, and the abundance and behavior of meso- and microzooplankton was compared with those outside of the patch. The surface chlorophyll-a concentration in the patch was high between da...

To better understand the mechanism underlying the bloom outbreaks of dinoflagellates, Ceratium furca, and Ceratium fusus in the temperate coastal area of Sagami Bay, we investigated the diel changes of vertical migration, swimming speed, cell volume, and cell division. Our results from both the field and laboratory indicate that C. furca and C. fus...

To assess the consequences of bottom-up effects on phytoplankton community composition during the rainy season, phytoplankton levels and environmental factors were monitored daily from 12 April to 22 July 2003 in Sagami Bay, Japan. The relevant environmental factors were analyzed using cross-correlation analyses. Based on time-series analysis, low...

The relationship between nutrients and phytoplankton dynamics was investigated daily from 12 April to 22 July 2003 in Sagami Bay, Japan. According to multidimensional scaling (MDS) and cluster analysis, phytoplankton community was divided into four distinct groups. The first group was consisted of centric diatom species, such as Guinardia spp., Det...

In order to study the influence of nutrients on the growth characteristics of the dominant dinoflagellates, Ceratium furca and Ceratium fusus, in the temperate coastal area of Sagami Bay, Japan, we conducted field monitoring from January 2000 to December 2005 and performed laboratory culture experiments. In the field study, population densities of...

To examine the population development of the dinoflagellates, Ceratium furca and Ceratium fusus, daily field monitoring was conducted between April and July 2003 in the temperate coastal water of Sagami Bay, Japan. During the study period, the concentrations of C. furca were always lower than those of C. fusus. A sharp increase in the densities of...

Seasonal changes of field populations and growth rates of two dinoflagellates, Ceratium furca and Ceratium fusus, were examined in the temperate coastal water of Sagami Bay, Japan. Weekly field sampling was conducted from August 2002 to August 2003, and laboratory experiments were also carried out to investigate effects of temperature, irradiance a...

To better understand the relationship between human-induced disturbance and the meiobenthic community in a harbor environment, sediment samples were collected at four stations (Sts. MP1 to 4) in Manazuru Port in Sagami Bay on eight occasions, approximately monthly between July, 2003, and March, 2004. Qualitative meiofaunal samples were collected by...

The seasonal abundance of the dominant dinoflagellate, Ceratium fusus, was investigated from January 2000 to December 2003 in a coastal region of Sagami Bay, Japan. The growth of this species was also examined under laboratory conditions. In Sagami Bay, C. fusus increased significantly from April to September, and decreased from November to Februar...

Seasonal occurrence, diel vertical migration (DVM), biomass (dry weight, carbon and nitrogen contents), growth and behavior of the two phytal-dwelling harpacticoid copepods, Ambunguipes rufocincta and Eudactylops spectabilis, were investigated using field samplings and laboratory experiments. The field samplings were conducted at a subtidal station...

Reproductive ecology of dinoflagellate, Ceratium furca, was studied in the coastal area of Sagami Bay. Field samplings and laboratory experiments were conducted to investigate seasonal changes of the field population and effects of temperature, salinity and irradiance on the growth rate of C. furca. Abundance of the species increased significantly...

A practical guideline for community-level ecological risk management is proposed, with particular emphasis on the mutual interdependencies of the scientific analysis, public consensus building, and an adaptive management. The procedure we recommend spans the screening of potential ecological risks, the involvement of related stakeholders, the conce...

Seasonal changes in diversity and community structure of planktonic copepods at a shelf site in Sagami Bay, Japan was studied in relation to cross-shelf interaction of species components. Seasonal mesozooplankton samples were collected from the shelf station (St. M) of the north-west part of Sagami Bay from 1995 to 1997. Vertical multi-layered samp...

Direct injection of CO(2) into the deep ocean is receiving increasing attention as a way to mitigate increasing atmospheric CO(2) concentration. To assess the potential impact of the environmental change associated with CO(2) sequestration in the ocean, we studied the lethal and sub-lethal effects of raised CO(2) concentration in seawater on adult...

Data concerning the effects of high CO2 concentrations on marine organisms are essential for both predicting future impacts of the increasing atmospheric CO2 concentration and assessing the effects of deep-sea CO2sequestration. Here we review our recent studies evaluating the effects of elevated CO2 concentrations in seawater on the mortality and e...

Diel vertical migration (DVM) and distributional patterns of copepods collected in the water column at shallow water site (Station M) in Tanabe Bay, Japan were investigated. Twenty-one taxa of zooplankton and 48 species of copepods at Station M had positive ΔZ values (subtraction of night-time weighted mean depth from daytime value) and performed n...

A new Ryocalanoid copepod, Ryocalanus spinifrons, collected by the MTD net system at a depth of 1400 m from the southwestern part of Sagami Bay, Japan, is described. The new species is morphologically very close to R. infelix Tanaka, 1956 (female unknown) from the Izu region of Sagami Bay. It is distinguished from other species by the presence of 1...

Reproduction, hatching success and population dynamics of the dominant copepod Acartia steueri were studied in Sagami Bay, Japan from February 2002 to December 2003. A. steueri occurred through the year in the water column, and it produced physiologically different eggs, subitaneous and diapausing. Subitaneous eggs were produced through the experim...

Spatio-temporal distribution patterns of bacterial abundance (BA) and production (BP), heterotrophic nanoflagellate abundance (HNFA), viral abundance (VA), and chlorophyll a concentrations (Chl a) were examined by annual monthly sampling of water from the surface to 100 m depth in a coastal area of Sagami Bay, Japan to investigate the changes of to...